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M Bader S, Calleja DJ, Devine SM, Kuchel NW, Lu BGC, Wu X, Birkinshaw RW, Bhandari R, Loi K, Volpe R, Khakham Y, Au AE, Blackmore TR, Mackiewicz L, Dayton M, Schaefer J, Scherer L, Stock AT, Cooney JP, Schoffer K, Maluenda A, Kleeman EA, Davidson KC, Allison CC, Ebert G, Chen G, Katneni K, Klemm TA, Nachbur U, Georgy SR, Czabotar PE, Hannan AJ, Putoczki TL, Tanzer M, Pellegrini M, Lechtenberg BC, Charman SA, Call MJ, Mitchell JP, Lowes KN, Lessene G, Doerflinger M, Komander D. A novel PLpro inhibitor improves outcomes in a pre-clinical model of long COVID. Nat Commun 2025; 16:2900. [PMID: 40180914 PMCID: PMC11969009 DOI: 10.1038/s41467-025-57905-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2024] [Accepted: 03/06/2025] [Indexed: 04/05/2025] Open
Abstract
The COVID-19 pandemic caused by the coronavirus SARS-CoV-2 has highlighted the vulnerability of a globally connected population to zoonotic viruses. The FDA-approved coronavirus antiviral Paxlovid targets the essential SARS-CoV-2 main protease, Mpro. Whilst effective in the acute phase of a COVID infection, Paxlovid cannot be used by all patients, can lead to viral recurrence, and does not protect against post-acute sequelae of COVID-19 (PASC), commonly known as long COVID, an emerging significant health burden that remains poorly understood and untreated. Alternative antivirals that are addressing broader patient needs are urgently required. We here report our drug discovery efforts to target PLpro, a further essential coronaviral protease, for which we report a novel chemical scaffold that targets SARS-CoV-2 PLpro with low nanomolar activity, and which exhibits activity against PLpro of other pathogenic coronaviruses. Our lead compound shows excellent in vivo efficacy in a mouse model of severe acute disease. Importantly, our mouse model recapitulates long-term pathologies matching closely those seen in PASC patients. Our lead compound offers protection against a range of PASC symptoms in this model, prevents lung pathology and reduces brain dysfunction. This provides proof-of-principle that PLpro inhibition may have clinical relevance for PASC prevention and treatment going forward.
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Affiliation(s)
- Stefanie M Bader
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Dale J Calleja
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Shane M Devine
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
- Department of Medical Biology, University of Melbourne, Melbourne, Australia.
| | - Nathan W Kuchel
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Bernadine G C Lu
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Xinyu Wu
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Richard W Birkinshaw
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Reet Bhandari
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Katie Loi
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Rohan Volpe
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Yelena Khakham
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Amanda E Au
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Timothy R Blackmore
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Liana Mackiewicz
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Merle Dayton
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Jan Schaefer
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Lena Scherer
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Angus T Stock
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - James P Cooney
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Kael Schoffer
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Ana Maluenda
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Elizabeth A Kleeman
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia
| | - Kathryn C Davidson
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Cody C Allison
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Gregor Ebert
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Gong Chen
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Kasiram Katneni
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Theresa A Klemm
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Ueli Nachbur
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Smitha Rose Georgy
- Anatomic Pathology - Veterinary Biosciences, Melbourne Veterinary School, University of Melbourne, Werribee, VIC, Australia
| | - Peter E Czabotar
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Anthony J Hannan
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia
- Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC, Australia
| | - Tracy L Putoczki
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
- Department of Surgery, University of Melbourne, Melbourne, Australia
| | - Maria Tanzer
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Marc Pellegrini
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
- Centenary Institute of Cancer Medicine and Cell Biology, Camperdown, NSW, Australia
| | - Bernhard C Lechtenberg
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Susan A Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Melissa J Call
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Jeffrey P Mitchell
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Kym N Lowes
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Guillaume Lessene
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
- Department of Medical Biology, University of Melbourne, Melbourne, Australia.
- Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Australia.
| | - Marcel Doerflinger
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
- Department of Medical Biology, University of Melbourne, Melbourne, Australia.
| | - David Komander
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
- Department of Medical Biology, University of Melbourne, Melbourne, Australia.
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Ngo LT, Jung W, Bui TT, Yun H, Chae J, Momper JD. Development of a physiologically-based pharmacokinetic model for Ritonavir characterizing exposure and drug interaction potential at both acute and steady-state conditions. CPT Pharmacometrics Syst Pharmacol 2025; 14:523-539. [PMID: 39714044 PMCID: PMC11919272 DOI: 10.1002/psp4.13293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 10/23/2024] [Accepted: 11/14/2024] [Indexed: 12/24/2024] Open
Abstract
Ritonavir (RTV) is a potent CYP3A inhibitor that is widely used as a pharmacokinetic (PK) enhancer to increase exposure to select protease inhibitors. However, as a strong and complex perpetrator of CYP3A interactions, RTV can also enhance the exposure of other co-administered CYP3A substrates, potentially causing toxicity. Therefore, the prediction of drug-drug interactions (DDIs) and estimation of dosing requirements for concomitantly administered drugs is imperative. In this study, we aimed to develop a physiologically-based PK (PBPK) model for RTV using the PK-sim® software platform. A total of 13 clinical PK studies of RTV covering a wide dose range (100 to 600 mg including both single and multiple dosing), and eight clinical DDI studies with RTV on CYP3A and P-gp substrates, including alprazolam, midazolam, rivaroxaban, clarithromycin, fluconazole, sildenafil, and digoxin were used for the model development and evaluation. Chronopharmacokinetic differences (between morning vs. evening doses) and limitations in parameter estimation for biochemical processes of RTV from in vitro studies were incorporated in the PBPK model. The final developed PBPK model predicted 100% of RTV AUClast and Cmax within a twofold dimension error. The geometric mean fold error (GMFE) from all PK datasets was 1.275 and 1.194, respectively. In addition, 97% of the DDI profiles were predicted with the DDI ratios within a twofold dimension error. The GMFE values from all DDI datasets were 1.297 and 1.212, respectively. Accordingly, this model could be applied to the prediction of DDI profiles of RTV and CYP3A substrates and used to estimate dosing requirements for concomitantly administered drugs.
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Affiliation(s)
- Lien Thi Ngo
- College of PharmacyChungnam National UniversityDaejeonKorea
- Faculty of PharmacyPHENIKAA UniversityHanoiVietnam
- PHENIKAA Research and Technology Institute (PRATI), A&A Green Phoenix Group JSCHanoiVietnam
| | - Woojin Jung
- College of PharmacyChungnam National UniversityDaejeonKorea
- Convergence Research CenterChungnam National UniversityDaejeonKorea
| | - Tham Thi Bui
- College of PharmacyChungnam National UniversityDaejeonKorea
| | - Hwi‐yeol Yun
- College of PharmacyChungnam National UniversityDaejeonKorea
- Convergence Research CenterChungnam National UniversityDaejeonKorea
- Department of Bio‐AI ConvergenceChungnam National UniversityDaejeonKorea
| | - Jung‐woo Chae
- College of PharmacyChungnam National UniversityDaejeonKorea
- Convergence Research CenterChungnam National UniversityDaejeonKorea
- Department of Bio‐AI ConvergenceChungnam National UniversityDaejeonKorea
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Jeremiah D. Momper
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San DiegoLa JollaCaliforniaUSA
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Wang X, Wang Z, Wang J, Yu Y, Wang Y, Xiong Z, Han S, Zhong XB, Wang P, Zhang L. Role of HNF4A-AS1/HNRNPC-mediated HNF4A ubiquitination protection against ritonavir-induced hepatotoxicity. Mol Pharmacol 2025; 107:100021. [PMID: 40037142 DOI: 10.1016/j.molpha.2025.100021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2024] [Revised: 01/07/2025] [Accepted: 01/31/2025] [Indexed: 03/06/2025] Open
Abstract
Ritonavir (RTV) is an important drug for anti-human immunodeficiency virus treatment and is mainly metabolized by cytochrome P450 (CYP) 3A4. Clinically, the most common side effect of RTV treatment is hepatoxicity. We previously showed that the long noncoding RNA hepatocyte nuclear factor 4 alpha (HNF4A) antisense 1 (HNF4A-AS1) negatively regulated CYP3A4 expression and participated in RTV-induced hepatotoxicity in vitro, but the mechanism has not been well understood. In this study, similar results were observed in the mouse, where liver-specific knockdown of Hnf4aos (homolog of human HNF4A-AS1) led to increased serum aspartate (∼1.8-fold) and alanine transaminase (∼2.4-fold) levels and enlarged and degenerated hepatocytes 24 hours after RTV administration. Meanwhile, endoplasmic reticulum stress markers GRP78, PDI, and XBP-1 increased about 2.4-fold, 2.1-fold, and 2.7-fold, respectively. The aggravated liver injury correlated with Hnf4aos knockdown, attributable to heightened Cyp3a11 (homolog of human CYP3A4) expression (mRNA and protein levels were 1.8-fold and 2.5-fold, respectively). Importantly, in vitro studies revealed the underlying mechanism that HNF4A-AS1 mediated the interaction between heterogeneous nuclear ribonucleoprotein C and HNF4A, whereas heterogeneous nuclear ribonucleoprotein C promoted HNF4A degradation through the ubiquitination pathway, thereby decreasing CYP3A4 expression and alleviating RTV-induced liver injury. Overall, our findings unveil a novel mechanism by which HNF4A-AS1 regulates CYP3A4 expression to influence RTV-induced liver injury. SIGNIFICANCE STATEMENT: HNF4A-AS1 negatively regulates the expression of CYP3A4, whose overexpression is highly correlated with ritonavir (RTV)-induced liver injury. In this study, the role of Hnf4aos (homolog of human HNF4A-AS1) in RTV-induced hepatotoxicity was confirmed in mice. We found that HNF4A-AS1 and HNRNPC form a complex and facilitate the ubiquitination and degradation of HNF4A protein, thereby decreasing CYP3A4 expression and alleviating RTV hepatotoxicity.
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Affiliation(s)
- Xiaofei Wang
- Academy of Medical Sciences, Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, China; Department of Pharmacology, School of Basic Medical Sciences, Open and Key Laboratory for Pharmacogenomics at Henan Universities, Zhengzhou University, Zhengzhou, China
| | - Zijing Wang
- Department of Pharmacology, School of Basic Medical Sciences, Open and Key Laboratory for Pharmacogenomics at Henan Universities, Zhengzhou University, Zhengzhou, China
| | - Jingya Wang
- Department of Pharmacology, School of Basic Medical Sciences, Open and Key Laboratory for Pharmacogenomics at Henan Universities, Zhengzhou University, Zhengzhou, China
| | - Yihang Yu
- Department of Pharmacology, School of Basic Medical Sciences, Open and Key Laboratory for Pharmacogenomics at Henan Universities, Zhengzhou University, Zhengzhou, China
| | - Yiting Wang
- Department of Clinical Pharmacology, School of Medicine, Henan University of Chinese Medicine, Zhengzhou, China
| | - Zaihuan Xiong
- Department of Pharmacology, School of Basic Medical Sciences, Open and Key Laboratory for Pharmacogenomics at Henan Universities, Zhengzhou University, Zhengzhou, China
| | - Shengna Han
- Department of Pharmacology, School of Basic Medical Sciences, Open and Key Laboratory for Pharmacogenomics at Henan Universities, Zhengzhou University, Zhengzhou, China
| | - Xiao-Bo Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Pei Wang
- Department of Pharmacology, School of Basic Medical Sciences, Open and Key Laboratory for Pharmacogenomics at Henan Universities, Zhengzhou University, Zhengzhou, China.
| | - Lirong Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Open and Key Laboratory for Pharmacogenomics at Henan Universities, Zhengzhou University, Zhengzhou, China.
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4
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Tabler CO, Tilton JC. Mechanism and Kinetics of HIV-1 Protease Activation. Viruses 2024; 16:1826. [PMID: 39772135 PMCID: PMC11680253 DOI: 10.3390/v16121826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2024] [Revised: 11/18/2024] [Accepted: 11/22/2024] [Indexed: 01/11/2025] Open
Abstract
The HIV-1 protease is a critical enzyme for viral replication. Because protease activity is necessary to generate mature infectious virions, it is a primary target of antiretroviral treatment. Here, we provide an overview of the mechanisms regulating protease activation and the methods available to assess protease activity. Finally, we will highlight some of the key discoveries regarding the kinetics of protease activation from the last decade, including how the manipulation of activation kinetics may provide novel HIV-1 treatment strategies.
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Affiliation(s)
| | - John C. Tilton
- Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA;
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Feys JR, Edwards K, Joyce MA, Saffran HA, Shields JA, Garcia K, Tyrrell DL, Fischer C. Peptide Aldehydes Incorporating Thiazol-4-yl Alanine Are Potent In Vitro Inhibitors of SARS-CoV-2 Main Protease. ACS Med Chem Lett 2024; 15:2046-2052. [PMID: 39563811 PMCID: PMC11571010 DOI: 10.1021/acsmedchemlett.4c00444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Revised: 10/28/2024] [Accepted: 10/30/2024] [Indexed: 11/21/2024] Open
Abstract
The main protease of SARS-CoV-2 is an essential enzyme required for polyprotein cleavage during viral replication and thus is an excellent target for development of direct-acting antiviral compounds. Continued research efforts have elucidated several peptidic small molecules like GC376, boceprevir, and nirmatrelvir with potent anticoronaviral activity bearing optimized amino acid side chain residues. To reduce synthetic complexity and cost, we used simple chemical surrogates that were commercially readily available to develop new inhibitors that mimic the potency of these drug compounds. We synthesized and tested several analogue chimeras of GC376 and boceprevir that have surrogate residues at the P1 and/or P2 position in order to further improve target binding. Both P1 variants with either a nonpolar cyclobutyl or polar thiazol-4-yl alanine resulted in low-micromolar to submicromolar Mpro inhibitors with strong antiviral activity in cell assays.
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Affiliation(s)
- Jenson R Feys
- Department of Chemistry, Barry University, Miami Shores, Florida 33161, United States
| | - Kyle Edwards
- Department of Chemistry, Barry University, Miami Shores, Florida 33161, United States
| | - Michael A Joyce
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2R3, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Holly A Saffran
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2R3, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Justin A Shields
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2R3, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Kassandra Garcia
- Department of Chemistry, Barry University, Miami Shores, Florida 33161, United States
| | - D Lorne Tyrrell
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2R3, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Conrad Fischer
- Department of Chemistry, Barry University, Miami Shores, Florida 33161, United States
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Sevrioukova IF. Interaction of CYP3A4 with the inhibitor cobicistat: Structural and mechanistic insights and comparison with ritonavir. Arch Biochem Biophys 2024; 758:110071. [PMID: 38909836 PMCID: PMC11286144 DOI: 10.1016/j.abb.2024.110071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 06/25/2024]
Abstract
Cobicistat is a derivative of ritonavir marketed as a pharmacoenhancer for anti-HIV therapy. This study investigated the interaction of cobicistat with the target protein, drug-metabolizing cytochrome P450 3A4 (CYP3A4), at the molecular level using spectral, kinetic, functional, and structural approaches. It was found that, similar to ritonavir, cobicistat directly coordinates to the heme via the thiazole nitrogen but its affinity and the binding rate are 2-fold lower: 0.030 μM and 0.72 s-1, respectively. The newly determined 2.5 Å crystal structure of cobicistat-bound CYP3A4 suggests that these changes arise from the inability of cobicistat to H-bond to the active site S119 and establish multiple stabilizing contacts with the F-F' connecting fragment, which becomes disordered upon steric clashing with the bulky morpholine moiety. Nonetheless, cobicistat inhibits recombinant CYP3A4 as potently as ritonavir (IC50 of 0.24 μM vs 0.22 μM, respectively) due to strong ligation to the heme and formation of extensive hydrophobic/aromatic interactions via the phenyl side-groups. To get insights into the inhibitory mechanism, the K257 residue, known to be solely and irreversibly modified by the reactive ritonavir metabolite, was substituted with alanine. Neither this nor control K266A mutation changed the extent of time-dependent inhibition of CYP3A4 by cobicistat and ritonavir, suggesting the existence of alternative inactivation mechanism(s). More importantly, K257 was found to be functionally important and contributed to CYP3A4 allosterism, possibly by modulating protein-ligand interactions through conformational dynamics.
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Affiliation(s)
- Irina F Sevrioukova
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697-3900, USA.
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Yadav J, Maldonato BJ, Roesner JM, Vergara AG, Paragas EM, Aliwarga T, Humphreys S. Enzyme-mediated drug-drug interactions: a review of in vivo and in vitro methodologies, regulatory guidance, and translation to the clinic. Drug Metab Rev 2024:1-33. [PMID: 39057923 DOI: 10.1080/03602532.2024.2381021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024]
Abstract
Enzyme-mediated pharmacokinetic drug-drug interactions can be caused by altered activity of drug metabolizing enzymes in the presence of a perpetrator drug, mostly via inhibition or induction. We identified a gap in the literature for a state-of-the art detailed overview assessing this type of DDI risk in the context of drug development. This manuscript discusses in vitro and in vivo methodologies employed during the drug discovery and development process to predict clinical enzyme-mediated DDIs, including the determination of clearance pathways, metabolic enzyme contribution, and the mechanisms and kinetics of enzyme inhibition and induction. We discuss regulatory guidance and highlight the utility of in silico physiologically-based pharmacokinetic modeling, an approach that continues to gain application and traction in support of regulatory filings. Looking to the future, we consider DDI risk assessment for targeted protein degraders, an emerging small molecule modality, which does not have recommended guidelines for DDI evaluation. Our goal in writing this report was to provide early-career researchers with a comprehensive view of the enzyme-mediated pharmacokinetic DDI landscape to aid their drug development efforts.
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Affiliation(s)
- Jaydeep Yadav
- Department of Pharmacokinetics, Dynamics, Metabolism & Bioanalytics (PDMB), Merck & Co., Inc., Boston, MA, USA
| | - Benjamin J Maldonato
- Department of Nonclinical Development and Clinical Pharmacology, Revolution Medicines, Inc., Redwood City, CA, USA
| | - Joseph M Roesner
- Department of Pharmacokinetics, Dynamics, Metabolism & Bioanalytics (PDMB), Merck & Co., Inc., Boston, MA, USA
| | - Ana G Vergara
- Department of Pharmacokinetics, Dynamics, Metabolism & Bioanalytics (PDMB), Merck & Co., Inc., Rahway, NJ, USA
| | - Erickson M Paragas
- Pharmacokinetics and Drug Metabolism Department, Amgen Research, South San Francisco, CA, USA
| | - Theresa Aliwarga
- Pharmacokinetics and Drug Metabolism Department, Amgen Research, South San Francisco, CA, USA
| | - Sara Humphreys
- Pharmacokinetics and Drug Metabolism Department, Amgen Research, South San Francisco, CA, USA
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8
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Lewis MA, Patil K, Ettayebi K, Estes MK, Atmar RL, Ramani S. Divergent responses of human intestinal organoid monolayers using commercial in vitro cytotoxicity assays. PLoS One 2024; 19:e0304526. [PMID: 38857221 PMCID: PMC11164375 DOI: 10.1371/journal.pone.0304526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/13/2024] [Indexed: 06/12/2024] Open
Abstract
In vitro models, such as primary cells and continuous cell lines routinely used for evaluating drug candidates, have limitations in their translational relevance to human diseases. Organotypic cultures are increasingly being used to assess therapeutics for various cancers and infectious diseases. Monitoring drug cytotoxicity in cell cultures is crucial in drug development, and several commercially available kits for cytotoxicity assessment offer distinct advantages and limitations. Given the complexity of organoid cultures, including donor-driven variability, we investigated drug-treated, tissue stem cell-derived human intestinal organoid responses with commonly used cell cytotoxicity assay kits. Using seven different compounds, we compared the cytotoxicity assay performance of two different leaky membrane-based and two metabolism-based assays. Significant variability was seen in reported viability outcomes across assays and organoid lines. High baseline activity of lactate dehydrogenase (LDH) in four human intestinal organoid lines required modification of the standard LDH assay protocol. Additionally, the LDH assay reported unique resilience to damage in a genetically-modified line contrasting results compared to other assays. This study highlights factors that can impact the measurement of cell cytotoxicity in intestinal organoid models, which are emerging as valuable new tools for research and pre-clinical drug testing and suggest the need for using multiple assay types to ensure reliable cytotoxicity assessment.
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Affiliation(s)
- Miranda A. Lewis
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ketki Patil
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Khalil Ettayebi
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Mary K. Estes
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Robert L. Atmar
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sasirekha Ramani
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
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Abdalla S, Compagnucci A, Riault Y, Chan MK, Bamford A, Nolan A, Ramos JT, Constant V, Nguyen TN, Zheng Y, Tréluyer JM, Froelicher-Bournaud L, Neveux N, Saidi Y, Cressey TR, Hirt D, on behalf of the SMILE study group. Simultaneous pharmacokinetic modeling of unbound and total darunavir with ritonavir in adolescents: a substudy of the SMILE trial. Antimicrob Agents Chemother 2024; 68:e0100423. [PMID: 38092664 PMCID: PMC10848770 DOI: 10.1128/aac.01004-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/14/2023] [Indexed: 02/08/2024] Open
Abstract
Darunavir (DRV) is an HIV protease inhibitor commonly used as part of antiretroviral treatment regimens globally for children and adolescents. It requires a pharmacological booster, such as ritonavir (RTV) or cobicistat. To better understand the pharmacokinetics (PK) of DRV in this younger population and the importance of the RTV boosting effect, a population PK substudy was conducted within SMILE trial, where the maintenance of HIV suppression with once daily integrate inhibitor + darunavir/ritonavir in children and adolescents is evaluated. A joint population PK model that simultaneously used total DRV, unbound DRV, and total RTV concentrations was developed. Competitive and non-competitive models were examined to define RTV's influence on DRV pharmacokinetics. Linear and non-linear equations were tested to assess DRV protein binding. A total of 443 plasma samples from 152 adolescents were included in this analysis. Darunavir PK was best described by a one-compartment model first-order absorption and elimination. The influence of RTV on DRV pharmacokinetics was best characterized by ritonavir area under the curve on DRV clearance using a power function. The association of non-linear and linear equations was used to describe DRV protein binding to alpha-1 glycoprotein and albumin, respectively. In our population, simulations indicate that 86.8% of total and unbound DRV trough concentrations were above 0.55 mg/L [10 times protein binding-adjusted EC50 for wild-type (WT) HIV-1] and 0.0243 mg/L (10 times EC90 for WT HIV-1) targets, respectively. Predictions were also in agreement with observed outcomes from adults receiving 800/100 mg DRV/r once a day. Administration of 800/100 mg of DRV/r once daily provides satisfactory concentrations and exposures for adolescents aged 12 years and older.
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Affiliation(s)
- Seef Abdalla
- Pharmacologie et évaluation des thérapeutiques chez l'enfant et la femme enceinte, Université Paris Cité, Paris, France
- Service de Pharmacologie Clinique, Hôpital Cochin, APHP Centre–Université Paris Cité, Paris, France
| | - Alexandra Compagnucci
- SC10-US019 Essais Thérapeutiques et Maladies Infectieuses, INSERM, Villejuif, France
| | - Yoann Riault
- SC10-US019 Essais Thérapeutiques et Maladies Infectieuses, INSERM, Villejuif, France
| | - Man K. Chan
- MRC Clinical Trials Unit at UCL, London, United Kingdom
| | - Alasdair Bamford
- MRC Clinical Trials Unit at UCL, London, United Kingdom
- Paediatric Infectious Diseases, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Aoife Nolan
- MRC Clinical Trials Unit at UCL, London, United Kingdom
| | - José T. Ramos
- Department of Pediatrics, Fundación de Investigación Biomédica Hospital Clínico San Carlos, Hospital Clínico San Carlos, Madrid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Universidad Complutense de Madrid, Madrid, Spain
| | - Valentin Constant
- Pharmacologie et évaluation des thérapeutiques chez l'enfant et la femme enceinte, Université Paris Cité, Paris, France
| | - Thao-Nguyen Nguyen
- Pharmacologie et évaluation des thérapeutiques chez l'enfant et la femme enceinte, Université Paris Cité, Paris, France
| | - Yi Zheng
- Pharmacologie et évaluation des thérapeutiques chez l'enfant et la femme enceinte, Université Paris Cité, Paris, France
| | - Jean-Marc Tréluyer
- Pharmacologie et évaluation des thérapeutiques chez l'enfant et la femme enceinte, Université Paris Cité, Paris, France
- Service de Pharmacologie Clinique, Hôpital Cochin, APHP Centre–Université Paris Cité, Paris, France
- Unité de Recherche Clinique, Hôpital Necker Enfants Malades, APHP Centre–Université Paris Cité, Paris, France
| | - Léo Froelicher-Bournaud
- Pharmacologie et évaluation des thérapeutiques chez l'enfant et la femme enceinte, Université Paris Cité, Paris, France
- Service de Pharmacologie Clinique, Hôpital Cochin, APHP Centre–Université Paris Cité, Paris, France
| | - Nathalie Neveux
- Service de Biochimie, Hôpital Cochin, APHP Centre–Université Paris Cité, Paris, France
| | - Yacine Saidi
- SC10-US019 Essais Thérapeutiques et Maladies Infectieuses, INSERM, Villejuif, France
| | - Tim R. Cressey
- AMS-PHPT Research Collaboration, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
| | - Déborah Hirt
- Pharmacologie et évaluation des thérapeutiques chez l'enfant et la femme enceinte, Université Paris Cité, Paris, France
- Service de Pharmacologie Clinique, Hôpital Cochin, APHP Centre–Université Paris Cité, Paris, France
| | - on behalf of the SMILE study group
- Pharmacologie et évaluation des thérapeutiques chez l'enfant et la femme enceinte, Université Paris Cité, Paris, France
- Service de Pharmacologie Clinique, Hôpital Cochin, APHP Centre–Université Paris Cité, Paris, France
- SC10-US019 Essais Thérapeutiques et Maladies Infectieuses, INSERM, Villejuif, France
- MRC Clinical Trials Unit at UCL, London, United Kingdom
- Paediatric Infectious Diseases, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
- Department of Pediatrics, Fundación de Investigación Biomédica Hospital Clínico San Carlos, Hospital Clínico San Carlos, Madrid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Universidad Complutense de Madrid, Madrid, Spain
- Unité de Recherche Clinique, Hôpital Necker Enfants Malades, APHP Centre–Université Paris Cité, Paris, France
- Service de Biochimie, Hôpital Cochin, APHP Centre–Université Paris Cité, Paris, France
- AMS-PHPT Research Collaboration, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
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10
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Bege M, Borbás A. The Design, Synthesis and Mechanism of Action of Paxlovid, a Protease Inhibitor Drug Combination for the Treatment of COVID-19. Pharmaceutics 2024; 16:217. [PMID: 38399271 PMCID: PMC10891713 DOI: 10.3390/pharmaceutics16020217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024] Open
Abstract
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has presented an enormous challenge to health care systems and medicine. As a result of global research efforts aimed at preventing and effectively treating SARS-CoV-2 infection, vaccines with fundamentally new mechanisms of action and some small-molecule antiviral drugs targeting key proteins in the viral cycle have been developed. The most effective small-molecule drug approved to date for the treatment of COVID-19 is PaxlovidTM, which is a combination of two protease inhibitors, nirmatrelvir and ritonavir. Nirmatrelvir is a reversible covalent peptidomimetic inhibitor of the main protease (Mpro) of SARS-CoV-2, which enzyme plays a crucial role in viral reproduction. In this combination, ritonavir serves as a pharmacokinetic enhancer, it irreversibly inhibits the cytochrome CYP3A4 enzyme responsible for the rapid metabolism of nirmatrelvir, thereby increasing the half-life and bioavailability of nirmatrelvir. In this tutorial review, we summarize the development and pharmaceutical chemistry aspects of Paxlovid, covering the evolution of protease inhibitors, the warhead design, synthesis and the mechanism of action of nirmatrelvir, as well as the synthesis of ritonavir and its CYP3A4 inhibition mechanism. The efficacy of Paxlovid to novel virus mutants is also overviewed.
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Affiliation(s)
- Miklós Bege
- Department of Pharmaceutical Chemistry, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary;
- HUN-REN-DE Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- Institute of Healthcare Industry, University of Debrecen, Nagyerdei krt 98, 4032 Debrecen, Hungary
| | - Anikó Borbás
- Department of Pharmaceutical Chemistry, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary;
- HUN-REN-DE Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- National Laboratory of Virology, University of Pécs, Ifjúság útja 20, 7624 Pécs, Hungary
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11
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Hemmati AA, Mojiri-Forushani H. Off-label Use of Medicines in COVID-19: A Lesson For Future. CORONAVIRUSES 2024; 5. [DOI: 10.2174/0126667975271719231107052426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/13/2023] [Accepted: 09/18/2023] [Indexed: 01/03/2025]
Abstract
Abstract:
The COVID-19 infection is rapidly spreading worldwide. Treating this new viral infection
is a great challenge worldwide. There is no specific and approved medication for its treatment,
so some medications are considered off-label. Antivirals, corticosteroids, antimalarial agents, and
antibiotics are proposed in different countries to treat COVID-19. This narrative review discussed the
off-label use of medications for COVID-19 and the beneficial and adverse effects of them. Evidence
was collected and sorted from the literature ranging from 2019 to 2022 on scientific databases such
as Web of Science, PubMed, and Scopus with suitable keywords. All papers, namely systematic
reviews, case studies, and clinical guidelines, were evaluated. Antimalarial agents, antivirals, antibiotics,
corticosteroids, NSAIDs, biological medicines, Ivermectin, and melatonin were reviewed in
this study. Some medications have direct antiviral effects, and many can reduce infection symptoms
and hospitalization. In some clinical trial trials, even some of them, such as corticosteroids, can lower
death rates, particularly during the cytokine storm period. However, the effectiveness of some
medications has not been understood. Besides, the side effects of off-label use of these medications
must be considered a serious concern. There are no proven medications for COVID-19 yet. Off-label
use of medications is a double-edged sword that can have advantages outweighing its disadvantages.
The COVID-19 crisis taught us many lessons about dealing with health-related crises and their
treatment management. One of the most important lessons is paying more attention to the discovery
and development of novel drugs and vaccines based on modern technology.
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Affiliation(s)
- Ali Asghar Hemmati
- Department of Pharmacology, Marine Pharmaceutical Science Research Center, School of Pharmacy, Ahvaz
Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Hoda Mojiri-Forushani
- Department of Pharmacology, School of Medicine, Abadan
University of Medical Sciences, Abadan, Iran
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12
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Loos NHC, Martins MLF, de Jong D, Lebre MC, Tibben M, Beijnen JH, Schinkel AH. Coadministration of ABCB1/P-glycoprotein inhibitor elacridar improves tissue distribution of ritonavir-boosted oral cabazitaxel in mice. Int J Pharm 2024; 650:123708. [PMID: 38135258 DOI: 10.1016/j.ijpharm.2023.123708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023]
Abstract
Developing an oral formulation for the chemotherapeutic cabazitaxel might improve its patient-friendliness, costs, and potentially exposure profile. Cabazitaxel oral availability is restricted by CYP3A-mediated first-pass metabolism, but can be substantially boosted with the CYP3A inhibitor ritonavir. We here tested whether adding the ABCB1/P-glycoprotein inhibitor elacridar to ritonavir-boosted oral cabazitaxel could further improve its tissue exposure using wild-type, CYP3A4-humanized and Abcb1a/b-/- mice. The plasma AUC0-2h of cabazitaxel was increased 2.3- and 1.9-fold in the ritonavir- and ritonavir-plus-elacridar groups of wild-type, and 10.5- and 8.8-fold in CYP3A4-humanized mice. Elacridar coadministration did not influence cabazitaxel plasma exposure. The brain-to-plasma ratio of cabazitaxel was not increased in the ritonavir group, 7.3-fold in the elacridar group and 13.4-fold in the combined booster group in wild-type mice. This was 0.4-, 4.6- and 3.6-fold in CYP3A4-humanized mice, illustrating that Abcb1 limited cabazitaxel brain exposure also during ritonavir boosting. Ritonavir itself was also a potent substrate for the Abcb1 efflux transporter, limiting its oral availability (3.3-fold) and brain penetration (10.6-fold). Both processes were fully reversed by elacridar. The tissue disposition of ritonavir-boosted oral cabazitaxel could thus be markedly enhanced by elacridar coadministration without affecting the plasma exposure. This approach should be verified in selected patient populations.
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Affiliation(s)
- Nancy H C Loos
- The Netherlands Cancer Institute, Division of Pharmacology, Amsterdam, The Netherlands
| | - Margarida L F Martins
- The Netherlands Cancer Institute, Division of Pharmacology, Amsterdam, The Netherlands
| | - Daniëlle de Jong
- The Netherlands Cancer Institute, Division of Pharmacy and Pharmacology, Amsterdam, The Netherlands
| | - Maria C Lebre
- The Netherlands Cancer Institute, Division of Pharmacology, Amsterdam, The Netherlands
| | - Matthijs Tibben
- The Netherlands Cancer Institute, Division of Pharmacy and Pharmacology, Amsterdam, The Netherlands
| | - Jos H Beijnen
- The Netherlands Cancer Institute, Division of Pharmacology, Amsterdam, The Netherlands; The Netherlands Cancer Institute, Division of Pharmacy and Pharmacology, Amsterdam, The Netherlands; Utrecht University, Faculty of Science, Department of Pharmaceutical Sciences, Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht, The Netherlands
| | - Alfred H Schinkel
- The Netherlands Cancer Institute, Division of Pharmacology, Amsterdam, The Netherlands.
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13
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Outteridge M, Nunn CM, Devine K, Patel B, McLean GR. Antivirals for Broader Coverage against Human Coronaviruses. Viruses 2024; 16:156. [PMID: 38275966 PMCID: PMC10820748 DOI: 10.3390/v16010156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/05/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
Coronaviruses (CoVs) are enveloped positive-sense single-stranded RNA viruses with a genome that is 27-31 kbases in length. Critical genes include the spike (S), envelope (E), membrane (M), nucleocapsid (N) and nine accessory open reading frames encoding for non-structural proteins (NSPs) that have multiple roles in the replication cycle and immune evasion (1). There are seven known human CoVs that most likely appeared after zoonotic transfer, the most recent being SARS-CoV-2, responsible for the COVID-19 pandemic. Antivirals that have been approved by the FDA for use against COVID-19 such as Paxlovid can target and successfully inhibit the main protease (MPro) activity of multiple human CoVs; however, alternative proteomes encoded by CoV genomes have a closer genetic similarity to each other, suggesting that antivirals could be developed now that target future CoVs. New zoonotic introductions of CoVs to humans are inevitable and unpredictable. Therefore, new antivirals are required to control not only the next human CoV outbreak but also the four common human CoVs (229E, OC43, NL63, HKU1) that circulate frequently and to contain sporadic outbreaks of the severe human CoVs (SARS-CoV, MERS and SARS-CoV-2). The current study found that emerging antiviral drugs, such as Paxlovid, could target other CoVs, but only SARS-CoV-2 is known to be targeted in vivo. Other drugs which have the potential to target other human CoVs are still within clinical trials and are not yet available for public use. Monoclonal antibody (mAb) treatment and vaccines for SARS-CoV-2 can reduce mortality and hospitalisation rates; however, they target the Spike protein whose sequence mutates frequently and drifts. Spike is also not applicable for targeting other HCoVs as these are not well-conserved sequences among human CoVs. Thus, there is a need for readily available treatments globally that target all seven human CoVs and improve the preparedness for inevitable future outbreaks. Here, we discuss antiviral research, contributing to the control of common and severe CoV replication and transmission, including the current SARS-CoV-2 outbreak. The aim was to identify common features of CoVs for antivirals, biologics and vaccines that could reduce the scientific, political, economic and public health strain caused by CoV outbreaks now and in the future.
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Affiliation(s)
- Mia Outteridge
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Christine M. Nunn
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Kevin Devine
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Bhaven Patel
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Gary R. McLean
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
- National Heart and Lung Institute, Imperial College London, London W2 1PG, UK
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14
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Richard AM, Wong NR, Harris K, Sundar R, Scott EE, Pochapsky TC. Selective steroidogenic cytochrome P450 haem iron ligation by steroid-derived isonitriles. Commun Chem 2023; 6:183. [PMID: 37660137 PMCID: PMC10475101 DOI: 10.1038/s42004-023-00994-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 08/23/2023] [Indexed: 09/04/2023] Open
Abstract
Alkyl isonitriles, R-NC, have previously been shown to ligate the heme (haem) iron of cytochromes P450 in both accessible oxidation states (ferrous, Fe2+, and ferric, Fe3+). Herein, the preparation of four steroid-derived isonitriles and their interactions with several P450s, including the steroidogenic CYP17A1 and CYP106A2, as well as the more promiscuous drug metabolizers CYP3A4 and CYP2D6, is described. It was found that successful ligation of the heme iron by the isonitrile functionality for a given P450 depends on both the position and stereochemistry of the isonitrile on the steroid skeleton. Spectral studies indicate that isonitrile ligation of the ferric heme is stable upon reduction to the ferrous form, with reoxidation resulting in the original complex. A crystallographic structure of CYP17A1 with an isonitrile derived from pregnanalone further confirmed the interaction and identified the absolute stereochemistry of the bound species.
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Affiliation(s)
- Alaina M Richard
- Chemical Biology Program, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Nathan R Wong
- Dept. of Biochemistry, Brandeis University, 415 South St., Waltham, 02454-9110, MA, USA
| | - Kurt Harris
- Department of Medicinal Chemistry, University of Michigan, 428 Church St., Ann Arbor, 48109-1065, MI, USA
| | - Reethy Sundar
- Dept. of Biochemistry, Brandeis University, 415 South St., Waltham, 02454-9110, MA, USA
| | - Emily E Scott
- Chemical Biology Program, University of Michigan, Ann Arbor, 48109, MI, USA
- Department of Medicinal Chemistry, University of Michigan, 428 Church St., Ann Arbor, 48109-1065, MI, USA
- Departments of Pharmacology and Biological Chemistry, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Thomas C Pochapsky
- Dept. of Biochemistry, Brandeis University, 415 South St., Waltham, 02454-9110, MA, USA.
- Dept. of Chemistry and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, 415 South St, Waltham, 02454-9110, MA, USA.
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15
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Geng ZZ, Atla S, Shaabani N, Vulupala V, Yang KS, Alugubelli YR, Khatua K, Chen PH, Xiao J, Blankenship LR, Ma XR, Vatansever EC, Cho CCD, Ma Y, Allen R, Ji H, Xu S, Liu WR. A Systematic Survey of Reversibly Covalent Dipeptidyl Inhibitors of the SARS-CoV-2 Main Protease. J Med Chem 2023; 66:11040-11055. [PMID: 37561993 PMCID: PMC10861299 DOI: 10.1021/acs.jmedchem.3c00221] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Indexed: 08/12/2023]
Abstract
SARS-CoV-2, the COVID-19 pathogen, relies on its main protease (MPro) for replication and pathogenesis. MPro is a demonstrated target for the development of antivirals for SARS-CoV-2. Past studies have systematically explored tripeptidyl inhibitors such as nirmatrelvir as MPro inhibitors. However, dipeptidyl inhibitors especially those with a spiro residue at their P2 position have not been systematically investigated. In this work, we synthesized about 30 dipeptidyl MPro inhibitors and characterized them on enzymatic inhibition potency, structures of their complexes with MPro, cellular MPro inhibition potency, antiviral potency, cytotoxicity, and in vitro metabolic stability. Our results indicated that MPro has a flexible S2 pocket to accommodate inhibitors with a large P2 residue and revealed that dipeptidyl inhibitors with a large P2 spiro residue such as (S)-2-azaspiro [4,4]nonane-3-carboxylate and (S)-2-azaspiro[4,5]decane-3-carboxylate have favorable characteristics. One compound, MPI60, containing a P2 (S)-2-azaspiro[4,4]nonane-3-carboxylate displayed high antiviral potency, low cellular cytotoxicity, and high in vitro metabolic stability.
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Affiliation(s)
- Zhi Zachary Geng
- Department
of Chemistry, Texas A&M Drug Discovery Laboratory, Texas A&M University, College Station, Texas 77843, United States
| | - Sandeep Atla
- Department
of Chemistry, Texas A&M Drug Discovery Laboratory, Texas A&M University, College Station, Texas 77843, United States
| | - Namir Shaabani
- Sorrento
Therapeutics, Inc. San Diego, California 92121, United States
| | - Veerabhadra Vulupala
- Department
of Chemistry, Texas A&M Drug Discovery Laboratory, Texas A&M University, College Station, Texas 77843, United States
| | - Kai S. Yang
- Department
of Chemistry, Texas A&M Drug Discovery Laboratory, Texas A&M University, College Station, Texas 77843, United States
| | - Yugendar R. Alugubelli
- Department
of Chemistry, Texas A&M Drug Discovery Laboratory, Texas A&M University, College Station, Texas 77843, United States
| | - Kaustav Khatua
- Department
of Chemistry, Texas A&M Drug Discovery Laboratory, Texas A&M University, College Station, Texas 77843, United States
| | - Peng-Hsun Chen
- Department
of Chemistry, Texas A&M Drug Discovery Laboratory, Texas A&M University, College Station, Texas 77843, United States
| | - Jing Xiao
- Department
of Chemistry, Texas A&M Drug Discovery Laboratory, Texas A&M University, College Station, Texas 77843, United States
| | - Lauren R. Blankenship
- Department
of Chemistry, Texas A&M Drug Discovery Laboratory, Texas A&M University, College Station, Texas 77843, United States
| | - Xinyu R. Ma
- Department
of Chemistry, Texas A&M Drug Discovery Laboratory, Texas A&M University, College Station, Texas 77843, United States
| | - Erol C. Vatansever
- Department
of Chemistry, Texas A&M Drug Discovery Laboratory, Texas A&M University, College Station, Texas 77843, United States
| | - Chia-Chuan D. Cho
- Department
of Chemistry, Texas A&M Drug Discovery Laboratory, Texas A&M University, College Station, Texas 77843, United States
| | - Yuying Ma
- Department
of Chemistry, Texas A&M Drug Discovery Laboratory, Texas A&M University, College Station, Texas 77843, United States
| | - Robert Allen
- Sorrento
Therapeutics, Inc. San Diego, California 92121, United States
| | - Henry Ji
- Sorrento
Therapeutics, Inc. San Diego, California 92121, United States
| | - Shiqing Xu
- Department
of Chemistry, Texas A&M Drug Discovery Laboratory, Texas A&M University, College Station, Texas 77843, United States
- Department
of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, Texas 77843, United States
| | - Wenshe Ray Liu
- Department
of Chemistry, Texas A&M Drug Discovery Laboratory, Texas A&M University, College Station, Texas 77843, United States
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
- Institute
of Biosciences and Technology and Department of Translational Medical
Sciences, College of Medicine, Texas A&M
University, Houston, Texas 77030, United States
- Department
of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, Texas 77843, United States
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16
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Labach DS, Kohio HP, Tse EA, Paparisto E, Friesen NJ, Pankovich J, Bazett M, Barr SD. The Metallodrug BOLD-100 Is a Potent Inhibitor of SARS-CoV-2 Replication and Has Broad-Acting Antiviral Activity. Biomolecules 2023; 13:1095. [PMID: 37509131 PMCID: PMC10377621 DOI: 10.3390/biom13071095] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 06/30/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
The COVID-19 pandemic has highlighted an urgent need to discover and test new drugs to treat patients. Metal-based drugs are known to interact with DNA and/or a variety of proteins such as enzymes and transcription factors, some of which have been shown to exhibit anticancer and antimicrobial effects. BOLD-100 (sodium trans-[tetrachlorobis(1H-indazole)ruthenate(III)]dihydrate) is a novel ruthenium-based drug currently being evaluated in a Phase 1b/2a clinical trial for the treatment of advanced gastrointestinal cancer. Given that metal-based drugs are known to exhibit antimicrobial activities, we asked if BOLD-100 exhibits antiviral activity towards SARS-CoV-2. We demonstrated that BOLD-100 potently inhibits SARS-CoV-2 replication and cytopathic effects in vitro. An RNA sequencing analysis showed that BOLD-100 inhibits virus-induced transcriptional changes in infected cells. In addition, we showed that the antiviral activity of BOLD-100 is not specific for SARS-CoV-2, but also inhibits the replication of the evolutionarily divergent viruses Human Immunodeficiency Virus type 1 and Human Adenovirus type 5. This study identifies BOLD-100 as a potentially novel broad-acting antiviral drug.
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Affiliation(s)
- Daniel S Labach
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada
| | - Hinissan P Kohio
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada
| | - Edwin A Tse
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada
| | - Ermela Paparisto
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada
| | - Nicole J Friesen
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada
| | - Jim Pankovich
- Bold Therapeutics Inc., 422 Richards St, Suite 170, Vancouver, BC V6N 2Z4, Canada
| | - Mark Bazett
- Bold Therapeutics Inc., 422 Richards St, Suite 170, Vancouver, BC V6N 2Z4, Canada
| | - Stephen D Barr
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada
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17
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Miners JO, Polasek TM, Hulin JA, Rowland A, Meech R. Drug-drug interactions that alter the exposure of glucuronidated drugs: Scope, UDP-glucuronosyltransferase (UGT) enzyme selectivity, mechanisms (inhibition and induction), and clinical significance. Pharmacol Ther 2023:108459. [PMID: 37263383 DOI: 10.1016/j.pharmthera.2023.108459] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 06/03/2023]
Abstract
Drug-drug interactions (DDIs) arising from the perturbation of drug metabolising enzyme activities represent both a clinical problem and a potential economic loss for the pharmaceutical industry. DDIs involving glucuronidated drugs have historically attracted little attention and there is a perception that interactions are of minor clinical relevance. This review critically examines the scope and aetiology of DDIs that result in altered exposure of glucuronidated drugs. Interaction mechanisms, namely inhibition and induction of UDP-glucuronosyltransferase (UGT) enzymes and the potential interplay with drug transporters, are reviewed in detail, as is the clinical significance of known DDIs. Altered victim drug exposure arising from modulation of UGT enzyme activities is relatively common and, notably, the incidence and importance of UGT induction as a DDI mechanism is greater than generally believed. Numerous DDIs are clinically relevant, resulting in either loss of efficacy or an increased risk of adverse effects, necessitating dose individualisation. Several generalisations relating to the likelihood of DDIs can be drawn from the known substrate and inhibitor selectivities of UGT enzymes, highlighting the importance of comprehensive reaction phenotyping studies at an early stage of drug development. Further, rigorous assessment of the DDI liability of new chemical entities that undergo glucuronidation to a significant extent has been recommended recently by regulatory guidance. Although evidence-based approaches exist for the in vitro characterisation of UGT enzyme inhibition and induction, the availability of drugs considered appropriate for use as 'probe' substrates in clinical DDI studies is limited and this should be research priority.
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Affiliation(s)
- John O Miners
- Discipline of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, Flinders University College of Medicine and Public Health, Flinders University, Adelaide, Australia.
| | - Thomas M Polasek
- Certara, Princeton, NJ, USA; Centre for Medicines Use and Safety, Monash University, Melbourne, Australia
| | - Julie-Ann Hulin
- Discipline of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, Flinders University College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Andrew Rowland
- Discipline of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, Flinders University College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Robyn Meech
- Discipline of Clinical Pharmacology and Flinders Centre for Innovation in Cancer, Flinders University College of Medicine and Public Health, Flinders University, Adelaide, Australia
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18
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Hong E, Shi A, Beringer P. Drug-drug interactions involving CFTR modulators: a review of the evidence and clinical implications. Expert Opin Drug Metab Toxicol 2023; 19:203-216. [PMID: 37259485 DOI: 10.1080/17425255.2023.2220960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/30/2023] [Indexed: 06/02/2023]
Abstract
INTRODUCTION Cystic fibrosis (CF) is characterized by mucus accumulation impairing the lungs, gastrointestinal tract, and other organs. Cystic fibrosis transmembrane conductance regulator (CFTR) modulators (ivacaftor, tezacaftor, elexacaftor, and lumacaftor) significantly improve lung function and nutritional status; however, they are substrates, inhibitors, and/or inducers of certain CYP enzymes and transporters, raising the risk of drug-drug interactions (DDI) with common CF medications. AREAS COVERED A literature search was conducted for DDIs involving CFTR modulators by reviewing new drug applications, drug package inserts, clinical studies, and validated databases of substrates, inhibitors, and inducers. Clinically, CYP3A inducers and inhibitors significantly decrease and increase systemic concentrations of elexacaftor/tezacaftor/ivacaftor, respectively. Additionally, lumacaftor and ivacaftor alter concentrations of CYP3A and P-gp substrates. Potential DDIs without current clinical evidence include ivacaftor and elexacaftor's effect on CYP2C9 and OATP1B1/3 substrates, respectively, and OATP1B1/3 and P-gp inhibitors' effect on tezacaftor. A literature review was conducted using PubMed. EXPERT OPINION Dosing recommendations for CFTR modulators with DDIs are relatively comprehensive; however, recommendations on timing of dosing transition of CFTR modulators when CYP3A inhibitors are initiated or discontinued is incomplete. Certain drug interactions may be managed by choosing an alternative treatment to avoid/minimize DDIs. Next generation CFTR modulator therapies under development are expected to provide increased activity with reduced DDI risk.
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Affiliation(s)
- Eunjin Hong
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Alan Shi
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Paul Beringer
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
- USC Anton Yelchin CF Clinic, Los Angeles, CA, USA
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19
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Muller S. The abscopal effect: Implications for drug discovery in autoimmunity. Autoimmun Rev 2023; 22:103315. [PMID: 36924921 DOI: 10.1016/j.autrev.2023.103315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/09/2023] [Indexed: 03/17/2023]
Abstract
The emergence of novel targeted therapies and the tools that increase the stability and delivery of drugs have greatly improved treatment outcomes in autoimmune diseases (ADs). Recently-developed strategies deplete specific deleterious T- and B-cell subsets, interrupt receptor-ligand interactions, and/or inhibit the secretion or activity of inflammatory mediators linked to tissue damage. Although generally efficient, these lines of intervention have limitations, with documented cases of drug-resistance and undesired side effects. They are also difficult to apply to non-organ-specific ADs, where the trigger and effector antigens are unknown and in which autoimmune activity is widely spread throughout the body. The potential of cellular modulators that act at a distance from the affected site, by abscopal effect, as described in the case of cancer radio- and immuno-therapy might be especially efficient in the context of ADs. Future research to discover small molecule- and peptide-based treatments will need to explore potential drugs with abscopal effects that could elicit potent immune tolerance and clinical quiescence to restore quality of life of affected patients.
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Affiliation(s)
- Sylviane Muller
- CNRS and Strasbourg University Unit Biotechnology and Cell signalling/Strasbourg Drug Discovery and Development Institute (IMS), Strasbourg, France; Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg University, Strasbourg, France; University of Strasbourg Institute for Advanced Study (USIAS), Strasbourg, France.
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20
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Hopkins AM, Sorich MJ, McLachlan AJ, Karapetis CS, Miners JO, van Dyk M, Rowland A. Understanding the Risk of Drug Interactions Between Ritonavir-Containing COVID-19 Therapies and Small-Molecule Kinase Inhibitors in Patients With Cancer. JCO Precis Oncol 2023; 7:e2200538. [PMID: 36787507 DOI: 10.1200/po.22.00538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
PURPOSE The introduction of COVID-19 therapies containing ritonavir has markedly expanded the scope of use for this medicine. As a strong cytochrome P450 3A4 inhibitor, the use of ritonavir is associated with a high drug interaction risk. There are currently no data to inform clinician regarding the likely magnitude and duration of interaction between ritonavir-containing COVID-19 therapies and small-molecule kinase inhibitors (KIs) in patients with cancer. METHODS Physiologically based pharmacokinetic modeling was used to conduct virtual clinical trials with a parallel group study design in the presence and absence of ritonavir (100 mg twice daily for 5 days). The magnitude and time course of changes in KI exposure when coadministered with ritonavir was evaluated as the primary outcome. RESULTS Dosing of ritonavir resulted in a > 2-fold increase in steady-state area under the plasma concentration-time curve and maximal concentration for six of the 10 KIs. When the KI was coadministered with ritonavir, dose reductions to between 10% and 75% of the original dose were required to achieve an area under the plasma concentration-time curve within 1.25-fold of the value in the absence of ritonavir. CONCLUSION To our knowledge, this study provides the first data to assist clinicians' understanding of the drug interaction risk associated with administering ritonavir-containing COVID-19 therapies to patients with cancer who are currently being treated with KIs. These data may support clinicians to make more informed dosing decisions for patients with cancer undergoing treatment with KIs who require treatment with ritonavir-containing COVID-19 antiviral therapies.
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Affiliation(s)
- Ashley M Hopkins
- College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Michael J Sorich
- College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Andrew J McLachlan
- Faculty of Medicine and Health, Sydney Pharmacy School, University of Sydney, Sydney, Australia
| | - Christos S Karapetis
- College of Medicine and Public Health, Flinders University, Adelaide, Australia.,Department of Medical Oncology, Flinders Medical Centre, Adelaide, Australia
| | - John O Miners
- College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Madelé van Dyk
- College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Andrew Rowland
- College of Medicine and Public Health, Flinders University, Adelaide, Australia
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21
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Gökçe F, Kaestli A, Lohasz C, de Geus M, Kaltenbach H, Renggli K, Bornhauser B, Hierlemann A, Modena M. Microphysiological Drug-Testing Platform for Identifying Responses to Prodrug Treatment in Primary Leukemia. Adv Healthc Mater 2023; 12:e2202506. [PMID: 36651229 PMCID: PMC11469234 DOI: 10.1002/adhm.202202506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/20/2022] [Indexed: 01/19/2023]
Abstract
Despite increasing survival rates of pediatric leukemia patients over the past decades, the outcome of some leukemia subtypes has remained dismal. Drug sensitivity and resistance testing on patient-derived leukemia samples provide important information to tailor treatments for high-risk patients. However, currently used well-based drug screening platforms have limitations in predicting the effects of prodrugs, a class of therapeutics that require metabolic activation to become effective. To address this issue, a microphysiological drug-testing platform is developed that enables co-culturing of patient-derived leukemia cells, human bone marrow mesenchymal stromal cells, and human liver microtissues within the same microfluidic platform. This platform also enables to control the physical interaction between the diverse cell types. Herein, it is made possible to recapitulate hepatic prodrug activation of ifosfamide in their platform, which is very difficult in traditional well-based assays. By testing the susceptibility of primary patient-derived leukemia samples to the prodrug ifosfamide, sample-specific sensitivities to ifosfamide in primary leukemia samples are identified. The microfluidic platform is found to enable the recapitulation of physiologically relevant conditions and the testing of prodrugs including short-lived and unstable metabolites. The platform holds great potential for clinical translation and precision chemotherapy selection.
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Affiliation(s)
- Furkan Gökçe
- Department of Biosystems Science and EngineeringETH ZurichBaselBS, 4058Switzerland
| | - Alicia Kaestli
- Department of Biosystems Science and EngineeringETH ZurichBaselBS, 4058Switzerland
| | - Christian Lohasz
- Department of Biosystems Science and EngineeringETH ZurichBaselBS, 4058Switzerland
| | - Martina de Geus
- Department of Biosystems Science and EngineeringETH ZurichBaselBS, 4058Switzerland
| | | | - Kasper Renggli
- Department of Biosystems Science and EngineeringETH ZurichBaselBS, 4058Switzerland
| | - Beat Bornhauser
- Children's Research CenterUniversity Children's Hospital ZurichZurichZH, 8008Switzerland
| | - Andreas Hierlemann
- Department of Biosystems Science and EngineeringETH ZurichBaselBS, 4058Switzerland
| | - Mario Modena
- Department of Biosystems Science and EngineeringETH ZurichBaselBS, 4058Switzerland
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22
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Chary MA, Barbuto AF, Izadmehr S, Tarsillo M, Fleischer E, Burns MM. COVID-19 Therapeutics: Use, Mechanism of Action, and Toxicity (Xenobiotics). J Med Toxicol 2023; 19:26-36. [PMID: 36525217 PMCID: PMC9756926 DOI: 10.1007/s13181-022-00918-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 emerged in 2019 and led to the COVID-19 pandemic. Efforts to develop therapeutics against SARS-Cov-2 led to both new treatments and attempts to repurpose existing medications. Here, we provide a narrative review of the xenobiotics and alternative remedies used or proposed to treat COVID-19. Most repositioned xenobiotics have had neither the feared toxicity nor the anticipated efficacy. Repurposed viral replication inhibitors are not efficacious and frequently associated with nausea, vomiting, and diarrhea. Antiviral medications designed specifically against SARS-CoV-2 may prevent progression to severe disease in at-risk individuals and appear to have a wide therapeutic index. Colloidal silver, zinc, and ivermectin have no demonstrated efficacy. Ivermectin has a wide therapeutic index but is not efficacious and acquiring it from veterinary sources poses additional danger. Chloroquine has a narrow therapeutic index and no efficacy. A companion review covers vaccines, monoclonal antibodies, and immunotherapies. Together, these two reviews form an update to our 2020 review.
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Affiliation(s)
- Michael A Chary
- Division of Medical Toxicology, Department of Emergency Medicine, Boston Children's Hospital, Boston, MA, USA.
- Regional Center for Poison Control and Prevention Serving Massachusetts and Rhode Island, Boston, MA, USA.
- Division of Medical Toxicology, Department of Emergency Medicine, Weill Cornell Medical College, New York, NY, USA.
| | - Alexander F Barbuto
- Division of Medical Toxicology, Department of Emergency Medicine, Boston Children's Hospital, Boston, MA, USA
- Regional Center for Poison Control and Prevention Serving Massachusetts and Rhode Island, Boston, MA, USA
- Department of Emergency Medicine, Carl R. Darnall Army Medical Center, Fort Hood, TX, USA
| | - Sudeh Izadmehr
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marc Tarsillo
- Division of Medical Toxicology, Department of Emergency Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Eduardo Fleischer
- Division of Medical Toxicology, Department of Emergency Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Michele M Burns
- Division of Medical Toxicology, Department of Emergency Medicine, Boston Children's Hospital, Boston, MA, USA
- Regional Center for Poison Control and Prevention Serving Massachusetts and Rhode Island, Boston, MA, USA
- Department of Emergency Medicine, Brigham and Women's Hospital, Boston, MA, USA
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23
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Loos NHC, Beijnen JH, Schinkel AH. The Mechanism-Based Inactivation of CYP3A4 by Ritonavir: What Mechanism? Int J Mol Sci 2022; 23:ijms23179866. [PMID: 36077262 PMCID: PMC9456214 DOI: 10.3390/ijms23179866] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Ritonavir is the most potent cytochrome P450 (CYP) 3A4 inhibitor in clinical use and is often applied as a booster for drugs with low oral bioavailability due to CYP3A4-mediated biotransformation, as in the treatment of HIV (e.g., lopinavir/ritonavir) and more recently COVID-19 (Paxlovid or nirmatrelvir/ritonavir). Despite its clinical importance, the exact mechanism of ritonavir-mediated CYP3A4 inactivation is still not fully understood. Nonetheless, ritonavir is clearly a potent mechanism-based inactivator, which irreversibly blocks CYP3A4. Here, we discuss four fundamentally different mechanisms proposed for this irreversible inactivation/inhibition, namely the (I) formation of a metabolic-intermediate complex (MIC), tightly coordinating to the heme group; (II) strong ligation of unmodified ritonavir to the heme iron; (III) heme destruction; and (IV) covalent attachment of a reactive ritonavir intermediate to the CYP3A4 apoprotein. Ritonavir further appears to inactivate CYP3A4 and CYP3A5 with similar potency, which is important since ritonavir is applied in patients of all ethnicities. Although it is currently not possible to conclude what the primary mechanism of action in vivo is, it is unlikely that any of the proposed mechanisms are fundamentally wrong. We, therefore, propose that ritonavir markedly inactivates CYP3A through a mixed set of mechanisms. This functional redundancy may well contribute to its overall inhibitory efficacy.
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Affiliation(s)
- Nancy H. C. Loos
- The Netherlands Cancer Institute, Division of Pharmacology, 1066 CX Amsterdam, The Netherlands
| | - Jos H. Beijnen
- Faculty of Science, Department of Pharmaceutical Sciences, Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht University, 3584 CS Utrecht, The Netherlands
- The Netherlands Cancer Institute, Division of Pharmacy and Pharmacology, 1066 CX Amsterdam, The Netherlands
| | - Alfred H. Schinkel
- The Netherlands Cancer Institute, Division of Pharmacology, 1066 CX Amsterdam, The Netherlands
- Correspondence: ; Tel.: +31-205122046
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24
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Clerbaux LA, Albertini MC, Amigó N, Beronius A, Bezemer GFG, Coecke S, Daskalopoulos EP, del Giudice G, Greco D, Grenga L, Mantovani A, Muñoz A, Omeragic E, Parissis N, Petrillo M, Saarimäki LA, Soares H, Sullivan K, Landesmann B. Factors Modulating COVID-19: A Mechanistic Understanding Based on the Adverse Outcome Pathway Framework. J Clin Med 2022; 11:4464. [PMID: 35956081 PMCID: PMC9369763 DOI: 10.3390/jcm11154464] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 12/10/2022] Open
Abstract
Addressing factors modulating COVID-19 is crucial since abundant clinical evidence shows that outcomes are markedly heterogeneous between patients. This requires identifying the factors and understanding how they mechanistically influence COVID-19. Here, we describe how eleven selected factors (age, sex, genetic factors, lipid disorders, heart failure, gut dysbiosis, diet, vitamin D deficiency, air pollution and exposure to chemicals) influence COVID-19 by applying the Adverse Outcome Pathway (AOP), which is well-established in regulatory toxicology. This framework aims to model the sequence of events leading to an adverse health outcome. Several linear AOPs depicting pathways from the binding of the virus to ACE2 up to clinical outcomes observed in COVID-19 have been developed and integrated into a network offering a unique overview of the mechanisms underlying the disease. As SARS-CoV-2 infectibility and ACE2 activity are the major starting points and inflammatory response is central in the development of COVID-19, we evaluated how those eleven intrinsic and extrinsic factors modulate those processes impacting clinical outcomes. Applying this AOP-aligned approach enables the identification of current knowledge gaps orientating for further research and allows to propose biomarkers to identify of high-risk patients. This approach also facilitates expertise synergy from different disciplines to address public health issues.
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Affiliation(s)
- Laure-Alix Clerbaux
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (S.C.); (E.P.D.); (N.P.); (M.P.); (B.L.)
| | | | - Núria Amigó
- Biosfer Teslab SL., 43204 Reus, Spain;
- Department of Basic Medical Sciences, Universitat Rovira i Virgili (URV), 23204 Reus, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Anna Beronius
- Institute of Environmental Medicine, Karolinska Institutet, 17177 Stockholm, Sweden;
| | - Gillina F. G. Bezemer
- Impact Station, 1223 JR Hilversum, The Netherlands;
- Department of Pharmaceutical Sciences, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Sandra Coecke
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (S.C.); (E.P.D.); (N.P.); (M.P.); (B.L.)
| | - Evangelos P. Daskalopoulos
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (S.C.); (E.P.D.); (N.P.); (M.P.); (B.L.)
| | - Giusy del Giudice
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, 33100 Tampere, Finland; (G.d.G.); (D.G.); (L.A.S.)
| | - Dario Greco
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, 33100 Tampere, Finland; (G.d.G.); (D.G.); (L.A.S.)
| | - Lucia Grenga
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, F-30200 Bagnols-sur-Ceze, France;
| | - Alberto Mantovani
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Amalia Muñoz
- European Commission, Joint Research Centre (JRC), 2440 Geel, Belgium;
| | - Elma Omeragic
- Faculty of Pharmacy, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina;
| | - Nikolaos Parissis
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (S.C.); (E.P.D.); (N.P.); (M.P.); (B.L.)
| | - Mauro Petrillo
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (S.C.); (E.P.D.); (N.P.); (M.P.); (B.L.)
| | - Laura A. Saarimäki
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, 33100 Tampere, Finland; (G.d.G.); (D.G.); (L.A.S.)
| | - Helena Soares
- Laboratory of Immunobiology and Pathogenesis, Chronic Diseases Research Centre, Faculdade de Ciências Médicas Medical School, University of Lisbon, 1649-004 Lisbon, Portugal;
| | - Kristie Sullivan
- Physicians Committee for Responsible Medicine, Washington, DC 20016, USA;
| | - Brigitte Landesmann
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (S.C.); (E.P.D.); (N.P.); (M.P.); (B.L.)
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25
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Swami D, Mudaliar P, Bichu YS, Kumar Sahu V, Devarajan S, Basu S, Aich J. Synergistic combination of ritonavir and cisplatin as an efficacious therapy in human cervical cancer cells: a computational drug discovery and in vitro insight. J Biomol Struct Dyn 2022:1-15. [PMID: 35818867 DOI: 10.1080/07391102.2022.2097312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
HIV-protease inhibitor Ritonavir (RTV) is a clinical-stage drug. We exhibit here the synergistic effect of RTV coupled with cisplatin as potential combination therapy for treatment of cervical cancer. Knowledge about the interaction of RTV with the high-expression signatures in cancer is limited. Therefore, we utilized computational techniques to understand and assess the drug-binding affinity and drug-target interaction of RTV with these altered protein signatures. Computational studies revealed the potential interaction ability of RTV along with few other HIV protease inhibitors against these altered cancer targets. All targets exhibited good affinity towards RTV and the highest affinity was exhibited by CYP450 3A4, PDGFR and ALK. RTV established stable interaction with PDGFR and molecular dynamics simulation confirms their frequent interaction for 300 ns. Control docking of PDGFR with standard PDGFR inhibitor exhibited lower binding affinity when compared with RTV-PDGFR complex. In search of drugs as a part of combination therapy to reduce side effects of Cisplatin, this paper further evaluated the effect of combination of RTV and Cisplatin in cervical cancer cells. We propose several combination models that combines anti-viral drug RTV and standard chemotherapeutic agent, Cisplatin to be synergistic with CI value ranging from of 0.01 to 1.14. These observations suggest that anti-viral compound (RTV) could act synergistically with Cisplatin for cervical cancer therapy. However, further studies are warranted to investigate the combinatorial mode of action of RTV and Cisplatin on different molecular pathways to have a translational outcome in cervical cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dayanand Swami
- School of Biotechnology and Bioinformatics, DY Patil Deemed to Be University, Navi Mumbai, Maharashtra, India
| | - Priyanka Mudaliar
- School of Biotechnology and Bioinformatics, DY Patil Deemed to Be University, Navi Mumbai, Maharashtra, India
| | - Yash Shrinivas Bichu
- School of Biotechnology and Bioinformatics, DY Patil Deemed to Be University, Navi Mumbai, Maharashtra, India
| | - Vishal Kumar Sahu
- Cancer and Translational Research Centre, Dr. D.Y. Patil Biotechnology & Bioinformatics Institute, Pune, Maharashtra, India
| | - Shine Devarajan
- School of Biotechnology and Bioinformatics, DY Patil Deemed to Be University, Navi Mumbai, Maharashtra, India
| | - Soumya Basu
- Cancer and Translational Research Centre, Dr. D.Y. Patil Biotechnology & Bioinformatics Institute, Pune, Maharashtra, India
| | - Jyotirmoi Aich
- School of Biotechnology and Bioinformatics, DY Patil Deemed to Be University, Navi Mumbai, Maharashtra, India
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26
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Interaction of CYP3A4 with Rationally Designed Ritonavir Analogues: Impact of Steric Constraints Imposed on the Heme-Ligating Group and the End-Pyridine Attachment. Int J Mol Sci 2022; 23:ijms23137291. [PMID: 35806297 PMCID: PMC9266530 DOI: 10.3390/ijms23137291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 02/04/2023] Open
Abstract
Controlled inhibition of drug-metabolizing cytochrome P450 3A4 (CYP3A4) is utilized to boost bioavailability of anti-viral and immunosuppressant pharmaceuticals. We investigate structure–activity relationships (SARs) in analogues of ritonavir, a potent CYP3A4 inhibitor marketed as pharmacoenhancer, to determine structural elements required for potent inhibition and whether the inhibitory potency can be further improved via a rational structure-based design. This study investigated eight (series VI) inhibitors differing in head- and end-moieties and their respective linkers. SAR analysis revealed the multifactorial regulation of inhibitory strength, with steric constraints imposed on the tethered heme-ligating moiety being a key factor. Minimization of these constraints by changing the linkers’ length/flexibility and N-heteroatom position strengthened heme coordination and markedly improved binding and/or inhibitory strength. Impact of the end-pyridine attachment was not uniform due to influence of other determinants controlling the ligand-binding mode. This interplay between pharmacophoric determinants and the end-group enlargement can be used for further inhibitor optimization.
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27
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Khalatbari A, Aghazadeh Z, Ji C. Adverse Effects of Anti-Covid-19 Drug Candidates and Alcohol on Cellular Stress Responses of Hepatocytes. Hepatol Commun 2022; 6:1262-1277. [PMID: 34910385 PMCID: PMC9134820 DOI: 10.1002/hep4.1887] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 11/16/2021] [Accepted: 12/12/2021] [Indexed: 12/15/2022] Open
Abstract
During the pandemic, dexamethasone (DEX), remdesivir (RDV), hydroxychloroquine (HCQ), thapsigargin (TG), camostat mesylate (CaM), and pralatrexate were repurposed drugs for coronavirus disease 2019 (COVID-19). However, the side effects on the liver associated with the anti-COVID therapies are unknown. Cellular stresses by these drugs at 0-30 μM were studied using HepG2, Huh7, and/or primary human hepatocytes. DEX or RDV induced endoplasmic reticulum stress with increased X-box binding protein 1 and autophagic response with increased accumulation of microtubule-associated protein 1A/1B-light chain 3 (LC3-II). DEX and RDV had additive effects on the stress responses in the liver cells, which further increased expression of activating transcription factor 4 and C/EBP homology protein 1 (CHOP), and cell death. Alcohol pretreatment (50 mM) and DEX induced greater cellular stress responses than DEX and RDV. Pralatrexate induced Golgi fragmentation, cell cycle arrest at G0/G1 phase, activations of poly (ADP-ribose) polymerase-1 (PARP) and caspases, and cell death. Pralatrexate and alcohol had synergistic effects on the cell death mediators of Bim, caspase3, and PARP. The protease inhibitor CaM and TG induced autophagic response and mitochondrial stress with altered mitochondrial membrane potential, B-cell lymphoma 2, and cytochrome C. TG and HCQ induced autophagic response markers of Unc-51 like autophagy activating kinase, LC3-II, Beclin1, and Atg5, and severe ER stress marker CHOP. Conclusion: These results suggest that the anti-COVID-19 drugs, especially with drug-drug or alcohol-drug combinations, cause cellular stress responses and injuries in the liver cells.
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Affiliation(s)
- Atousa Khalatbari
- Department of MedicineKeck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCAUSA
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28
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Hong E, Almond LM, Chung PS, Rao AP, Beringer PM. Physiologically-Based Pharmacokinetic-Led Guidance for Patients With Cystic Fibrosis Taking Elexacaftor-Tezacaftor-Ivacaftor With Nirmatrelvir-Ritonavir for the Treatment of COVID-19. Clin Pharmacol Ther 2022; 111:1324-1333. [PMID: 35292968 PMCID: PMC9087007 DOI: 10.1002/cpt.2585] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 03/04/2022] [Indexed: 12/11/2022]
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) modulating therapies, including elexacaftor-tezacaftor-ivacaftor, are primarily eliminated through cytochrome P450 (CYP) 3A-mediated metabolism. This creates a therapeutic challenge to the treatment of coronavirus disease 2019 (COVID-19) with nirmatrelvir-ritonavir in people with cystic fibrosis (CF) due to the potential for significant drug-drug interactions (DDIs). However, the population with CF is more at risk of serious illness following COVID-19 infection and hence it is important to manage the DDI risk and provide treatment options. CYP3A-mediated DDI of elexacaftor-tezacaftor-ivacaftor was evaluated using a physiologically-based pharmacokinetic modeling approach. Modeling was performed incorporating physiological information and drug-dependent parameters of elexacaftor-tezacaftor-ivacaftor to predict the effect of ritonavir (the CYP3A inhibiting component of the combination) on the pharmacokinetics of elexacaftor-tezacaftor-ivacaftor. The elexacaftor-tezacaftor-ivacaftor models were verified using independent clinical pharmacokinetic and DDI data of elexacaftor-tezacaftor-ivacaftor with a range of CYP3A modulators. When ritonavir was administered on Days 1 through 5, the predicted area under the curve (AUC) ratio of ivacaftor (the most sensitive CYP3A substrate) on Day 6 was 9.31, indicating that its metabolism was strongly inhibited. Based on the predicted DDI, the dose of elexacaftor-tezacaftor-ivacaftor should be reduced when coadministered with nirmatrelvir-ritonavir to elexacaftor 200 mg-tezacaftor 100 mg-ivacaftor 150 mg on Days 1 and 5, with delayed resumption of full-dose elexacaftor-tezacaftor-ivacaftor on Day 9, considering the residual inhibitory effect of ritonavir as a mechanism-based inhibitor. The simulation predicts a regimen of elexacaftor-tezacaftor-ivacaftor administered concomitantly with nirmatrelvir-ritonavir in people with CF that will likely decrease the impact of the drug interaction.
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Affiliation(s)
- Eunjin Hong
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California, USA
| | | | - Peter S Chung
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.,University of Southern California, Anton Yelchin Cystic Fibrosis Clinic, Los Angeles, California, USA
| | - Adupa P Rao
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.,University of Southern California, Anton Yelchin Cystic Fibrosis Clinic, Los Angeles, California, USA
| | - Paul M Beringer
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California, USA.,University of Southern California, Anton Yelchin Cystic Fibrosis Clinic, Los Angeles, California, USA
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Ridhwan MJM, Bakar SIA, Latip NA, Ghani NA, Ismail NH. A Comprehensive Analysis of Human CYP3A4 Crystal Structures as a Potential Tool for Molecular Docking-Based Site of Metabolism and Enzyme Inhibition Studies. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2022; 21:259-285. [DOI: 10.1142/s2737416522300012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
The notable ability of human liver cytochrome P450 3A4 (CYP3A4) to metabolize diverse xenobiotics encourages researchers to explore in-depth the mechanism of enzyme action. Numerous CYP3A4 protein crystal structures have been deposited in protein data bank (PDB) and are majorly used in molecular docking analysis. The quality of the molecular docking results depends on the three-dimensional CYP3A4 protein crystal structures from the PDB. Present review endeavors to provide a brief outline of some technical parameters of CYP3A4 PDB entries as valuable information for molecular docking research. PDB entries between 22 April 2004 and 2 June 2021 were compiled and the active sites were thoroughly observed. The present review identified 76 deposited PDB entries and described basic information that includes CYP3A4 from human genetic, Escherichia coli (E. coli) use for protein expression, crystal structure obtained from X-ray diffraction method, taxonomy ID 9606, Uniprot ID P08684, ligand–protein structure description, co-crystal ligand, protein site deposit and resolution ranges between 1.7[Formula: see text]Å and 2.95[Formula: see text]Å. The observation of protein–ligand interactions showed the various residues on the active site depending on the ligand. The residues Ala305, Ser119, Ala370, Phe304, Phe108, Phe213 and Phe215 have been found to frequently interact with ligands from CYP3A4 PDB. Literature surveys of 17 co-crystal ligands reveal multiple mechanisms that include competitive inhibition, noncompetitive inhibition, mixed-mode inhibition, mechanism-based inhibition, substrate with metabolite, inducer, or combination modes of action. This overview may help researchers choose a trustworthy CYP3A4 protein structure from the PDB database to apply the protein in molecular docking analysis for drug discovery.
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Affiliation(s)
- Mohamad Jemain Mohamad Ridhwan
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), Shah Alam 40450, Selangor, Malaysia
- Atta-ur-Rahman Institute for Natural Products Discovery, Universiti Teknologi MARA (UiTM), Puncak Alam 42300, Selangor, Malaysia
| | - Syahrul Imran Abu Bakar
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), Shah Alam 40450, Selangor, Malaysia
- Atta-ur-Rahman Institute for Natural Products Discovery, Universiti Teknologi MARA (UiTM), Puncak Alam 42300, Selangor, Malaysia
| | - Normala Abd Latip
- Atta-ur-Rahman Institute for Natural Products Discovery, Universiti Teknologi MARA (UiTM), Puncak Alam 42300, Selangor, Malaysia
- Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), Puncak Alam 42300, Selangor, Malaysia
| | - Nurunajah Ab Ghani
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), Shah Alam 40450, Selangor, Malaysia
- Atta-ur-Rahman Institute for Natural Products Discovery, Universiti Teknologi MARA (UiTM), Puncak Alam 42300, Selangor, Malaysia
| | - Nor Hadiani Ismail
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), Shah Alam 40450, Selangor, Malaysia
- Atta-ur-Rahman Institute for Natural Products Discovery, Universiti Teknologi MARA (UiTM), Puncak Alam 42300, Selangor, Malaysia
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Girardin F, Manuel O, Marzolini C, Buclin T. Evaluating the risk of drug-drug interactions with pharmacokinetic boosters: the case of ritonavir-enhanced nirmatrelvir to prevent severe COVID-19. Clin Microbiol Infect 2022; 28:1044-1046. [PMID: 35358684 PMCID: PMC8958820 DOI: 10.1016/j.cmi.2022.03.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 01/14/2023]
Affiliation(s)
- François Girardin
- Division of Clinical Pharmacology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital, Faculty of Medicine, University of Lausanne, Lausanne, Switzerland; Division of Clinical Pharmacology and Toxicology, Department of Anesthesiology, Clinical Pharmacology, Intensive Care and Emergency Medicine, Geneva University Hospitals, Geneva, Switzerland.
| | - Oriol Manuel
- Infectious Diseases Service and Transplantation Centre, Lausanne, Lausanne University Hospital, Faculty of Medicine, University of Lausanne, Lausanne, Switzerland
| | - Catia Marzolini
- Division of Infectious Diseases and Hospital Epidemiology, Departments of Medicine and Clinical Research, University Hospital of Basel and University of Basel, Basel, Switzerland; Department of Molecular and Clinical Pharmacology, University of Liverpool, United Kingdom
| | - Thierry Buclin
- Division of Clinical Pharmacology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital, Faculty of Medicine, University of Lausanne, Lausanne, Switzerland
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Riffle M, Hoopmann MR, Jaschob D, Zhong G, Moritz RL, MacCoss MJ, Davis TN, Isoherranen N, Zelter A. Discovery and Visualization of Uncharacterized Drug-Protein Adducts Using Mass Spectrometry. Anal Chem 2022; 94:3501-3509. [PMID: 35184559 PMCID: PMC8892443 DOI: 10.1021/acs.analchem.1c04101] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Drugs are often metabolized
to reactive intermediates that form
protein adducts. Adducts can inhibit protein activity, elicit immune
responses, and cause life-threatening adverse drug reactions. The
masses of reactive metabolites are frequently unknown, rendering traditional
mass spectrometry-based proteomics approaches incapable of adduct
identification. Here, we present Magnum, an open-mass search algorithm
optimized for adduct identification, and Limelight, a web-based data
processing package for analysis and visualization of data from all
existing algorithms. Limelight incorporates tools for sample comparisons
and xenobiotic-adduct discovery. We validate our tools with three
drug/protein combinations and apply our label-free workflow to identify
novel xenobiotic-protein adducts in CYP3A4. Our new methods and software
enable accurate identification of xenobiotic-protein adducts with
no prior knowledge of adduct masses or protein targets. Magnum outperforms
existing label-free tools in xenobiotic-protein adduct discovery,
while Limelight fulfills a major need in the rapidly developing field
of open-mass searching, which until now lacked comprehensive data
visualization tools.
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Affiliation(s)
- Michael Riffle
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | | | - Daniel Jaschob
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Guo Zhong
- Department of Pharmaceutics, University of Washington, Seattle, Washington 98195, United States
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Nina Isoherranen
- Department of Pharmaceutics, University of Washington, Seattle, Washington 98195, United States
| | - Alex Zelter
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
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Perazzolo S, Shireman LM, Shen DD, Ho RJY. Physiologically Based Pharmacokinetic Modeling of 3 HIV Drugs in Combination and the Role of Lymphatic System after Subcutaneous Dosing. Part 1: Model for the Free-Drug Mixture. J Pharm Sci 2022; 111:529-541. [PMID: 34673093 PMCID: PMC9272351 DOI: 10.1016/j.xphs.2021.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/11/2021] [Accepted: 10/11/2021] [Indexed: 02/03/2023]
Abstract
Drug-combination nanoparticles (DcNP) allow the formulation of multiple HIV drugs in one injectable. In nonhuman primates (NHP), all drugs in DcNP have demonstrated long-acting pharmacokinetics (PK) in the blood and lymph nodes, rendering it suitable for a Targeted Long-acting Antiretroviral Therapy (TLC-ART). To support the translation of TLC-ART into the clinic, the objective is to present a physiologically based PK (PBPK) model tool to control mechanisms affecting the rather complex DcNP-drug PK. Two species contribute simultaneously to the drug PK: drugs that dissociate from DcNP (Part 1) and drugs retained in DcNP (Part 2, presented separately). Here, we describe the PBPK modeling of the nanoparticle-free drugs. The free-drug model was built on subcutaneous injections of suspended lopinavir, ritonavir, and tenofovir in NHP, and validated by external experiments. A novelty was the design of a lymphatic network as part of a whole-body PBPK system which included major lymphatic regions: the cervical, axillary, hilar, mesenteric, and inguinal nodes. This detailed/regionalized description of the lymphatic system and mononuclear cells represents an unprecedented level of prediction that renders the free-drug model extendible to other small-drug molecules targeting the lymphatic system at both the regional and cellular levels.
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Affiliation(s)
- Simone Perazzolo
- Department of Pharmaceutics, University of Washington, Seattle, WA, 98195, USA.
| | - Laura M Shireman
- Department of Pharmaceutics, University of Washington, Seattle, WA, 98195, USA
| | - Danny D Shen
- Department of Pharmaceutics, University of Washington, Seattle, WA, 98195, USA
| | - Rodney J Y Ho
- Department of Pharmaceutics, University of Washington, Seattle, WA, 98195, USA; Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA.
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Law MF, Ho R, Law KWT, Cheung CKM. Gastrointestinal and hepatic side effects of potential treatment for COVID-19 and vaccination in patients with chronic liver diseases. World J Hepatol 2021; 13:1850-1874. [PMID: 35069994 PMCID: PMC8727202 DOI: 10.4254/wjh.v13.i12.1850] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/20/2021] [Accepted: 11/15/2021] [Indexed: 02/06/2023] Open
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) is a global pandemic. Many clinical trials have been performed to investigate potential treatments or vaccines for this disease to reduce the high morbidity and mortality. The drugs of higher interest include umifenovir, bromhexine, remdesivir, lopinavir/ritonavir, steroid, tocilizumab, interferon alpha or beta, ribavirin, fivapiravir, nitazoxanide, ivermectin, molnupiravir, hydroxychloroquine/chloroquine alone or in combination with azithromycin, and baricitinib. Gastrointestinal (GI) symptoms and liver dysfunction are frequently seen in patients with COVID-19, which can make it difficult to differentiate disease manifestations from treatment adverse effects. GI symptoms of COVID-19 include anorexia, dyspepsia, nausea, vomiting, diarrhea and abdominal pain. Liver injury can be a result of systemic inflammation or cytokine storm, or due to the adverse drug effects in patients who have been receiving different treatments. Regular monitoring of liver function should be performed. COVID-19 vaccines have been rapidly developed with different technologies including mRNA, viral vectors, inactivated viruses, recombinant DNA, protein subunits and live attenuated viruses. Patients with chronic liver disease or inflammatory bowel disease and liver transplant recipients are encouraged to receive vaccination as the benefits outweigh the risks. Vaccination against COVID-19 is also recommended to family members and healthcare professionals caring for these patients to reduce exposure to the severe acute respiratory syndrome coronavirus 2 virus.
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Affiliation(s)
- Man Fai Law
- Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China.
| | - Rita Ho
- Department of Medicine, North District Hospital, Hong Kong, China
| | | | - Carmen Ka Man Cheung
- Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
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34
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Maze EA, Agit B, Reeves S, Hilton DA, Parkinson DB, Laraba L, Ercolano E, Kurian KM, Hanemann CO, Belshaw RD, Ammoun S. Human endogenous retrovirus type K promotes proliferation and confers sensitivity to anti-retroviral drugs in Merlin-negative schwannoma and meningioma. Cancer Res 2021; 82:235-247. [PMID: 34853069 DOI: 10.1158/0008-5472.can-20-3857] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/04/2021] [Accepted: 11/15/2021] [Indexed: 11/16/2022]
Abstract
Deficiency of the tumour suppressor Merlin causes development of schwannoma, meningioma, and ependymoma tumours, which can occur spontaneously or in the hereditary disease neurofibromatosis type 2 (NF2). Merlin mutations are also relevant in a variety of other tumours. Surgery and radiotherapy are current first-line treatments; however, tumours frequently recur with limited treatment options. Here, we use human Merlin-negative schwannoma and meningioma primary cells to investigate the involvement of the endogenous retrovirus HERV-K in tumour development. HERV-K proteins previously implicated in tumorigenesis were overexpressed in schwannoma and all meningioma grades, and disease-associated CRL4DCAF1 and YAP/TEAD pathways were implicated in this overexpression. In normal Schwann cells, ectopic overexpression of HERV-K Env increased proliferation and upregulated expression of c-Jun and pERK1/2, which are key components of known tumorigenic pathways in schwannoma, JNK/c-Jun and RAS/RAF/MEK/ERK. Furthermore, FDA-approved retroviral protease inhibitors ritonavir, atazanavir, and lopinavir reduced proliferation of schwannoma and grade I meningioma cells. These results identify HERV-K as a critical regulator of progression in Merlin-deficient tumours and offer potential strategies for therapeutic intervention.
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Affiliation(s)
- Emmanuel A Maze
- School of Biomedical Sciences, Faculty of Health Medicine, Dentistry and Human Sciences, Plymouth University
| | - Bora Agit
- Faculty of Health Medicine, Dentistry and Human Sciences, Plymouth University
| | - Shona Reeves
- Faculty of Health Medicine, Dentistry and Human Sciences, Plymouth University
| | - David A Hilton
- Faculty of Health Medicine, Dentistry and Human Sciences, Plymouth University
| | - David B Parkinson
- Institute of Translational and Stratified Medicine, Plymouth University Peninsula Schools of Medicine and Dentistry
| | - Liyam Laraba
- Institute of Translational and Stratified Medicine, Plymouth University Peninsula Schools of Medicine and Dentistry
| | | | - Kathreena M Kurian
- Department of Neuropathology, Brain Tumour Research Group, Frenchay Hospital, University of Bristol
| | - C Oliver Hanemann
- Institute of Translational and Stratified Medicine, Plymouth University Peninsula Schools of Medicine and Dentistry
| | | | - Sylwia Ammoun
- Faculty of Health Medicine, Dentistry and Human Sciences, Plymouth University
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35
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Thomas L, Birangal SR, Ray R, Sekhar Miraj S, Munisamy M, Varma M, S V CS, Banerjee M, Shenoy GG, Rao M. Prediction of potential drug interactions between repurposed COVID-19 and antitubercular drugs: an integrational approach of drug information software and computational techniques data. Ther Adv Drug Saf 2021; 12:20420986211041277. [PMID: 34471515 PMCID: PMC8404633 DOI: 10.1177/20420986211041277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 07/24/2021] [Indexed: 01/02/2023] Open
Abstract
Introduction: Tuberculosis is a major respiratory disease globally with a higher prevalence in Asian and African countries than rest of the world. With a larger population of tuberculosis patients anticipated to be co-infected with COVID-19 infection, an ongoing pandemic, identifying, preventing and managing drug–drug interactions is inevitable for maximizing patient benefits for the current repurposed COVID-19 and antitubercular drugs. Methods: We assessed the potential drug–drug interactions between repurposed COVID-19 drugs and antitubercular drugs using the drug interaction checker of IBM Micromedex®. Extensive computational studies were performed at a molecular level to validate and understand the drug–drug interactions found from the Micromedex drug interaction checker database at a molecular level. The integrated knowledge derived from Micromedex and computational data was collated and curated for predicting potential drug–drug interactions between repurposed COVID-19 and antitubercular drugs. Results: A total of 91 potential drug–drug interactions along with their severity and level of documentation were identified from Micromedex between repurposed COVID-19 drugs and antitubercular drugs. We identified 47 pharmacodynamic, 42 pharmacokinetic and 2 unknown DDIs. The majority of our molecular modelling results were in line with drug–drug interaction data obtained from the drug information software. QT prolongation was identified as the most common type of pharmacodynamic drug–drug interaction, whereas drug–drug interactions associated with cytochrome P450 3A4 (CYP3A4) and P-glycoprotein (P-gp) inhibition and induction were identified as the frequent pharmacokinetic drug–drug interactions. The results suggest antitubercular drugs, particularly rifampin and second-line agents, warrant high alert and monitoring while prescribing with the repurposed COVID-19 drugs. Conclusion: Predicting these potential drug–drug interactions, particularly related to CYP3A4, P-gp and the human Ether-à-go-go-Related Gene proteins, could be used in clinical settings for screening and management of drug–drug interactions for delivering safer chemotherapeutic tuberculosis and COVID-19 care. The current study provides an initial propulsion for further well-designed pharmacokinetic-pharmacodynamic-based drug–drug interaction studies. Plain Language Summary
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Affiliation(s)
- Levin Thomas
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Sumit Raosaheb Birangal
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Rajdeep Ray
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Sonal Sekhar Miraj
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Murali Munisamy
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Muralidhar Varma
- Department of Infectious Diseases, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | | | - Mithu Banerjee
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Rajasthan, India
| | - Gautham G Shenoy
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Mahadev Rao
- Professor and Head, Department of Pharmacy Practice, Coordinator, Centre for Translational Research, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
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Tarazona JV, Martínez M, Martínez MA, Anadón A. Environmental impact assessment of COVID-19 therapeutic solutions. A prospective analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 778:146257. [PMID: 33721651 PMCID: PMC7943388 DOI: 10.1016/j.scitotenv.2021.146257] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 02/26/2021] [Accepted: 02/28/2021] [Indexed: 05/08/2023]
Abstract
Several medicinal products for human use are currently under consideration as potential treatment for COVID-19 pandemic. As proposals cover also prophylactic use, the treatment could be massive, resulting in unprecedent levels of antiviral emissions to the aquatic environment. We have adapted previous models and used available information for predicting the environmental impact of representative medicinal products, covering the main groups under consideration: multitarget antiparasitic (chloroquines and ivermectin), glucocorticoids, macrolide antibiotics and antiviral drugs including their pharmacokinetic boosters. The retrieved information has been sufficient for conducting a conventional environmental risk assessment for the group of miscellaneous medicines; results suggest low concern for the chloroquines and dexamethasone while very high impact for ivermectin and azithromycin, even at use levels well below the default value of 1% of the population. The information on the ecotoxicity of the antiviral medicines is very scarce, thus we have explored an innovative pharmacodynamic-based approach, combining read-across, quantitative structure-activity relationship (QSAR), US EPA's Toxicity Forecaster (ToxCast) in vitro data, pharmacological modes of action, and the observed adverse effects. The results highlight fish sublethal effects as the most sensitive target and identify possible concerns. These results offer guidance for minimizing the environmental risk of treatment medication for COVID-19.
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Affiliation(s)
- José V Tarazona
- Royal Academy of Veterinary Sciences of Spain (RACVE), Maestro Ripoll, 8, 28006 Madrid, Spain; Scientific Committee and Emerging Risks Unit, European Food Safety Authority (EFSA), Via Carlo Magno 1/A, I-43126 Parma, Italy.
| | - Marta Martínez
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Universidad Complutense de Madrid (UCM) and Research Institute Hospital 12 de Octubre (i+12), 28040 Madrid, Spain
| | - María-Aránzazu Martínez
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Universidad Complutense de Madrid (UCM) and Research Institute Hospital 12 de Octubre (i+12), 28040 Madrid, Spain
| | - Arturo Anadón
- Royal Academy of Veterinary Sciences of Spain (RACVE), Maestro Ripoll, 8, 28006 Madrid, Spain; Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Universidad Complutense de Madrid (UCM) and Research Institute Hospital 12 de Octubre (i+12), 28040 Madrid, Spain
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Toupin N, Steinke SJ, Nadella S, Li A, Rohrabaugh TN, Samuels ER, Turro C, Sevrioukova IF, Kodanko JJ. Photosensitive Ru(II) Complexes as Inhibitors of the Major Human Drug Metabolizing Enzyme CYP3A4. J Am Chem Soc 2021; 143:9191-9205. [PMID: 34110801 DOI: 10.1021/jacs.1c04155] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We report the synthesis and photochemical and biological characterization of the first selective and potent metal-based inhibitors of cytochrome P450 3A4 (CYP3A4), the major human drug metabolizing enzyme. Five Ru(II)-based derivatives were prepared from two analogs of the CYP3A4 inhibitor ritonavir, 4 and 6: [Ru(tpy)(L)(6)]Cl2 (tpy = 2,2':6',2″-terpyridine) with L = 6,6'-dimethyl-2,2'-bipyridine (Me2bpy; 8), dimethylbenzo[i]dipyrido[3,2-a:2',3'-c]phenazine (Me2dppn; 10) and 3,6-dimethyl-10,15-diphenylbenzo[i]dipyrido[3,2-a:2',3'-c]phenazine (Me2Ph2dppn; 11), [Ru(tpy)(Me2bpy)(4)]Cl2 (7) and [Ru(tpy)(Me2dppn)(4)]Cl2 (9). Photochemical release of 4 or 6 from 7-11 was demonstrated, and the spectrophotometric evaluation of 7 showed that it behaves similarly to free 4 (type II heme ligation) after irradiation with visible light but not in the dark. Unexpectedly, the intact Ru(II) complexes 7 and 8 were found to inhibit CYP3A4 potently and specifically through direct binding to the active site without heme ligation. Caged inhibitors 9-11 showed dual action properties by combining photoactivated dissociation of 4 or 6 with efficient 1O2 production. In prostate adenocarcinoma DU-145 cells, compound 9 had the best synergistic effect with vinblastine, the anticancer drug primarily metabolized by CYP3A4 in vivo. Thus, our study establishes a new paradigm in CYP inhibition using metalated complexes and suggests possible utilization of photoactive CYP3A4 inhibitory compounds in clinical applications, such as enhancement of therapeutic efficacy of anticancer drugs.
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Affiliation(s)
- Nicholas Toupin
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Sean J Steinke
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sandeep Nadella
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Ao Li
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Thomas N Rohrabaugh
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | | | - Claudia Turro
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | | | - Jeremy J Kodanko
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States.,Barbara Ann Karmanos Cancer Institute, Detroit, Michigan 48201, United States
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38
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Descriptors of Cytochrome Inhibitors and Useful Machine Learning Based Methods for the Design of Safer Drugs. Pharmaceuticals (Basel) 2021; 14:ph14050472. [PMID: 34067565 PMCID: PMC8156202 DOI: 10.3390/ph14050472] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 11/16/2022] Open
Abstract
Roughly 2.8% of annual hospitalizations are a result of adverse drug interactions in the United States, representing more than 245,000 hospitalizations. Drug-drug interactions commonly arise from major cytochrome P450 (CYP) inhibition. Various approaches are routinely employed in order to reduce the incidence of adverse interactions, such as altering drug dosing schemes and/or minimizing the number of drugs prescribed; however, often, a reduction in the number of medications cannot be achieved without impacting therapeutic outcomes. Nearly 80% of drugs fail in development due to pharmacokinetic issues, outlining the importance of examining cytochrome interactions during preclinical drug design. In this review, we examined the physiochemical and structural properties of small molecule inhibitors of CYPs 3A4, 2D6, 2C19, 2C9, and 1A2. Although CYP inhibitors tend to have distinct physiochemical properties and structural features, these descriptors alone are insufficient to predict major cytochrome inhibition probability and affinity. Machine learning based in silico approaches may be employed as a more robust and accurate way of predicting CYP inhibition. These various approaches are highlighted in the review.
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Mutiti CS, Kapungu NN, Kanji CR, Stadler N, Stingl J, Nhachi C, Hakim J, Masimirembwa C, Thelingwani RS. Clinically relevant enantiomer specific R- and S-praziquantel pharmacokinetic drug-drug interactions with efavirenz and ritonavir. Pharmacol Res Perspect 2021; 9:e00769. [PMID: 33929078 PMCID: PMC8085964 DOI: 10.1002/prp2.769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 03/11/2021] [Indexed: 11/05/2022] Open
Abstract
We conducted a clinical study to determine the effect of efavirenz and ritonavir on the pharmacokinetics of R- and S-PZQ in healthy male participants. This was toward evaluating the risk of drug-drug interactions, which may occur after PZQ administration to HIV patients on efavirenz or ritonavir containing regimens. A non-randomized, open-label, single-dose, one sequence crossover study with 2 arms was conducted. We gave 26 healthy volunteers a single oral dose of 40 mg/kg PZQ followed by a daily oral dose of either 400 mg efavirenz or 100 mg ritonavir for 14 consecutive days. On day 14, they ingested a single 40 mg/kg dose of PZQ. We measured plasma levels up to 12 h on day 1 and day 14. Samples were analyzed by LC-MS. Pharmacokinetic analysis was conducted in WinNonlin to determine the primary endpoints (plasma T1/2 , Cmin , and AUC). Efavirenz had a significant effect on the pharmacokinetics of PZQ (p < .05), reducing the AUC by 4-fold (1213.15 vs. 281.35 h·ng/ml for R-PZQ and 5669 vs. 871.84 h·ng/ml for S-PZQ). Ritonavir had no significant effect on R-PZQ but increased the AUC 2-fold for S-PZQ (p < .05) (4154.79 vs. 7291.05 h·ng/ml). Using PZQ in HIV patients needs investigation, as there is a risk of both treatment failure and adverse effects because of induction and inhibition, respectively.
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Affiliation(s)
- Chenai Sheilla Mutiti
- Department of Pharmaceutical Medicine, African Institute of Biomedical Science and Technology Block C Wilkins Hospital, Harare, Zimbabwe.,Clinical Pharmacology Department, University of Zimbabwe College of Health Sciences, Harare, Zimbabwe
| | - Nyasha Nicole Kapungu
- Department of Pharmaceutical Medicine, African Institute of Biomedical Science and Technology Block C Wilkins Hospital, Harare, Zimbabwe.,Clinical Pharmacology Department, University of Zimbabwe College of Health Sciences, Harare, Zimbabwe
| | - Comfort Ropafadzo Kanji
- Department of Pharmaceutical Medicine, African Institute of Biomedical Science and Technology Block C Wilkins Hospital, Harare, Zimbabwe.,Clinical Pharmacology Department, University of Zimbabwe College of Health Sciences, Harare, Zimbabwe
| | - Nadina Stadler
- Research Division Federal Institute for Drugs and Medical Devices, Bonn, Germany
| | - Julia Stingl
- Institute of Pharmacology and Toxicology, RWTG Aachen University Hospital, Aachen, Germany
| | - Charles Nhachi
- Clinical Pharmacology Department, University of Zimbabwe College of Health Sciences, Harare, Zimbabwe
| | - James Hakim
- Department of Medicine, University of Zimbabwe College of Health Sciences, Harare, Zimbabwe
| | - Collen Masimirembwa
- Department of Pharmaceutical Medicine, African Institute of Biomedical Science and Technology Block C Wilkins Hospital, Harare, Zimbabwe
| | - Roslyn Stella Thelingwani
- Department of Pharmaceutical Medicine, African Institute of Biomedical Science and Technology Block C Wilkins Hospital, Harare, Zimbabwe
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40
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Rational Design of CYP3A4 Inhibitors: A One-Atom Linker Elongation in Ritonavir-Like Compounds Leads to a Marked Improvement in the Binding Strength. Int J Mol Sci 2021; 22:ijms22020852. [PMID: 33467005 PMCID: PMC7830545 DOI: 10.3390/ijms22020852] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/09/2021] [Accepted: 01/12/2021] [Indexed: 12/11/2022] Open
Abstract
Inhibition of the major human drug-metabolizing cytochrome P450 3A4 (CYP3A4) by pharmaceuticals and other xenobiotics could lead to toxicity, drug–drug interactions and other adverse effects, as well as pharmacoenhancement. Despite serious clinical implications, the structural basis and attributes required for the potent inhibition of CYP3A4 remain to be established. We utilized a rational inhibitor design to investigate the structure–activity relationships in the analogues of ritonavir, the most potent CYP3A4 inhibitor in clinical use. This study elucidated the optimal length of the head-group spacer using eleven (series V) analogues with the R1/R2 side-groups as phenyls or R1–phenyl/R2–indole/naphthalene in various stereo configurations. Spectral, functional and structural characterization of the inhibitory complexes showed that a one-atom head-group linker elongation, from pyridyl–ethyl to pyridyl–propyl, was beneficial and markedly improved Ks, IC50 and thermostability of CYP3A4. In contrast, a two-atom linker extension led to a multi-fold decrease in the binding and inhibitory strength, possibly due to spatial and/or conformational constraints. The lead compound, 3h, was among the best inhibitors designed so far and overall, the strongest binder (Ks and IC50 of 0.007 and 0.090 µM, respectively). 3h was the fourth structurally simpler inhibitor superior to ritonavir, which further demonstrates the power of our approach.
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41
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Guengerich FP, McCarty KD, Chapman JG. Kinetics of cytochrome P450 3A4 inhibition by heterocyclic drugs defines a general sequential multistep binding process. J Biol Chem 2021; 296:100223. [PMID: 33449875 PMCID: PMC7948456 DOI: 10.1074/jbc.ra120.016855] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 11/21/2022] Open
Abstract
Cytochrome P450 (P450) 3A4 is the enzyme most involved in the metabolism of drugs and can also oxidize numerous steroids. This enzyme is also involved in one-half of pharmacokinetic drug-drug interactions, but details of the exact mechanisms of P450 3A4 inhibition are still unclear in many cases. Ketoconazole, clotrimazole, ritonavir, indinavir, and itraconazole are strong inhibitors; analysis of the kinetics of reversal of inhibition with the model substrate 7-benzoyl quinoline showed lag phases in several cases, consistent with multiple structures of P450 3A4 inhibitor complexes. Lags in the onset of inhibition were observed when inhibitors were added to P450 3A4 in 7-benzoyl quinoline O-debenzylation reactions, and similar patterns were observed for inhibition of testosterone 6β-hydroxylation by ritonavir and indinavir. Upon mixing with inhibitors, P450 3A4 showed rapid binding as judged by a spectral shift with at least partial high-spin iron character, followed by a slower conversion to a low-spin iron-nitrogen complex. The changes were best described by two intermediate complexes, one being a partial high-spin form and the second another intermediate, with half-lives of seconds. The kinetics could be modeled in a system involving initial loose binding of inhibitor, followed by a slow step leading to a tighter complex on a multisecond time scale. Although some more complex possibilities cannot be dismissed, these results describe a system in which conformationally distinct forms of P450 3A4 bind inhibitors rapidly and two distinct P450-inhibitor complexes exist en route to the final enzyme-inhibitor complex with full inhibitory activity.
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
| | - Kevin D McCarty
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Jesse G Chapman
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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42
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Vlachakis D, Papakonstantinou E, Mitsis T, Pierouli K, Diakou I, Chrousos G, Bacopoulou F. Molecular mechanisms of the novel coronavirus SARS-CoV-2 and potential anti-COVID19 pharmacological targets since the outbreak of the pandemic. Food Chem Toxicol 2020; 146:111805. [PMID: 33038452 PMCID: PMC7543766 DOI: 10.1016/j.fct.2020.111805] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 12/26/2022]
Abstract
The novel coronavirus SARS-CoV-2 has emerged as a severe threat against public health and global economies. COVID-19, the disease caused by this virus, is highly contagious and has led to an ongoing pandemic. SARS-CoV-2 affects, mainly, the respiratory system, with most severe cases primarily showcasing acute respiratory distress syndrome. Currently, no targeted therapy exists, and since the number of infections and death toll keeps rising, it has become a necessity to study possible therapeutic targets. Antiviral drugs can target various stages of the viral infection, and in the case of SARS-CoV-2, both structural and non-structural proteins have been proposed as potential drug targets. This review focuses on the most researched SARS-CoV-2 proteins, their structure, function, and possible therapeutic approaches.
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Affiliation(s)
- Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos, Athens, 11855, Greece; University Research Institute of Maternal and Child Health & Precision Medicine, and UNESCO Chair on Adolescent Health Care, National and Kapodistrian University of Athens, Aghia Sophia Children's Hospital, 8 Levadias Street, Athens, 11527, Greece; Lab of Molecular Endocrinology, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou Street, Athens, 11527, Greece; Department of Informatics, Faculty of Natural and Mathematical Sciences, King's College London, Strand, London WC2R 2LS, UK
| | - Eleni Papakonstantinou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos, Athens, 11855, Greece
| | - Thanasis Mitsis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos, Athens, 11855, Greece
| | - Katerina Pierouli
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos, Athens, 11855, Greece
| | - Io Diakou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos, Athens, 11855, Greece
| | - George Chrousos
- University Research Institute of Maternal and Child Health & Precision Medicine, and UNESCO Chair on Adolescent Health Care, National and Kapodistrian University of Athens, Aghia Sophia Children's Hospital, 8 Levadias Street, Athens, 11527, Greece; Lab of Molecular Endocrinology, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou Street, Athens, 11527, Greece
| | - Flora Bacopoulou
- University Research Institute of Maternal and Child Health & Precision Medicine, and UNESCO Chair on Adolescent Health Care, National and Kapodistrian University of Athens, Aghia Sophia Children's Hospital, 8 Levadias Street, Athens, 11527, Greece.
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43
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Chan SW. Current and Future Direct-Acting Antivirals Against COVID-19. Front Microbiol 2020; 11:587944. [PMID: 33262747 PMCID: PMC7688518 DOI: 10.3389/fmicb.2020.587944] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/23/2020] [Indexed: 01/18/2023] Open
Abstract
The coronavirus disease of 2019 (COVID-19) has caused an unprecedented global crisis. The etiological agent is a new virus called the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). As of October, 2020 there have been 45.4 million confirmed cases with a mortality rate of 2.6% globally. With the lack of a vaccine and effective treatments, the race is on to find a cure for the virus infection using specific antivirals. The viral RNA-dependent RNA polymerase, proteases, spike protein-host angiotensin-converting enzyme 2 binding and fusion have presented as attractive targets for pan-coronavirus and broad spectrum direct-acting antivirals (DAAs). This review presents a perspective on current re-purposing treatments and future DAAs.
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44
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Shah N, Davariya V, Gupta SK, Gajjar P, Parmar J, D'Cruz L. Review: An insight into coronaviruses: Challenges, security and scope. Rev Med Virol 2020; 30:1-8. [PMID: 32754974 PMCID: PMC7435549 DOI: 10.1002/rmv.2138] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/27/2020] [Accepted: 06/09/2020] [Indexed: 12/24/2022]
Abstract
SARS-CoV2 is a novel coronavirus; the seventh of its species to infect humans. The spread of this virus emerged in Wuhan, China in late December, 2019. Since then, this virus has spread to more than 200 countries and has caused a worldwide pandemic. Being a new species of coronaviruses, any cure or vaccines for this virus has not yet been obtained. A large amount of scientific studies and clinical trials are being carried out across the world to find a potential vaccine for this virus. Current work reports a review of potential drugs and vaccines that may be effective against this virus. Different scientific therapies that may potentially be effective against the SARS-CoV2 virus are also reviewed. The mechanisms of various drugs, their efficiency in various clinical trials and their side effects are also studied.
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Affiliation(s)
- Niyati Shah
- Computational Materials and Nanoscience Group, Department of Physics and ElectronicsSt. Xavier's CollegeAhmedabadIndia
| | - Vipul Davariya
- Research and Development LabVigor Life SciencesAhmedabadIndia
| | - Sanjeev K. Gupta
- Computational Materials and Nanoscience Group, Department of Physics and ElectronicsSt. Xavier's CollegeAhmedabadIndia
| | - Pankaj Gajjar
- Department of PhysicsGujarat UniversityAhmedabadIndia
| | - Jitendra Parmar
- Bioavailability and BioequivalenceVeeda Clinical ResearchAhmedabadIndia
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45
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Lohasz C, Bonanini F, Hoelting L, Renggli K, Frey O, Hierlemann A. Predicting Metabolism-Related Drug-Drug Interactions Using a Microphysiological Multitissue System. ACTA ACUST UNITED AC 2020; 4:e2000079. [PMID: 33073544 DOI: 10.1002/adbi.202000079] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 09/30/2020] [Indexed: 12/20/2022]
Abstract
Drug-drug interactions (DDIs) occur when the pharmacological activity of one drug is altered by a second drug. As multimorbidity and polypharmacotherapy are becoming more common due to the increasing age of the population, the risk of DDIs is massively increasing. Therefore, in vitro testing methods are needed to capture such multiorgan events. Here, a scalable, gravity-driven microfluidic system featuring 3D microtissues (MTs) that represent different organs for the prediction of drug-drug interactions is used. Human liver microtissues (hLiMTs) are combined with tumor microtissues (TuMTs) and treated with drug combinations that are known to cause DDIs in vivo. The testing system is able to capture and quantify DDIs upon co-administration of the anticancer prodrugs cyclophosphamide or ifosfamide with the antiretroviral drug ritonavir. Dosage of ritonavir inhibits hepatic metabolization of the two prodrugs to different extents and decreases their efficacy in acting on TuMTs. The flexible MT compartment design of the system, the use of polystyrene as chip material, and the assembly of several chips in stackable plates offer the potential to significantly advance preclinical substance testing. The possibility of testing a broad variety of drug combinations to identify possible DDIs will improve the drug development process and increase patient safety.
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Affiliation(s)
- Christian Lohasz
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, 4058, Switzerland
| | - Flavio Bonanini
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, 4058, Switzerland
| | | | - Kasper Renggli
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, 4058, Switzerland
| | | | - Andreas Hierlemann
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, 4058, Switzerland
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46
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Stanković B, Kotur N, Gašić V, Klaassen K, Ristivojević B, Stojiljković M, Pavlović S, Zukić B. Pharmacogenomics landscape of COVID-19 therapy response in Serbian population and comparison with worldwide populations. J Med Biochem 2020; 39:488-499. [PMID: 33312066 PMCID: PMC7710379 DOI: 10.5937/jomb0-26725] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/12/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Since there are no certified therapeutics to treat COVID-19 patients, drug repurposing became important. With lack of time to test individual pharmacogenomics markers, population pharmacogenomics could be helpful in predicting a higher risk of developing adverse reactions and treatment failure in COVID-19 patients. Aim of our study was to identify pharmacogenes and pharmacogenomics markers associated with drugs recommended for COVID-19 treatment, chloroquine/hydroxychloroquine, azithromycin, lopinavir and ritonavir, in population of Serbia and other world populations. METHODS Genotype information of 143 individuals of Serbian origin was extracted from database previously obtained using TruSight One Gene Panel (Illumina). Genotype data of individuals from different world populations were extracted from the 1000 Genome Project. Fisher's exact test was used for comparison of allele frequencies. RESULTS We have identified 11 potential pharmacogenomics markers in 7 pharmacogenes relevant for COVID-19 treatment. Based on high alternative allele frequencies in population and the functional effect of the variants, ABCB1 rs1045642 and rs2032582 could be relevant for reduced clearance of azithromycin, lopinavir and ritonavir drugs and UGT1A7 rs17868323 for hyperbilirubinemia in ritonavir treated COVID-19 patients in Serbian population. SLCO1B1 rs4149056 is a potential marker of lopinavir response, especially in Italian population. Our results confirmed that pharmacogenomics profile of African population is different from the rest of the world. CONCLUSIONS Considering population specific pharmacogenomics landscape, preemptive testing for pharmacogenes relevant for drugs used in COVID-19 treatment could contribute to better understanding of the inconsistency in therapy response and could be applied to improve the outcome of the COVID-19 patients.
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Affiliation(s)
- Biljana Stanković
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
| | - Nikola Kotur
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
| | - Vladimir Gašić
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
| | - Kristel Klaassen
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
| | - Bojan Ristivojević
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
| | - Maja Stojiljković
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
| | - Sonja Pavlović
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
| | - Branka Zukić
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
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47
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Chary MA, Barbuto AF, Izadmehr S, Hayes BD, Burns MM. COVID-19: Therapeutics and Their Toxicities. J Med Toxicol 2020; 16:284-294. [PMID: 32356252 PMCID: PMC7192319 DOI: 10.1007/s13181-020-00777-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/09/2020] [Accepted: 04/09/2020] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 is a novel coronavirus that emerged in 2019 and is causing the COVID-19 pandemic. There is no current standard of care. Clinicians need to be mindful of the toxicity of a wide variety of possibly unfamiliar substances being tested or repurposed to treat COVID-19. The United States Food and Drug Administration (FDA) has provided emergency authorization for the use of chloroquine and hydroxychloroquine. These two medications may precipitate ventricular dysrhythmias, necessitating cardiac and electrolyte monitoring, and in severe cases, treatment with epinephrine and high-doses of diazepam. Recombinant protein therapeutics may cause serum sickness or immune complex deposition. Nucleic acid vaccines may introduce mutations into the human genome. ACE inhibitors and ibuprofen have been suggested to exacerbate the pathogenesis of COVID-19. Here, we review the use, mechanism of action, and toxicity of proposed COVID-19 therapeutics.
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Affiliation(s)
- Michael A Chary
- Division of Emergency Medicine, Harvard Medical Toxicology Fellowship, Boston Children's Hospital, Boston, MA, USA.
- Regional Center for Poison Control and Prevention Serving Massachusetts and Rhode Island, Boston, MA, USA.
- Department of Emergency Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| | - Alexander F Barbuto
- Division of Emergency Medicine, Harvard Medical Toxicology Fellowship, Boston Children's Hospital, Boston, MA, USA
- Regional Center for Poison Control and Prevention Serving Massachusetts and Rhode Island, Boston, MA, USA
- Department of Emergency Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Sudeh Izadmehr
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bryan D Hayes
- Department of Pharmacy, Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Michele M Burns
- Division of Emergency Medicine, Harvard Medical Toxicology Fellowship, Boston Children's Hospital, Boston, MA, USA
- Regional Center for Poison Control and Prevention Serving Massachusetts and Rhode Island, Boston, MA, USA
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48
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Barr JT, Wang Z, Min X, Wienkers HJ, Rock BM, Rock DA, Wienkers LC. Mechanistic Studies of Cytochrome P450 3A4 Time-Dependent Inhibition Using Two Cysteine-Targeting Electrophiles. Drug Metab Dispos 2020; 48:508-514. [PMID: 32193357 DOI: 10.1124/dmd.119.089813] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 02/21/2020] [Indexed: 02/13/2025] Open
Abstract
Experiments designed to identify the mechanism of cytochrome P450 inactivation are critical to drug discovery. Small molecules irreversibly inhibit P450 enzymatic activity via two primary mechanisms: apoprotein adduct formation or heme modification. Understanding the interplay between chemical structures of reactive electrophiles and the impact on CYP3A4 structure and function can ultimately provide insights into drug design to minimize P450 inactivation. In a previous study, raloxifene and N-(1-pyrene) iodoacetamide (PIA) alkylated CYP3A4 in vitro; however, only raloxifene influenced enzyme activity. Here, two alkylating agents with cysteine selectivity, PIA and pyrene maleimide (PM), were used to investigate this apparent compound-dependent disconnect between CYP3A4 protein alkylation and activity loss. The compound's effect on 1) enzymatic activity, 2) carbon monoxide (CO) binding capacity, 3) intact heme content, and 4) protein conformation were measured. Results showed that PM had a large time-dependent loss of enzyme activity, whereas PIA did not. The differential effect on enzymatic activity between PM and PIA was mirrored in the CO binding data. Despite disruption of CO binding, neither compound affected the heme concentrations, inferring there was no destruction or alkylation of the heme. Lastly, differential scanning fluorescence showed PM-treated CYP3A4 caused a shift in the onset temperature required to induce protein aggregation, which was not observed for CYP3A4 treated with PIA. In conclusion, alkylation of CYP3A4 apoprotein can have a variable impact on catalytic activity, CO binding, and protein conformation that may be compound-dependent. These results highlight the need for careful interpretation of experimental results aimed at characterizing the nature of P450 enzyme inactivation. SIGNIFICANCE STATEMENT: Understanding the mechanism of CYP3A4 time-dependent inhibition is critical to drug discovery. In this study, we use two cysteine-targeting electrophiles to probe how subtle variation in inhibitor structure may impact the mechanism of CYP3A4 time-dependent inhibition and confound interpretation of traditional diagnostic experiments. Ultimately, this simplified system was used to reveal insights into CYP3A4 biochemical behavior. The insights may have implications that aid in understanding the susceptibility of CYP enzymes to the effects of electrophilic intermediates generated via bioactivation.
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Affiliation(s)
- John T Barr
- Amgen Research, Pharmacokinetics and Drug Metabolism, Amgen Inc., South San Francisco, California
| | - Zhican Wang
- Amgen Research, Pharmacokinetics and Drug Metabolism, Amgen Inc., South San Francisco, California
| | - Xiaoshan Min
- Amgen Research, Pharmacokinetics and Drug Metabolism, Amgen Inc., South San Francisco, California
| | - Henry J Wienkers
- Amgen Research, Pharmacokinetics and Drug Metabolism, Amgen Inc., South San Francisco, California
| | - Brooke M Rock
- Amgen Research, Pharmacokinetics and Drug Metabolism, Amgen Inc., South San Francisco, California
| | - Dan A Rock
- Amgen Research, Pharmacokinetics and Drug Metabolism, Amgen Inc., South San Francisco, California
| | - Larry C Wienkers
- Amgen Research, Pharmacokinetics and Drug Metabolism, Amgen Inc., South San Francisco, California
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49
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Eng H, Tseng E, Cerny MA, Goosen TC, Obach RS. Cytochrome P450 3A Time-Dependent Inhibition Assays Are Too Sensitive for Identification of Drugs Causing Clinically Significant Drug-Drug Interactions: A Comparison of Human Liver Microsomes and Hepatocytes and Definition of Boundaries for Inactivation Rate Constants. Drug Metab Dispos 2020; 49:442-450. [PMID: 33811106 DOI: 10.1124/dmd.121.000356] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 03/18/2021] [Indexed: 02/06/2023] Open
Abstract
Time-dependent inhibition (TDI) of CYP3A is an important mechanism underlying numerous drug-drug interactions (DDIs), and assays to measure this are done to support early drug research efforts. However, measuring TDI of CYP3A in human liver microsomes (HLMs) frequently yields overestimations of clinical DDIs and thus can lead to the erroneous elimination of many viable drug candidates from further development. In this investigation, 50 drugs were evaluated for TDI in HLMs and suspended human hepatocytes (HHEPs) to define appropriate boundary lines for the TDI parameter rate constant for inhibition (kobs) at a concentration of 30 µM. In HLMs, a kobs value of 0.002 minute-1 was statistically distinguishable from control; however, many drugs show kobs greater than this but do not cause DDI. A boundary line defined by the drug with the lowest kobs that causes a DDI (diltiazem) was established at 0.01 minute-1 Even with this boundary, of the 33 drugs above this value, only 61% cause a DDI (true positive rate). A corresponding analysis was done using HHEPs; kobs of 0.0015 minute-1 was statistically distinguishable from control, and the boundary was established at 0.006 minute-1 Values of kobs in HHEPs were almost always lower than those in HLMs. These findings offer a practical guide to the use of TDI data for CYP3A in early drug-discovery research. SIGNIFICANCE STATEMENT: Time-dependent inhibition of CYP3A is responsible for many drug interactions. In vitro assays are employed in early drug research to identify and remove CYP3A time-dependent inhibitors from further consideration. This analysis demonstrates suitable boundaries for inactivation rates to better delineate drug candidates for their potential to cause clinically significant drug interactions.
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Affiliation(s)
- Heather Eng
- Medicine Design, Pfizer Inc., Groton, Connecticut
| | - Elaine Tseng
- Medicine Design, Pfizer Inc., Groton, Connecticut
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50
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Yadav J, Paragas E, Korzekwa K, Nagar S. Time-dependent enzyme inactivation: Numerical analyses of in vitro data and prediction of drug-drug interactions. Pharmacol Ther 2020; 206:107449. [PMID: 31836452 PMCID: PMC6995442 DOI: 10.1016/j.pharmthera.2019.107449] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cytochrome P450 (CYP) enzyme kinetics often do not conform to Michaelis-Menten assumptions, and time-dependent inactivation (TDI) of CYPs displays complexities such as multiple substrate binding, partial inactivation, quasi-irreversible inactivation, and sequential metabolism. Additionally, in vitro experimental issues such as lipid partitioning, enzyme concentrations, and inactivator depletion can further complicate the parameterization of in vitro TDI. The traditional replot method used to analyze in vitro TDI datasets is unable to handle complexities in CYP kinetics, and numerical approaches using ordinary differential equations of the kinetic schemes offer several advantages. Improvement in the parameterization of CYP in vitro kinetics has the potential to improve prediction of clinical drug-drug interactions (DDIs). This manuscript discusses various complexities in TDI kinetics of CYPs, and numerical approaches to model these complexities. The extrapolation of CYP in vitro TDI parameters to predict in vivo DDIs with static and dynamic modeling is discussed, along with a discussion on current gaps in knowledge and future directions to improve the prediction of DDI with in vitro data for CYP catalyzed drug metabolism.
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Affiliation(s)
- Jaydeep Yadav
- Amgen Inc., 360 Binney Street, Cambridge, MA 02142, United States; Department of Pharmaceutical Sciences, Temple University, Philadelphia, PA 19140, United States
| | - Erickson Paragas
- Department of Pharmaceutical Sciences, Temple University, Philadelphia, PA 19140, United States
| | - Ken Korzekwa
- Department of Pharmaceutical Sciences, Temple University, Philadelphia, PA 19140, United States
| | - Swati Nagar
- Department of Pharmaceutical Sciences, Temple University, Philadelphia, PA 19140, United States.
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