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Zhang W, Xiao L, Li D, Hu Y, Yu W. New Strategies for Responding to SARS-CoV-2: The Present and Future of Dual-Target Drugs. J Med Chem 2024; 67:11522-11542. [PMID: 38967785 DOI: 10.1021/acs.jmedchem.4c00384] [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: 07/06/2024]
Abstract
The 2019 coronavirus disease (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in millions of deaths, posing a serious threat to public health and safety. Rapid mutations of SARS-CoV-2 and complex interactions among multiple targets during infection pose a risk of expiry for small molecule inhibitors. This suggests that the traditional concept of "one bug, one drug" could be ineffective in dealing with the coronavirus. The dual-target drug strategy is expected to be the key to ending coronavirus infections. However, the lack of design method and improper combination of dual-targets poses obstacle to the discovery of new dual-target drugs. In this Perspective, we summarized the profiles concerning drug design methods, structure-activity relationships, and pharmacological parameters of dual-target drugs for the treatment of COVID-19. Importantly, we underscored how target combination and rational drug design illuminate the development of dual-target drugs for SARS-CoV-2.
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Affiliation(s)
- Wenyi Zhang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Lecheng Xiao
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Dianyang Li
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yuxuan Hu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Wenying Yu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
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2
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Klevanski M, Kim H, Heilemann M, Kuner T, Bartenschlager R. Glycan-directed SARS-CoV-2 inhibition by leek extract and lectins with insights into the mode-of-action of Concanavalin A. Antiviral Res 2024; 225:105856. [PMID: 38447646 DOI: 10.1016/j.antiviral.2024.105856] [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: 01/02/2024] [Revised: 02/26/2024] [Accepted: 03/04/2024] [Indexed: 03/08/2024]
Abstract
Four years after its outbreak, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains a global challenge for human health. At its surface, SARS-CoV-2 features numerous extensively glycosylated spike proteins. This glycan coat supports virion docking and entry into host cells and at the same time renders the virus less susceptible to neutralizing antibodies. Given the high genetic plasticity of SARS-CoV-2 and the rapid emergence of immune escape variants, targeting the glycan shield by carbohydrate-binding agents emerges as a promising strategy. However, the potential of carbohydrate-targeting reagents as viral inhibitors remains underexplored. Here, we tested seven plant-derived carbohydrate-binding proteins, called lectins, and one crude plant extract for their antiviral activity against SARS-CoV-2 in two types of human lung cells: A549 cells ectopically expressing the ACE2 receptor and Calu-3 cells. We identified three lectins and an Allium porrum (leek) extract inhibiting SARS-CoV-2 infection in both cell systems with selectivity indices (SI) ranging between >2 and >299. Amongst these, the lectin Concanavalin A (Con A) exerted the most potent and broad activity against a panel of SARS-CoV-2 variants. We used multiplex super-resolution microscopy to address lectin interactions with SARS-CoV-2 and its host cells. Notably, we discovered that Con A not only binds to SARS-CoV-2 virions and their host cells, but also causes SARS-CoV-2 aggregation. Thus, Con A exerts a dual mode-of-action comprising both, antiviral and virucidal, mechanisms. These results establish Con A and other plant lectins as candidates for COVID-19 prevention and basis for further drug development.
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Affiliation(s)
- Maja Klevanski
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120, Heidelberg, Germany.
| | - Heeyoung Kim
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120, Heidelberg, Germany; German Center for Infection Research (DZIF), Partner Site Heidelberg, 69120, Heidelberg, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Thomas Kuner
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120, Heidelberg, Germany; German Center for Lung Research (DZL), Partner Site Heidelberg (TLRC), Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120, Heidelberg, Germany; German Center for Infection Research (DZIF), Partner Site Heidelberg, 69120, Heidelberg, Germany; Division Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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3
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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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4
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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 PMCID: PMC11193659 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, The 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, The University of Texas Medical Branch; Galveston, TX 77555, USA
| | - Aleksandra Drelich
- Department of Microbiology and Immunology, The University of Texas Medical Branch; Galveston, TX 77555, USA
| | - Bi-Hung Peng
- Department of Neuroscience, Cell Biology, and Anatomy, The 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, The University of Texas Medical Branch; Galveston, TX 77555, USA
- Department of Pathology, The University of Texas Medical Branch; Galveston, TX 77555, USA
- Department of Neuroscience, Cell Biology, and Anatomy, The 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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5
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Braulke T, Carette JE, Palm W. Lysosomal enzyme trafficking: from molecular mechanisms to human diseases. Trends Cell Biol 2024; 34:198-210. [PMID: 37474375 DOI: 10.1016/j.tcb.2023.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/22/2023]
Abstract
Lysosomes degrade and recycle macromolecules that are delivered through the biosynthetic, endocytic, and autophagic routes. Hydrolysis of the different classes of macromolecules is catalyzed by about 70 soluble enzymes that are transported from the Golgi apparatus to lysosomes in a mannose 6-phosphate (M6P)-dependent process. The molecular machinery that generates M6P tags for receptor-mediated targeting of lysosomal enzymes was thought to be understood in detail. However, recent studies on the M6P pathway have identified a previously uncharacterized core component, yielded structural insights in known components, and uncovered functions in various human diseases. Here we review molecular mechanisms of lysosomal enzyme trafficking and discuss its relevance for rare lysosomal disorders, cancer, and viral infection.
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Affiliation(s)
- Thomas Braulke
- Department of Osteology and Biomechanics, Cell Biology of Rare Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Wilhelm Palm
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
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6
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Ciaglia T, Vestuto V, Di Sarno V, Musella S, Smaldone G, Di Matteo F, Napolitano V, Miranda MR, Pepe G, Basilicata MG, Novi S, Capolupo I, Bifulco G, Campiglia P, Gomez-Monterrey I, Snoeck R, Andrei G, Manfra M, Ostacolo C, Lauro G, Bertamino A. Peptidomimetics as potent dual SARS-CoV-2 cathepsin-L and main protease inhibitors: In silico design, synthesis and pharmacological characterization. Eur J Med Chem 2024; 266:116128. [PMID: 38232463 DOI: 10.1016/j.ejmech.2024.116128] [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: 11/06/2023] [Revised: 12/11/2023] [Accepted: 01/04/2024] [Indexed: 01/19/2024]
Abstract
In this paper we present the design, synthesis, and biological evaluation of a new series of peptidomimetics acting as potent anti-SARS-CoV-2 agents. Starting from our previously described Main Protease (MPro) and Papain Like Protease (PLPro) dual inhibitor, CV11, here we disclose its high inhibitory activity against cathepsin L (CTSL) (IC50 = 19.80 ± 4.44 nM), an emerging target in SARS-CoV-2 infection machinery. An in silico design, inspired by the structure of CV11, led to the development of a library of peptidomimetics showing interesting activities against CTSL and Mpro, allowing us to trace the chemical requirements for the binding to both enzymes. The screening in Vero cells infected with 5 different SARS-CoV-2 variants of concerns, highlighted sub-micromolar activities for most of the synthesized compounds (13, 15, 16, 17 and 31) in agreement with the enzymatic inhibition assays results. The compounds showed lack of activity against several different RNA viruses except for the 229E and OC43 human coronavirus strains, also characterized by a cathepsin-L dependent release into the host cells. The most promising derivatives were also evaluated for their chemical and metabolic in-vitro stability, with derivatives 15 and 17 showing a suitable profile for further preclinical characterization.
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Affiliation(s)
- Tania Ciaglia
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Vincenzo Vestuto
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Veronica Di Sarno
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Simona Musella
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Gerardina Smaldone
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Francesca Di Matteo
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Valeria Napolitano
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Maria Rosaria Miranda
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Giacomo Pepe
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | | | - Sara Novi
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Ilaria Capolupo
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Giuseppe Bifulco
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Pietro Campiglia
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy; European Biomedical Research Institute (EBRIS), Via S. De Renzi 50, 84125, Salerno, Italy
| | - Isabel Gomez-Monterrey
- Department of Pharmacy, University Federico II of Naples, Via D. Montesano 49, 80131, Naples, Italy
| | - Robert Snoeck
- Rega Institute for Medical Research, Department of Microbiology, Immunology, and Transplantation, KU Leuven, BE-3000, Leuven, Belgium
| | - Graciela Andrei
- Rega Institute for Medical Research, Department of Microbiology, Immunology, and Transplantation, KU Leuven, BE-3000, Leuven, Belgium
| | - Michele Manfra
- Department of Science, University of Basilicata, Via Dell'Ateneo Lucano 10, 85100, Potenza, Italy
| | - Carmine Ostacolo
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Gianluigi Lauro
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy.
| | - Alessia Bertamino
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy.
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7
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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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8
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Wang R, Chen X, Li H, Chen X, Sun D, Yu D, Lu J, Xie Y, Zhang Q, Xu J, Zhang W, Chen H, Liu S, Chen L. Danshensu inhibits SARS-CoV-2 by targeting its main protease as a specific covalent inhibitor and discovery of bifunctional compounds eliciting antiviral and anti-inflammatory activity. Int J Biol Macromol 2024; 257:128623. [PMID: 38070810 DOI: 10.1016/j.ijbiomac.2023.128623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/30/2023] [Accepted: 12/02/2023] [Indexed: 12/17/2023]
Abstract
The coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed a serious threat to human. Since there are still no effective treatment options against the new emerging variants of SARS-CoV-2, it is necessary to devote a continuous endeavor for more targeted drugs and the preparation for the next pandemic. Salvia miltiorrhiza and its active ingredients possess wide antiviral activities, including against SARS-CoV-2. Danshensu, as one of the most important active ingredients in Salvia miltiorrhiza, has been reported to inhibit the entry of SARS-CoV-2 into ACE2 (angiotensin-converting enzyme 2)-overexpressed HEK-293T cells and Vero-E6 cells. However, there is a paucity of information regarding its detailed target and mechanism against SARS-CoV-2. Here, we present Danshensu as a covalent inhibitor of 3-chymotrypsin-like protease (3CLpro) against SARS-CoV-2 by the time-dependent inhibition assay (TDI) and mass spectrometry analysis. Further molecular docking, site-directed mutagenesis, circular dichroism (CD) and fluorescence spectra revealed that Danshensu covalently binds to C145 of SARS-CoV-2 3CLpro, meanwhile forming the hydrogen bonds with S144, H163 and E166 in the S1 site. Structure-based optimization of Danshensu led to the discovery of the promising compounds with good inhibitory activity and microsomal stability in vitro. Due to Danshensu inhibiting lung inflammation in the mouse model, we found that Danshensu derivatives also showed better anti-inflammatory activity than Danshensu in lipopolysaccharide (LPS)-stimulated RAW264.7 macrophage cells. Thus, our study provides not only the clue of the efficacy of Salvia miltiorrhiza against SARS-CoV-2, but also a detailed mechanistic insight into the covalent mode of action of Danshensu for design of covalent inhibitors against SARS-CoV-2 3CLpro, highlighting its potential as a bifunctional molecule with antivirus and anti-inflammation.
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Affiliation(s)
- Ruyu Wang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xuwen Chen
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - 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
| | - 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
| | - Donghui Sun
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, 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
| | - 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
| | - Yuanyuan Xie
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Qian Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, 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; Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Weidong Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Shanghai Institute of Infectious Diseases and Biosafety, 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
| | - Shunying Liu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, 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.
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9
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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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10
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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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11
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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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12
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Zhao S, Jiang M, Qing H, Ni J. Cathepsins and SARS-CoV-2 infection: From pathogenic factors to potential therapeutic targets. Br J Pharmacol 2023; 180:2455-2481. [PMID: 37403614 DOI: 10.1111/bph.16187] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 05/04/2023] [Accepted: 06/20/2023] [Indexed: 07/06/2023] Open
Abstract
Coronavirus disease-19 (COVID-19) is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection. The COVID-19 pandemic began in March 2020 and has wrought havoc on health and economic systems worldwide. Efficacious treatment for COVID-19 is lacking: Only preventive measures as well as symptomatic and supportive care are available. Preclinical and clinical studies have indicated that lysosomal cathepsins might contribute to the pathogenesis and disease outcome of COVID-19. Here, we discuss cutting-edge evidence on the pathological roles of cathepsins in SARS-CoV-2 infection, host immune dysregulations, and the possible underlying mechanisms. Cathepsins are attractive drug targets because of their defined substrate-binding pockets, which can be exploited as binding sites for pharmaceutical enzyme inhibitors. Accordingly, the potential modulatory strategies of cathepsin activity are discussed. These insights could shed light on the development of cathepsin-based interventions for COVID-19.
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Affiliation(s)
- Shuxuan Zhao
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Muzhou Jiang
- Department of Periodontics, Liaoning Provincial Key Laboratory of Oral Diseases, School and Hospital of Stomatology, China Medical University, Shenyang, China
| | - Hong Qing
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Junjun Ni
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
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13
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Tucci AR, da Rosa RM, Rosa AS, Augusto Chaves O, Ferreira VNS, Oliveira TKF, Coutinho Souza DD, Borba NRR, Dornelles L, Rocha NS, Mayer JCP, da Rocha JBT, Rodrigues OED, Miranda MD. Antiviral Effect of 5'-Arylchalcogeno-3-aminothymidine Derivatives in SARS-CoV-2 Infection. Molecules 2023; 28:6696. [PMID: 37764472 PMCID: PMC10537738 DOI: 10.3390/molecules28186696] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/04/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
The understanding that zidovudine (ZDV or azidothymidine, AZT) inhibits the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 and that chalcogen atoms can increase the bioactivity and reduce the toxicity of AZT has directed our search for the discovery of novel potential anti-coronavirus compounds. Here, the antiviral activity of selenium and tellurium containing AZT derivatives in human type II pneumocytes cell model (Calu-3) and monkey kidney cells (Vero E6) infected with SARS-CoV-2, and their toxic effects on these cells, was evaluated. Cell viability analysis revealed that organoselenium (R3a-R3e) showed lower cytotoxicity than organotellurium (R3f, R3n-R3q), with CC50 ≥ 100 µM. The R3b and R3e were particularly noteworthy for inhibiting viral replication in both cell models and showed better selectivity index. In Vero E6, the EC50 values for R3b and R3e were 2.97 ± 0.62 µM and 1.99 ± 0.42 µM, respectively, while in Calu-3, concentrations of 3.82 ± 1.42 µM and 1.92 ± 0.43 µM (24 h treatment) and 1.33 ± 0.35 µM and 2.31 ± 0.54 µM (48 h) were observed, respectively. The molecular docking calculations were carried out to main protease (Mpro), papain-like protease (PLpro), and RdRp following non-competitive, competitive, and allosteric inhibitory approaches. The in silico results suggested that the organoselenium is a potential non-competitive inhibitor of RdRp, interacting in the allosteric cavity located in the palm region. Overall, the cell-based results indicated that the chalcogen-zidovudine derivatives were more potent than AZT in inhibiting SARS-CoV-2 replication and that the compounds R3b and R3e play an important inhibitory role, expanding the knowledge about the promising therapeutic capacity of organoselenium against COVID-19.
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Affiliation(s)
- Amanda Resende Tucci
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (A.S.R.); (V.N.S.F.); (T.K.F.O.); (D.D.C.S.); (N.R.R.B.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Raquel Mello da Rosa
- LabSelen-NanoBio—Departamento de Química, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil; (R.M.d.R.); (L.D.); (N.S.R.); (J.C.P.M.)
| | - Alice Santos Rosa
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (A.S.R.); (V.N.S.F.); (T.K.F.O.); (D.D.C.S.); (N.R.R.B.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Otávio Augusto Chaves
- CQC-IMS, Departamento de Química, Universidade de Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
- Laboratório de Imunofarmacologia, Centro de Pesquisa, Inovação e Vigilância em COVID-19 e Emergências Sanitárias (CPIV), Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-900, RJ, Brazil
| | - Vivian Neuza Santos Ferreira
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (A.S.R.); (V.N.S.F.); (T.K.F.O.); (D.D.C.S.); (N.R.R.B.)
| | - Thamara Kelcya Fonseca Oliveira
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (A.S.R.); (V.N.S.F.); (T.K.F.O.); (D.D.C.S.); (N.R.R.B.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Daniel Dias Coutinho Souza
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (A.S.R.); (V.N.S.F.); (T.K.F.O.); (D.D.C.S.); (N.R.R.B.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Nathalia Roberto Resende Borba
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (A.S.R.); (V.N.S.F.); (T.K.F.O.); (D.D.C.S.); (N.R.R.B.)
| | - Luciano Dornelles
- LabSelen-NanoBio—Departamento de Química, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil; (R.M.d.R.); (L.D.); (N.S.R.); (J.C.P.M.)
| | - Nayra Salazar Rocha
- LabSelen-NanoBio—Departamento de Química, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil; (R.M.d.R.); (L.D.); (N.S.R.); (J.C.P.M.)
| | - João Candido Pilar Mayer
- LabSelen-NanoBio—Departamento de Química, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil; (R.M.d.R.); (L.D.); (N.S.R.); (J.C.P.M.)
| | - João B. Teixeira da Rocha
- Programa de Pós-Graduação em Bioquímica Toxicológica, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil;
| | - Oscar Endrigo D. Rodrigues
- LabSelen-NanoBio—Departamento de Química, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil; (R.M.d.R.); (L.D.); (N.S.R.); (J.C.P.M.)
| | - Milene Dias Miranda
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (A.S.R.); (V.N.S.F.); (T.K.F.O.); (D.D.C.S.); (N.R.R.B.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
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14
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D′Oliviera A, Dai X, Mottaghinia S, Geissler EP, Etienne L, Zhang Y, Mugridge JS. Recognition and Cleavage of Human tRNA Methyltransferase TRMT1 by the SARS-CoV-2 Main Protease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.20.529306. [PMID: 36865253 PMCID: PMC9980103 DOI: 10.1101/2023.02.20.529306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
The SARS-CoV-2 main protease (Mpro) is critical for the production of functional viral proteins during infection and, like many viral proteases, can also target host proteins to subvert their cellular functions. Here, we show that the human tRNA methyltransferase TRMT1 can be recognized and cleaved by SARS-CoV-2 Mpro. TRMT1 installs the N2,N2-dimethylguanosine (m2,2G) modification on mammalian tRNAs, which promotes global protein synthesis and cellular redox homeostasis. We find that Mpro can cleave endogenous TRMT1 in human cell lysate, resulting in removal of the TRMT1 zinc finger domain required for tRNA modification activity in cells. Evolutionary analysis shows that the TRMT1 cleavage site is highly conserved in mammals, except in Muroidea, where TRMT1 may be resistant to cleavage. In primates, regions outside the cleavage site with rapid evolution could indicate adaptation to ancient viral pathogens. We determined the structure of a TRMT1 peptide in complex with Mpro, revealing a substrate binding conformation distinct from the majority of available Mpro-peptide complexes. Kinetic parameters for peptide cleavage showed that the TRMT1(526-536) sequence is cleaved with comparable efficiency to the Mpro-targeted nsp8/9 viral cleavage site. Mutagenesis studies and molecular dynamics simulations together indicate that kinetic discrimination occurs during a later step of Mpro-mediated proteolysis that follows substrate binding. Our results provide new information about the structural basis for Mpro substrate recognition and cleavage that could help inform future therapeutic design and raise the possibility that proteolysis of human TRMT1 during SARS-CoV-2 infection suppresses protein translation and oxidative stress response to impact viral pathogenesis.
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Affiliation(s)
- Angel D′Oliviera
- Department of Chemistry & Biochemistry, University of Delaware, Newark, DE 19716
| | - Xuhang Dai
- Department of Chemistry, New York University, New York, NY 10003
| | - Saba Mottaghinia
- CIRI (Centre International de Recherche en Infectiologie), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Evan P. Geissler
- Department of Chemistry & Biochemistry, University of Delaware, Newark, DE 19716
| | - Lucie Etienne
- CIRI (Centre International de Recherche en Infectiologie), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY 10003
- Simons Center for Computational Physical Chemistry at New York University, New York, NY 10003
| | - Jeffrey S. Mugridge
- Department of Chemistry & Biochemistry, University of Delaware, Newark, DE 19716
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15
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Citarella A, Dimasi A, Moi D, Passarella D, Scala A, Piperno A, Micale N. Recent Advances in SARS-CoV-2 Main Protease Inhibitors: From Nirmatrelvir to Future Perspectives. Biomolecules 2023; 13:1339. [PMID: 37759739 PMCID: PMC10647625 DOI: 10.3390/biom13091339] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/28/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
The main protease (Mpro) plays a pivotal role in the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is considered a highly conserved viral target. Disruption of the catalytic activity of Mpro produces a detrimental effect on the course of the infection, making this target one of the most attractive for the treatment of COVID-19. The current success of the SARS-CoV-2 Mpro inhibitor Nirmatrelvir, the first oral drug for the treatment of severe forms of COVID-19, has further focused the attention of researchers on this important viral target, making the search for new Mpro inhibitors a thriving and exciting field for the development of antiviral drugs active against SARS-CoV-2 and related coronaviruses.
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Affiliation(s)
- Andrea Citarella
- Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milano, Italy; (A.D.); (D.P.)
| | - Alessandro Dimasi
- Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milano, Italy; (A.D.); (D.P.)
| | - Davide Moi
- Department of Chemical and Geological Sciences, University of Cagliari, S.P. 8 CA, 09042 Cagliari, Italy;
| | - Daniele Passarella
- Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milano, Italy; (A.D.); (D.P.)
| | - Angela Scala
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D’Alcontres 31, 98166 Messina, Italy; (A.S.); (A.P.)
| | - Anna Piperno
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D’Alcontres 31, 98166 Messina, Italy; (A.S.); (A.P.)
| | - Nicola Micale
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D’Alcontres 31, 98166 Messina, Italy; (A.S.); (A.P.)
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16
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Nicolau I, Hădade ND, Matache M, Funeriu DP. Synthetic Approaches of Epoxysuccinate Chemical Probes. Chembiochem 2023; 24:e202300157. [PMID: 37096389 DOI: 10.1002/cbic.202300157] [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: 02/26/2023] [Revised: 04/21/2023] [Accepted: 04/23/2023] [Indexed: 04/26/2023]
Abstract
Synthetic chemical probes are powerful tools for investigating biological processes. They are particularly useful for proteomic studies such as activity-based protein profiling (ABPP). These chemical methods initially used mimics of natural substrates. As the techniques gained prominence, more and more elaborate chemical probes with increased specificity towards given enzyme/protein families and amenability to various reaction conditions were used. Among the chemical probes, peptidyl-epoxysuccinates represent one of the first types of compounds used to investigate the activity of the cysteine protease papain-like family of enzymes. Structurally derived from the natural substrate, a wide body of inhibitors and activity- or affinity-based probes bearing the electrophilic oxirane unit for covalent labeling of active enzymes now exists. Herein, we review the literature regarding the synthetic approaches to epoxysuccinate-based chemical probes together with their reported applications, from biological chemistry and inhibition studies to supramolecular chemistry and the formation of protein arrays.
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Affiliation(s)
- Ioana Nicolau
- University of Bucharest, Faculty of Chemistry, Department of Organic Chemistry, Biochemistry and Catalysis, Research Centre of Applied Organic Chemistry, 90 Panduri Street, 050663, Bucharest, Romania
| | - Niculina D Hădade
- Babes-Bolyai University, Faculty of Chemistry and Chemical Engineering, Supramolecular and Organometallic Chemistry Centre, 11 Arany Janos Street, 400028, Cluj-Napoca, Romania
| | - Mihaela Matache
- University of Bucharest, Faculty of Chemistry, Department of Organic Chemistry, Biochemistry and Catalysis, Research Centre of Applied Organic Chemistry, 90 Panduri Street, 050663, Bucharest, Romania
| | - Daniel P Funeriu
- University of Bucharest, Faculty of Chemistry, Department of Organic Chemistry, Biochemistry and Catalysis, Research Centre of Applied Organic Chemistry, 90 Panduri Street, 050663, Bucharest, Romania
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17
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Wildner G, Tucci AR, Prestes ADS, Muller T, Rosa ADS, Borba NRR, Ferreira VN, Rocha JBT, Miranda MD, Barbosa NV. Ebselen and Diphenyl Diselenide Inhibit SARS-CoV-2 Replication at Non-Toxic Concentrations to Human Cell Lines. Vaccines (Basel) 2023; 11:1222. [PMID: 37515038 PMCID: PMC10384302 DOI: 10.3390/vaccines11071222] [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: 04/27/2023] [Revised: 06/18/2023] [Accepted: 06/25/2023] [Indexed: 07/30/2023] Open
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was the causative agent of the COVID-19 pandemic, a global public health problem. Despite the numerous studies for drug repurposing, there are only two FDA-approved antiviral agents (Remdesivir and Nirmatrelvir) for non-hospitalized patients with mild-to-moderate COVID-19 symptoms. Consequently, it is pivotal to search for new molecules with anti-SARS-CoV-2 activity and to study their effects in the human immune system. Ebselen (Eb) is an organoselenium compound that is safe for humans and has antioxidant, anti-inflammatory, and antimicrobial properties. Diphenyl diselenide ((PhSe)2) shares several pharmacological properties with Eb and is of low toxicity to mammals. Herein, we investigated Eb and (PhSe)2 anti-SARS-CoV-2 activity in a human pneumocytes cell model (Calu-3) and analyzed their toxic effects on human peripheral blood mononuclear cells (PBMCs). Both compounds significantly inhibited the SARS-CoV-2 replication in Calu-3 cells. The EC50 values for Eb and (PhSe)2 after 24 h post-infection (hpi) were 3.8 µM and 3.9 µM, respectively, and after 48 hpi were 2.6 µM and 3.4 µM. These concentrations are safe for non-infected cells, since the CC50 values found for Eb and (PhSe)2 on Calu-3 were greater than 200 µM. Importantly, the concentration rates tested on viral replication were not toxic to human PBMCs. Therefore, our findings reinforce the efficacy of Eb and demonstrate (PhSe)2 as a new candidate to be tested in future trials against SARS-CoV-2 infection/inflammation conditions.
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Affiliation(s)
- Guilherme Wildner
- Programa de Pós-Graduação em Bioquímica Toxicológica, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil
| | - Amanda Resende Tucci
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Alessandro de Souza Prestes
- Programa de Pós-Graduação em Bioquímica Toxicológica, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil
| | - Talise Muller
- Programa de Pós-Graduação em Bioquímica Toxicológica, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil
| | - Alice Dos Santos Rosa
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Nathalia Roberto R Borba
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Vivian Neuza Ferreira
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - João Batista Teixeira Rocha
- Programa de Pós-Graduação em Bioquímica Toxicológica, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil
| | - Milene Dias Miranda
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Nilda Vargas Barbosa
- Programa de Pós-Graduação em Bioquímica Toxicológica, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil
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Wang L, Ma C, Sacco MD, Xue S, Mahmoud M, Calcul L, Chen Y, Wang J, Cai J. Development of the Safe and Broad-Spectrum Aldehyde and Ketoamide Mpro inhibitors Derived from the Constrained α, γ-AA Peptide Scaffold. Chemistry 2023; 29:e202300476. [PMID: 36920943 PMCID: PMC10330001 DOI: 10.1002/chem.202300476] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/16/2023]
Abstract
SARS-CoV-2 is still wreaking havoc all over the world with surging morbidity and high mortality. The main protease (Mpro ) is essential in the replication of SARS-CoV-2, enabling itself an active target for antiviral development. Herein, we reported the design and synthesis of a new class of peptidomimetics-constrained α, γ-AA peptides, based on which a series of aldehyde and ketoamide inhibitors of the Mpro of SARS-CoV-2 were prepared. The lead compounds showed excellent inhibitory activity in the FRET-based Mpro enzymatic assay not only for the Mpro of SARS-CoV-2 but also for SARS-CoV and MERS-CoV, along with HCoVs like HCoV-OC43, HCoV-229E, HCoV-NL63 and HKU1. The X-ray crystallographic results demonstrated that our compounds form a covalent bond with the catalytic Cys145. They also demonstrated effective antiviral activity against live SARS-CoV-2. Overall, the results suggest that α, γ-AA peptide could be a promising molecular scaffold in designing novel Mpro inhibitors of SARS-CoV-2 and other coronaviruses.
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Affiliation(s)
- Lei Wang
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, FL 33620, USA
| | - Chunlong Ma
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona, 85721, USA
| | - Michael Dominic Sacco
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 4202 E. Fowler Ave., Tampa, FL 33620, USA
| | - Songyi Xue
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, FL 33620, USA
| | - Mentalla Mahmoud
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, FL 33620, USA
| | - Laurent Calcul
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, FL 33620, USA
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 4202 E. Fowler Ave., Tampa, FL 33620, USA
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona, 85721, USA
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, University of New Jersey, Piscataway, NJ, USA
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, FL 33620, USA
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19
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Pang X, Xu W, Liu Y, Li H, Chen L. The research progress of SARS-CoV-2 main protease inhibitors from 2020 to 2022. Eur J Med Chem 2023; 257:115491. [PMID: 37244162 DOI: 10.1016/j.ejmech.2023.115491] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/06/2023] [Accepted: 05/14/2023] [Indexed: 05/29/2023]
Abstract
The novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide. The main protease (Mpro) of SARS-CoV-2 plays a central role in viral replication and transcription and represents an attractive drug target for fighting COVID-19. Many SARS-CoV-2 Mpro inhibitors have been reported, including covalent and noncovalent inhibitors. The SARS-CoV-2 Mpro inhibitor PF-07321332 (Nirmatrelvir) designed by Pfizer has been put on the market. This paper briefly introduces the structural characteristics of SARS-CoV-2 Mpro and summarizes the research progress of SARS-CoV-2 Mpro inhibitors from the aspects of drug repurposing and drug design. These information will provide a basis for the drug development of treating the infection of SARS-CoV-2 and even other coronaviruses in the future.
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Affiliation(s)
- Xiaojing Pang
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Wei Xu
- Institute of Structural Pharmacology & TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, China
| | - Yang Liu
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Hua Li
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China; Institute of Structural Pharmacology & TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, China.
| | - Lixia Chen
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China.
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20
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Ahmad S, Mirza MU, Trant JF. Dock-able linear and homodetic di, tri, tetra and pentapeptide library from canonical amino acids: SARS-CoV-2 Mpro as a case study. J Pharm Anal 2023; 13:523-534. [PMID: 37275125 PMCID: PMC10104786 DOI: 10.1016/j.jpha.2023.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/07/2023] [Accepted: 04/13/2023] [Indexed: 06/07/2023] Open
Abstract
Peptide-based therapeutics are increasingly pushing to the forefront of biomedicine with their promise of high specificity and low toxicity. Although noncanonical residues can always be used, employing only the natural 20 residues restricts the chemical space to a finite dimension allowing for comprehensive in silico screening. Towards this goal, the dataset comprising all possible di-, tri-, and tetra-peptide combinations of the canonical residues has been previously reported. However, with increasing computational power, the comprehensive set of pentapeptides is now also feasible for screening as the comprehensive set of cyclic peptides comprising four or five residues. Here, we provide both the complete and prefiltered libraries of all di-, tri-, tetra-, and penta-peptide sequences from 20 canonical amino acids and their homodetic (N-to-C-terminal) cyclic homologues. The FASTA, simplified molecular-input line-entry system (SMILES), and structure-data file (SDF)-three dimension (3D) libraries can be readily used for screening against protein targets. We also provide a simple method and tool for conducting identity-based filtering. Access to this dataset will accelerate small peptide screening workflows and encourage their use in drug discovery campaigns. As a case study, the developed library was screened against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease to identify potential small peptide inhibitors.
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Affiliation(s)
- Sarfraz Ahmad
- Department of Chemistry and Biochemistry, University of Windsor, Windsor N9B 3P4, Ontario, Canada
- Binary Star Research Services, LaSalle N9J 3X8, Ontario, Canada
| | - Muhammad Usman Mirza
- Department of Chemistry and Biochemistry, University of Windsor, Windsor N9B 3P4, Ontario, Canada
- Binary Star Research Services, LaSalle N9J 3X8, Ontario, Canada
| | - John F Trant
- Department of Chemistry and Biochemistry, University of Windsor, Windsor N9B 3P4, Ontario, Canada
- Binary Star Research Services, LaSalle N9J 3X8, Ontario, Canada
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21
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Zabiegala A, Kim Y, Chang KO. Roles of host proteases in the entry of SARS-CoV-2. ANIMAL DISEASES 2023; 3:12. [PMID: 37128508 PMCID: PMC10125864 DOI: 10.1186/s44149-023-00075-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/07/2023] [Indexed: 05/03/2023] Open
Abstract
The spike protein (S) of SARS-CoV-2 is responsible for viral attachment and entry, thus a major factor for host susceptibility, tissue tropism, virulence and pathogenicity. The S is divided with S1 and S2 region, and the S1 contains the receptor-binding domain (RBD), while the S2 contains the hydrophobic fusion domain for the entry into the host cell. Numerous host proteases have been implicated in the activation of SARS-CoV-2 S through various cleavage sites. In this article, we review host proteases including furin, trypsin, transmembrane protease serine 2 (TMPRSS2) and cathepsins in the activation of SARS-CoV-2 S. Many betacoronaviruses including SARS-CoV-2 have polybasic residues at the S1/S2 site which is subjected to the cleavage by furin. The S1/S2 cleavage facilitates more assessable RBD to the receptor ACE2, and the binding triggers further conformational changes and exposure of the S2' site to proteases such as type II transmembrane serine proteases (TTPRs) including TMPRSS2. In the presence of TMPRSS2 on the target cells, SARS-CoV-2 can utilize a direct entry route by fusion of the viral envelope to the cellular membrane. In the absence of TMPRSS2, SARS-CoV-2 enter target cells via endosomes where multiple cathepsins cleave the S for the successful entry. Additional host proteases involved in the cleavage of the S were discussed. This article also includes roles of 3C-like protease inhibitors which have inhibitory activity against cathepsin L in the entry of SARS-CoV-2, and discussed the dual roles of such inhibitors in virus replication.
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Affiliation(s)
- Alexandria Zabiegala
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506 USA
| | - Yunjeong Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506 USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506 USA
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22
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Doijen J, Temmerman K, Van den Eynde C, Diels A, Van den Broeck N, Van Gool M, Heo I, Jaensch S, Zwaagstra M, Diosa Toro M, Chiu W, De Jonghe S, Leyssen P, Bojkova D, Ciesek S, Cinatl J, Verschueren L, Buyck C, Van Kuppeveld F, Neyts J, Van Loock M, Van Damme E. Identification of Z-Tyr-Ala-CHN 2, a Cathepsin L Inhibitor with Broad-Spectrum Cell-Specific Activity against Coronaviruses, including SARS-CoV-2. Microorganisms 2023; 11:717. [PMID: 36985290 PMCID: PMC10055926 DOI: 10.3390/microorganisms11030717] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/17/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
The ongoing COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is partly under control by vaccination. However, highly potent and safe antiviral drugs for SARS-CoV-2 are still needed to avoid development of severe COVID-19. We report the discovery of a small molecule, Z-Tyr-Ala-CHN2, which was identified in a cell-based antiviral screen. The molecule exerts sub-micromolar antiviral activity against SARS-CoV-2, SARS-CoV-1, and human coronavirus 229E. Time-of-addition studies reveal that Z-Tyr-Ala-CHN2 acts at the early phase of the infection cycle, which is in line with the observation that the molecule inhibits cathepsin L. This results in antiviral activity against SARS-CoV-2 in VeroE6, A549-hACE2, and HeLa-hACE2 cells, but not in Caco-2 cells or primary human nasal epithelial cells since the latter two cell types also permit entry via transmembrane protease serine subtype 2 (TMPRSS2). Given their cell-specific activity, cathepsin L inhibitors still need to prove their value in the clinic; nevertheless, the activity profile of Z-Tyr-Ala-CHN2 makes it an interesting tool compound for studying the biology of coronavirus entry and replication.
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Affiliation(s)
- Jordi Doijen
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Koen Temmerman
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | | | - Annick Diels
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | | | | | - Inha Heo
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Steffen Jaensch
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Marleen Zwaagstra
- Faculty of Veterinary Medicine, Yalelaan 1, Virology Division, Department of Biomolecular Health Sciences, Infectious Diseases and Immunology, Utrecht University, 3584 Utrecht, The Netherlands
| | - Mayra Diosa Toro
- Faculty of Veterinary Medicine, Yalelaan 1, Virology Division, Department of Biomolecular Health Sciences, Infectious Diseases and Immunology, Utrecht University, 3584 Utrecht, The Netherlands
| | - Winston Chiu
- Laboratory of Virology and Chemotherapy, Herestraat 49, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Steven De Jonghe
- Laboratory of Virology and Chemotherapy, Herestraat 49, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Pieter Leyssen
- Laboratory of Virology and Chemotherapy, Herestraat 49, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Denisa Bojkova
- Institute for Medical Virology, University Hospital, Paul-Ehrlich-Str. 40, Frankfurt University, 60596 Frankfurt am Main, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital, Paul-Ehrlich-Str. 40, Frankfurt University, 60596 Frankfurt am Main, Germany
| | - Jindrich Cinatl
- Institute for Medical Virology, University Hospital, Paul-Ehrlich-Str. 40, Frankfurt University, 60596 Frankfurt am Main, Germany
| | - Lore Verschueren
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Christophe Buyck
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Frank Van Kuppeveld
- Faculty of Veterinary Medicine, Yalelaan 1, Virology Division, Department of Biomolecular Health Sciences, Infectious Diseases and Immunology, Utrecht University, 3584 Utrecht, The Netherlands
| | - Johan Neyts
- Laboratory of Virology and Chemotherapy, Herestraat 49, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Marnix Van Loock
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Ellen Van Damme
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
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23
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Vanhoutte R, Barniol-Xicota M, Chiu W, Vangeel L, Jochmans D, De Jonghe S, Zidane H, Barr HM, London N, Neyts J, Verhelst SHL. Azapeptide activity-based probes for the SARS-CoV-2 main protease enable visualization of inhibition in infected cells. Chem Sci 2023; 14:1666-1672. [PMID: 36819852 PMCID: PMC9931053 DOI: 10.1039/d2sc04147b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/02/2023] [Indexed: 01/08/2023] Open
Abstract
The COVID-19 pandemic has revealed the vulnerability of the modern, global society. With expected waves of future infections by SARS-CoV-2, treatment options for infected individuals will be crucial in order to decrease mortality and hospitalizations. The SARS-CoV-2 main protease is a validated drug target, for which the first inhibitor has been approved for use in patients. To facilitate future work on this drug target, we designed a solid-phase synthesis route towards azapeptide activity-based probes that are capped with a cysteine-reactive electrophile for covalent modification of the active site of Mpro. This design led to the most potent ABP for Mpro and one of the most potent inhibitors reported thus far. We demonstrate that this ABP can be used to visualize Mpro activity and target engagement by drugs in infected cells.
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Affiliation(s)
- Roeland Vanhoutte
- Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, KU Leuven Herestraat 49 box 802 3000 Leuven Belgium
| | - Marta Barniol-Xicota
- Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, KU Leuven Herestraat 49 box 802 3000 Leuven Belgium
| | - Winston Chiu
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU LeuvenHerestraat 49, Box 10433000LeuvenBelgium
| | - Laura Vangeel
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU LeuvenHerestraat 49, Box 10433000LeuvenBelgium
| | - Dirk Jochmans
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU LeuvenHerestraat 49, Box 10433000LeuvenBelgium
| | - Steven De Jonghe
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU LeuvenHerestraat 49, Box 10433000LeuvenBelgium
| | - Hadeer Zidane
- Maurice and Vivienne Wohl Institute for Drug Discovery, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, The Weizmann Institute of ScienceRehovot 7610001Israel
| | - Haim M. Barr
- Maurice and Vivienne Wohl Institute for Drug Discovery, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, The Weizmann Institute of ScienceRehovot 7610001Israel
| | - Nir London
- Department of Chemical and Structural Biology, Weizmann Institute of ScienceRehovot 7610001Israel
| | - Johan Neyts
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU LeuvenHerestraat 49, Box 10433000LeuvenBelgium
| | - Steven H. L. Verhelst
- Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, KU LeuvenHerestraat 49 box 8023000 LeuvenBelgium,AG Chemical Proteomics, Leibniz Institute for Analytical Sciences ISASOtto-Hahn-Str. 6b44227 DortmundGermany
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24
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Moloney A, Maple HJ. Developing, Choosing, and Using the Chemical Toolbox for Infectious Diseases Research. ACS Infect Dis 2023; 9:2-4. [PMID: 36511756 DOI: 10.1021/acsinfecdis.2c00539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Scientific progress is built on "what went before". As research in a field or discipline progresses, laying strong and scientifically correct foundations for each incremental discovery ultimately accelerates progress. The importance of "research tools" (e.g., chemical probes, antibodies, assays) that underpin researchers' efforts to probe and understand biological systems and pathways should therefore not be underestimated. Appropriate validation, protocol development, and ultimately availability of research tools are critical, in parallel with education on the appropriate selection and use of these tools.
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Affiliation(s)
- Alex Moloney
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Bristol BS11 9QD, U.K
| | - Hannah J Maple
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Bristol BS11 9QD, U.K
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25
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Mondal S, Chen Y, Lockbaum GJ, Sen S, Chaudhuri S, Reyes AC, Lee JM, Kaur AN, Sultana N, Cameron MD, Shaffer SA, Schiffer CA, Fitzgerald KA, Thompson PR. Dual Inhibitors of Main Protease (M Pro) and Cathepsin L as Potent Antivirals against SARS-CoV2. J Am Chem Soc 2022; 144:21035-21045. [PMID: 36356199 PMCID: PMC9662648 DOI: 10.1021/jacs.2c04626] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Indexed: 11/12/2022]
Abstract
Given the current impact of SARS-CoV2 and COVID-19 on human health and the global economy, the development of direct acting antivirals is of paramount importance. Main protease (MPro), a cysteine protease that cleaves the viral polyprotein, is essential for viral replication. Therefore, MPro is a novel therapeutic target. We identified two novel MPro inhibitors, D-FFRCMKyne and D-FFCitCMKyne, that covalently modify the active site cysteine (C145) and determined cocrystal structures. Medicinal chemistry efforts led to SM141 and SM142, which adopt a unique binding mode within the MPro active site. Notably, these inhibitors do not inhibit the other cysteine protease, papain-like protease (PLPro), involved in the life cycle of SARS-CoV2. SM141 and SM142 block SARS-CoV2 replication in hACE2 expressing A549 cells with IC50 values of 8.2 and 14.7 nM. Detailed studies indicate that these compounds also inhibit cathepsin L (CatL), which cleaves the viral S protein to promote viral entry into host cells. Detailed biochemical, proteomic, and knockdown studies indicate that the antiviral activity of SM141 and SM142 results from the dual inhibition of MPro and CatL. Notably, intranasal and intraperitoneal administration of SM141 and SM142 lead to reduced viral replication, viral loads in the lung, and enhanced survival in SARS-CoV2 infected K18-ACE2 transgenic mice. In total, these data indicate that SM141 and SM142 represent promising scaffolds on which to develop antiviral drugs against SARS-CoV2.
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Affiliation(s)
- Santanu Mondal
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Yongzhi Chen
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Gordon J. Lockbaum
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Sudeshna Sen
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Sauradip Chaudhuri
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Archie C. Reyes
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Jeong Min Lee
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Arshia N. Kaur
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Nadia Sultana
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Michael D. Cameron
- Department of Molecular Medicine, The Scripps Research Institute,130 Scripps Way, Jupiter, FL 33458, USA
| | - Scott A. Shaffer
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Katherine A. Fitzgerald
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Paul R. Thompson
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
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26
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Identification of fungal lignocellulose-degrading biocatalysts secreted by Phanerochaete chrysosporium via activity-based protein profiling. Commun Biol 2022; 5:1254. [DOI: 10.1038/s42003-022-04141-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 10/20/2022] [Indexed: 11/17/2022] Open
Abstract
AbstractActivity-based protein profiling (ABPP) has emerged as a versatile biochemical method for studying enzyme activity under various physiological conditions, with applications so far mainly in biomedicine. Here, we show the potential of ABPP in the discovery of biocatalysts from the thermophilic and lignocellulose-degrading white rot fungus Phanerochaete chrysosporium. By employing a comparative ABPP-based functional screen, including a direct profiling of wood substrate-bound enzymes, we identify those lignocellulose-degrading carbohydrate esterase (CE1 and CE15) and glycoside hydrolase (GH3, GH5, GH16, GH17, GH18, GH25, GH30, GH74 and GH79) enzymes specifically active in presence of the substrate. As expression of fungal enzymes remains challenging, our ABPP-mediated approach represents a preselection procedure for focusing experimental efforts on the most promising biocatalysts. Furthermore, this approach may also allow the functional annotation of domains-of-unknown functions (DUFs). The ABPP-based biocatalyst screening described here may thus allow the identification of active enzymes in a process of interest and the elucidation of novel biocatalysts that share no sequence similarity to known counterparts.
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27
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Fàbrega-Ferrer M, Herrera-Morandé A, Muriel-Goñi S, Pérez-Saavedra J, Bueno P, Castro V, Garaigorta U, Gastaminza P, Coll M. Structure and inhibition of SARS-CoV-1 and SARS-CoV-2 main proteases by oral antiviral compound AG7404. Antiviral Res 2022; 208:105458. [PMID: 36336176 PMCID: PMC9632241 DOI: 10.1016/j.antiviral.2022.105458] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 10/26/2022] [Accepted: 10/29/2022] [Indexed: 11/05/2022]
Abstract
Severe acute respiratory syndrome coronaviruses 1 and 2 (SARS-CoV-1 and SARS-CoV-2) pose a threat to global public health. The 3C-like main protease (Mpro), which presents structural similarity with the active site domain of enterovirus 3C protease, is one of the best-characterized drug targets of these viruses. Here we studied the antiviral activity of the orally bioavailable enterovirus protease inhibitor AG7404 against SARS-CoV-1 and SARS-CoV-2 from a structural, biochemical, and cellular perspective, comparing it with the related molecule rupintrivir (AG7800). Crystallographic structures of AG7404 in complex with SARS-CoV-1 Mpro and SARS-CoV-2 Mpro and of rupintrivir in complex with SARS-CoV-2 Mpro were solved, revealing that all protein residues interacting with the inhibitors are conserved between the two proteins. A detailed analysis of protein-inhibitor interactions indicates that AG7404 has a better fit to the active site of the target protease than rupintrivir. This observation was further confirmed by biochemical FRET assays showing IC50 values of 47 μM and 101 μM for AG7404 and rupintrivir, respectively, in the case of SARS-CoV-2 Mpro. Equivalent IC50 values for SARS-CoV-1 also revealed greater inhibitory capacity of AG7404, with a value of 29 μM vs. 66 μM for rupintrivir. Finally, the antiviral activity of the two inhibitors against SARS-CoV-2 was confirmed in a human cell culture model of SARS-CoV-2 infection, although rupintrivir showed a higher potency and selectivity index in this assay.
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Affiliation(s)
- Montserrat Fàbrega-Ferrer
- Institute for Research in Biomedicine IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain,Institut de Biologia Molecular de Barcelona IBMB-CSIC, Baldiri Reixac 10, Barcelona, 08028, Spain
| | - Alejandra Herrera-Morandé
- Institute for Research in Biomedicine IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain,Institut de Biologia Molecular de Barcelona IBMB-CSIC, Baldiri Reixac 10, Barcelona, 08028, Spain
| | - Sara Muriel-Goñi
- Institute for Research in Biomedicine IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain,Institut de Biologia Molecular de Barcelona IBMB-CSIC, Baldiri Reixac 10, Barcelona, 08028, Spain
| | - Julia Pérez-Saavedra
- Institute for Research in Biomedicine IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain,Institut de Biologia Molecular de Barcelona IBMB-CSIC, Baldiri Reixac 10, Barcelona, 08028, Spain
| | - Paula Bueno
- Centro Nacional de Biotecnología, CNB-CSIC, Darwin 3, Madrid, 28049, Spain
| | - Victoria Castro
- Centro Nacional de Biotecnología, CNB-CSIC, Darwin 3, Madrid, 28049, Spain
| | - Urtzi Garaigorta
- Centro Nacional de Biotecnología, CNB-CSIC, Darwin 3, Madrid, 28049, Spain
| | - Pablo Gastaminza
- Centro Nacional de Biotecnología, CNB-CSIC, Darwin 3, Madrid, 28049, Spain
| | - Miquel Coll
- Institute for Research in Biomedicine IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain,Institut de Biologia Molecular de Barcelona IBMB-CSIC, Baldiri Reixac 10, Barcelona, 08028, Spain,Corresponding author. Institute for Research in Biomedicine IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
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28
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Cooper MS, Zhang L, Ibrahim M, Zhang K, Sun X, Röske J, Göhl M, Brönstrup M, Cowell JK, Sauerhering L, Becker S, Vangeel L, Jochmans D, Neyts J, Rox K, Marsh GP, Maple HJ, Hilgenfeld R. Diastereomeric Resolution Yields Highly Potent Inhibitor of SARS-CoV-2 Main Protease. J Med Chem 2022; 65:13328-13342. [PMID: 36179320 PMCID: PMC9574927 DOI: 10.1021/acs.jmedchem.2c01131] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Indexed: 12/02/2022]
Abstract
SARS-CoV-2 is the causative agent behind the COVID-19 pandemic. The main protease (Mpro, 3CLpro) of SARS-CoV-2 is a key enzyme that processes polyproteins translated from the viral RNA. Mpro is therefore an attractive target for the design of inhibitors that block viral replication. We report the diastereomeric resolution of the previously designed SARS-CoV-2 Mpro α-ketoamide inhibitor 13b. The pure (S,S,S)-diastereomer, 13b-K, displays an IC50 of 120 nM against the Mpro and EC50 values of 0.8-3.4 μM for antiviral activity in different cell types. Crystal structures have been elucidated for the Mpro complexes with each of the major diastereomers, the active (S,S,S)-13b (13b-K), and the nearly inactive (R,S,S)-13b (13b-H); results for the latter reveal a novel binding mode. Pharmacokinetic studies show good levels of 13b-K after inhalative as well as after peroral administration. The active inhibitor (13b-K) is a promising candidate for further development as an antiviral treatment for COVID-19.
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Affiliation(s)
- Mark S. Cooper
- Bio-Techne
(Tocris), The Watkins
Building, Atlantic Road, Bristol, BS11 9QD, U.K.
| | - Linlin Zhang
- Institute
of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
| | - Mohamed Ibrahim
- Institute
of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
| | - Kaixuan Zhang
- Institute
of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
| | - Xinyuanyuan Sun
- Institute
of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
| | - Judith Röske
- Institute
of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
| | - Matthias Göhl
- Department
of Chemical Biology, Helmholtz Centre for
Infection Research (HZI), 38124 Braunschweig, Germany
| | - Mark Brönstrup
- Department
of Chemical Biology, Helmholtz Centre for
Infection Research (HZI), 38124 Braunschweig, Germany
- German
Center for Infection Research (DZIF), Partner
Site Braunschweig-Hannover, 38124 Braunschweig, Germany
| | - Justin K. Cowell
- Bio-Techne
(Tocris), The Watkins
Building, Atlantic Road, Bristol, BS11 9QD, U.K.
| | - Lucie Sauerhering
- Institute
of Virology, University of Marburg, 35043 Marburg, Germany
| | - Stephan Becker
- Institute
of Virology, University of Marburg, 35043 Marburg, Germany
- German Center
for Infection Research (DZIF), Marburg-Gießen-Langen
Site, 35043 Marburg, Germany
| | - Laura Vangeel
- Rega
Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, B-3000 Leuven, Belgium
| | - Dirk Jochmans
- Rega
Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, B-3000 Leuven, Belgium
| | - Johan Neyts
- Rega
Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, B-3000 Leuven, Belgium
| | - Katharina Rox
- Department
of Chemical Biology, Helmholtz Centre for
Infection Research (HZI), 38124 Braunschweig, Germany
- German
Center for Infection Research (DZIF), Partner
Site Braunschweig-Hannover, 38124 Braunschweig, Germany
| | - Graham P. Marsh
- Bio-Techne
(Tocris), The Watkins
Building, Atlantic Road, Bristol, BS11 9QD, U.K.
| | - Hannah J. Maple
- Bio-Techne
(Tocris), The Watkins
Building, Atlantic Road, Bristol, BS11 9QD, U.K.
| | - Rolf Hilgenfeld
- Institute
of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
- German
Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems
Site, University of Lübeck, 23562 Lübeck, Germany
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29
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Cui Z, Zeng C, Huang F, Yuan F, Yan J, Zhao Y, Zhou Y, Hankey W, Jin VX, Huang J, Staats HF, Everitt JI, Sempowski GD, Wang H, Dong Y, Liu SL, Wang Q. Cas13d knockdown of lung protease Ctsl prevents and treats SARS-CoV-2 infection. Nat Chem Biol 2022; 18:1056-1064. [PMID: 35879545 PMCID: PMC10082993 DOI: 10.1038/s41589-022-01094-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/24/2022] [Indexed: 12/11/2022]
Abstract
SARS-CoV-2 entry into cells requires specific host proteases; however, no successful in vivo applications of host protease inhibitors have yet been reported for treatment of SARS-CoV-2 pathogenesis. Here we describe a chemically engineered nanosystem encapsulating CRISPR-Cas13d, developed to specifically target lung protease cathepsin L (Ctsl) messenger RNA to block SARS-CoV-2 infection in mice. We show that this nanosystem decreases lung Ctsl expression in normal mice efficiently, specifically and safely. We further show that this approach extends survival of mice lethally infected with SARS-CoV-2, correlating with decreased lung virus burden, reduced expression of proinflammatory cytokines/chemokines and diminished severity of pulmonary interstitial inflammation. Postinfection treatment by this nanosystem dramatically lowers the lung virus burden and alleviates virus-induced pathological changes. Our results indicate that targeting lung protease mRNA by Cas13d nanosystem represents a unique strategy for controlling SARS-CoV-2 infection and demonstrate that CRISPR can be used as a potential treatment for SARS-CoV-2 infection.
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Affiliation(s)
- Zhifen Cui
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Cong Zeng
- Viruses and Emerging Pathogens Program, Infectious Diseases Institute, Center for Retrovirus Research and Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
| | - Furong Huang
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Fuwen Yuan
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Jingyue Yan
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Department of Biomedical Engineering, The Ohio State University, Columbus, OH, USA
| | - Yue Zhao
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
- Department of Pathology, College of Basic Medical Sciences and First Affiliated Hospital, China Medical University, Shenyang, China
| | - Yufan Zhou
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - William Hankey
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Victor X Jin
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Jiaoti Huang
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Herman F Staats
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
- Duke Human Vaccine Institute and Regional Biocontainment Laboratory, Duke University School of Medicine, Durham, NC, USA
| | - Jeffrey I Everitt
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Gregory D Sempowski
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
- Duke Human Vaccine Institute and Regional Biocontainment Laboratory, Duke University School of Medicine, Durham, NC, USA
| | - Hongyan Wang
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Yizhou Dong
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Department of Biomedical Engineering, The Ohio State University, Columbus, OH, USA.
| | - Shan-Lu Liu
- Viruses and Emerging Pathogens Program, Infectious Diseases Institute, Center for Retrovirus Research and Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA.
| | - Qianben Wang
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA.
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30
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Goyal R, Gautam RK, Chopra H, Dubey AK, Singla RK, Rayan RA, Kamal MA. Comparative highlights on MERS-CoV, SARS-CoV-1, SARS-CoV-2, and NEO-CoV. EXCLI JOURNAL 2022; 21:1245-1272. [PMID: 36483910 PMCID: PMC9727256 DOI: 10.17179/excli2022-5355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 09/23/2022] [Indexed: 01/25/2023]
Abstract
The severe acute respiratory syndrome (SARS-CoV, now SARS-CoV-1), middle east respiratory syndrome (MERS-CoV), Neo-CoV, and 2019 novel coronavirus (SARS-CoV-2/COVID-19) are the most notable coronaviruses, infecting the number of people worldwide by targeting the respiratory system. All these viruses are of zoonotic origin, predominantly from bats which are one of the natural reservoir hosts for coronaviruses. Thus, the major goal of our review article is to compare and contrast the characteristics and attributes of these coronaviruses. The SARS-CoV-1, MERS-CoV, and COVID-19 have many viral similarities due to their classification, they are not genetically related. COVID-19 shares approximately 79 % of its genome with SARS-CoV-1 and about 50 % with MERS-CoV. The shared receptor protein, ACE2 exhibit the most striking genetic similarities between SARS-CoV-1 and SARS-CoV-2. SARS-CoV primarily replicates in the epithelial cells of the respiratory system, but it may also affect macrophages, monocytes, activated T cells, and dendritic cells. MERS-CoV not only infects and replicates inside the epithelial and immune cells, but it may lyse them too, which is one of the common reasons for MERS's higher mortality rate. The details of infections caused by SARS-CoV-2 and lytic replication mechanisms in host cells are currently mysterious. In this review article, we will discuss the comparative highlights of SARS-CoV-1, MERS-CoV, SARS-CoV-2, and Neo-CoV, concerning their structural features, morphological characteristics, sources of virus origin and their evolutionary transitions, infection mechanism, computational study approaches, pathogenesis and their severity towards several diseases, possible therapeutic approaches, and preventive measures.
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Affiliation(s)
- Rajat Goyal
- MM College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, Haryana, India,MM School of Pharmacy, Maharishi Markandeshwar University, Sadopur-Ambala, India
| | - Rupesh K. Gautam
- Department of Pharmacology, Indore Institute of Pharmacy, Rau, Indore, India-453331,*To whom correspondence should be addressed: Rupesh K. Gautam, Department of Pharmacology, Indore Institute of Pharmacy, IIST Campus, Opposite IIM Indore, Rau-Pithampur Road, Indore – 453331 (M.P.), India; Tel.: +91 9413654324, E-mail:
| | - Hitesh Chopra
- Chitkara College of Pharmacy, Chitkara University, Punjab, India-140401
| | | | - Rajeev K. Singla
- Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China,School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab-144411, India
| | - Rehab A. Rayan
- Department of Epidemiology, High Institute of Public Health, Alexandria University, 5422031, Egypt
| | - Mohammad Amjad Kamal
- Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China,King Fahd Medical Research Center, King Abdulaziz University, Saudi Arabia,Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Bangladesh,Enzymoics, 7 Peterlee Place, Hebersham NSW 2770; Novel Global Community Educational Foundation, Australia
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31
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Zhong L, Zhao Z, Peng X, Zou J, Yang S. Recent advances in small-molecular therapeutics for COVID-19. PRECISION CLINICAL MEDICINE 2022; 5:pbac024. [PMID: 36268466 PMCID: PMC9579963 DOI: 10.1093/pcmedi/pbac024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/21/2022] [Indexed: 12/14/2022] Open
Abstract
The COVID-19 pandemic poses a fundamental challenge to global health. Since the outbreak of SARS-CoV-2, great efforts have been made to identify antiviral strategies and develop therapeutic drugs to combat the disease. There are different strategies for developing small molecular anti-SARS-CoV-2 drugs, including targeting coronavirus structural proteins (e.g. spike protein), non-structural proteins (nsp) (e.g. RdRp, Mpro, PLpro, helicase, nsp14, and nsp16), host proteases (e.g. TMPRSS2, cathepsin, and furin) and the pivotal proteins mediating endocytosis (e.g. PIKfyve), as well as developing endosome acidification agents and immune response modulators. Favipiravir and chloroquine are the anti-SARS-CoV-2 agents that were identified earlier in this epidemic and repurposed for COVID-19 clinical therapy based on these strategies. However, their efficacies are controversial. Currently, three small molecular anti-SARS-CoV-2 agents, remdesivir, molnupiravir, and Paxlovid (PF-07321332 plus ritonavir), have been granted emergency use authorization or approved for COVID-19 therapy in many countries due to their significant curative effects in phase III trials. Meanwhile, a large number of promising anti-SARS-CoV-2 drug candidates have entered clinical evaluation. The development of these drugs brings hope for us to finally conquer COVID-19. In this account, we conducted a comprehensive review of the recent advances in small molecule anti-SARS-CoV-2 agents according to the target classification. Here we present all the approved drugs and most of the important drug candidates for each target, and discuss the challenges and perspectives for the future research and development of anti-SARS-CoV-2 drugs.
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Affiliation(s)
| | | | - Xuerun Peng
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | | | - Shengyong Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China School of Medicine, Sichuan University, Chengdu 610041, China
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32
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Samrat SK, Xu J, Xie X, Gianti E, Chen H, Zou J, Pattis JG, Elokely K, Lee H, Li Z, Klein ML, Shi PY, Zhou J, Li H. Allosteric inhibitors of the main protease of SARS-CoV-2. Antiviral Res 2022; 205:105381. [PMID: 35835291 PMCID: PMC9272661 DOI: 10.1016/j.antiviral.2022.105381] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 12/19/2022]
Abstract
SARS-CoV-2 has raised the alarm to search for effective therapy for this virus. To date several vaccines have been approved but few available drugs reported recently still need approval from FDA. Remdesivir was approved for emergency use only. In this report, the SARS-CoV-2 3CLpro was expressed and purified. By using a FRET-based enzymatic assay, we have screened a library consisting of more than 300 different niclosamide derivatives and identified three molecules JMX0286, JMX0301, and JMX0941 as potent allosteric inhibitors against SARS-CoV-2 3CLpro, with IC50 values similar to that of known covalent inhibitor boceprevir. In a cell-based antiviral assay, these inhibitors can inhibit the virus growth with EC50 in the range of 2-3 μM. The mechanism of action of JMX0286, JMX0301, and JMX0941 were characterized by enzyme kinetics, affinity binding and protein-based substrate digestion. Molecular docking, molecular dynamics (MD) simulations and hydration studies suggested that JMX0286, JMX0301, JMX0941 bind specifically to an allosteric pocket of the SARS-CoV-2 3CL protease. This study provides three potent compounds for further studies.
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Affiliation(s)
- Subodh Kumar Samrat
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ, 85721-0207, USA.
| | - Jimin Xu
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Eleonora Gianti
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA, 19122, USA
| | - Haiying Chen
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Jing Zou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Jason G Pattis
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA, 19122, USA
| | - Khaled Elokely
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA, 19122, USA
| | - Hyun Lee
- Department of Pharmaceutical Sciences at College of Pharmacy and Biophysics Core at Research Resources Center, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Zhong Li
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ, 85721-0207, USA
| | - Michael L Klein
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA, 19122, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, 77555, USA; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, 77555, USA; Institute for Drug Discovery, University of Texas Medical Branch, Galveston, TX, 77555, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
| | - Hongmin Li
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ, 85721-0207, USA; BIO5 Institute, The University of Arizona, Tucson, Tucson, AZ, 85721, USA.
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33
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Evaluation of the anti-SARS-CoV-2 properties of essential oils and aromatic extracts. Sci Rep 2022; 12:14230. [PMID: 35987981 PMCID: PMC9392441 DOI: 10.1038/s41598-022-18676-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 08/17/2022] [Indexed: 01/18/2023] Open
Abstract
Essential oils and aromatic extracts (oleoresins, absolutes, concretes, resinoids) are often used as food flavorings and constituents of fragrance compositions. The flavor and fragrance industry observed significant growth in the sales of some natural materials during the COVID-19 outbreak. Some companies worldwide are making false claims regarding the effectiveness of their essential oils or blends (or indirectly point toward this conclusion) against coronaviruses, even though the available data on the activity of plant materials against highly pathogenic human coronaviruses are very scarce. Our exploratory study aimed to develop pioneering knowledge and provide the first experimental results on the inhibitory properties of hundreds of flavor and fragrance materials against SARS-CoV-2 main and papain-like proteases and the antiviral potential of the most active protease inhibitors. As essential oils are volatile products, they could provide an interesting therapeutic strategy for subsidiary inhalation in the long term.
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34
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Liu H, Iketani S, Zask A, Khanizeman N, Bednarova E, Forouhar F, Fowler B, Hong SJ, Mohri H, Nair MS, Huang Y, Tay NES, Lee S, Karan C, Resnick SJ, Quinn C, Li W, Shion H, Xia X, Daniels JD, Bartolo-Cruz M, Farina M, Rajbhandari P, Jurtschenko C, Lauber MA, McDonald T, Stokes ME, Hurst BL, Rovis T, Chavez A, Ho DD, Stockwell BR. Development of optimized drug-like small molecule inhibitors of the SARS-CoV-2 3CL protease for treatment of COVID-19. Nat Commun 2022; 13:1891. [PMID: 35393402 PMCID: PMC8989888 DOI: 10.1038/s41467-022-29413-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 03/14/2022] [Indexed: 11/29/2022] Open
Abstract
The SARS-CoV-2 3CL protease is a critical drug target for small molecule COVID-19 therapy, given its likely druggability and essentiality in the viral maturation and replication cycle. Based on the conservation of 3CL protease substrate binding pockets across coronaviruses and using screening, we identified four structurally distinct lead compounds that inhibit SARS-CoV-2 3CL protease. After evaluation of their binding specificity, cellular antiviral potency, metabolic stability, and water solubility, we prioritized the GC376 scaffold as being optimal for optimization. We identified multiple drug-like compounds with <10 nM potency for inhibiting SARS-CoV-2 3CL and the ability to block SARS-CoV-2 replication in human cells, obtained co-crystal structures of the 3CL protease in complex with these compounds, and determined that they have pan-coronavirus activity. We selected one compound, termed coronastat, as an optimized lead and characterized it in pharmacokinetic and safety studies in vivo. Coronastat represents a new candidate for a small molecule protease inhibitor for the treatment of SARS-CoV-2 infection for eliminating pandemics involving coronaviruses. Small molecule drugs promise to remain a valuable tool in controlling the ongoing COVID-19 pandemic. Here the authors describe optimized drug-like small molecule inhibitors of the SARS-CoV-2 3CL protease for potential treatment of COVID-19.
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Affiliation(s)
- Hengrui Liu
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, 10032, USA.,Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Arie Zask
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Nisha Khanizeman
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Eva Bednarova
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Farhad Forouhar
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Brandon Fowler
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Seo Jung Hong
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Hiroshi Mohri
- Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Manoj S Nair
- Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Nicholas E S Tay
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Sumin Lee
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Charles Karan
- Sulzberger Columbia Genome Center, Columbia University, New York, NY, 10032, USA
| | - Samuel J Resnick
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA.,Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Colette Quinn
- Waters Corporation, 34 Maple Street, Milford, MA, 01757, USA
| | - Wenjing Li
- Waters Corporation, 34 Maple Street, Milford, MA, 01757, USA
| | - Henry Shion
- Waters Corporation, 34 Maple Street, Milford, MA, 01757, USA
| | - Xin Xia
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Jacob D Daniels
- Department of Pharmacology and Molecular Therapeutics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | | | - Marcelo Farina
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.,Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Presha Rajbhandari
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | | | | | - Thomas McDonald
- Waters Corporation, 34 Maple Street, Milford, MA, 01757, USA
| | - Michael E Stokes
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Brett L Hurst
- Institute for Antiviral Research, Utah State University, Logan, UT, 84322, USA
| | - Tomislav Rovis
- Department of Chemistry, Columbia University, New York, NY, 10027, USA.
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, 10032, USA.
| | - Brent R Stockwell
- Department of Chemistry, Columbia University, New York, NY, 10027, USA. .,Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.
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35
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Wang J, Hu Y, Zheng M. Enterovirus A71 antivirals: Past, present, and future. Acta Pharm Sin B 2022; 12:1542-1566. [PMID: 35847514 PMCID: PMC9279511 DOI: 10.1016/j.apsb.2021.08.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/28/2021] [Accepted: 08/12/2021] [Indexed: 02/07/2023] Open
Abstract
Enterovirus A71 (EV-A71) is a significant human pathogen, especially in children. EV-A71 infection is one of the leading causes of hand, foot, and mouth diseases (HFMD), and can lead to neurological complications such as acute flaccid myelitis (AFM) in severe cases. Although three EV-A71 vaccines are available in China, they are not broadly protective and have reduced efficacy against emerging strains. There is currently no approved antiviral for EV-A71. Significant progress has been made in developing antivirals against EV-A71 by targeting both viral proteins and host factors. However, viral capsid inhibitors and protease inhibitors failed in clinical trials of human rhinovirus infection due to limited efficacy or side effects. This review discusses major discoveries in EV-A71 antiviral development, analyzes the advantages and limitations of each drug target, and highlights the knowledge gaps that need to be addressed to advance the field forward.
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Affiliation(s)
- Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy, the University of Arizona, Tucson, AZ 85721, USA
| | - Yanmei Hu
- Department of Pharmacology and Toxicology, College of Pharmacy, the University of Arizona, Tucson, AZ 85721, USA
| | - Madeleine Zheng
- Department of Pharmacology and Toxicology, College of Pharmacy, the University of Arizona, Tucson, AZ 85721, USA
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36
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Wang J. Editorial of Special Column on Antiviral Drug Discovery and Pharmacology. Acta Pharm Sin B 2022; 12:1540-1541. [PMID: 35474901 PMCID: PMC9023784 DOI: 10.1016/j.apsb.2022.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
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37
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Wu Q, Yan S, Wang Y, Li M, Xiao Y, Li Y. Discovery of 4'-O-methylscutellarein as a potent SARS-CoV-2 main protease inhibitor. Biochem Biophys Res Commun 2022; 604:76-82. [PMID: 35303682 PMCID: PMC8907111 DOI: 10.1016/j.bbrc.2022.03.052] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/05/2022] [Accepted: 03/09/2022] [Indexed: 12/25/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in millions of deaths and seriously threatened public health and safety. Despite COVID-19 vaccines being readily popularized worldwide, targeted therapeutic agents for the treatment of this disease remain very limited. Here, we studied the inhibitory activity of the scutellarein and its methylated derivatives against SARS-CoV-2 main protease (Mpro) by the fluorescence resonance energy transfer (FRET) assay. Among all the methylated derivatives we studied, 4'-O-methylscutellarein exhibited the most promising enzyme inhibitory activity in vitro, with the half-maximal inhibitory concentration value (IC50) of 0.40 ± 0.03 μM. Additionally, the mechanism of action of the hits was further characterized through enzyme kinetic studies and molecular docking. Overall, our results implied that 4'-O-methylscutellarein could be a primary lead compound with clinical potential for the development of inhibitors against the SARS-CoV-2 Mpro.
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Affiliation(s)
- Qianqian Wu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Shiqiang Yan
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Yujie Wang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Maotian Li
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Yibei Xiao
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Yingxia Li
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China.
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38
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Kitamura N, Sacco MD, Ma C, Hu Y, Townsend JA, Meng X, Zhang F, Zhang X, Ba M, Szeto T, Kukuljac A, Marty MT, Schultz D, Cherry S, Xiang Y, Chen Y, Wang J. Expedited Approach toward the Rational Design of Noncovalent SARS-CoV-2 Main Protease Inhibitors. J Med Chem 2022; 65:2848-2865. [PMID: 33891389 PMCID: PMC8536799 DOI: 10.1021/acs.jmedchem.1c00509] [Citation(s) in RCA: 92] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The main protease (Mpro) of SARS-CoV-2 is a validated antiviral drug target. Several Mpro inhibitors have been reported with potent enzymatic inhibition and cellular antiviral activity, including GC376, boceprevir, calpain inhibitors II, and XII, with each containing a reactive warhead that covalently modifies the catalytic Cys145. Coupling structure-based drug design with the one-pot Ugi four-component reaction, we discovered one of the most potent noncovalent inhibitors, 23R (Jun8-76-3A) that is structurally distinct from the canonical Mpro inhibitor GC376. Significantly, 23R is highly selective compared with covalent inhibitors such as GC376, especially toward host proteases. The cocrystal structure of SARS-CoV-2 Mpro with 23R revealed a previously unexplored binding site located in between the S2 and S4 pockets. Overall, this study discovered 23R, one of the most potent and selective noncovalent SARS-CoV-2 Mpro inhibitors reported to date, and a novel binding pocket in Mpro that can be explored for inhibitor design.
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Affiliation(s)
- Naoya Kitamura
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Michael Dominic Sacco
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Chunlong Ma
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Yanmei Hu
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Julia Alma Townsend
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, United States
| | - Xiangzhi Meng
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, United States
| | - Fushun Zhang
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, United States
| | - Xiujun Zhang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Mandy Ba
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Tommy Szeto
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Adis Kukuljac
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Michael Thomas Marty
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, United States
| | - David Schultz
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, United States
| | - Sara Cherry
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States
| | - Yan Xiang
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, 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 Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
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39
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Ashhurst A, Tang AH, Fajtová P, Yoon MC, Aggarwal A, Bedding MJ, Stoye A, Beretta L, Pwee D, Drelich A, Skinner D, Li L, Meek TD, McKerrow JH, Hook V, Tseng CT, Larance M, Turville S, Gerwick WH, O’Donoghue AJ, Payne RJ. Potent Anti-SARS-CoV-2 Activity by the Natural Product Gallinamide A and Analogues via Inhibition of Cathepsin L. J Med Chem 2022; 65:2956-2970. [PMID: 34730959 PMCID: PMC8577376 DOI: 10.1021/acs.jmedchem.1c01494] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Indexed: 12/15/2022]
Abstract
Cathepsin L is a key host cysteine protease utilized by coronaviruses for cell entry and is a promising drug target for novel antivirals against SARS-CoV-2. The marine natural product gallinamide A and several synthetic analogues were identified as potent inhibitors of cathepsin L with IC50 values in the picomolar range. Lead molecules possessed selectivity over other cathepsins and alternative host proteases involved in viral entry. Gallinamide A directly interacted with cathepsin L in cells and, together with two lead analogues, potently inhibited SARS-CoV-2 infection in vitro, with EC50 values in the nanomolar range. Reduced antiviral activity was observed in cells overexpressing transmembrane protease, serine 2 (TMPRSS2); however, a synergistic improvement in antiviral activity was achieved when combined with a TMPRSS2 inhibitor. These data highlight the potential of cathepsin L as a COVID-19 drug target as well as the likely need to inhibit multiple routes of viral entry to achieve efficacy.
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Affiliation(s)
- Anneliese
S. Ashhurst
- School
of Chemistry, The University of Sydney, Sydney, NSW2006, Australia
- School
of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW2006, Australia
| | - Arthur H. Tang
- School
of Chemistry, The University of Sydney, Sydney, NSW2006, Australia
| | - Pavla Fajtová
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California92093, United States
- Institute
of Organic Chemistry and Biochemistry, Academy
of Sciences of the Czech Republic, 16610Prague, Czech Republic
| | - Michael C. Yoon
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California92093, United States
| | - Anupriya Aggarwal
- Kirby
Institute, University of New South Wales, Sydney, NSW2052, Australia
| | - Max J. Bedding
- School
of Chemistry, The University of Sydney, Sydney, NSW2006, Australia
| | - Alexander Stoye
- School
of Chemistry, The University of Sydney, Sydney, NSW2006, Australia
| | - Laura Beretta
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California92093, United States
| | - Dustin Pwee
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California92093, United States
| | - Aleksandra Drelich
- Department
of Microbiology and Immunology, University
of Texas, Medical Branch, 3000 University Boulevard, Galveston, Texas77755-1001, United States
| | - Danielle Skinner
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California92093, United States
| | - Linfeng Li
- Department
of Biochemistry and Biophysics, Texas A&M
University, 301 Old Main
Drive, College Station, Texas77843, United States
| | - Thomas D. Meek
- Department
of Biochemistry and Biophysics, Texas A&M
University, 301 Old Main
Drive, College Station, Texas77843, United States
| | - James H. McKerrow
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California92093, United States
| | - Vivian Hook
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California92093, United States
| | - Chien-Te Tseng
- Department
of Microbiology and Immunology, University
of Texas, Medical Branch, 3000 University Boulevard, Galveston, Texas77755-1001, United States
| | - Mark Larance
- Charles
Perkins Centre and School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW2006, Australia
| | - Stuart Turville
- Kirby
Institute, University of New South Wales, Sydney, NSW2052, Australia
| | - William H. Gerwick
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California92093, United States
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California92093, United States
| | - Anthony J. O’Donoghue
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California92093, United States
| | - Richard J. Payne
- School
of Chemistry, The University of Sydney, Sydney, NSW2006, Australia
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, The University of Sydney, Sydney, NSW2006, Australia
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40
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Jin Z, Mantri Y, Retout M, Cheng Y, Zhou J, Jorns A, Fajtova P, Yim W, Moore C, Xu M, Creyer MN, Borum RM, Zhou J, Wu Z, He T, Penny WF, O’Donoghue A, Jokerst JV. A Charge-Switchable Zwitterionic Peptide for Rapid Detection of SARS-CoV-2 Main Protease. Angew Chem Int Ed Engl 2022; 61:e202112995. [PMID: 34936725 PMCID: PMC8854333 DOI: 10.1002/anie.202112995] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Indexed: 11/06/2022]
Abstract
The transmission of SARS-CoV-2 coronavirus has led to the COVID-19 pandemic. Nucleic acid testing while specific has limitations for mass surveillance. One alternative is the main protease (Mpro ) due to its functional importance in mediating the viral life cycle. Here, we describe a combination of modular substrate and gold colloids to detect Mpro via visual readout. The strategy involves zwitterionic peptide that carries opposite charges at the C-/N-terminus to exploit the specific recognition by Mpro . Autolytic cleavage releases a positively charged moiety that assembles the nanoparticles with rapid color changes (t<10 min). We determine a limit of detection for Mpro in breath condensate matrices <10 nM. We further assayed ten COVID-negative subjects and found no false-positive result. In the light of simplicity, our test for viral protease is not limited to an equipped laboratory, but also is amenable to integrating as portable point-of-care devices including those on face-coverings.
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Affiliation(s)
- Zhicheng Jin
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Yash Mantri
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Maurice Retout
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Yong Cheng
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Jiajing Zhou
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Alec Jorns
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Pavla Fajtova
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Wonjun Yim
- Materials Science and Engineering Program, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Colman Moore
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Ming Xu
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Matthew N. Creyer
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Raina M. Borum
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Jingcheng Zhou
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Zhuohong Wu
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Tengyu He
- Materials Science and Engineering Program, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - William F. Penny
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Anthony O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Jesse V. Jokerst
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Materials Science and Engineering Program, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
- Department of Radiology, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
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41
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Cheng Y, Borum RM, Clark AE, Jin Z, Moore C, Fajtová P, O'Donoghue AJ, Carlin AF, Jokerst JV. A Dual-Color Fluorescent Probe Allows Simultaneous Imaging of Main and Papain-like Proteases of SARS-CoV-2-Infected Cells for Accurate Detection and Rapid Inhibitor Screening. Angew Chem Int Ed Engl 2022; 61:e202113617. [PMID: 34889013 PMCID: PMC8854376 DOI: 10.1002/anie.202113617] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Indexed: 11/15/2022]
Abstract
The main protease (Mpro ) and papain-like protease (PLpro ) play critical roles in SARS-CoV-2 replication and are promising targets for antiviral inhibitors. The simultaneous visualization of Mpro and PLpro is extremely valuable for SARS-CoV-2 detection and rapid inhibitor screening. However, such a crucial investigation has remained challenging because of the lack of suitable probes. We have now developed a dual-color probe (3MBP5) for the simultaneous detection of Mpro and PLpro by fluorescence (or Förster) resonance energy transfer (FRET). This probe produces fluorescence from both the Cy3 and Cy5 fluorophores that are cleaved by Mpro and PLpro . 3MBP5-activatable specificity was demonstrated with recombinant proteins, inhibitors, plasmid-transfected HEK 293T cells, and SARS-CoV-2-infected TMPRSS2-Vero cells. Results from the dual-color probe first verified the simultaneous detection and intracellular distribution of SARS-CoV-2 Mpro and PLpro . This is a powerful tool for the simultaneous detection of different proteases with value for the rapid screening of inhibitors.
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Affiliation(s)
- Yong Cheng
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
| | - Raina M. Borum
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
| | - Alex E. Clark
- Department of MedicineUniversity of California, San DiegoLa JollaCA 92093USA
| | - Zhicheng Jin
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
| | - Colman Moore
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San DiegoLa JollaCA 92093USA
| | - Anthony J. O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San DiegoLa JollaCA 92093USA
| | - Aaron F. Carlin
- Department of MedicineUniversity of California, San DiegoLa JollaCA 92093USA
| | - Jesse V. Jokerst
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
- Materials Science and Engineering ProgramUniversity of California, San DiegoLa JollaCA 92093USA
- Department of RadiologyUniversity of California, San DiegoLa JollaCA 92093USA
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42
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Lv Z, Cano KE, Jia L, Drag M, Huang TT, Olsen SK. Targeting SARS-CoV-2 Proteases for COVID-19 Antiviral Development. Front Chem 2022; 9:819165. [PMID: 35186898 PMCID: PMC8850931 DOI: 10.3389/fchem.2021.819165] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 12/20/2021] [Indexed: 12/18/2022] Open
Abstract
The emergence of severe acute respiratory syndrome (SARS-CoV-2) in 2019 marked the third occurrence of a highly pathogenic coronavirus in the human population since 2003. As the death toll surpasses 5 million globally and economic losses continue, designing drugs that could curtail infection and disease progression is critical. In the US, three highly effective Food and Drug Administration (FDA)-authorized vaccines are currently available, and Remdesivir is approved for the treatment of hospitalized patients. However, moderate vaccination rates and the sustained evolution of new viral variants necessitate the ongoing search for new antivirals. Several viral proteins have been prioritized as SARS-CoV-2 antiviral drug targets, among them the papain-like protease (PLpro) and the main protease (Mpro). Inhibition of these proteases would target viral replication, viral maturation, and suppression of host innate immune responses. Knowledge of inhibitors and assays for viruses were quickly adopted for SARS-CoV-2 protease research. Potential candidates have been identified to show inhibitory effects against PLpro and Mpro, both in biochemical assays and viral replication in cells. These results encourage further optimizations to improve prophylactic and therapeutic efficacy. In this review, we examine the latest developments of potential small-molecule inhibitors and peptide inhibitors for PLpro and Mpro, and how structural biology greatly facilitates this process.
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Affiliation(s)
- Zongyang Lv
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Kristin E. Cano
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Lijia Jia
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Tony T. Huang
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, United States
| | - Shaun K. Olsen
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
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43
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Cryptococcal Protease(s) and the Activation of SARS-CoV-2 Spike (S) Protein. Cells 2022; 11:cells11030437. [PMID: 35159253 PMCID: PMC8834071 DOI: 10.3390/cells11030437] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/22/2022] [Accepted: 01/26/2022] [Indexed: 12/04/2022] Open
Abstract
In this contribution, we report on the possibility that cryptococcal protease(s) could activate the SARS-CoV-2 spike (S) protein. The S protein is documented to have a unique four-amino-acid sequence (underlined, SPRRAR↓S) at the interface between the S1 and S2 sites, that serves as a cleavage site for the human protease, furin. We compared the biochemical efficiency of cryptococcal protease(s) and furin to mediate the proteolytic cleavage of the S1/S2 site in a fluorogenic peptide. We show that cryptococcal protease(s) processes this site in a manner comparable to the efficiency of furin (p > 0.581). We conclude the paper by discussing the impact of these findings in the context of a SARS-CoV-2 disease manifesting while there is an underlying cryptococcal infection.
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44
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Cheng Y, Borum RM, Clark AE, Jin Z, Moore C, Fajtová P, O'Donoghue AJ, Carlin AF, Jokerst JV. A Dual‐Color Fluorescent Probe Allows Simultaneous Imaging of Main and Papain‐like Proteases of SARS‐CoV‐2‐Infected Cells for Accurate Detection and Rapid Inhibitor Screening. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113617] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yong Cheng
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
| | - Raina M. Borum
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
| | - Alex E. Clark
- Department of Medicine University of California, San Diego La Jolla CA 92093 USA
| | - Zhicheng Jin
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
| | - Colman Moore
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical Sciences University of California, San Diego La Jolla CA 92093 USA
| | - Anthony J. O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences University of California, San Diego La Jolla CA 92093 USA
| | - Aaron F. Carlin
- Department of Medicine University of California, San Diego La Jolla CA 92093 USA
| | - Jesse V. Jokerst
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
- Materials Science and Engineering Program University of California, San Diego La Jolla CA 92093 USA
- Department of Radiology University of California, San Diego La Jolla CA 92093 USA
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Jin Z, Mantri Y, Retout M, Cheng Y, Zhou J, Jorns A, Fajtova P, Yim W, Moore C, Xu M, Creyer MN, Borum RM, Zhou J, Wu Z, He T, Penny WF, O'Donoghue AJ, Jokerst JV. A Charge‐Switchable Zwitterionic Peptide for Rapid Detection of SARS‐CoV‐2 Main Protease. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Zhicheng Jin
- Department of NanoEngineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Yash Mantri
- Department of Bioengineering University of California San Diego 9500 Gilman Drive La Jolla California 92093 USA
| | - Maurice Retout
- Department of NanoEngineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Yong Cheng
- Department of NanoEngineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Jiajing Zhou
- Department of NanoEngineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Alec Jorns
- Department of NanoEngineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Pavla Fajtova
- Skaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego 9500 Gilman Drive La Jolla California 92093 USA
| | - Wonjun Yim
- Materials Science and Engineering Program University of California San Diego 9500 Gilman Drive La Jolla California 92093 USA
| | - Colman Moore
- Department of NanoEngineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Ming Xu
- Department of NanoEngineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Matthew N. Creyer
- Department of NanoEngineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Raina M. Borum
- Department of NanoEngineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Jingcheng Zhou
- Department of NanoEngineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Zhuohong Wu
- Department of NanoEngineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Tengyu He
- Materials Science and Engineering Program University of California San Diego 9500 Gilman Drive La Jolla California 92093 USA
| | - William F. Penny
- Department of Medicine University of California San Diego 9500 Gilman Drive La Jolla California 92093 USA
| | - Anthony J. O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego 9500 Gilman Drive La Jolla California 92093 USA
| | - Jesse V. Jokerst
- Department of NanoEngineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
- Materials Science and Engineering Program University of California San Diego 9500 Gilman Drive La Jolla California 92093 USA
- Department of Radiology University of California San Diego 9500 Gilman Drive La Jolla California 92093 USA
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Asiimwe N, Lee J, Hong K, murale D, Haque MM, Kim DH, Lee JS. Temporal control of protein labeling by photo-caged benzaldehyde motif and discovery of host cell factors of avian influenza virus infection. Chem Commun (Camb) 2022; 58:9345-9348. [DOI: 10.1039/d2cc04091c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photo-caged benzaldehyde probes using o-nitrophenylethylene glycol were designed for photo-activated electrophile generation. Unlike radical reaction that produce uncontrolled multiple reaction paths resulting low yield of crosslinking, reaction of electrophile has...
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Bhowmick S, Saha A, AlFaris NA, ALTamimi JZ, ALOthman ZA, Aldayel TS, Wabaidur SM, Islam MA. Identification of potent food constituents as SARS-CoV-2 papain-like protease modulators through advanced pharmacoinformatics approaches. J Mol Graph Model 2021; 111:108113. [PMID: 34959151 PMCID: PMC8688376 DOI: 10.1016/j.jmgm.2021.108113] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/05/2021] [Accepted: 12/18/2021] [Indexed: 12/15/2022]
Abstract
The current ongoing pandemic of COVID-19 urges immediate treatment measures for controlling the highly contagious SARS-CoV-2 infections. The papain-like protease (PLpro), which is released from nsp3, is presently being evaluated as a significant anti-viral drug target for COVID-19 therapy development. Particularly, PLpro is implicated in the cleavage of viral polyproteins and antagonizes the host innate immune response through its deubiquitinating and deISGylating actions, thus making it a high-profile antiviral therapeutic target. The present study reports a few specific food compounds that can bind tightly with the SARS-CoV-2 PLpro protein identified through extensive computational screening techniques. Precisely, extensive advanced computational approaches combining target-based virtual screening, particularly employing sub-structure based similarity search, molecular docking, molecular dynamics (MD) simulations, and MM-GBSA based binding free energy calculations have been employed for the identification of the most promising food compounds with substantial functional implications as SARS-CoV-2 PLpro protein inhibitors/modulators. Observations from the present research investigation also provide a deeper understanding of the binding modes of the proposed four food compounds with SARS-CoV-2 PLpro protein. In docking analyses, all compounds have established essential inter-molecular interaction profiles at the active site cavity of the SARS-CoV-2 PLpro protein. Similarly, the long-range 100 ns conventional MD simulation studies also provided an in-depth understanding of probable interactions and dynamic behaviour of the SARS-CoV-2 PLpro protein-food compound complexes. Binding free energies of all molecular systems revealed a strong interaction affinity of food compounds towards the SARS-CoV-2 PLpro protein. Moreover, clear-cut comparative analyses against the known standard inhibitor also suggest that proposed food compounds may act as potential active chemical entities for modulating the action of the SARS-CoV-2 PLpro protein.
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Affiliation(s)
- Shovonlal Bhowmick
- Department of Chemical Technology, University of Calcutta, 92, A.P.C. Road, Kolkata, 700009, India
| | - Achintya Saha
- Department of Chemical Technology, University of Calcutta, 92, A.P.C. Road, Kolkata, 700009, India.
| | - Nora Abdullah AlFaris
- Nutrition and Food Science, Department of Physical Sport Science, Princess Nourah bint Abdulrahman University, P. O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Jozaa Zaidan ALTamimi
- Nutrition and Food Science, Department of Physical Sport Science, Princess Nourah bint Abdulrahman University, P. O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Zeid A ALOthman
- Department of Chemistry, P.O. Box 2455, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Tahany Saleh Aldayel
- Nutrition and Food Science, Department of Physical Sport Science, Princess Nourah bint Abdulrahman University, P. O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Saikh Mohammad Wabaidur
- Department of Chemistry, P.O. Box 2455, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Md Ataul Islam
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom.
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Ma C, Xia Z, Sacco MD, Hu Y, Townsend JA, Meng X, Choza J, Tan H, Jang J, Gongora MV, Zhang X, Zhang F, Xiang Y, Marty MT, Chen Y, Wang J. Discovery of Di- and Trihaloacetamides as Covalent SARS-CoV-2 Main Protease Inhibitors with High Target Specificity. J Am Chem Soc 2021; 143:20697-20709. [PMID: 34860011 PMCID: PMC8672434 DOI: 10.1021/jacs.1c08060] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Indexed: 12/17/2022]
Abstract
The main protease (Mpro) is a validated antiviral drug target of SARS-CoV-2. A number of Mpro inhibitors have now advanced to animal model study and human clinical trials. However, one issue yet to be addressed is the target selectivity over host proteases such as cathepsin L. In this study we describe the rational design of covalent SARS-CoV-2 Mpro inhibitors with novel cysteine reactive warheads including dichloroacetamide, dibromoacetamide, tribromoacetamide, 2-bromo-2,2-dichloroacetamide, and 2-chloro-2,2-dibromoacetamide. The promising lead candidates Jun9-62-2R (dichloroacetamide) and Jun9-88-6R (tribromoacetamide) had not only potent enzymatic inhibition and antiviral activity but also significantly improved target specificity over caplain and cathepsins. Compared to GC-376, these new compounds did not inhibit the host cysteine proteases including calpain I, cathepsin B, cathepsin K, cathepsin L, and caspase-3. To the best of our knowledge, they are among the most selective covalent Mpro inhibitors reported thus far. The cocrystal structures of SARS-CoV-2 Mpro with Jun9-62-2R and Jun9-57-3R reaffirmed our design hypothesis, showing that both compounds form a covalent adduct with the catalytic C145. Overall, these novel compounds represent valuable chemical probes for target validation and drug candidates for further development as SARS-CoV-2 antivirals.
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Affiliation(s)
- Chunlong Ma
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Zilei Xia
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Michael Dominic Sacco
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Yanmei Hu
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Julia Alma Townsend
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, United States
| | - Xiangzhi Meng
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, United States
| | - Juliana Choza
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Haozhou Tan
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Janice Jang
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
| | - Maura V Gongora
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Xiujun Zhang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Fushun Zhang
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, United States
| | - Yan Xiang
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, United States
| | - Michael Thomas Marty
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, 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 Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, United States
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Abstract
The development of effective antiviral therapy for COVID-19 is critical for those awaiting vaccination, as well as for those who do not respond robustly to vaccination. This review summarizes 1 year of progress in the race to develop antiviral therapies for COVID-19, including research spanning preclinical and clinical drug development efforts, with an emphasis on antiviral compounds that are in clinical development or that are high priorities for clinical development. The review is divided into sections on compounds that inhibit SARS-CoV-2 enzymes, including its polymerase and proteases; compounds that inhibit virus entry, including monoclonal antibodies; interferons; and repurposed drugs that inhibit host processes required for SARS-CoV-2 replication. The review concludes with a summary of the lessons to be learned from SARS-CoV-2 drug development efforts and the challenges to continued progress.
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Affiliation(s)
- Kaiming Tao
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
| | - Philip L. Tzou
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
| | - Janin Nouhin
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
| | - Hector Bonilla
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
| | - Prasanna Jagannathan
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
| | - Robert W. Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
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50
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Design, synthesis and in vitro evaluation of novel SARS-CoV-2 3CL pro covalent inhibitors. Eur J Med Chem 2021; 229:114046. [PMID: 34995923 PMCID: PMC8665847 DOI: 10.1016/j.ejmech.2021.114046] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/17/2021] [Accepted: 12/01/2021] [Indexed: 12/20/2022]
Abstract
Severe diseases such as the ongoing COVID-19 pandemic, as well as the previous SARS and MERS outbreaks, are the result of coronavirus infections and have demonstrated the urgent need for antiviral drugs to combat these deadly viruses. Due to its essential role in viral replication and function, 3CLpro (main coronaviruses cysteine-protease) has been identified as a promising target for the development of antiviral drugs. Previously reported SARS-CoV 3CLpro non-covalent inhibitors were used as a starting point for the development of covalent inhibitors of SARS-CoV-2 3CLpro. We report herein our efforts in the design and synthesis of submicromolar covalent inhibitors when the enzymatic activity of the viral protease was used as a screening platform.
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