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O'Brien Laramy MN, Bezawada P, Horst R, Jaini R, Lillis J, Liu Y, Luthra S, Nguyen B, Patel N, Soni S, Sullivan BP, Thiel A, Ticehurst MD. Self-Assembly Properties of an Amphiphilic Phosphate Ester Prodrug Designed for the Treatment of COVID-19. J Pharm Sci 2024; 113:1515-1522. [PMID: 37543257 DOI: 10.1016/j.xphs.2023.07.024] [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: 04/06/2023] [Revised: 07/10/2023] [Accepted: 07/29/2023] [Indexed: 08/07/2023]
Abstract
PF-07304814 is a water-soluble phosphate ester prodrug of a small molecule inhibitor for the SARS CoV-2 3CL protease designed for the treatment of COVID-19. The amphiphilicity and self-assembly behavior of the prodrug was investigated computationally and experimentally via multiple orthogonal techniques to better design formulations for intravenous infusion. The self-assembly of PF-07304814 into micellar structures enabled an increase in the solubility of lipophilic impurities by up to 1900x in clinically relevant formulations. The observed solubilization could help extend the drug product shelf-life and in use stability through inhibition of precipitation, without the need for solubilizing excipients. The work presented in this manuscript provides a roadmap for the characterization of prodrug self-assembly and highlights the potential for prodrug modifications to enhance solubility of both active ingredients and impurities and to extend drug product shelf-life.
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Affiliation(s)
| | - Padmavani Bezawada
- Pfizer Inc., Worldwide Research, Development, & Medical, Lake Forest, IL 60045, USA
| | - Reto Horst
- Pfizer Inc., Worldwide Research, Development, & Medical, Groton 06340, CT
| | - Rohit Jaini
- Pfizer Inc., Worldwide Research, Development, & Medical, Lake Forest, IL 60045, USA
| | - Jonathan Lillis
- Pfizer Inc., Worldwide Research, Development, & Medical, Sandwich, UK
| | - Yizhou Liu
- Pfizer Inc., Worldwide Research, Development, & Medical, Groton 06340, CT
| | - Suman Luthra
- Pfizer Inc., Worldwide Research, Development, & Medical, Cambridge, MA 02139, USA
| | - Bao Nguyen
- Pfizer Inc., Worldwide Research, Development, & Medical, Groton 06340, CT
| | - Nandini Patel
- Pfizer Inc., Worldwide Research, Development, & Medical, Cambridge, MA 02139, USA
| | - Smita Soni
- Pfizer Inc., Worldwide Research, Development, & Medical, Lake Forest, IL 60045, USA
| | - Bradley P Sullivan
- Pfizer Inc., Worldwide Research, Development, & Medical, Lake Forest, IL 60045, USA
| | - Andrew Thiel
- Pfizer Inc., Worldwide Research, Development, & Medical, Lake Forest, IL 60045, USA
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2
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Salgado-Benvindo C, Tas A, Zevenhoven-Dobbe JC, van der Meer Y, Sidorov IA, Leijs AA, Wanningen P, Gelderloos AT, van Kasteren PB, Snijder EJ, van Hemert MJ. Characterization of SARS-CoV-2 replication in human H1299/ACE2 cells: A versatile and practical infection model for antiviral research and beyond. Antiviral Res 2024; 227:105903. [PMID: 38723907 DOI: 10.1016/j.antiviral.2024.105903] [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: 01/23/2024] [Revised: 04/12/2024] [Accepted: 05/06/2024] [Indexed: 05/18/2024]
Abstract
A range of cell culture infection models have been used to study SARS-CoV-2 and perform antiviral drug research. Commonly used African green monkey Vero, human lung-derived Calu-3 and ACE2+TMPRSS2-expressing A549 cells, each have their limitations. Here, we describe human ACE2-expressing H1299 lung cells as a more efficient and robust model for SARS-CoV-2 research. These cells are as easy to handle as Vero cells, support SARS-CoV-2 replication to high titers, display a functional innate immune response and are suitable for plaque assays, microscopy, the production of (genetically stable) virus stocks and antiviral assays. H1299/ACE2-based (CPE reduction) assays can be performed without adding a P-gP drug efflux pump inhibitor, which is often required in Vero-based assays. Moreover, H1299/ACE2 cells allowed us to perform CPE reduction assays with omicron variants that did not work in Vero-based assays. In summary, H1299/ACE2 cells are a versatile infection model to study SARS-CoV-2 replication in the context of antiviral drug development and virus-host interaction studies.
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Affiliation(s)
- Clarisse Salgado-Benvindo
- Molecular Virology Laboratory, Center for Infectious Diseases, Leiden University Medical Center, 2333 ZA, Leiden, the Netherlands
| | - Ali Tas
- Molecular Virology Laboratory, Center for Infectious Diseases, Leiden University Medical Center, 2333 ZA, Leiden, the Netherlands
| | - Jessika C Zevenhoven-Dobbe
- Molecular Virology Laboratory, Center for Infectious Diseases, Leiden University Medical Center, 2333 ZA, Leiden, the Netherlands
| | - Yvonne van der Meer
- Molecular Virology Laboratory, Center for Infectious Diseases, Leiden University Medical Center, 2333 ZA, Leiden, the Netherlands
| | - Igor A Sidorov
- Molecular Virology Laboratory, Center for Infectious Diseases, Leiden University Medical Center, 2333 ZA, Leiden, the Netherlands
| | - Anouk A Leijs
- Molecular Virology Laboratory, Center for Infectious Diseases, Leiden University Medical Center, 2333 ZA, Leiden, the Netherlands
| | - Patrick Wanningen
- Molecular Virology Laboratory, Center for Infectious Diseases, Leiden University Medical Center, 2333 ZA, Leiden, the Netherlands
| | - Anne T Gelderloos
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3720 BA, Bilthoven, the Netherlands
| | - Puck B van Kasteren
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3720 BA, Bilthoven, the Netherlands
| | - Eric J Snijder
- Molecular Virology Laboratory, Center for Infectious Diseases, Leiden University Medical Center, 2333 ZA, Leiden, the Netherlands
| | - Martijn J van Hemert
- Molecular Virology Laboratory, Center for Infectious Diseases, Leiden University Medical Center, 2333 ZA, Leiden, the Netherlands.
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3
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Xie F, Zhu Q. The regulation of cGAS-STING signaling by RNA virus-derived components. Virol J 2024; 21:101. [PMID: 38693578 PMCID: PMC11064393 DOI: 10.1186/s12985-024-02359-1] [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: 02/04/2024] [Accepted: 04/04/2024] [Indexed: 05/03/2024] Open
Abstract
The Cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) serves as a key innate immune signaling axis involved in the regulation of various human diseases. It has been found that cGAS-STING pathway can recognize a variety of cytosolic double-stranded DNA (dsDNA), contributing to cause a robust type I interferon response thereby affecting the occurrence and progression of viral infection. Accumulating evidence indicates RNA virus-derived components play an important role in regulating cGAS-STING signaling, either as protective or pathogenic factors in the pathogenesis of diseases. Thus, a comprehensive understanding of the function of RNA virus-derived components in regulating cGAS-STING signaling will provide insights into developing novel therapies. Here, we review the existing literature on cGAS-STING pathway regulated by RNA virus-derived components to propose insights into pharmacologic strategies targeting the cGAS-STING pathway.
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Affiliation(s)
- Feiting Xie
- Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, 310006, Hangzhou, China.
| | - Qiugang Zhu
- Department of Laboratory Medicine, Shangyu People's Hospital of Shaoxing, Shaoxing, China
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4
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Iketani S, Ho DD. SARS-CoV-2 resistance to monoclonal antibodies and small-molecule drugs. Cell Chem Biol 2024; 31:632-657. [PMID: 38640902 PMCID: PMC11084874 DOI: 10.1016/j.chembiol.2024.03.008] [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: 09/07/2023] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/21/2024]
Abstract
Over four years have passed since the beginning of the COVID-19 pandemic. The scientific response has been rapid and effective, with many therapeutic monoclonal antibodies and small molecules developed for clinical use. However, given the ability for viruses to become resistant to antivirals, it is perhaps no surprise that the field has identified resistance to nearly all of these compounds. Here, we provide a comprehensive review of the resistance profile for each of these therapeutics. We hope that this resource provides an atlas for mutations to be aware of for each agent, particularly as a springboard for considerations for the next generation of antivirals. Finally, we discuss the outlook and thoughts for moving forward in how we continue to manage this, and the next, pandemic.
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Affiliation(s)
- Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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5
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Chan JFW, Yuan S, Chu H, Sridhar S, Yuen KY. COVID-19 drug discovery and treatment options. Nat Rev Microbiol 2024:10.1038/s41579-024-01036-y. [PMID: 38622352 DOI: 10.1038/s41579-024-01036-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2024] [Indexed: 04/17/2024]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused substantial morbidity and mortality, and serious social and economic disruptions worldwide. Unvaccinated or incompletely vaccinated older individuals with underlying diseases are especially prone to severe disease. In patients with non-fatal disease, long COVID affecting multiple body systems may persist for months. Unlike SARS-CoV and Middle East respiratory syndrome coronavirus, which have either been mitigated or remained geographically restricted, SARS-CoV-2 has disseminated globally and is likely to continue circulating in humans with possible emergence of new variants that may render vaccines less effective. Thus, safe, effective and readily available COVID-19 therapeutics are urgently needed. In this Review, we summarize the major drug discovery approaches, preclinical antiviral evaluation models, representative virus-targeting and host-targeting therapeutic options, and key therapeutics currently in clinical use for COVID-19. Preparedness against future coronavirus pandemics relies not only on effective vaccines but also on broad-spectrum antivirals targeting conserved viral components or universal host targets, and new therapeutics that can precisely modulate the immune response during infection.
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Affiliation(s)
- Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Infectious Diseases and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Shatin, Hong Kong Special Administrative Region, China
| | - Shuofeng Yuan
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Infectious Diseases and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Shatin, Hong Kong Special Administrative Region, China
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Infectious Diseases and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Shatin, Hong Kong Special Administrative Region, China
| | - Siddharth Sridhar
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Infectious Diseases and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.
- Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.
- Department of Infectious Diseases and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China.
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Shatin, Hong Kong Special Administrative Region, China.
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Li H, Sun M, Lei F, Liu J, Chen X, Li Y, Wang Y, Lu J, Yu D, Gao Y, Xu J, Chen H, Li M, Yi Z, He X, Chen L. Methyl rosmarinate is an allosteric inhibitor of SARS-CoV-2 3 CL protease as a potential candidate against SARS-cov-2 infection. Antiviral Res 2024; 224:105841. [PMID: 38408645 DOI: 10.1016/j.antiviral.2024.105841] [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: 11/10/2023] [Revised: 02/09/2024] [Accepted: 02/24/2024] [Indexed: 02/28/2024]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been ongoing for more than three years and urgently needs to be addressed. Traditional Chinese medicine (TCM) prescriptions have played an important role in the clinical treatment of patients with COVID-19 in China. However, it is difficult to uncover the potential molecular mechanisms of the active ingredients in these TCM prescriptions. In this paper, we developed a new approach by integrating the experimental assay, virtual screening, and the experimental verification, exploring the rapid discovery of active ingredients from TCM prescriptions. To achieve this goal, 4 TCM prescriptions in clinical use for different indications were selected to find the antiviral active ingredients in TCMs. The 3-chymotrypsin-like protease (3CLpro), an important target for fighting COVID-19, was utilized to determine the inhibitory activity of the TCM prescriptions and single herb. It was found that 10 single herbs had better inhibitory activity than other herbs by using a fluorescence resonance energy transfer (FRET) - based enzymatic assay of SARS-CoV-2 3CLpro. The ingredients contained in 10 herbs were thus virtually screened and the predicted active ingredients were experimentally validated. Thus, such a research strategy firstly removed many single herbs with no inhibitory activity against SARS-CoV-2 3CLpro at the very beginning by FRET-based assay, making our subsequent virtual screening more effective. Finally, 4 active components were found to have stronger inhibitory effects on SARS-CoV-2 3CLpro, and their inhibitory mechanism was subsequently investigated. Among of them, methyl rosmarinate as an allosteric inhibitor of SARS-CoV-2 3CLpro was confirmed and its ability to inhibit viral replication was demonstrated by the SARS-CoV-2 replicon system. To validate the binding mode via docking, the mutation experiment, circular dichroism (CD), enzymatic inhibition and surface plasmon resonance (SPR) assay were performed, demonstrating that methyl rosmarinate bound to the allosteric site of SARS-CoV-2 3CLpro. In conclusion, this paper provides the new ideas for the rapid discovery of active ingredients in TCM prescriptions based on a specific target, and methyl rosmarinate has the potential to be developed as an antiviral therapeutic candidate against SARS-CoV-2 infection.
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Affiliation(s)
- Hongtao Li
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Meng Sun
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Fuzhi Lei
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, and Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China; Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - Xixiang Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yaqi Li
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China; Peptide and small Molecule Drug R&D Plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China; DP Technology, Beijing, China
| | - Ying Wang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China; Peptide and small Molecule Drug R&D Plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China
| | - Jiani Lu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Danmei Yu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yueqiu Gao
- Department of Hepatopathy, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China; Laboratory of Cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Infectious Diseases of Integrated Traditional Chinese and Western Medicine, China
| | - Jianrong Xu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Hongzhuan Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Man Li
- Laboratory of Cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Zhigang Yi
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, and Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China; Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China; New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai, 200062, China.
| | - Lili Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China; Longhua Hospital Shanghai University of Traditional Chinese Medicine, 725 South Wanping Road, Shanghai, 200032, China.
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7
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Carney DW, Leffler AE, Bell JA, Chandrasinghe AS, Cheng C, Chang E, Dornford A, Dougan DR, Frye LL, Grimes ME, Knehans T, Knight JL, Komandla M, Lane W, Li H, Newman SR, Phimister K, Saikatendu KS, Silverstein H, Vafaei S. Exploiting high-energy hydration sites for the discovery of potent peptide aldehyde inhibitors of the SARS-CoV-2 main protease with cellular antiviral activity. Bioorg Med Chem 2024; 103:117577. [PMID: 38518735 DOI: 10.1016/j.bmc.2023.117577] [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: 11/28/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 03/24/2024]
Abstract
Small-molecule antivirals that prevent the replication of the SARS-CoV-2 virus by blocking the enzymatic activity of its main protease (Mpro) are and will be a tenet of pandemic preparedness. However, the peptidic nature of such compounds often precludes the design of compounds within favorable physical property ranges, limiting cellular activity. Here we describe the discovery of peptide aldehyde Mpro inhibitors with potent enzymatic and cellular antiviral activity. This structure-activity relationship (SAR) exploration was guided by the use of calculated hydration site thermodynamic maps (WaterMap) to drive potency via displacement of waters from high-energy sites. Thousands of diverse compounds were designed to target these high-energy hydration sites and then prioritized for synthesis by physics- and structure-based Free-Energy Perturbation (FEP+) simulations, which accurately predicted biochemical potencies. This approach ultimately led to the rapid discovery of lead compounds with unique SAR that exhibited potent enzymatic and cellular activity with excellent pan-coronavirus coverage.
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Affiliation(s)
- Daniel W Carney
- Takeda Development Center Americas, Inc, 9625 Towne Centre Drive, San Diego, CA 92121, United States.
| | - Abba E Leffler
- Schrödinger, Inc, 1540 Broadway, New York, NY 10036, United States.
| | - Jeffrey A Bell
- Schrödinger, Inc, 1540 Broadway, New York, NY 10036, United States
| | | | - Cecilia Cheng
- Schrödinger, Inc, 9868 Scranton Road, Suite 3200, San Diego, CA 92121, United States
| | - Edcon Chang
- Takeda Development Center Americas, Inc, 9625 Towne Centre Drive, San Diego, CA 92121, United States
| | - Adam Dornford
- Schrödinger, Inc, 1 Main St, 11th Floor, Cambridge, MA 02142, United States
| | - Douglas R Dougan
- Takeda Development Center Americas, Inc, 9625 Towne Centre Drive, San Diego, CA 92121, United States
| | - Leah L Frye
- Schrödinger, Inc, 101 SW Main Street, Suite 1300, Portland, OR 97204, United States
| | - Mary E Grimes
- Schrödinger, Inc, 101 SW Main Street, Suite 1300, Portland, OR 97204, United States
| | - Tim Knehans
- Schrödinger GmbH, Glücksteinallee 25, 68163 Mannheim, Germany
| | | | - Mallareddy Komandla
- Takeda Development Center Americas, Inc, 9625 Towne Centre Drive, San Diego, CA 92121, United States
| | - Weston Lane
- Treeline Biosciences, 500 Arsenal Way, Watertown, MA 02472, United States
| | - Hubert Li
- Schrödinger, Inc, 9868 Scranton Road, Suite 3200, San Diego, CA 92121, United States
| | - Sophia R Newman
- Schrödinger, Inc, 101 SW Main Street, Suite 1300, Portland, OR 97204, United States
| | - Katalin Phimister
- Schrödinger Technologies Limited, 1st Floor West, Davidson House, Forbury Square, Reading RG1 3EU, United Kingdom
| | - Kumar S Saikatendu
- Takeda Development Center Americas, Inc, 9625 Towne Centre Drive, San Diego, CA 92121, United States
| | - Hercules Silverstein
- Schrödinger, Inc, 101 SW Main Street, Suite 1300, Portland, OR 97204, United States
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8
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Chen X, Huang X, Ma Q, Kuzmič P, Zhou B, Zhang S, Chen J, Xu J, Liu B, Jiang H, Zhang W, Yang C, Wu S, Huang J, Li H, Long C, Zhao X, Xu H, Sheng Y, Guo Y, Niu C, Xue L, Xu Y, Liu J, Zhang T, Spencer J, Zhu Z, Deng W, Chen X, Chen SH, Zhong N, Xiong X, Yang Z. Preclinical evaluation of the SARS-CoV-2 M pro inhibitor RAY1216 shows improved pharmacokinetics compared with nirmatrelvir. Nat Microbiol 2024; 9:1075-1088. [PMID: 38553607 PMCID: PMC10994847 DOI: 10.1038/s41564-024-01618-9] [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: 02/27/2023] [Accepted: 01/22/2024] [Indexed: 04/06/2024]
Abstract
Although vaccines are available for SARS-CoV-2, antiviral drugs such as nirmatrelvir are still needed, particularly for individuals in whom vaccines are less effective, such as the immunocompromised, to prevent severe COVID-19. Here we report an α-ketoamide-based peptidomimetic inhibitor of the SARS-CoV-2 main protease (Mpro), designated RAY1216. Enzyme inhibition kinetic analysis shows that RAY1216 has an inhibition constant of 8.4 nM and suggests that it dissociates about 12 times slower from Mpro compared with nirmatrelvir. The crystal structure of the SARS-CoV-2 Mpro:RAY1216 complex shows that RAY1216 covalently binds to the catalytic Cys145 through the α-ketoamide group. In vitro and using human ACE2 transgenic mouse models, RAY1216 shows antiviral activities against SARS-CoV-2 variants comparable to those of nirmatrelvir. It also shows improved pharmacokinetics in mice and rats, suggesting that RAY1216 could be used without ritonavir, which is co-administered with nirmatrelvir. RAY1216 has been approved as a single-component drug named 'leritrelvir' for COVID-19 treatment in China.
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Affiliation(s)
- Xiaoxin Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
- Guangdong Raynovent Biotech Co., Ltd, Guangzhou, China
| | - Xiaodong Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Qinhai Ma
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | | | - Biao Zhou
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangzhou National Laboratory, Guangzhou, China
| | - Sai Zhang
- Guangzhou National Laboratory, Guangzhou, China
| | | | - Jinxin Xu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Bin Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Haiming Jiang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenjie Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chunguang Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shiguan Wu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | | | - Haijun Li
- Guangdong Raynovent Biotech Co., Ltd, Guangzhou, China
| | - Chaofeng Long
- Guangdong Raynovent Biotech Co., Ltd, Guangzhou, China
| | - Xin Zhao
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center Guangzhou), Guangzhou, China
| | - Hongrui Xu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yanan Sheng
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yaoting Guo
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Chuanying Niu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Lu Xue
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yong Xu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jinsong Liu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | | | - Wenbin Deng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Xinwen Chen
- Guangzhou National Laboratory, Guangzhou, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | | | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Guangzhou National Laboratory, Guangzhou, China.
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), China.
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
| | - Zifeng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Guangzhou National Laboratory, Guangzhou, China.
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), China.
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9
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Zengin IN, Koca MS, Tayfuroglu O, Yildiz M, Kocak A. Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 M pro. J Comput Aided Mol Des 2024; 38:15. [PMID: 38532176 DOI: 10.1007/s10822-024-00554-4] [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: 01/03/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024]
Abstract
Here, we introduce the use of ANI-ML potentials as a rescoring function in the host-guest interaction in molecular docking. Our results show that the "docking power" of ANI potentials can compete with the current scoring functions at the same level of computational cost. Benchmarking studies on CASF-2016 dataset showed that ANI is ranked in the top 5 scoring functions among the other 34 tested. In particular, the ANI predicted interaction energies when used in conjunction with GOLD-PLP scoring function can boost the top ranked solution to be the closest to the x-ray structure. Rapid and accurate calculation of interaction energies between ligand and protein also enables screening of millions of drug candidates/docking poses. Using a unique protocol in which docking by GOLD-PLP, rescoring by ANI-ML potentials and extensive MD simulations along with end state free energy methods are combined, we have screened FDA approved drugs against the SARS-CoV-2 main protease (Mpro). The top six drug molecules suggested by the consensus of these free energy methods have already been in clinical trials or proposed as potential drug molecules in previous theoretical and experimental studies, approving the validity and the power of accuracy in our screening method.
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Affiliation(s)
- Irem N Zengin
- Department of Chemistry, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey
| | - M Serdar Koca
- Department of Molecular Biology and Genetics, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey
- Pfizer - Universidad de Granada - Junta de Andalucía Centre for Genomics and Oncological Research (GENYO), 18016, Granada, Spain
| | - Omer Tayfuroglu
- Department of Chemistry, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey
| | - Muslum Yildiz
- Department of Molecular Biology and Genetics, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey
| | - Abdulkadir Kocak
- Department of Chemistry, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey.
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10
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Amblard F, LeCher JC, De R, Zhou S, Liu P, Goh SL, Tao S, Patel D, Downs-Bowen J, Zandi K, Zhang H, Chaudhry G, McBrayer T, Muczynski M, Al-Homoudi A, Engel J, Lan S, Sarafianos SG, Kovari LC, Schinazi RF. Synthesis and biological evaluation of novel peptidomimetic inhibitors of the coronavirus 3C-like protease. Eur J Med Chem 2024; 268:116263. [PMID: 38432056 DOI: 10.1016/j.ejmech.2024.116263] [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: 12/13/2023] [Revised: 02/13/2024] [Accepted: 02/17/2024] [Indexed: 03/05/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and related variants, are responsible for the devastating coronavirus disease 2019 (COVID-19) pandemic. The SARS-CoV-2 main protease (Mpro) plays a central role in the replication of the virus and represents an attractive drug target. Herein, we report the discovery of novel SARS-CoV-2 Mpro covalent inhibitors, including highly effective compound NIP-22c which displays high potency against several key variants and clinically relevant nirmatrelvir Mpro E166V mutants.
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Affiliation(s)
- Franck Amblard
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA.
| | - Julia C LeCher
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Ramyani De
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Shaoman Zhou
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Peng Liu
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Shu Ling Goh
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Sijia Tao
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Dharmeshkumar Patel
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Jessica Downs-Bowen
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Keivan Zandi
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Huanchun Zhang
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Gitika Chaudhry
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Tamara McBrayer
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Michael Muczynski
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Abdullah Al-Homoudi
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Joseph Engel
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Shuiyun Lan
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Stefan G Sarafianos
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Ladislau C Kovari
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Raymond F Schinazi
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA.
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11
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Shurtleff VW, Layton ME, Parish CA, Perkins JJ, Schreier JD, Wang Y, Adam GC, Alvarez N, Bahmanjah S, Bahnck-Teets CM, Boyce CW, Burlein C, Cabalu TD, Campbell BT, Carroll SS, Chang W, de Lera Ruiz M, Dolgov E, Fay JF, Fox NG, Goh SL, Hartingh TJ, Hurzy DM, Kelly MJ, Klein DJ, Klingler FM, Krishnamurthy H, Kudalkar S, Mayhood TW, McKenna PM, Murray EM, Nahas D, Nawrat CC, Park S, Qian D, Roecker AJ, Sharma V, Shipe WD, Su J, Taggart RV, Truong Q, Wu Y, Zhou X, Zhuang N, Perlin DS, Olsen DB, Howe JA, McCauley JA. Invention of MK-7845, a SARS-CoV-2 3CL Protease Inhibitor Employing a Novel Difluorinated Glutamine Mimic. J Med Chem 2024; 67:3935-3958. [PMID: 38365209 DOI: 10.1021/acs.jmedchem.3c02248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Abstract
As SARS-CoV-2 continues to circulate, antiviral treatments are needed to complement vaccines. The virus's main protease, 3CLPro, is an attractive drug target in part because it recognizes a unique cleavage site, which features a glutamine residue at the P1 position and is not utilized by human proteases. Herein, we report the invention of MK-7845, a novel reversible covalent 3CLPro inhibitor. While most covalent inhibitors of SARS-CoV-2 3CLPro reported to date contain an amide as a Gln mimic at P1, MK-7845 bears a difluorobutyl substituent at this position. SAR analysis and X-ray crystallographic studies indicate that this group interacts with His163, the same residue that forms a hydrogen bond with the amide substituents typically found at P1. In addition to promising in vivo efficacy and an acceptable projected human dose with unboosted pharmacokinetics, MK-7845 exhibits favorable properties for both solubility and absorption that may be attributable to the unusual difluorobutyl substituent.
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Affiliation(s)
| | - Mark E Layton
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Craig A Parish
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - James J Perkins
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - John D Schreier
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Yunyi Wang
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Gregory C Adam
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Nadine Alvarez
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | | | | | | | | | - Tamara D Cabalu
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Brian T Campbell
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Steven S Carroll
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Wonsuk Chang
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | - Enriko Dolgov
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - John F Fay
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Nicholas G Fox
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Shih Lin Goh
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | | | - Danielle M Hurzy
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Michael J Kelly
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Daniel J Klein
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | | | | | - Shalley Kudalkar
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Todd W Mayhood
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Philip M McKenna
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Edward M Murray
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Debbie Nahas
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | | | - Steven Park
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | | | | | - Vijeta Sharma
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - William D Shipe
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Jing Su
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Robert V Taggart
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Quang Truong
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Yin Wu
- Viva Biotech Ltd., Shanghai 201318, China
| | - Xiaoyan Zhou
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - David B Olsen
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - John A Howe
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - John A McCauley
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
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12
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Westberg M, Su Y, Zou X, Huang P, Rustagi A, Garhyan J, Patel PB, Fernandez D, Wu Y, Hao C, Lo CW, Karim M, Ning L, Beck A, Saenkham-Huntsinger P, Tat V, Drelich A, Peng BH, Einav S, Tseng CTK, Blish C, Lin MZ. An orally bioavailable SARS-CoV-2 main protease inhibitor exhibits improved affinity and reduced sensitivity to mutations. Sci Transl Med 2024; 16:eadi0979. [PMID: 38478629 DOI: 10.1126/scitranslmed.adi0979] [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: 04/03/2023] [Accepted: 02/21/2024] [Indexed: 05/09/2024]
Abstract
Inhibitors of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro) such as nirmatrelvir (NTV) and ensitrelvir (ETV) have proven effective in reducing the severity of COVID-19, but the presence of resistance-conferring mutations in sequenced viral genomes raises concerns about future drug resistance. Second-generation oral drugs that retain function against these mutants are thus urgently needed. We hypothesized that the covalent hepatitis C virus protease inhibitor boceprevir (BPV) could serve as the basis for orally bioavailable drugs that inhibit SARS-CoV-2 Mpro more efficiently than existing drugs. Performing structure-guided modifications of BPV, we developed a picomolar-affinity inhibitor, ML2006a4, with antiviral activity, oral pharmacokinetics, and therapeutic efficacy similar or superior to those of NTV. A crucial feature of ML2006a4 is a derivatization of the ketoamide reactive group that improves cell permeability and oral bioavailability. Last, ML2006a4 was found to be less sensitive to several mutations that cause resistance to NTV or ETV and occur in the natural SARS-CoV-2 population. Thus, anticipatory design can preemptively address potential resistance mechanisms to expand future treatment options against coronavirus variants.
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Affiliation(s)
- Michael Westberg
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus C, Denmark
| | - Yichi Su
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
- Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200032, China
| | - Xinzhi Zou
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Pinghan Huang
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Arjun Rustagi
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Jaishree Garhyan
- Stanford In Vitro Biosafety Level 3 Service Center, Stanford University, Stanford, CA 94305, USA
| | - Puja Bhavesh Patel
- Stanford In Vitro Biosafety Level 3 Service Center, Stanford University, Stanford, CA 94305, USA
| | - Daniel Fernandez
- Program in Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA 94305, USA
- Sarafan ChEM-H, Macromolecular Structure Knowledge Center, Stanford University, Stanford, CA 94305, USA
| | - Yan Wu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Chenzhou Hao
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
| | - Chieh-Wen Lo
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Marwah Karim
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Lin Ning
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
| | - Aimee Beck
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | | | - Vivian Tat
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Aleksandra Drelich
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Bi-Hung Peng
- Department of Neuroscience, Cell Biology, and Anatomy, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Shirit Einav
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Chien-Te K Tseng
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Neuroscience, Cell Biology, and Anatomy, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Catherine Blish
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Michael Z Lin
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
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13
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Lee D, Jung HG, Park D, Bang J, Cheong DY, Jang JW, Kim Y, Lee S, Lee SW, Lee G, Kim YH, Hong JH, Hwang KS, Lee JH, Yoon DS. Bioengineered amyloid peptide for rapid screening of inhibitors against main protease of SARS-CoV-2. Nat Commun 2024; 15:2108. [PMID: 38453923 PMCID: PMC10920794 DOI: 10.1038/s41467-024-46296-7] [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: 05/13/2023] [Accepted: 02/22/2024] [Indexed: 03/09/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has evoked a worldwide pandemic. As the emergence of variants has hampered the neutralization capacity of currently available vaccines, developing effective antiviral therapeutics against SARS-CoV-2 and its variants becomes a significant challenge. The main protease (Mpro) of SARS-CoV-2 has received increased attention as an attractive pharmaceutical target because of its pivotal role in viral replication and proliferation. Here, we generated a de novo Mpro-inhibitor screening platform to evaluate the efficacies of Mpro inhibitors based on Mpro cleavage site-embedded amyloid peptide (MCAP)-coated gold nanoparticles (MCAP-AuNPs). We fabricated MCAPs comprising an amyloid-forming sequence and Mpro-cleavage sequence, mimicking in vivo viral replication process mediated by Mpro. By measuring the proteolytic activity of Mpro and the inhibitory efficacies of various drugs, we confirmed that the MCAP-AuNP-based platform was suitable for rapid screening potential of Mpro inhibitors. These results demonstrated that our MCAP-AuNP-based platform has great potential for discovering Mpro inhibitors and may accelerate the development of therapeutics against COVID-19.
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Affiliation(s)
- Dongtak Lee
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Hyo Gi Jung
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, 02841, South Korea
| | - Dongsung Park
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul, 02447, South Korea
| | - Junho Bang
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, 02841, South Korea
| | - Da Yeon Cheong
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, 30019, South Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong, 30019, South Korea
| | - Jae Won Jang
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, 02841, South Korea
| | - Yonghwan Kim
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, 02841, South Korea
| | - Seungmin Lee
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Department of Electrical Engineering, Kwangwoon University, Seoul, 01897, South Korea
| | - Sang Won Lee
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Terasaki Institute for Biomedical Innovation, Los Angeles, CA, 90064, USA
| | - Gyudo Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, 30019, South Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong, 30019, South Korea
| | - Yeon Ho Kim
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, 02841, South Korea
| | - Ji Hye Hong
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Department of Electrical Engineering, Kwangwoon University, Seoul, 01897, South Korea
| | - Kyo Seon Hwang
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul, 02447, South Korea.
| | - Jeong Hoon Lee
- Department of Electrical Engineering, Kwangwoon University, Seoul, 01897, South Korea.
| | - Dae Sung Yoon
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea.
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, 02841, South Korea.
- Astrion Inc, Seoul, 02841, South Korea.
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14
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Li P, Kim Y, Dampalla CS, Nhat Nguyen H, Meyerholz DK, Johnson DK, Lovell S, Groutas WC, Perlman S, Chang KO. Potent 3CLpro inhibitors effective against SARS-CoV-2 and MERS-CoV in animal models by therapeutic treatment. mBio 2024; 15:e0287823. [PMID: 38126789 PMCID: PMC10865860 DOI: 10.1128/mbio.02878-23] [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: 10/31/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Middle East respiratory syndrome coronavirus (MERS-CoV) are zoonotic betacoronaviruses that continue to have a significant impact on public health. Timely development and introduction of vaccines and antivirals against SARS-CoV-2 into the clinic have substantially mitigated the burden of COVID-19. However, a limited or lacking therapeutic arsenal for SARS-CoV-2 and MERS-CoV infections, respectively, calls for an expanded and diversified portfolio of antivirals against these coronavirus infections. In this report, we examined the efficacy of two potent 3CLpro inhibitors, 5d and 11d, in fatal animal models of SARS-CoV-2 and MERS-CoV to demonstrate their broad-spectrum activity against both viral infections. These compounds significantly increased the survival of mice in both models when treatment started 1 day post infection compared to no treatment which led to 100% fatality. Especially, the treatment with compound 11d resulted in 80% and 90% survival in SARS-CoV-2 and MERS-CoV-infected mice, respectively. Amelioration of lung viral load and histopathological changes in treated mice correlated well with improved survival in both infection models. Furthermore, compound 11d exhibited significant antiviral activities in K18-hACE2 mice infected with SARS-CoV-2 Omicron subvariant XBB.1.16. The results suggest that these are promising candidates for further development as broad-spectrum direct-acting antivirals against highly virulent human coronaviruses.IMPORTANCEHuman coronaviruses such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Middle East respiratory syndrome coronavirus (MERS-CoV) continue to have a significant impact on public health. A limited or lacking therapeutic arsenal for SARS-CoV-2 and MERS-CoV infections calls for an expanded and diversified portfolio of antivirals against these coronavirus infections. We have previously reported a series of small-molecule 3C-like protease (3CLpro) inhibitors against human coronaviruses. In this report, we demonstrated the in vivo efficacy of 3CLpro inhibitors for their broad-spectrum activity against both SARS-CoV-2 and MERS-CoV infections using the fatal animal models. The results suggest that these are promising candidates for further development as broad-spectrum direct-acting antivirals against highly virulent human coronaviruses.
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Affiliation(s)
- Pengfei Li
- Department of Microbiology and Immunology, The University of Iowa, lowa, USA
| | - Yunjeong Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | | | - Harry Nhat Nguyen
- Department of Chemistry, Wichita State University, Wichita, Kansas, USA
| | | | - David K. Johnson
- Computational Chemical Biology Core, The University of Kansas, Lawrence, Kansas, USA
| | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas, USA
| | | | - Stanley Perlman
- Department of Microbiology and Immunology, The University of Iowa, lowa, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
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15
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Janin YL. On the origins of SARS-CoV-2 main protease inhibitors. RSC Med Chem 2024; 15:81-118. [PMID: 38283212 PMCID: PMC10809347 DOI: 10.1039/d3md00493g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/13/2023] [Indexed: 01/30/2024] Open
Abstract
In order to address the world-wide health challenge caused by the COVID-19 pandemic, the 3CL protease/SARS-CoV-2 main protease (SARS-CoV-2-Mpro) coded by its nsp5 gene became one of the biochemical targets for the design of antiviral drugs. In less than 3 years of research, 4 inhibitors of SARS-CoV-2-Mpro have actually been authorized for COVID-19 treatment (nirmatrelvir, ensitrelvir, leritrelvir and simnotrelvir) and more such as EDP-235, FB-2001 and STI-1558/Olgotrelvir or five undisclosed compounds (CDI-988, ASC11, ALG-097558, QLS1128 and H-10517) are undergoing clinical trials. This review is an attempt to picture this quite unprecedented medicinal chemistry feat and provide insights on how these cysteine protease inhibitors were discovered. Since many series of covalent SARS-CoV-2-Mpro inhibitors owe some of their origins to previous work on other proteases, we first provided a description of various inhibitors of cysteine-bearing human caspase-1 or cathepsin K, as well as inhibitors of serine proteases such as human dipeptidyl peptidase-4 or the hepatitis C protein complex NS3/4A. This is then followed by a description of the results of the approaches adopted (repurposing, structure-based and high throughput screening) to discover coronavirus main protease inhibitors.
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Affiliation(s)
- Yves L Janin
- Structure et Instabilité des Génomes (StrInG), Muséum National d'Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université 75005 Paris France
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16
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Tian L, Qiang T, Yang X, Gao Y, Zhai X, Kang K, Du C, Lu Q, Gao H, Zhang D, Xie X, Liang C. Development of de-novo coronavirus 3-chymotrypsin-like protease (3CL pro) inhibitors since COVID-19 outbreak: A strategy to tackle challenges of persistent virus infection. Eur J Med Chem 2024; 264:115979. [PMID: 38048696 DOI: 10.1016/j.ejmech.2023.115979] [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: 09/18/2023] [Revised: 10/30/2023] [Accepted: 11/18/2023] [Indexed: 12/06/2023]
Abstract
Although no longer a public health emergency of international concern, COVID-19 remains a persistent and critical health concern. The development of effective antiviral drugs could serve as the ultimate piece of the puzzle to curbing this global crisis. 3-chymotrypsin-like protease (3CLpro), with its substrate specificity mirroring that of the main picornavirus 3C protease and conserved across various coronaviruses, emerges as an ideal candidate for broad-spectrum antiviral drug development. Moreover, it holds the potential as a reliable contingency option to combat emerging SARS-CoV-2 variants. In this light, the approved drugs, promising candidates, and de-novo small molecule therapeutics targeting 3CLpro since the COVID-19 outbreak in 2020 are discussed. Emphasizing the significance of diverse structural characteristics in inhibitors, be they peptidomimetic or nonpeptidic, with a shared mission to minimize the risk of cross-resistance. Moreover, the authors propose an innovative optimization strategy for 3CLpro reversible covalent PROTACs, optimizing pharmacodynamics and pharmacokinetics to better prepare for potential future viral outbreaks.
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Affiliation(s)
- Lei Tian
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Taotao Qiang
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, PR China.
| | - Xiuding Yang
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Yue Gao
- College of Pharmacy, Jinan University, Guangzhou, 511436, PR China
| | - Xiaopei Zhai
- Department of Pharmaceutics, School of Pharmacy, Air Force Medical University, Xi'an, 710032, PR China
| | - Kairui Kang
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Cong Du
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Qi Lu
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Hong Gao
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; Shaanxi Pioneer Biotech Co., Ltd., Xi'an, 710021, PR China
| | - Dezhu Zhang
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; Shaanxi Panlong Pharmaceutical Group Co., Ltd., Xi'an, 710025, PR China
| | - Xiaolin Xie
- Shaanxi Panlong Pharmaceutical Group Co., Ltd., Xi'an, 710025, PR China
| | - Chengyuan Liang
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China.
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17
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Zhang H, Zhou J, Chen H, Mao J, Tang Y, Yan W, Zhang T, Li C, Chen S, Li G, Zhang G, Ding Y, Liu L. Phase I study, and dosing regimen selection for a pivotal COVID-19 trial of GST-HG171. Antimicrob Agents Chemother 2024; 68:e0111523. [PMID: 38099673 PMCID: PMC10777829 DOI: 10.1128/aac.01115-23] [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: 08/28/2023] [Accepted: 10/28/2023] [Indexed: 01/11/2024] Open
Abstract
This study is aimed to evaluate the safety, tolerability, and pharmacokinetics (PK), as well as to select an appropriate dosing regimen for the pivotal clinical trial of GST-HG171, an orally bioavailable, potent, and selective 3CL protease inhibitor by a randomized, double-blind, and placebo-controlled phase I trial in healthy subjects. We conducted a Ph1 study involving 78 healthy subjects to assess the safety, tolerability, and PK of single ascending doses (150-900 mg) as well as multiple ascending doses (MADs) (150 and 300 mg) of GST-HG171. Additionally, we examined the food effect and drug-drug interaction of GST-HG171 in combination with ritonavir through a MAD regimen of GST-HG171/ritonavir (BID or TID) for 5 days. Throughout the course of these studies, no serious AEs or deaths occurred, and no AEs necessitated study discontinuation. We observed that food had no significant impact on the exposure of GST-HG171. However, the presence of ritonavir substantially increased the exposure of GST-HG171, which facilitated the selection of the GST-HG171/ritonavir dose and regimen (150/100 mg BID) for subsequent phase II/III trials. The selected dose regimen was achieved through concentrations continuously at 6.2-9.9-fold above the levels required for protein-binding adjusted 50% inhibition (IC50) of viral replication in vitro. The combination of 150 mg GST-HG171/100 mg ritonavir demonstrated favorable safety and tolerability profiles. The PK data obtained from GST-HG171/ritonavir administration guided the selection of appropriate dose for a pivotal phase II/III trial currently in progress. (This study has been registered at ClinicalTrials.gov under identifier NCT05668897).
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Affiliation(s)
- Hong Zhang
- 1 Phase I Clinical Research Center, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Jing Zhou
- 1 Phase I Clinical Research Center, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Hong Chen
- 1 Phase I Clinical Research Center, The First Hospital of Jilin University, Changchun, Jilin, China
| | - John Mao
- Fujian Akeylink Biotechnology Co., Ltd., Fuzhou, Fujian, China
| | - Yanan Tang
- Fujian Akeylink Biotechnology Co., Ltd., Fuzhou, Fujian, China
| | - Wenhao Yan
- Fujian Akeylink Biotechnology Co., Ltd., Fuzhou, Fujian, China
| | - Tianxiang Zhang
- Fujian Akeylink Biotechnology Co., Ltd., Fuzhou, Fujian, China
| | - Chuanjing Li
- Fujian Akeylink Biotechnology Co., Ltd., Fuzhou, Fujian, China
| | - Shikui Chen
- Fujian Cosunter Pharmaceutical Co., Ltd., Fuzhou, Fujian, China
| | - Guoping Li
- Fujian Cosunter Pharmaceutical Co., Ltd., Fuzhou, Fujian, China
| | - George Zhang
- Fujian Akeylink Biotechnology Co., Ltd., Fuzhou, Fujian, China
| | - Yanhua Ding
- 1 Phase I Clinical Research Center, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Li Liu
- Department of Pediatrics, The First Hospital of Jilin University, Changchun, Jilin, China
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18
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Khan N, Sathish J, Rohde CM. Discovery and development of COVID-19 vaccines and therapeutics: nonclinical perspectives. J Toxicol Sci 2024; 49:79-94. [PMID: 38432955 DOI: 10.2131/jts.49.79] [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] [Indexed: 03/05/2024]
Abstract
The development and regulatory review of BNT162b2, a COVID-19 vaccine, and PaxlovidTM (nirmatrelvir tablets/ritonavir tablets), a COVID-19 therapeutic, are benchmarks for accelerated innovation during a global pandemic. Rapid choice of the SARS-CoV-2 spike protein and main protease (Mpro) as targets for the vaccine and therapeutic, respectively, leveraged the available knowledge of the biology of SARS-CoV-2 and related viruses. The nonclinical immunogenicity and safety of BNT162b2 was rigorously assessed. Likewise, a comprehensive nonclinical safety assessment was conducted for the therapeutic candidates, lufotrelvir (PF-07304814) and nirmatrelvir (PF-07321332). The development and regulatory review of BNT162b2 and Paxlovid was enabled through close collaboration of the pharmaceutical industry with regulatory agencies and public health organizations. This experience highlights approaches that could be adopted for pandemic preparedness including risk-based investment strategies, conduct of activities in parallel that normally are conducted sequentially, quick kill decisions, simultaneous evaluation of multiple candidates, and use of flexible, established vaccine platforms.
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Affiliation(s)
- Nasir Khan
- Pfizer Research and Development, Pfizer Inc, Groton, CT, USA
| | - Jean Sathish
- Pfizer Research and Development, Pfizer Inc, Pearl River, NY, USA
| | - Cynthia M Rohde
- Pfizer Research and Development, Pfizer Inc, Pearl River, NY, USA
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19
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Tantra T, Singh Y, Patekar R, Kulkarni S, Kumar P, Thareja S. Phosphate Prodrugs: An Approach to Improve the Bioavailability of Clinically Approved Drugs. Curr Med Chem 2024; 31:336-357. [PMID: 36757029 DOI: 10.2174/0929867330666230209094738] [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: 09/19/2022] [Revised: 11/17/2022] [Accepted: 11/23/2022] [Indexed: 02/10/2023]
Abstract
The phosphate prodrug approach has emerged as a viable option for increasing the bioavailability of a drug candidate with low hydrophilicity and poor cell membrane permeability. When a phosphoric acid moiety is attached to the parent drug, it results in a several-fold elevation in aqueous solubility which helps to achieve desired bioavailability of the pharmaceutically active parental molecule. The neutral phosphate prodrugs have rapid diffusion ability through the plasma membrane as compared to their charged counterpart. The presence of phosphate mono ester breaking alkaline phosphatase (ALP) enzyme throughout the whole human body, is the main consideration behind the development of phosphate prodrug strategy. The popularity of this phosphate prodrug strategy is increasing nowadays due to the fulfillment of different desired pharmacokinetic characteristics required to get pharmaceutical and therapeutic responses without showing any serious adverse drug reactions (ADR). This review article mainly focuses on various phosphate prodrugs synthesized within the last decade to get an improved pharmacological response of the parent moiety along with various preclinical and clinical challenges associated with this approach. Emphasis is also given to the chemical mechanism to release the parent moiety from the prodrug.
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Affiliation(s)
- Tanmoy Tantra
- Department of Pharmaceutical Sciences and Natural Products, School of Health Sciences, Central University of Punjab, Bathinda, Punjab, 151401, India
| | - Yogesh Singh
- Department of Pharmaceutical Sciences and Natural Products, School of Health Sciences, Central University of Punjab, Bathinda, Punjab, 151401, India
| | - Rohan Patekar
- Department of Pharmaceutical Sciences and Natural Products, School of Health Sciences, Central University of Punjab, Bathinda, Punjab, 151401, India
| | - Swanand Kulkarni
- Department of Pharmaceutical Sciences and Natural Products, School of Health Sciences, Central University of Punjab, Bathinda, Punjab, 151401, India
| | - Pradeep Kumar
- Department of Pharmaceutical Sciences and Natural Products, School of Health Sciences, Central University of Punjab, Bathinda, Punjab, 151401, India
| | - Suresh Thareja
- Department of Pharmaceutical Sciences and Natural Products, School of Health Sciences, Central University of Punjab, Bathinda, Punjab, 151401, India
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20
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Zhang H, Li J, Toth K, Tollefson AE, Jing L, Gao S, Liu X, Zhan P. Identification of Ebselen derivatives as novel SARS-CoV-2 main protease inhibitors: Design, synthesis, biological evaluation, and structure-activity relationships exploration. Bioorg Med Chem 2023; 96:117531. [PMID: 37972434 DOI: 10.1016/j.bmc.2023.117531] [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: 08/12/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/19/2023]
Abstract
The main protease (Mpro) represents one of the most effective and attractive targets for designing anti-SARS-CoV-2 drugs. In this study, we designed and synthesized a novel series of Ebselen derivatives by incorporating privileged fragments from different pockets of the Mpro active site. Among these compounds, 11 compounds showed submicromolar activity in the FRET-based SARS-CoV-2 Mpro inhibition assay, with IC50 values ranging from 233 nM to 550 nM. Notably, compound 3a displayed submicromolar Mpro activity (IC50 = 364 nM) and low micromolar antiviral activity (EC50 = 8.01 µM), comparable to that of Ebselen (IC50 = 339 nM, EC50 = 3.78 µM). Time-dependent inhibition assay confirmed that these compounds acted as covalent inhibitors. Taken together, our optimization campaigns thoroughly explored the structural diversity of Ebselen and verified the impact of specific modifications on potency against Mpro.
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Affiliation(s)
- Heng Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China
| | - Jing Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China
| | - Karoly Toth
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri 63104, United States; Saint Louis University Institute for Drug and Biotherapeutic Innovation, St. Louis, Missouri 63104, United States
| | - Ann E Tollefson
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri 63104, United States; Saint Louis University Institute for Drug and Biotherapeutic Innovation, St. Louis, Missouri 63104, United States
| | - Lanlan Jing
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China
| | - Shenghua Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China.
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21
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Gao S, Song L, Sylvester K, Mercorelli B, Loregian A, Toth K, Weiße RH, Useini A, Sträter N, Yang M, Ye B, Tollefson AE, Müller CE, Liu X, Zhan P. Design, Synthesis, and Biological Evaluation of Trisubstituted Piperazine Derivatives as Noncovalent Severe Acute Respiratory Syndrome Coronavirus 2 Main Protease Inhibitors with Improved Antiviral Activity and Favorable Druggability. J Med Chem 2023; 66:16426-16440. [PMID: 37992202 DOI: 10.1021/acs.jmedchem.3c01876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
The ongoing transmission of SARS-CoV-2 necessitates the development of additional potent antiviral agents capable of combating the current highly infectious variants and future coronaviruses. Here, we present the discovery of potent nonpeptide main protease (Mpro) inhibitors with prominent antiviral activity and improved pharmacokinetic properties. Three series of 1,2,4-trisubstituted piperazine derivatives were designed and synthesized, and the optimal GC-78-HCl demonstrated high enzyme-inhibitory potency (IC50 = 0.19 μM) and exhibited excellent antiviral activity (EC50 = 0.40 μM), reaching the same level as Nirmatrelvir (EC50 = 0.38 μM). Additionally, GC-78-HCl displayed potent antiviral activities against various SARS-CoV-2 variants as well as HCoV-OC43 and HCoV-229E, indicating its potential broad-spectrum anticoronaviral activity. Notably, the pharmacokinetic properties of GC-78-HCl were somewhat enhanced compared to those of the lead compound. Furthermore, the cocrystal and molecular docking elucidated the mechanism of action. In conclusion, we discovered a novel nonpeptidic Mpro inhibitor with promising antiviral activity and a favorable pharmacokinetic profile.
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Affiliation(s)
- Shenghua Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
- Shenzhen Research Institute of Shandong University, A301 Virtual University Park in South District of Shenzhen, Shenzhen, Guangdong 518057, PR China
| | - Letian Song
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Katharina Sylvester
- PharmaCenter Bonn & Pharmaceutical Institute, Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53113 Bonn, Germany
| | - Beatrice Mercorelli
- Department of Molecular Medicine, University of Padua, Via Gabelli 63, 35121 Padua, Italy
| | - Arianna Loregian
- Department of Molecular Medicine, University of Padua, Via Gabelli 63, 35121 Padua, Italy
| | - Karoly Toth
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri 63103, United States
| | - Renato H Weiße
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, Leipzig 04103, Germany
| | - Abibe Useini
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, Leipzig 04103, Germany
| | - Norbert Sträter
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, Leipzig 04103, Germany
| | - Mianling Yang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Bing Ye
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Ann E Tollefson
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri 63103, United States
| | - Christa E Müller
- PharmaCenter Bonn & Pharmaceutical Institute, Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53113 Bonn, Germany
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
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22
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Lan Q, Yan Y, Zhang G, Xia S, Zhou J, Lu L, Jiang S. Clinical development of antivirals against SARS-CoV-2 and its variants. CURRENT RESEARCH IN MICROBIAL SCIENCES 2023; 6:100208. [PMID: 38149085 PMCID: PMC10750039 DOI: 10.1016/j.crmicr.2023.100208] [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] [Indexed: 12/28/2023] Open
Abstract
The unceasing global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) calls for the development of novel therapeutics. Although many newly developed antivirals and repurposed antivirals have been applied to the treatment of coronavirus disease 2019 (COVID-19), antivirals showing satisfactory clinical efficacy are few in number. In addition, the loss of sensitivity to variants of concern (VOCs) and lack of oral bioavailability have also limited the clinical application of some antivirals. These facts remind us to develop more potent and broad-spectrum antivirals with better pharmacokinetic/pharmacodynamic properties to fight against infections from SARS-CoV-2, its variants, and other human coronaviruses (HCoVs). In this review, we summarize the latest advancements in the clinical development of antivirals against infections by SARS-CoV-2 and its variants.
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Affiliation(s)
- Qiaoshuai Lan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, China
| | - Yan Yan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Guangxu Zhang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Shuai Xia
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Jie Zhou
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
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23
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Trivedi A, Kardam V, Inampudi KK, Vrati S, Gupta D, Singh A, Kayampeta SR, Appaiahgari MB, Sehgal D. Identification of a novel inhibitor of SARS-CoV-2 main protease: an in silico, biochemical, and cell-based approach. FEBS J 2023; 290:5496-5513. [PMID: 37657928 DOI: 10.1111/febs.16947] [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: 05/25/2023] [Revised: 07/06/2023] [Accepted: 08/31/2023] [Indexed: 09/03/2023]
Abstract
The recurrent nature of coronavirus outbreaks, severity of the COVID-19 pandemic, rapid emergence of novel variants, and concerns over the effectiveness of existing vaccines against novel variants have highlighted the need to develop therapeutic interventions. Targeted efforts to identify inhibitors of crucial viral proteins are the preferred strategy. In this study, we screened FDA-approved and natural product libraries using in silico approach for potential hits against the SARS-CoV-2 main protease (Mpro) and experimentally validated their potency using in vitro biochemical and cell-based assays. Seven potential hits were identified through in silico screening and were subsequently evaluated in SARS-CoV-2-based cell-free assays, followed by testing in the HCoV-229E-based culture system. Of the tested compounds, 4-(3,4-dihydroxyphenyl)-6,7-dihydroxy-1-isopropyl-1H-benzofuro[3,2-b]pyrazolo[4,3-e]pyridin-3(2H)-one (PubChem CID:71755304, hereafter referred to as STL522228) exhibited significant antiviral activity. Subsequently, its potential as a novel COVID therapeutic molecule was validated in the SARS-CoV-2-culture system, where STL522228 demonstrated superior antiviral activity (EC50 = 0.44 μm) compared to Remdesivir (EC50 = 0.62 μm). Based on these findings, we report the strong anti-coronavirus activity of STL522228, and propose that it as a promising pan-coronavirus Mpro inhibitor for further experimental and preclinical validation.
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Affiliation(s)
- Aditya Trivedi
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence, Greater Noida, Uttar Pradesh, India
| | - Vandana Kardam
- Department of Chemistry, School of Natural Sciences, Shiv Nadar Institution of Eminence, Greater Noida, Uttar Pradesh, India
| | | | - Sudhanshu Vrati
- Laboratory of Virology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Dharmender Gupta
- Laboratory of Virology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Aekagra Singh
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence, Greater Noida, Uttar Pradesh, India
| | - Sarala Rani Kayampeta
- Research and Development Division, Srikara Biologicals Private Limited, Tirupati, India
| | | | - Deepak Sehgal
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence, Greater Noida, Uttar Pradesh, India
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24
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Feral A, Martin AR, Desfoux A, Amblard M, Vezenkov LL. Covalent-reversible peptide-based protease inhibitors. Design, synthesis, and clinical success stories. Amino Acids 2023; 55:1775-1800. [PMID: 37330416 DOI: 10.1007/s00726-023-03286-1] [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: 03/30/2023] [Accepted: 05/22/2023] [Indexed: 06/19/2023]
Abstract
Dysregulated human peptidases are implicated in a large variety of diseases such as cancer, hypertension, and neurodegeneration. Viral proteases for their part are crucial for the pathogens' maturation and assembly. Several decades of research were devoted to exploring these precious therapeutic targets, often addressing them with synthetic substrate-based inhibitors to elucidate their biological roles and develop medications. The rational design of peptide-based inhibitors offered a rapid pathway to obtain a variety of research tools and drug candidates. Non-covalent modifiers were historically the first choice for protease inhibition due to their reversible enzyme binding mode and thus presumably safer profile. However, in recent years, covalent-irreversible inhibitors are having a resurgence with dramatic increase of their related publications, preclinical and clinical trials, and FDA-approved drugs. Depending on the context, covalent modifiers could provide more effective and selective drug candidates, hence requiring lower doses, thereby limiting off-target effects. Additionally, such molecules seem more suitable to tackle the crucial issue of cancer and viral drug resistances. At the frontier of reversible and irreversible based inhibitors, a new drug class, the covalent-reversible peptide-based inhibitors, has emerged with the FDA approval of Bortezomib in 2003, shortly followed by 4 other listings to date. The highlight in the field is the breathtakingly fast development of the first oral COVID-19 medication, Nirmatrelvir. Covalent-reversible inhibitors can hipothetically provide the safety of the reversible modifiers combined with the high potency and specificity of their irreversible counterparts. Herein, we will present the main groups of covalent-reversible peptide-based inhibitors, focusing on their design, synthesis, and successful drug development programs.
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Affiliation(s)
- Anthony Feral
- IBMM, University Montpellier, CNRS, ENSCM, Montpellier, France
| | | | | | - Muriel Amblard
- IBMM, University Montpellier, CNRS, ENSCM, Montpellier, France
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25
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Li X, Song Y. Structure and function of SARS-CoV and SARS-CoV-2 main proteases and their inhibition: A comprehensive review. Eur J Med Chem 2023; 260:115772. [PMID: 37659195 PMCID: PMC10529944 DOI: 10.1016/j.ejmech.2023.115772] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 09/04/2023]
Abstract
Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) identified in 2003 infected ∼8000 people in 26 countries with 800 deaths, which was soon contained and eradicated by syndromic surveillance and enhanced quarantine. A closely related coronavirus SARS-CoV-2, the causative agent of COVID-19 identified in 2019, has been dramatically more contagious and catastrophic. It has infected and caused various flu-like symptoms of billions of people in >200 countries, including >6 million people died of or with the virus. Despite the availability of several vaccines and antiviral drugs against SARS-CoV-2, finding new therapeutics is needed because of viral evolution and a possible emerging coronavirus in the future. The main protease (Mpro) of these coronaviruses plays important roles in their life cycle and is essential for the viral replication. This article represents a comprehensive review of the function, structure and inhibition of SARS-CoV and -CoV-2 Mpro, including structure-activity relationships, protein-inhibitor interactions and clinical trial status.
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Affiliation(s)
- Xin Li
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
| | - Yongcheng Song
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
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26
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Tan B, Sacco M, Tan H, Li K, Joyce R, Zhang X, Chen Y, Wang J. Exploring diverse reactive warheads for the design of SARS-CoV-2 main protease inhibitors. Eur J Med Chem 2023; 259:115667. [PMID: 37482021 PMCID: PMC10529912 DOI: 10.1016/j.ejmech.2023.115667] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 07/25/2023]
Abstract
SARS-CoV-2 main protease (Mpro) is a validated antiviral drug target of nirmatrelvir, the active ingredient in Pfizer's oral drug Paxlovid. Drug-drug interactions limit the use of Paxlovid. In addition, drug-resistant Mpro mutants against nirmatrelvir have been identified from cell culture viral passage and naturally occurring variants. As such, there is a need for a second generation of Mpro inhibitors. In this study, we explored several reactive warheads in the design of Mpro inhibitors. We identified Jun11119R (vinyl sulfonamide warhead), Jun10221R (propiolamide warhead), Jun1112R (4-chlorobut-2-ynamide warhead), Jun10541R (nitrile warhead), and Jun10963R (dually activated nitrile warhead) as potent Mpro inhibitors. Jun10541R and Jun10963R also had potent antiviral activity against SARS-CoV-2 in Calu-3 cells with EC50 values of 2.92 and 6.47 μM, respectively. X-ray crystal structures of Mpro with Jun10541R and Jun10221 revealed covalent modification of Cys145. These Mpro inhibitors with diverse reactive warheads collectively represent promising candidates for further development.
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Affiliation(s)
- Bin Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, United States
| | - Michael Sacco
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Haozhou Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, United States
| | - Kan Li
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, United States
| | - Ryan Joyce
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, United States
| | - Xiujun Zhang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, United States.
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27
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Agno KC, Yang K, Byun SH, Oh S, Lee S, Kim H, Kim K, Cho S, Jeong WI, Jeong JW. A temperature-responsive intravenous needle that irreversibly softens on insertion. Nat Biomed Eng 2023:10.1038/s41551-023-01116-z. [PMID: 37903901 DOI: 10.1038/s41551-023-01116-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 09/26/2023] [Indexed: 11/01/2023]
Abstract
The high stiffness of intravenous needles can cause tissue injury and increase the risk of transmission of blood-borne pathogens through accidental needlesticks. Here we describe the development and performance of an intravenous needle whose stiffness and shape depend on body temperature. The needle is sufficiently stiff for insertion into soft tissue yet becomes irreversibly flexible after insertion, adapting to the shape of the blood vessel and reducing the risk of needlestick injury on removal, as we show in vein phantoms and ex vivo porcine tissue. In mice, the needles had similar fluid-delivery performance and caused substantially less inflammation than commercial devices for intravenous access of similar size. We also show that an intravenous needle integrated with a thin-film temperature sensor can monitor core body temperature in mice and detect fluid leakage in porcine tissue ex vivo. Temperature-responsive intravenous needles may improve patient care.
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Affiliation(s)
- Karen-Christian Agno
- School of Electrical Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Keungmo Yang
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sang-Hyuk Byun
- School of Electrical Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Subin Oh
- School of Electrical Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Simok Lee
- School of Electrical Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Heesoo Kim
- School of Electrical Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Kyurae Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Sungwoo Cho
- School of Electrical Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Won-Il Jeong
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.
| | - Jae-Woong Jeong
- School of Electrical Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.
- KAIST Institute for Health Science and Technology, Daejeon, Republic of Korea.
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28
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Liu M, Li J, Liu W, Yang Y, Zhang M, Ye Y, Zhu W, Zhou C, Zhai H, Xu Z, Zhang G, Huang H. The S1'-S3' Pocket of the SARS-CoV-2 Main Protease Is Critical for Substrate Selectivity and Can Be Targeted with Covalent Inhibitors. Angew Chem Int Ed Engl 2023; 62:e202309657. [PMID: 37609788 DOI: 10.1002/anie.202309657] [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: 07/07/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 08/24/2023]
Abstract
The main protease (Mpro ) of SARS-CoV-2 is a well-characterized target for antiviral drug discovery. To date, most antiviral drug discovery efforts have focused on the S4-S1' pocket of Mpro ; however, it is still unclear whether the S1'-S3' pocket per se can serve as a new site for drug discovery. In this study, the S1'-S3' pocket of Mpro was found to differentially recognize viral peptidyl substrates. For instance, S3' in Mpro strongly favors Phe or Trp, and S1' favors Ala. The peptidyl inhibitor D-4-77, which possesses an α-bromoacetamide warhead, was discovered to be a promising inhibitor of Mpro , with an IC50 of 0.95 μM and an antiviral EC50 of 0.49 μM. The Mpro /inhibitor co-crystal structure confirmed the binding mode of the inhibitor to the S1'-S3' pocket and revealed a covalent mechanism. In addition, D-4-77 functions as an immune protectant and suppresses SARS-CoV-2 Mpro -induced antagonism of the host NF-κB innate immune response. These findings indicate that the S1'-S3' pocket of SARS-CoV-2 Mpro is druggable, and that inhibiting SARS-CoV-2 Mpro can simultaneously protect human innate immunity and inhibit virion assembly.
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Affiliation(s)
- Ming Liu
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Laboratory of Structural Biology and Drug Discovery, Laboratory of Ubiquitination and Targeted Therapy, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, China
| | - Jihui Li
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Laboratory of Structural Biology and Drug Discovery, Laboratory of Ubiquitination and Targeted Therapy, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, China
| | - Wenqi Liu
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong, 518112, China
| | - Ying Yang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Laboratory of Structural Biology and Drug Discovery, Laboratory of Ubiquitination and Targeted Therapy, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, China
| | - Manman Zhang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Laboratory of Structural Biology and Drug Discovery, Laboratory of Ubiquitination and Targeted Therapy, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, China
| | - Yuxin Ye
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Laboratory of Structural Biology and Drug Discovery, Laboratory of Ubiquitination and Targeted Therapy, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, China
| | - Wenning Zhu
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Laboratory of Structural Biology and Drug Discovery, Laboratory of Ubiquitination and Targeted Therapy, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, China
| | - Cuiyan Zhou
- National Protein Science Facility, School of Life Science, Tsinghua University, Beijing, 100084, China
| | - Hongbin Zhai
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Laboratory of Structural Biology and Drug Discovery, Laboratory of Ubiquitination and Targeted Therapy, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, China
| | - Zhengshuang Xu
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Laboratory of Structural Biology and Drug Discovery, Laboratory of Ubiquitination and Targeted Therapy, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, China
| | - Guoliang Zhang
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong, 518112, China
| | - Hao Huang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Laboratory of Structural Biology and Drug Discovery, Laboratory of Ubiquitination and Targeted Therapy, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, China
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China
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29
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Cheruvu N, van Duijn E, Spigt PA, Barbu IM, Toussi SS, Schildknegt K, Jones RM, Obach RS. The Metabolism of Lufotrelvir, a Prodrug Investigated for the Treatment of SARS-COV2 in Humans Following Intravenous Administration. Drug Metab Dispos 2023; 51:1419-1427. [PMID: 37429728 DOI: 10.1124/dmd.123.001416] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 06/30/2023] [Accepted: 07/05/2023] [Indexed: 07/12/2023] Open
Abstract
The metabolism of lufotrelvir, a novel phosphate prodrug of PF-00835231 for the treatment of COVID-19, was evaluated in healthy human volunteers and clinical trial participants with COVID-19 following intravenous infusion. The prodrug was completely converted to PF-00835231 that was subsequently cleared by hydrolysis, hydroxylation, ketoreduction, epimerization, renal clearance, and secretion into the feces. The main circulating metabolite was a hydrolysis product (M7) that was present at concentrations greater than PF-00835231, and this was consistent between healthy volunteers and participants with COVID-19. On administration of [14C]lufotrelvir, only 63% of the dose was obtained in excreta over 10 days and total drug-related material demonstrated a prolonged terminal phase half-life in plasma. A considerable portion of the labeled material was unextractable from fecal homogenate and plasma. The position of the carbon-14 atom in the labeled material was at a leucine carbonyl, and pronase digestion of the pellet derived from extraction of the fecal homogenate showed that [14C]leucine was released. SIGNIFICANCE STATEMENT: Lufotrelvir is an experimental phosphate prodrug intravenous therapy investigated for the potential treatment of COVID-19 in a hospital setting. The overall metabolism of lufotrelvir was determined in human healthy volunteers and clinical trial participants with COVID-19. Conversion of the phosphate prodrug to the active drug PF-00835231 was complete and the subsequent metabolic clearance of the active drug was largely via amide bond hydrolysis. Substantial drug-related material was not recovered due to loss of the carbon-14 label to endogenous metabolism.
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Affiliation(s)
- Narayan Cheruvu
- Pfizer Worldwide Research, Development and Medical, Groton, Connecticut (R.S.O., K.S.); Pfizer Worldwide Research, Development and Medical, La Jolla, California (R.M.J.); Pfizer Worldwide Research, Development and Medical, Collegeville, Pennsylvania (N.C.); Pfizer Worldwide Research, Development and Medical, Pearl River, New York (S.S.T.); and The Netherlands Organization for Applied Scientific Research (T.N.O.), Zeist, Netherlands (E.v.D., P.A.S., I.M.B.)
| | - Esther van Duijn
- Pfizer Worldwide Research, Development and Medical, Groton, Connecticut (R.S.O., K.S.); Pfizer Worldwide Research, Development and Medical, La Jolla, California (R.M.J.); Pfizer Worldwide Research, Development and Medical, Collegeville, Pennsylvania (N.C.); Pfizer Worldwide Research, Development and Medical, Pearl River, New York (S.S.T.); and The Netherlands Organization for Applied Scientific Research (T.N.O.), Zeist, Netherlands (E.v.D., P.A.S., I.M.B.)
| | - Pieter A Spigt
- Pfizer Worldwide Research, Development and Medical, Groton, Connecticut (R.S.O., K.S.); Pfizer Worldwide Research, Development and Medical, La Jolla, California (R.M.J.); Pfizer Worldwide Research, Development and Medical, Collegeville, Pennsylvania (N.C.); Pfizer Worldwide Research, Development and Medical, Pearl River, New York (S.S.T.); and The Netherlands Organization for Applied Scientific Research (T.N.O.), Zeist, Netherlands (E.v.D., P.A.S., I.M.B.)
| | - Ioana M Barbu
- Pfizer Worldwide Research, Development and Medical, Groton, Connecticut (R.S.O., K.S.); Pfizer Worldwide Research, Development and Medical, La Jolla, California (R.M.J.); Pfizer Worldwide Research, Development and Medical, Collegeville, Pennsylvania (N.C.); Pfizer Worldwide Research, Development and Medical, Pearl River, New York (S.S.T.); and The Netherlands Organization for Applied Scientific Research (T.N.O.), Zeist, Netherlands (E.v.D., P.A.S., I.M.B.)
| | - Sima S Toussi
- Pfizer Worldwide Research, Development and Medical, Groton, Connecticut (R.S.O., K.S.); Pfizer Worldwide Research, Development and Medical, La Jolla, California (R.M.J.); Pfizer Worldwide Research, Development and Medical, Collegeville, Pennsylvania (N.C.); Pfizer Worldwide Research, Development and Medical, Pearl River, New York (S.S.T.); and The Netherlands Organization for Applied Scientific Research (T.N.O.), Zeist, Netherlands (E.v.D., P.A.S., I.M.B.)
| | - Klaas Schildknegt
- Pfizer Worldwide Research, Development and Medical, Groton, Connecticut (R.S.O., K.S.); Pfizer Worldwide Research, Development and Medical, La Jolla, California (R.M.J.); Pfizer Worldwide Research, Development and Medical, Collegeville, Pennsylvania (N.C.); Pfizer Worldwide Research, Development and Medical, Pearl River, New York (S.S.T.); and The Netherlands Organization for Applied Scientific Research (T.N.O.), Zeist, Netherlands (E.v.D., P.A.S., I.M.B.)
| | - Rhys M Jones
- Pfizer Worldwide Research, Development and Medical, Groton, Connecticut (R.S.O., K.S.); Pfizer Worldwide Research, Development and Medical, La Jolla, California (R.M.J.); Pfizer Worldwide Research, Development and Medical, Collegeville, Pennsylvania (N.C.); Pfizer Worldwide Research, Development and Medical, Pearl River, New York (S.S.T.); and The Netherlands Organization for Applied Scientific Research (T.N.O.), Zeist, Netherlands (E.v.D., P.A.S., I.M.B.)
| | - R Scott Obach
- Pfizer Worldwide Research, Development and Medical, Groton, Connecticut (R.S.O., K.S.); Pfizer Worldwide Research, Development and Medical, La Jolla, California (R.M.J.); Pfizer Worldwide Research, Development and Medical, Collegeville, Pennsylvania (N.C.); Pfizer Worldwide Research, Development and Medical, Pearl River, New York (S.S.T.); and The Netherlands Organization for Applied Scientific Research (T.N.O.), Zeist, Netherlands (E.v.D., P.A.S., I.M.B.)
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30
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Alam MNE, Hosen MM, Ullah AKMA, Maksud MA, Khan SR, Lutfa LN, Choudhury TR, Quraishi SB. Lead Exposure of Four Biologically Important Common Branded and Non-branded Spices: Relative Analysis and Health Implication. Biol Trace Elem Res 2023; 201:4972-4984. [PMID: 36627477 PMCID: PMC9838428 DOI: 10.1007/s12011-022-03553-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/30/2022] [Indexed: 01/12/2023]
Abstract
Technological advances and socioeconomic development of Bangladesh are leading to the best choice between branded and non-branded powdered spices. But toxic metal issues can be another factor to elect them. So lead (Pb) exposure and its consequence on the human body for these two categories of four common spices have been ascertained here. A validated laboratory method using hot plate digestion and flame atomic absorption spectrometry (FAAS) has been used for that. The obtained mean concentration of Pb in branded and non-branded spice powders followed the decreasing order of turmeric > coriander > red chili > cumin powder and turmeric > red chili > cumin > coriander powder, respectively, where, in any analysis mode, the non-branded items are potentially ahead of Pb exposure. The market-based mean concentration between these two categories was not a significant difference (t-test). Approximately 90% of the spice samples have shown within the maximum allowable limit by Bangladesh Standard. The sum of estimated daily intake indicated that most of the city market (67%) for non-branded items and some branded (33%) samples have crossed the maximum tolerable daily intake (> 0.21 mg/kg). So, the human health risk assumption for the inhabitant of studied areas suggests there is no significant level of risk for them due to the consumption of spices regarding non-carcinogenic risk factor (THQ and total THQ) and carcinogenic risk factor (CR). But the development of a quality control process for loose spice powders as well as toxic metal screening from raw materials to finish products urgently needed and continuous monitoring with identifying the source of toxic metal is highly recommended.
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Affiliation(s)
- M. Nur E. Alam
- Analytical Chemistry Laboratory, Atomic Energy Center, Bangladesh, Atomic Energy Commission, Dhaka, 1000 Bangladesh
| | - M. Mozammal Hosen
- Analytical Chemistry Laboratory, Atomic Energy Center, Bangladesh, Atomic Energy Commission, Dhaka, 1000 Bangladesh
| | - A. K. M. Atique Ullah
- Analytical Chemistry Laboratory, Atomic Energy Center, Bangladesh, Atomic Energy Commission, Dhaka, 1000 Bangladesh
| | - M. A. Maksud
- Analytical Chemistry Laboratory, Atomic Energy Center, Bangladesh, Atomic Energy Commission, Dhaka, 1000 Bangladesh
| | - S. R. Khan
- Analytical Chemistry Laboratory, Atomic Energy Center, Bangladesh, Atomic Energy Commission, Dhaka, 1000 Bangladesh
| | - L. N. Lutfa
- Analytical Chemistry Laboratory, Atomic Energy Center, Bangladesh, Atomic Energy Commission, Dhaka, 1000 Bangladesh
| | - Tasrina Rabia Choudhury
- Analytical Chemistry Laboratory, Atomic Energy Center, Bangladesh, Atomic Energy Commission, Dhaka, 1000 Bangladesh
| | - Shamshad B. Quraishi
- Analytical Chemistry Laboratory, Atomic Energy Center, Bangladesh, Atomic Energy Commission, Dhaka, 1000 Bangladesh
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31
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Lokhande KB, Kale A, Shahakar B, Shrivastava A, Nawani N, Swamy KV, Singh A, Pawar SV. Terpenoid phytocompounds from mangrove plant Xylocarpus moluccensis as possible inhibitors against SARS-CoV-2: In silico strategy. Comput Biol Chem 2023; 106:107912. [PMID: 37454399 DOI: 10.1016/j.compbiolchem.2023.107912] [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: 05/19/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Abstract
COVID-19 shook the world during the pandemic, where the climax it reached was vaccine manufacturing at an unfathomable pace. Alternative promising solutions to prevent infection from SARS-CoV-2 and its variants will remain crucial in the years to come. Due to its key role in viral replication, the major protease (Mpro) enzyme of SARS-CoV-2 can be an attractive therapeutic target. In the present work, natural terpenoids from mangrove medicinal plant Xylocarpus moluccensis (Lam.) M. Roem. were screened using computational methods for inhibition of Mpro protein. Out of sixty-seven terpenoids, Angolensic acid methyl ester, Moluccensin V, Thaixylomolin F, Godavarin J, and Xylomexicanolide A were shortlisted based on their docking scores and interaction affinities (- 13.502 to - 15.52 kcal/mol). The efficacy was validated by the 100 ns molecular dynamics study. Lead terpenoids were within the acceptable range of RMSD and RMSF with a mean value of 2.5 Å and 1.5 Å, respectively indicating that they bound tightly within Mpro and there was minimal fluctuation and stability of Mpro upon binding of these terpenoids. The utmost favorable binding strengths as calculated by MM-GBSA, were of Angolensic acid methyl ester and Moluccensin V with binding free energies (ΔGbind) of - 39.084, and - 43.160 kcal/mol, respectively. The terpenoids showed no violations in terms of Drug Likeliness and ADMET predictions. Overall, the findings indicate that Angolensic acid methyl ester and Moluccensin V are effective terpenoids having strong binding interaction with Mpro protein, which must be tested in vitro as an effective anti-SARS-CoV-2 drug.
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Affiliation(s)
- Kiran Bharat Lokhande
- Bioinformatics Research Laboratory, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune 411033, Maharashtra, India; Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, India
| | - Arti Kale
- Microbial Diversity Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune 411033, Maharashtra, India
| | - Bhagyashree Shahakar
- Microbial Diversity Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune 411033, Maharashtra, India
| | - Ashish Shrivastava
- Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, India
| | - Neelu Nawani
- Microbial Diversity Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune 411033, Maharashtra, India.
| | - K Venkateswara Swamy
- MIT School of Bioengineering Sciences & Research, MIT Art, Design and Technology University, Pune, Maharashtra, India
| | - Ashutosh Singh
- Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, India
| | - Sarika Vishnu Pawar
- Microbial Diversity Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune 411033, Maharashtra, India.
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32
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Wu J, Zhang HX, Zhang J. The molecular mechanism of non-covalent inhibitor WU-04 targeting SARS-CoV-2 3CLpro and computational evaluation of its effectiveness against mainstream coronaviruses. Phys Chem Chem Phys 2023; 25:23555-23567. [PMID: 37655706 DOI: 10.1039/d3cp03828a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
There is an urgent need for highly effective therapeutic agents to interrupt the continued spread of SARS-CoV-2. As a pivotal protease in the replication process of coronaviruses, the 3CLpro protein is considered as a potential target of drug development to stop the spread and infection of the virus. In this work, molecular dynamics (MD) simulations were used to elucidate the molecular mechanism of a novel and highly effective non-covalent inhibitor, WU-04, targeting the SARS-CoV-2 3CLpro protein. The difference in dynamic behavior between the apo-3CLpro and the holo-3CLpro systems suggests that the presence of WU-04 inhibits the motion amplitude of the 3CLpro protein relative to the apo-3CLpro system, thus maintaining a stable conformational binding state. The energy calculations and interaction analysis show that the hot-spot residues Q189, M165, M49, E166, and H41 and the warm-spot residues H163 and C145 have a strong binding capacity to WU-04 by forming multiple hydrogen bonds and hydrophobic interactions, which stabilizes the binding of the inhibitor. After that, the resistance of WU-04 to the six SARS-CoV-2 variants (Alpha, Beta, Gamma, Delta, Lambda, and Omicron) and two other mainstream coronavirus (SARS-CoV and MERS-CoV) 3CLpro proteins was further investigated. Excitingly, the slight difference in energy values relative to the SARS-CoV-2 system indicates that WU-04 is still highly effective against the coronaviruses, which becomes crucial evidence that WU-04 is a pan-inhibitor of the 3CLpro protein in various SARS-CoV-2 variants and other mainstream coronaviruses. The study will hopefully provide theoretical insights for the future rational design and improvement of novel non-covalent inhibitors targeting the 3CLpro protein.
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Affiliation(s)
- Jianhua Wu
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, Jilin, People's Republic of China.
| | - Hong-Xing Zhang
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, Jilin, People's Republic of China.
| | - Jilong Zhang
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, Jilin, People's Republic of China.
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33
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Lin C, Jiang H, Li W, Zeng P, Zhou X, Zhang J, Li J. Structural basis for the inhibition of coronaviral main proteases by ensitrelvir. Structure 2023; 31:1016-1024.e3. [PMID: 37421945 DOI: 10.1016/j.str.2023.06.010] [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: 02/07/2023] [Revised: 03/31/2023] [Accepted: 06/13/2023] [Indexed: 07/10/2023]
Abstract
Main protease (Mpro) is a highly conserved cysteine protease that plays a vital role in the replication of coronaviruses, making it an attractive pan-coronaviral therapeutic target. Ensitrelvir (S-217622), developed by Shionogi, is the first orally active non-covalent, non-peptidic SARS-CoV-2 Mpro inhibitor, which also displays antiviral efficacy against other human coronaviruses as well as SARS-CoV-2 variants of concern (VOCs) and variants of interest (VOIs). Here, we report the crystal structures of the main proteases from SARS-CoV-2, SARS-CoV-2 VOC/VOIs, SARS-CoV, MERS-CoV, and HCoV-NL63 bound to the inhibitor S-217622. A detailed analysis of these structures illuminates key structural determinants essential for inhibition and elucidates the binding modes of the main proteases from different coronaviruses. Given the importance of the main protease for the treatment of coronaviral infection, structural insights obtained from this study could accelerate the design of novel antivirals with broad-spectrum efficacy against different human coronaviruses.
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Affiliation(s)
- Cheng Lin
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China
| | - Haihai Jiang
- School of Basic Medical Sciences, Nanchang University, Nanchang 330031, China
| | - Wenwen Li
- Shenzhen Crystalo Biopharmaceutical Co., Ltd., Shenzhen 518118, China; Jiangxi Jmerry Biopharmaceutical Co., Ltd., Ganzhou 341000, China
| | - Pei Zeng
- Jiangxi Jmerry Biopharmaceutical Co., Ltd., Ganzhou 341000, China
| | - Xuelan Zhou
- Jiangxi Jmerry Biopharmaceutical Co., Ltd., Ganzhou 341000, China
| | - Jin Zhang
- School of Basic Medical Sciences, Nanchang University, Nanchang 330031, China.
| | - Jian Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China.
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34
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Yang L, Wang Z. Bench-to-bedside: Innovation of small molecule anti-SARS-CoV-2 drugs in China. Eur J Med Chem 2023; 257:115503. [PMID: 37229831 PMCID: PMC10193775 DOI: 10.1016/j.ejmech.2023.115503] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/19/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023]
Abstract
The ongoing COVID-19 pandemic has resulted in millions of deaths globally, highlighting the need to develop potent prophylactic and therapeutic strategies against SARS-CoV-2. Small molecule inhibitors (remdesivir, Paxlovid, and molnupiravir) are essential complements to vaccines and play important roles in clinical treatment of SARS-CoV-2. Many advances have been made in development of anti-SARS-CoV-2 inhibitors in China, but progress in discovery and characterization of pharmacological activity, antiviral mechanisms, and clinical efficacy are limited. We review development of small molecule anti-SARS-CoV-2 drugs (azvudine [approved by the NMPA of China on July 25, 2022], VV116 [approved by the NMPA of China on January 29, 2023], FB2001, WPV01, pentarlandir, and cepharanthine) in China and summarize their pharmacological activity, potential mechanisms of action, clinical trials and use, and important milestones in their discovery. The role of structural biology in drug development is also reviewed. Future studies should focus on development of diverse second-generation inhibitors with excellent oral bioavailability, superior plasma half-life, increased antiviral activity against SARS-CoV-2 and its variants, high target specificity, minimal side effects, reduced drug-drug interactions, and improved lung histopathology.
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Affiliation(s)
- Liyan Yang
- School of Physics and Physical Engineering, Qufu Normal University, Qufu, 273165, PR China; Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Zhonglei Wang
- Key Laboratory of Green Natural Products and Pharmaceutical Intermediates in Colleges and Universities of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, 273165, PR China; School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus, Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, PR China.
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35
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Guo M, Xiong M, Peng J, Guan T, Su H, Huang Y, Yang CG, Li Y, Boraschi D, Pillaiyar T, Wang G, Yi C, Xu Y, Chen C. Multi-omics for COVID-19: driving development of therapeutics and vaccines. Natl Sci Rev 2023; 10:nwad161. [PMID: 37936830 PMCID: PMC10627145 DOI: 10.1093/nsr/nwad161] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 11/09/2023] Open
Abstract
The ongoing COVID-19 pandemic caused by SARS-CoV-2 has raised global concern for public health and economy. The development of therapeutics and vaccines to combat this virus is continuously progressing. Multi-omics approaches, including genomics, transcriptomics, proteomics, metabolomics, epigenomics and metallomics, have helped understand the structural and molecular features of the virus, thereby assisting in the design of potential therapeutics and accelerating vaccine development for COVID-19. Here, we provide an up-to-date overview of the latest applications of multi-omics technologies in strategies addressing COVID-19, in order to provide suggestions towards the development of highly effective knowledge-based therapeutics and vaccines.
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Affiliation(s)
- Mengyu Guo
- CAS Key Laboratory of Biomedical Effects of Nanomaterials and Nanosafety, and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Muya Xiong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinying Peng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Tong Guan
- CAS Key Laboratory of Biomedical Effects of Nanomaterials and Nanosafety, and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haixia Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanyi Huang
- Biomedical Pioneering Innovation Centre, Peking University, Beijing 100871, China
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 528107, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Cai-Guang Yang
- State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Li
- Laboratory of Immunology and Nanomedicine, and China-Italy Joint Laboratory of Pharmacobiotechnology for Medical Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Diana Boraschi
- Laboratory of Immunology and Nanomedicine, and China-Italy Joint Laboratory of Pharmacobiotechnology for Medical Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Institute of Biochemistry and Cell Biology, National Research Council, Napoli 80131, Italy
| | - Thanigaimalai Pillaiyar
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tuebingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Tübingen 72076, Germany
| | - Guanbo Wang
- Biomedical Pioneering Innovation Centre, Peking University, Beijing 100871, China
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 528107, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
- Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yechun Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunying Chen
- CAS Key Laboratory of Biomedical Effects of Nanomaterials and Nanosafety, and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- GBA National Institute for Nanotechnology Innovation, Guangzhou 510700, China
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36
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Leonard RA, Rao VN, Bartlett A, Froggatt HM, Luftig MA, Heaton BE, Heaton NS. A low-background, fluorescent assay to evaluate inhibitors of diverse viral proteases. J Virol 2023; 97:e0059723. [PMID: 37578235 PMCID: PMC10506478 DOI: 10.1128/jvi.00597-23] [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: 04/20/2023] [Accepted: 06/11/2023] [Indexed: 08/15/2023] Open
Abstract
Multiple coronaviruses (CoVs) can cause respiratory diseases in humans. While prophylactic vaccines designed to prevent infection are available for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), incomplete vaccine efficacy, vaccine hesitancy, and the threat of other pathogenic CoVs for which vaccines do not exist have highlighted the need for effective antiviral therapies. While antiviral compounds targeting the viral polymerase and protease are already in clinical use, their sensitivity to potential resistance mutations as well as their breadth against the full range of human and preemergent CoVs remain incompletely defined. To begin to fill that gap in knowledge, we report here the development of an improved, noninfectious, cell-based fluorescent assay with high sensitivity and low background that reports on the activity of viral proteases, which are key drug targets. We demonstrate that the assay is compatible with not only the SARS-CoV-2 Mpro protein but also orthologues from a range of human and nonhuman CoVs as well as clinically reported SARS-CoV-2 drug-resistant Mpro variants. We then use this assay to define the breadth of activity of two clinically used protease inhibitors, nirmatrelvir and ensitrelvir. Continued use of this assay will help define the strengths and limitations of current therapies and may also facilitate the development of next-generation protease inhibitors that are broadly active against both currently circulating and preemergent CoVs. IMPORTANCE Coronaviruses (CoVs) are important human pathogens with the ability to cause global pandemics. Working in concert with vaccines, antivirals specifically limit viral disease in people who are actively infected. Antiviral compounds that target CoV proteases are already in clinical use; their efficacy against variant proteases and preemergent zoonotic CoVs, however, remains incompletely defined. Here, we report an improved, noninfectious, and highly sensitive fluorescent method of defining the sensitivity of CoV proteases to small molecule inhibitors. We use this approach to assay the activity of current antiviral therapies against clinically reported SARS-CoV-2 protease mutants and a panel of highly diverse CoV proteases. Additionally, we show this system is adaptable to other structurally nonrelated viral proteases. In the future, this assay can be used to not only better define the strengths and limitations of current therapies but also help develop new, broadly acting inhibitors that more broadly target viral families.
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Affiliation(s)
- Rebecca A. Leonard
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Vishwas N. Rao
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Medical Scientist Training Program, Duke University School of Medicine, Durham, North Carolina, USA
| | - Alexandria Bartlett
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Heather M. Froggatt
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Micah A. Luftig
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Center for Virology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Brook E. Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Nicholas S. Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Center for Virology, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
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37
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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: 6] [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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38
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Hu Y, Lewandowski EM, Tan H, Zhang X, Morgan RT, Zhang X, Jacobs LMC, Butler SG, Gongora MV, Choy J, Deng X, Chen Y, Wang J. Naturally Occurring Mutations of SARS-CoV-2 Main Protease Confer Drug Resistance to Nirmatrelvir. ACS CENTRAL SCIENCE 2023; 9:1658-1669. [PMID: 37637734 PMCID: PMC10451032 DOI: 10.1021/acscentsci.3c00538] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Indexed: 08/29/2023]
Abstract
The SARS-CoV-2 main protease (Mpro) is the drug target of Pfizer's oral drug nirmatrelvir. The emergence of SARS-CoV-2 variants with mutations in Mpro raised the alarm of potential drug resistance. To identify potential clinically relevant drug-resistant mutants, we systematically characterized 102 naturally occurring Mpro mutants located at 12 residues at the nirmatrelvir-binding site, among which 22 mutations in 5 residues, including S144M/F/A/G/Y, M165T, E166 V/G/A, H172Q/F, and Q192T/S/L/A/I/P/H/V/W/C/F, showed comparable enzymatic activity to the wild-type (kcat/Km < 10-fold change) while being resistant to nirmatrelvir (Ki > 10-fold increase). X-ray crystal structures were determined for six representative mutants with and/or without GC-376/nirmatrelvir. Using recombinant SARS-CoV-2 viruses generated from reverse genetics, we confirmed the drug resistance in the antiviral assay and showed that Mpro mutants with reduced enzymatic activity had attenuated viral replication. Overall, our study identified several drug-resistant hotspots in Mpro that warrant close monitoring for possible clinical evidence of nirmatrelvir resistance, some of which have already emerged in independent viral passage assays conducted by others.
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Affiliation(s)
- Yanmei Hu
- Department
of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, New Brunswick, New Jersey 08854, United States
| | - Eric M. Lewandowski
- Department
of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Haozhou Tan
- Department
of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, New Brunswick, New Jersey 08854, United States
| | - Xiaoming Zhang
- Department
Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, Oklahoma 74078, United States
- Oklahoma
Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Ryan T. Morgan
- Department
of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Xiujun Zhang
- Department
of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Lian M. C. Jacobs
- Department
of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Shane G. Butler
- Department
of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Maura V. Gongora
- Department
of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - John Choy
- Department
Biology, School of Arts and Sciences, the
Catholic University of America, Washington, DC 20064, United States
| | - Xufang Deng
- Department
Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, Oklahoma 74078, United States
- Oklahoma
Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Yu Chen
- Department
of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Jun Wang
- Department
of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, New Brunswick, New Jersey 08854, United States
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39
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Stubbing LA, Hubert JG, Bell-Tyrer J, Hermant YO, Yang SH, McSweeney AM, McKenzie-Goldsmith GM, Ward VK, Furkert DP, Brimble MA. P 1 Glutamine isosteres in the design of inhibitors of 3C/3CL protease of human viruses of the Pisoniviricetes class. RSC Chem Biol 2023; 4:533-547. [PMID: 37547456 PMCID: PMC10398354 DOI: 10.1039/d3cb00075c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 06/19/2023] [Indexed: 08/08/2023] Open
Abstract
Viral infections are one of the leading causes of acute morbidity in humans and much endeavour has been made by the synthetic community for the development of drugs to treat associated diseases. Peptide-based enzyme inhibitors, usually short sequences of three or four residues, are one of the classes of compounds currently under development for enhancement of their activity and pharmaceutical properties. This review reports the advances made in the design of inhibitors targeting the family of highly conserved viral proteases 3C/3CLpro, which play a key role in viral replication and present minimal homology with mammalian proteases. Particular focus is put on the reported development of P1 glutamine isosteres to generate potent inhibitors mimicking the natural substrate sequence at the site of recognition.'
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Affiliation(s)
- Louise A Stubbing
- School of Chemical Sciences, The University of Auckland 23 Symonds Street and 3b Symonds Street Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 3b Symonds Street Auckland 1142 New Zealand
| | - Jonathan G Hubert
- School of Chemical Sciences, The University of Auckland 23 Symonds Street and 3b Symonds Street Auckland 1142 New Zealand
| | - Joseph Bell-Tyrer
- School of Chemical Sciences, The University of Auckland 23 Symonds Street and 3b Symonds Street Auckland 1142 New Zealand
| | - Yann O Hermant
- School of Chemical Sciences, The University of Auckland 23 Symonds Street and 3b Symonds Street Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 3b Symonds Street Auckland 1142 New Zealand
| | - Sung Hyun Yang
- School of Chemical Sciences, The University of Auckland 23 Symonds Street and 3b Symonds Street Auckland 1142 New Zealand
| | - Alice M McSweeney
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 3b Symonds Street Auckland 1142 New Zealand
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago PO Box 56, 720 Cumberland Street Dunedin 9054 New Zealand
| | - Geena M McKenzie-Goldsmith
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 3b Symonds Street Auckland 1142 New Zealand
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago PO Box 56, 720 Cumberland Street Dunedin 9054 New Zealand
| | - Vernon K Ward
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 3b Symonds Street Auckland 1142 New Zealand
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago PO Box 56, 720 Cumberland Street Dunedin 9054 New Zealand
| | - Daniel P Furkert
- School of Chemical Sciences, The University of Auckland 23 Symonds Street and 3b Symonds Street Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 3b Symonds Street Auckland 1142 New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, The University of Auckland 23 Symonds Street and 3b Symonds Street Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 3b Symonds Street Auckland 1142 New Zealand
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40
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Jiang H, Zou X, Zeng P, Zeng X, Zhou X, Wang J, Zhang J, Li J. Crystal structures of main protease (M pro) mutants of SARS-CoV-2 variants bound to PF-07304814. MOLECULAR BIOMEDICINE 2023; 4:23. [PMID: 37532968 PMCID: PMC10397169 DOI: 10.1186/s43556-023-00134-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 06/08/2023] [Indexed: 08/04/2023] Open
Abstract
There is an urgent need to develop effective antiviral drugs to prevent the viral infection caused by constantly circulating SARS-CoV-2 as well as its variants. The main protease (Mpro) of SARS-CoV-2 is a salient enzyme that plays a vital role in viral replication and serves as a fascinating therapeutic target. PF-07304814 is a covalent inhibitor targeting SARS-CoV-2 Mpro with favorable inhibition potency and drug-like properties, thus making it a promising drug candidate for the treatment of COVID-19. We previously solved the structure of PF-07304814 in complex with SARS-CoV-2 Mpro. However, the binding modes of PF-07304814 with Mpros from evolving SARS-CoV-2 variants is under-determined. In the current study, we expressed six Mpro mutants (G15S, K90R, M49I, S46F, V186F, and Y54C) that have been identified in Omicron variants including the recently emerged XBB.1.16 subvariant and solved the crystal structures of PF-07304814 bound to Mpro mutants. Structural analysis provided insight into the key molecular determinants responsible for the interaction between PF-07304814 and these mutant Mpros. Patterns for PF-07304814 to bind with these investigated Mpro mutants and the wild-type Mpro are generally similar but with some differences as revealed by detailed structural comparison. Structural insights presented in this study will inform the development of novel drugs against SARS-CoV-2 and the possible conformation changes of Mpro mutants when bound to an inhibitor.
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Affiliation(s)
- Haihai Jiang
- School of Basic Medical Sciences, Nanchang University, Nanchang, 330031, China
| | - Xiaofang Zou
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, China
| | - Pei Zeng
- Shenzhen Crystalo Biopharmaceutical Co., Ltd., Shenzhen, 518118, China
- Jiangxi Jmerry Biopharmaceutical Co., Ltd., Ganzhou, 341000, China
| | - Xiangyi Zeng
- Shenzhen Crystalo Biopharmaceutical Co., Ltd., Shenzhen, 518118, China
- Jiangxi Jmerry Biopharmaceutical Co., Ltd., Ganzhou, 341000, China
| | - Xuelan Zhou
- Shenzhen Crystalo Biopharmaceutical Co., Ltd., Shenzhen, 518118, China
- Jiangxi Jmerry Biopharmaceutical Co., Ltd., Ganzhou, 341000, China
| | - Jie Wang
- Shenzhen Crystalo Biopharmaceutical Co., Ltd., Shenzhen, 518118, China
- Jiangxi Jmerry Biopharmaceutical Co., Ltd., Ganzhou, 341000, China
| | - Jin Zhang
- School of Basic Medical Sciences, Nanchang University, Nanchang, 330031, China.
| | - Jian Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, China.
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41
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Ou J, Lewandowski EM, Hu Y, Lipinski AA, Aljasser A, Colon-Ascanio M, Morgan RT, Jacobs LMC, Zhang X, Bikowitz MJ, Langlais PR, Tan H, Wang J, Chen Y, Choy JS. A yeast-based system to study SARS-CoV-2 Mpro structure and to identify nirmatrelvir resistant mutations. PLoS Pathog 2023; 19:e1011592. [PMID: 37651467 PMCID: PMC10499260 DOI: 10.1371/journal.ppat.1011592] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 09/13/2023] [Accepted: 07/31/2023] [Indexed: 09/02/2023] Open
Abstract
The SARS-CoV-2 main protease (Mpro) is a major therapeutic target. The Mpro inhibitor, nirmatrelvir, is the antiviral component of Paxlovid, an orally available treatment for COVID-19. As Mpro inhibitor use increases, drug resistant mutations will likely emerge. We have established a non-pathogenic system, in which yeast growth serves as an approximation for Mpro activity, enabling rapid identification of mutants with altered enzymatic activity and drug sensitivity. The E166 residue is known to be a potential hot spot for drug resistance and yeast assays identified substitutions which conferred strong nirmatrelvir resistance and others that compromised activity. On the other hand, N142A and the P132H mutation, carried by the Omicron variant, caused little to no change in drug response and activity. Standard enzymatic assays confirmed the yeast results. In turn, we solved the structures of Mpro E166R, and Mpro E166N, providing insights into how arginine may drive drug resistance while asparagine leads to reduced activity. The work presented here will help characterize novel resistant variants of Mpro that may arise as Mpro antivirals become more widely used.
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Affiliation(s)
- Jin Ou
- Department of Biology, School of Arts and Sciences, The Catholic University of America, Washington, Washington DC, United States of America
| | - Eric M. Lewandowski
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Yanmei Hu
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Austin A. Lipinski
- Department of Medicine, College of Medicine, University of Arizona, Tucson, Arizona, United States of America
| | - Ali Aljasser
- Department of Biology, School of Arts and Sciences, The Catholic University of America, Washington, Washington DC, United States of America
| | - Mariliz Colon-Ascanio
- Department of Biology, School of Arts and Sciences, The Catholic University of America, Washington, Washington DC, United States of America
| | - Ryan T. Morgan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Lian M. C. Jacobs
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
- Drug Discovery Department, Moffit Cancer Center, Tampa, Florida, United States of America
| | - Xiujun Zhang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Melissa J. Bikowitz
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Paul R. Langlais
- Department of Medicine, College of Medicine, University of Arizona, Tucson, Arizona, United States of America
| | - Haozhou Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - John S. Choy
- Department of Biology, School of Arts and Sciences, The Catholic University of America, Washington, Washington DC, United States of America
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Robinson P, Toussi SS, Aggarwal S, Bergman A, Zhu T, Hackman F, Sathish JG, Updyke L, Loudon P, Krishna G, Clevenbergh P, Hernandez-Mora MG, Cisneros Herreros JM, Albertson TE, Dougan M, Thacker A, Baniecki ML, Soares H, Whitlock M, Nucci G, Menon S, Anderson AS, Binks M. Safety, Tolerability, and Pharmacokinetics of Single and Multiple Ascending Intravenous Infusions of PF-07304814 (Lufotrelvir) in Participants Hospitalized With COVID-19. Open Forum Infect Dis 2023; 10:ofad355. [PMID: 37559753 PMCID: PMC10407246 DOI: 10.1093/ofid/ofad355] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 07/06/2023] [Indexed: 08/11/2023] Open
Abstract
BACKGROUND An urgent need remains for antiviral therapies to treat patients hospitalized with COVID-19. PF-07304814-the prodrug (lufotrelvir) and its active moiety (PF-00835231)-is a potent inhibitor of the SARS-CoV-2 3CL protease. METHOD Eligible participants were 18 to 79 years old and hospitalized with confirmed COVID-19. This first-in-human phase 1b study was designed with 2 groups: single ascending dose (SAD) and multiple ascending dose (MAD). Participants could receive local standard-of-care therapy. In SAD, participants were randomized to receive a 24-hour infusion of lufotrelvir/placebo. In MAD, participants were randomized to receive a 120-hour infusion of lufotrelvir/placebo. The primary endpoint was to assess the safety and tolerability of lufotrelvir. The secondary endpoint was to evaluate the pharmacokinetics of lufotrelvir and PF-00835231. RESULTS In SAD, participants were randomized to receive 250 mg lufotrelvir (n = 2), 500 mg lufotrelvir (n = 2), or placebo (n = 4) by continuous 24-hour infusion. In MAD, participants were randomized to receive 250 mg lufotrelvir (n = 7), 500 mg lufotrelvir (n = 6), or placebo (n = 4) by continuous 120-hour infusion. No adverse events or serious adverse events were considered related to lufotrelvir. At doses of 250 and 500 mg, concentrations for the prodrug lufotrelvir and active moiety PF-00835231 increased in a dose-related manner. Unbound concentrations of the lufotrelvir active metabolite reached steady state approximately 2- and 4-fold that of in vitro EC90 following 250- and 500-mg doses, respectively. CONCLUSIONS These safety and pharmacokinetic findings support the continued evaluation of lufotrelvir in clinical studies. Clinical Trials Registration. ClinicalTrials.gov NCT04535167.
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Affiliation(s)
- Philip Robinson
- Infectious Disease, Hoag Memorial Hospital Presbyterian, Newport Beach, California, USA
| | - Sima S Toussi
- Pfizer Worldwide Research, Development and Medical, Pfizer Inc, Pearl River, New York, USA
| | - Sudeepta Aggarwal
- Early Clinical Development, Pfizer Inc, Cambridge, Massachusetts, USA
| | - Arthur Bergman
- Pfizer Worldwide Research, Development and Medical, Pfizer Inc, Cambridge, Massachusetts, USA
| | - Tong Zhu
- Pfizer Worldwide Research, Development and Medical, Pfizer Inc, Cambridge, Massachusetts, USA
| | - Frances Hackman
- Pfizer Worldwide Research, Development and Medical, Pfizer Ltd, Cambridge, UK
| | - Jean G Sathish
- Drug Safety Unit, Pfizer Inc, Pearl River, New York, USA
| | | | | | | | | | | | | | | | - Michael Dougan
- Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | | | - Holly Soares
- Early Clinical Development, Pfizer Inc, Cambridge, Massachusetts, USA
| | - Mark Whitlock
- Early Clinical Development, Pfizer Inc, Cambridge, UK
| | - Gianluca Nucci
- Pfizer Worldwide Research, Development and Medical, Pfizer Ltd, Cambridge, UK
| | - Sandeep Menon
- Pfizer Worldwide Research, Development and Medical, Pfizer Ltd, Cambridge, UK
| | | | - Michael Binks
- Pfizer Worldwide Research, Development and Medical, Pfizer Ltd, Cambridge, UK
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43
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Tang P, Sun D, Xu W, Li H, Chen L. Long non‑coding RNAs as potential therapeutic targets in non‑small cell lung cancer (Review). Int J Mol Med 2023; 52:68. [PMID: 37350412 PMCID: PMC10413047 DOI: 10.3892/ijmm.2023.5271] [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: 12/17/2022] [Accepted: 05/02/2023] [Indexed: 06/24/2023] Open
Abstract
Non‑small cell lung cancer (NSCLC) is one of the most common malignancies with a high morbidity and mortality rate. Long non‑coding RNAs (lncRNAs) have been reported to be closely associated with the occurrence and progression of NSCLC. In addition, lncRNAs have been documented to participate in the development of drug resistance and radiation sensitivity in patients with NSCLC. Due to their extensive functional characterization, high tissue specificity and sex specificity, lncRNAs have been proposed to be novel biomarkers and therapeutic targets for NSCLC. Therefore, in the current review, the functional classification of lncRNAs were presented, whilst the potential roles of lncRNAs in NSCLC were also summarized. Various physiological aspects, including proliferation, invasion and drug resistance, were all discussed. It is anticipated that the present review will provide a perspective on lncRNAs as potential diagnostic molecular biomarkers and therapeutic targets for NSCLC.
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Affiliation(s)
- Peiyu Tang
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016
| | - Dejuan Sun
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016
| | - Wei Xu
- Institute of Structural Pharmacology and TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Hua Li
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016
- Institute of Structural Pharmacology and TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Lixia Chen
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016
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Kiso M, Yamayoshi S, Iida S, Furusawa Y, Hirata Y, Uraki R, Imai M, Suzuki T, Kawaoka Y. In vitro and in vivo characterization of SARS-CoV-2 resistance to ensitrelvir. Nat Commun 2023; 14:4231. [PMID: 37454219 PMCID: PMC10349878 DOI: 10.1038/s41467-023-40018-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023] Open
Abstract
Ensitrelvir, an oral antiviral agent that targets a SARS-CoV-2 main protease (3CLpro or Nsp5), is clinically useful against SARS-CoV-2 including its omicron variants. Since most omicron subvariants have reduced sensitivity to most monoclonal antibody therapies, SARS-CoV-2 resistance to other antivirals including main protease inhibitors such as ensitrelvir is a major public health concern. Here, repeating passages of SARS-CoV-2 in the presence of ensitrelvir revealed that the M49L and E166A substitutions in Nsp5 are responsible for reduced sensitivity to ensitrelvir. Both substitutions reduced in vitro virus growth in the absence of ensitrelvir. The combination of the M49L and E166A substitutions allowed the virus to largely evade the suppressive effect of ensitrelvir in vitro. The virus possessing Nsp5-M49L showed similar pathogenicity to wild-type virus, whereas the virus possessing Nsp5-E166A or Nsp5-M49L/E166A slightly attenuated. Ensitrelvir treatment of hamsters infected with the virus possessing Nsp5-M49L/E166A was ineffective; however, nirmatrelvir or molnupiravir treatment was effective. Therefore, it is important to closely monitor the emergence of ensitrelvir-resistant SARS-CoV-2 variants to guide antiviral treatment selection.
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Affiliation(s)
- Maki Kiso
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Seiya Yamayoshi
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan.
- International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan.
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan.
| | - Shun Iida
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuri Furusawa
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Yuichiro Hirata
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ryuta Uraki
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Masaki Imai
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan.
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan.
- The University of Tokyo Pandemic Preparedness, Infection and Advanced Research Center, Tokyo, Japan.
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.
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She Z, Yao Y, Wang C, Li Y, Xiong X, Liu Y. M pro-targeted anti-SARS-CoV-2 inhibitor-based drugs. JOURNAL OF CHEMICAL RESEARCH 2023; 47:17475198231184799. [PMID: 37455837 PMCID: PMC10333551 DOI: 10.1177/17475198231184799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023]
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 is a global health emergency. The main protease is an important drug target in coronaviruses. It plays an important role in the processing of viral RNA-translated polyproteins and is highly conserved in the amino acid sequence and three-dimensional structure, making it a good drug target for which several small molecule inhibitors are available. This paper describes the various anti-severe acute respiratory syndrome coronavirus 2 inhibitor drugs targeting Mpro discovered since the severe acute respiratory syndrome coronavirus 2 outbreak at the end of 2019, with all these compounds inhibiting severe acute respiratory syndrome coronavirus 2 Mpro activity in vitro. This provides a reference for the development of severe acute respiratory syndrome coronavirus 2 Mpro-targeted inhibitors and the design of therapeutic approaches to address newly emerged severe acute respiratory syndrome coronavirus 2 mutant strains with immune evasion capabilities.
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Affiliation(s)
- Zhuxin She
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, P.R. China
| | - Yinuo Yao
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, P.R. China
| | - Conglong Wang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, P.R. China
| | - Yi Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, P.R. China
| | - Xiaohui Xiong
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, P.R. China
| | - Yuanyuan Liu
- School of Pharmaceutical and Chemical Engineering, ChengXian College, Southeast University, Nanjing, P.R. China
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Navitha Reddy G, Jogvanshi A, Naikwadi S, Sonti R. Nirmatrelvir and ritonavir combination: an antiviral therapy for COVID-19. Expert Rev Anti Infect Ther 2023; 21:943-955. [PMID: 37525997 DOI: 10.1080/14787210.2023.2241638] [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: 03/15/2023] [Accepted: 07/24/2023] [Indexed: 08/02/2023]
Abstract
INTRODUCTION The emergence of the Omicron SARS-CoV-2 variant of concern in late November 2021 presaged yet another stage of the COVID-19 pandemic. Paxlovid, a co-packaged dosage form of two antiviral drugs (nirmatrelvir and ritonavir) developed by Pfizer, received its first FDA Emergency Use Authorization (EUA) and conditional marketing by European Medical Agency in patients at high risk of developing severe COVID-19. AREAS COVERED We reviewed the timeline of the drug nirmatrelvir from its discovery to authorization by FDA. After 1 year of its authorization, numerous studies and reports on paxlovid's use and post-use consequences are available. This review summarizes the complete journey of paxlovid from its development, preclinical studies, clinical trials, regulatory approvals, ongoing clinical trials, and safety measures, followed by discussions on recent updates on drug-drug interactions, adverse effects, and relapse of COVID-19. EXPERT OPINION Paxlovid, a new oral antiviral therapy for COVID-19, has shown promising results in clinical trials and has the potential to be effective against the pandemic, particularly for individuals at high risk of severe illness. Comorbidity usage and pharmacovigilance will play a significant stake in the future of paxlovid development. Second-generation Mpro inhibitors play an important role in the upcoming problems associated with COVID-19.
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Affiliation(s)
- Gangireddy Navitha Reddy
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
| | - Akanksha Jogvanshi
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
| | - Sana Naikwadi
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
| | - Rajesh Sonti
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
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von Delft A, Hall MD, Kwong AD, Purcell LA, Saikatendu KS, Schmitz U, Tallarico JA, Lee AA. Accelerating antiviral drug discovery: lessons from COVID-19. Nat Rev Drug Discov 2023; 22:585-603. [PMID: 37173515 PMCID: PMC10176316 DOI: 10.1038/s41573-023-00692-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2023] [Indexed: 05/15/2023]
Abstract
During the coronavirus disease 2019 (COVID-19) pandemic, a wave of rapid and collaborative drug discovery efforts took place in academia and industry, culminating in several therapeutics being discovered, approved and deployed in a 2-year time frame. This article summarizes the collective experience of several pharmaceutical companies and academic collaborations that were active in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antiviral discovery. We outline our opinions and experiences on key stages in the small-molecule drug discovery process: target selection, medicinal chemistry, antiviral assays, animal efficacy and attempts to pre-empt resistance. We propose strategies that could accelerate future efforts and argue that a key bottleneck is the lack of quality chemical probes around understudied viral targets, which would serve as a starting point for drug discovery. Considering the small size of the viral proteome, comprehensively building an arsenal of probes for proteins in viruses of pandemic concern is a worthwhile and tractable challenge for the community.
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Affiliation(s)
- Annette von Delft
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Oxford Biomedical Research Centre, National Institute for Health Research, University of Oxford, Oxford, UK.
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | | | | | | | | | | | - Alpha A Lee
- PostEra, Inc., Cambridge, MA, USA.
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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48
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Pagliano P, Spera A, Sellitto C, Scarpati G, Folliero V, Piazza O, Franci G, Conti V, Ascione T. Preclinical discovery and development of nirmatrelvir/ritonavir combinational therapy for the treatment of COVID-19 and the lessons learned from SARS-COV-2 variants. Expert Opin Drug Discov 2023; 18:1301-1311. [PMID: 37614103 DOI: 10.1080/17460441.2023.2248879] [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: 03/25/2023] [Accepted: 08/14/2023] [Indexed: 08/25/2023]
Abstract
INTRODUCTION Nirmatrelvir/ritonavir (Paxlovid®) represent an oral antiviral therapy approved for the treatment of COVID-19. Extensive in vitro and in vivo studies have reported the promising activity of nirmatrelvir/ritonavir against numerous emerging viruses. This combination consists of nirmatrelvir, a protease reversible inhibitor of coronavirus 3CLpro mainly metabolized by cytochrome P450 (CYP)3A4, and ritonavir, an inhibitor of the CYP3A isoforms that enhances the efficacy of nirmatrelvir by fixing its suboptimal pharmacokinetic properties. AREAS COVERED This review comprehensively examines the efficacy of nirmatrelvir/ritonavir through rigorous analysis of in vitro and in vivo studies. Moreover, it thoroughly assesses its safety, tolerability, pharmacokinetics, and antiviral efficacy against SARS-COV-2 infection, based on the main pre-authorization randomized controlled trials. EXPERT OPINION Nirmatrelvir/ritonavir has a good tolerability profile. Its administration during the early stages of mild-to-moderate COVID-19 holds potential benefits, as it can help prevent the onset of an aberrant immune response that could lead to pulmonary and extra-pulmonary complications. However, its drug - drug interactions can be a factor limiting its use, at least in populations on some chronic therapies, along with the risk of infection relapse after treatment.
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Affiliation(s)
- Pasquale Pagliano
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", Unit of Infectious Diseases, University of Salerno, Baronissi, Italy
| | - Annamaria Spera
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", Unit of Infectious Diseases, University of Salerno, Baronissi, Italy
| | - Carmine Sellitto
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", Unit of Pharmacology, University of Salerno, Baronissi, Italy
| | - Giuliana Scarpati
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", Unit of Anesthesiology, University of Salerno, Baronissi, Italy
| | - Veronica Folliero
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Unit of Microbiology, University of Salerno, Baronissi, Italy
| | - Ornella Piazza
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", Unit of Anesthesiology, University of Salerno, Baronissi, Italy
| | - Gianluigi Franci
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Unit of Microbiology, University of Salerno, Baronissi, Italy
| | - Valeria Conti
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", Unit of Pharmacology, University of Salerno, Baronissi, Italy
| | - Tiziana Ascione
- Department of Medicine, Service of Infectious Diseases, Cardarelli Hospital, Naples, Italy
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49
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Luo J, Wang W, Jiang H, Li W, Zeng P, Wang J, Zhou X, Zou X, Chen S, Wang Q, Zhang J, Li J. Crystal structures of main proteases of SARS-CoV-2 variants bound to a benzothiazole-based inhibitor. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1257-1264. [PMID: 37357528 PMCID: PMC10448042 DOI: 10.3724/abbs.2023053] [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: 12/23/2022] [Accepted: 02/20/2023] [Indexed: 06/27/2023] Open
Abstract
Main protease (M pro) serves as an indispensable factor in the life cycle of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as well as its constantly emerging variants and is therefore considered an attractive target for antiviral drug development. Benzothiazole-based inhibitors targeting M pro have recently been investigated by several groups and proven to be promising leads for coronaviral drug development. In the present study, we determine the crystal structures of a benzothiazole-based inhibitor, YH-53, bound to M pro mutants from SARS-CoV-2 variants of concern (VOCs) or variants of interest (VOIs), including K90R (Beta, B.1.351), G15S (Lambda, C.37), Y54C (Delta, AY.4), M49I (Omicron, BA.5) and P132H (Omicron, B.1.1.529). The structures show that the benzothiazole group in YH-53 forms a C-S covalent bond with the sulfur atom of catalytic residue Cys145 in SARS-CoV-2 M pro mutants. Structural analysis reveals the key molecular determinants necessary for interaction and illustrates the binding mode of YH-53 to these mutant M pros. In conclusion, structural insights from this study offer more information to develop benzothiazole-based drugs that are broader spectrum, more effective and safer.
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Affiliation(s)
- Jiqing Luo
- College of Pharmaceutical SciencesGannan Medical UniversityGanzhou341000China
| | - Weiwei Wang
- Shanghai Advanced Research InstituteChinese Academy of SciencesShanghai201204China
| | - Haihai Jiang
- School of Basic Medical SciencesNanchang UniversityNanchang330031China
| | - Wenwen Li
- Shenzhen Crystalo Biopharmaceutical Co.Ltd.Shenzhen518118China
- Jiangxi Jmerry Biopharmaceutical Co.Ltd.Ganzhou341000China
| | - Pei Zeng
- Jiangxi Jmerry Biopharmaceutical Co.Ltd.Ganzhou341000China
| | - Jie Wang
- Jiangxi Jmerry Biopharmaceutical Co.Ltd.Ganzhou341000China
| | - Xuelan Zhou
- Jiangxi Jmerry Biopharmaceutical Co.Ltd.Ganzhou341000China
| | - Xiaofang Zou
- Jiangxi Jmerry Biopharmaceutical Co.Ltd.Ganzhou341000China
| | | | - Qisheng Wang
- Shanghai Advanced Research InstituteChinese Academy of SciencesShanghai201204China
| | - Jin Zhang
- School of Basic Medical SciencesNanchang UniversityNanchang330031China
| | - Jian Li
- College of Pharmaceutical SciencesGannan Medical UniversityGanzhou341000China
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50
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Chatterjee S, Bhattacharya M, Dhama K, Lee SS, Chakraborty C. Resistance to nirmatrelvir due to mutations in the Mpro in the subvariants of SARS-CoV-2 Omicron: Another concern? MOLECULAR THERAPY - NUCLEIC ACIDS 2023; 32:263-266. [PMID: 37041859 PMCID: PMC10078092 DOI: 10.1016/j.omtn.2023.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
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