1
|
Philippsen GS, Seixas FAV. In silico identification of D449-0032 compound as a putative SARS-CoV-2 M pro inhibitor. J Biomol Struct Dyn 2024; 42:6440-6447. [PMID: 37424215 DOI: 10.1080/07391102.2023.2234045] [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: 01/10/2023] [Accepted: 07/03/2023] [Indexed: 07/11/2023]
Abstract
The SARS-CoV-2 pandemic originated the urgency in developing therapeutic resources for the treatment of COVID-19. Despite the current availability of vaccines and some antivirals, the occurence of severe cases of the disease and the risk of the emergence of new virus variants still motivate research in this field. In this context, this study aimed at the computational prospection of likely inhibitors of the main protease (Mpro) of SARS-CoV-2 since inhibiting this enzyme leads to disruption of the viral replication process. The virtual screening of the antiviral libraries Asinex, ChemDiv, and Enamine targeting SARS-CoV-2 Mpro was performed, indicating the D449-0032 compound as a promising inhibitor. Molecular dynamics simulations showed the stability of the protein-ligand complex and in silico predictions of toxicity and pharmacokinetic parameters indicated the probable drug-like behavior of the compound. In vitro and in vivo studies are essential to confirm the Mpro inhibition by the D449-0032.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
| | - Flavio Augusto Vicente Seixas
- Laboratory of Structural Biochemistry, Departamento de Tecnologia, Universidade Estadual de Maringá, Umuarama, Brazil
| |
Collapse
|
2
|
Dampalla CS, Kim Y, Zabiegala A, Howard DJ, Nguyen HN, Madden TK, Thurman HA, Cooper A, Liu L, Battaile KP, Lovell S, Chang KO, Groutas WC. Structure-Guided Design of Potent Coronavirus Inhibitors with a 2-Pyrrolidone Scaffold: Biochemical, Crystallographic, and Virological Studies. J Med Chem 2024. [PMID: 38953866 DOI: 10.1021/acs.jmedchem.4c00551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Zoonotic coronaviruses are known to produce severe infections in humans and have been the cause of significant morbidity and mortality worldwide. SARS-CoV-2 was the largest and latest contributor of fatal cases, even though MERS-CoV has the highest case-fatality ratio among zoonotic coronaviruses. These infections pose a high risk to public health worldwide warranting efforts for the expeditious discovery of antivirals. Hence, we hereby describe a novel series of inhibitors of coronavirus 3CLpro embodying an N-substituted 2-pyrrolidone scaffold envisaged to exploit favorable interactions with the S3-S4 subsites and connected to an invariant Leu-Gln P2-P1 recognition element. Several inhibitors showed nanomolar antiviral activity in enzyme and cell-based assays, with no significant cytotoxicity. High-resolution crystal structures of inhibitors bound to the 3CLpro were determined to probe and identify the molecular determinants associated with binding, to inform the structure-guided optimization of the inhibitors, and to confirm the mechanism of action of the inhibitors.
Collapse
Affiliation(s)
- Chamandi S Dampalla
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, United States
| | - Alexandria Zabiegala
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, United States
| | - Dennis J Howard
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Harry Nhat Nguyen
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Trent K Madden
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Hayden A Thurman
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Anne Cooper
- Protein Structure and X-ray Crystallography Laboratory, The University of Kansas, Lawrence, Kansas 66047, United States
| | - Lijun Liu
- Protein Structure and X-ray Crystallography Laboratory, The University of Kansas, Lawrence, Kansas 66047, United States
| | - Kevin P Battaile
- NYX, New York Structural Biology Center, Upton, New York 11973, United States
| | - Scott Lovell
- Protein Structure and X-ray Crystallography Laboratory, The University of Kansas, Lawrence, Kansas 66047, United States
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, United States
| | - William C Groutas
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
| |
Collapse
|
3
|
Krismer L, Schöppe H, Rauch S, Bante D, Sprenger B, Naschberger A, Costacurta F, Fürst A, Sauerwein A, Rupp B, Kaserer T, von Laer D, Heilmann E. Study of key residues in MERS-CoV and SARS-CoV-2 main proteases for resistance against clinically applied inhibitors nirmatrelvir and ensitrelvir. NPJ VIRUSES 2024; 2:23. [PMID: 38933182 PMCID: PMC11196219 DOI: 10.1038/s44298-024-00028-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 03/14/2024] [Indexed: 06/28/2024]
Abstract
The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is an epidemic, zoonotically emerging pathogen initially reported in Saudi Arabia in 2012. MERS-CoV has the potential to mutate or recombine with other coronaviruses, thus acquiring the ability to efficiently spread among humans and become pandemic. Its high mortality rate of up to 35% and the absence of effective targeted therapies call for the development of antiviral drugs for this pathogen. Since the beginning of the SARS-CoV-2 pandemic, extensive research has focused on identifying protease inhibitors for the treatment of SARS-CoV-2. Our intention was therefore to assess whether these protease inhibitors are viable options for combating MERS-CoV. To that end, we used previously established protease assays to quantify inhibition of SARS-CoV-2, MERS-CoV and other main proteases. Nirmatrelvir inhibited several of these proteases, whereas ensitrelvir was less broadly active. To simulate nirmatrelvir's clinical use against MERS-CoV and subsequent resistance development, we applied a safe, surrogate virus-based system. Using the surrogate virus, we previously selected hallmark mutations of SARS-CoV-2-Mpro, such as T21I, M49L, S144A, E166A/K/V and L167F. In the current study, we selected a pool of MERS-CoV-Mpro mutants, characterized the resistance and modelled the steric effect of catalytic site mutants S142G, S142R, S147Y and A171S.
Collapse
Affiliation(s)
- Laura Krismer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020 Austria
| | - Helge Schöppe
- Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, 6020 Austria
| | - Stefanie Rauch
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020 Austria
| | - David Bante
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020 Austria
| | - Bernhard Sprenger
- Institute of Biochemistry, University of Innsbruck, CMBI – Center for Molecular Biosciences Innsbruck, Innsbruck, 6020 Austria
| | - Andreas Naschberger
- Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology KAUST, Thuwal, Saudi Arabia
| | | | - Anna Fürst
- Institute of Molecular Immunology, Technical University of Munich, Munich, 81675 Germany
| | - Anna Sauerwein
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020 Austria
| | - Bernhard Rupp
- Division of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, 6020 Austria
| | - Teresa Kaserer
- Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, 6020 Austria
| | - Dorothee von Laer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020 Austria
| | - Emmanuel Heilmann
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020 Austria
| |
Collapse
|
4
|
Amorim VMDF, Soares EP, Ferrari ASDA, Merighi DGS, de Souza RF, Guzzo CR, de Souza AS. 3-Chymotrypsin-like Protease (3CLpro) of SARS-CoV-2: Validation as a Molecular Target, Proposal of a Novel Catalytic Mechanism, and Inhibitors in Preclinical and Clinical Trials. Viruses 2024; 16:844. [PMID: 38932137 PMCID: PMC11209289 DOI: 10.3390/v16060844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 05/21/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
Proteases represent common targets in combating infectious diseases, including COVID-19. The 3-chymotrypsin-like protease (3CLpro) is a validated molecular target for COVID-19, and it is key for developing potent and selective inhibitors for inhibiting viral replication of SARS-CoV-2. In this review, we discuss structural relationships and diverse subsites of 3CLpro, shedding light on the pivotal role of dimerization and active site architecture in substrate recognition and catalysis. Our analysis of bioinformatics and other published studies motivated us to investigate a novel catalytic mechanism for the SARS-CoV-2 polyprotein cleavage by 3CLpro, centering on the triad mechanism involving His41-Cys145-Asp187 and its indispensable role in viral replication. Our hypothesis is that Asp187 may participate in modulating the pKa of the His41, in which catalytic histidine may act as an acid and/or a base in the catalytic mechanism. Recognizing Asp187 as a crucial component in the catalytic process underscores its significance as a fundamental pharmacophoric element in drug design. Next, we provide an overview of both covalent and non-covalent inhibitors, elucidating advancements in drug development observed in preclinical and clinical trials. By highlighting various chemical classes and their pharmacokinetic profiles, our review aims to guide future research directions toward the development of highly selective inhibitors, underscore the significance of 3CLpro as a validated therapeutic target, and propel the progression of drug candidates through preclinical and clinical phases.
Collapse
Affiliation(s)
| | | | | | | | | | - Cristiane Rodrigues Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 5508-900, Brazil; (V.M.d.F.A.); (E.P.S.); (A.S.d.A.F.); (D.G.S.M.); (R.F.d.S.)
| | - Anacleto Silva de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 5508-900, Brazil; (V.M.d.F.A.); (E.P.S.); (A.S.d.A.F.); (D.G.S.M.); (R.F.d.S.)
| |
Collapse
|
5
|
Mesaros EF, Dugan BJ, Gao M, Sheraz M, McGovern-Gooch K, Xu F, Fan KY, Nguyen D, Kultgen SG, Lindstrom A, Stever K, Tercero B, Binder RJ, Liu F, Micolochick Steuer HM, Mani N, Harasym TO, Thi EP, Cuconati A, Dorsey BD, Cole AG, Lam AM, Sofia MJ. Discovery of C-Linked Nucleoside Analogues with Antiviral Activity against SARS-CoV-2. ACS Infect Dis 2024; 10:1780-1792. [PMID: 38651692 DOI: 10.1021/acsinfecdis.4c00122] [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] [Indexed: 04/25/2024]
Abstract
The recent COVID-19 pandemic underscored the limitations of currently available direct-acting antiviral treatments against acute respiratory RNA-viral infections and stimulated major research initiatives targeting anticoronavirus agents. Two novel nsp5 protease (MPro) inhibitors have been approved, nirmatrelvir and ensitrelvir, along with two existing nucleos(t)ide analogues repurposed as nsp12 polymerase inhibitors, remdesivir and molnupiravir, but a need still exists for therapies with improved potency and systemic exposure with oral dosing, better metabolic stability, and reduced resistance and toxicity risks. Herein, we summarize our research toward identifying nsp12 inhibitors that led to nucleoside analogues 10e and 10n, which showed favorable pan-coronavirus activity in cell-infection screens, were metabolized to active triphosphate nucleotides in cell-incubation studies, and demonstrated target (nsp12) engagement in biochemical assays.
Collapse
Affiliation(s)
- Eugen F Mesaros
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Benjamin J Dugan
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Min Gao
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Muhammad Sheraz
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | | | - Fran Xu
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Kristi Yi Fan
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Duyan Nguyen
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Steven G Kultgen
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Aaron Lindstrom
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Kim Stever
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Breanna Tercero
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Randall J Binder
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Fei Liu
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | | | - Nagraj Mani
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Troy O Harasym
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Emily P Thi
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Andrea Cuconati
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Bruce D Dorsey
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Andrew G Cole
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Angela M Lam
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Michael J Sofia
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| |
Collapse
|
6
|
Pereira F, Bedda L, Tammam MA, Alabdullah AK, Arafa R, El-Demerdash A. Investigating the antiviral therapeutic potentialities of marine polycyclic lamellarin pyrrole alkaloids as promising inhibitors for SARS-CoV-2 and Zika main proteases (Mpro). J Biomol Struct Dyn 2024; 42:3983-4001. [PMID: 37232419 DOI: 10.1080/07391102.2023.2217513] [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: 01/04/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023]
Abstract
The new coronavirus variant (SARS-CoV-2) and Zika virus are two world-wide health pandemics. Along history, natural products-based drugs have always crucially recognized as a main source of valuable medications. Considering the SARS-CoV-2 and Zika main proteases (Mpro) as the re-production key element of the viral cycle and its main target, herein we report an intensive computer-aided virtual screening for a focused list of 39 marine lamellarins pyrrole alkaloids, against SARS-CoV-2 and Zika main proteases (Mpro) using a set of combined modern computational methodologies including molecular docking (MDock), molecule dynamic simulations (MDS) and structure-activity relationships (SARs) as well. Indeed, the molecular docking studies had revealed four promising marine alkaloids including [lamellarin H (14)/K (17)] and [lamellarin S (26)/Z (39)], according to their notable ligand-protein energy scores and relevant binding affinities with the SARS-CoV-2 and Zika (Mpro) pocket residues, respectively. Consequentially, these four chemical hits were further examined thermodynamically though investigating their MD simulations at 100 ns, where they showed prominent stability within the accommodated (Mpro) pockets. Moreover, in-deep SARs studies suggested the crucial roles of the rigid fused polycyclic ring system, particularly aromatic A- and F- rings, position of the phenolic -OH and δ-lactone functionalities as essential structural and pharmacophoric features. Finally, these four promising lamellarins alkaloids were investigated for their in-silico ADME using the SWISS ADME platform, where they displayed appropriated drug-likeness properties. Such motivating outcomes are greatly recommending further in vitro/vivo examinations regarding those lamellarins pyrrole alkaloids (LPAs).Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Florbela Pereira
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Loay Bedda
- Drug Design and Discovery Laboratory, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Mohamed A Tammam
- Department of Biochemistry, Faculty of Agriculture, Fayoum University, Fayoum, Egypt
| | | | - Reem Arafa
- Drug Design and Discovery Laboratory, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Amr El-Demerdash
- Division of Organic Chemistry, Department of Chemistry, Faculty of Sciences, Mansoura University, Mansoura, Egypt
- Department of Biochemistry and Metabolism, the John Innes Centre, Norwich Research Park, Norwich, UK
| |
Collapse
|
7
|
Humayun F, Khan F, Khan A, Alshammari A, Ji J, Farhan A, Fawad N, Alam W, Ali A, Wei DQ. De novo generation of dual-target ligands for the treatment of SARS-CoV-2 using deep learning, virtual screening, and molecular dynamic simulations. J Biomol Struct Dyn 2024; 42:3019-3029. [PMID: 37449757 DOI: 10.1080/07391102.2023.2234481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 04/30/2023] [Indexed: 07/18/2023]
Abstract
De novo generation of molecules with the necessary features offers a promising opportunity for artificial intelligence, such as deep generative approaches. However, creating novel compounds having biological activities toward two distinct targets continues to be a very challenging task. In this study, we develop a unique computational framework for the de novo synthesis of bioactive compounds directed at two predetermined therapeutic targets. This framework is referred to as the dual-target ligand generative network. Our approach uses a stochastic policy to explore chemical spaces called a sequence-based simple molecular input line entry system (SMILES) generator. The steps in the high-level workflow would be to gather and prepare the training data for both targets' molecules, build a neural network model and train it to make molecules, create new molecules using generative AI, and then virtually screen the newly validated molecules against the SARS-CoV-2 PLpro and 3CLpro drug targets. Results shows that novel molecules generated have higher binding affinity with both targets than the conventional drug i.e. Remdesivir being used for the treatment of SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Fahad Humayun
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Fatima Khan
- National Institute of Health, Islamabad, Pakistan
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Jun Ji
- Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, PR China
| | - Ali Farhan
- Department of Chemistry, Chung Yuan Christian University, Taoyuan, Taiwan
| | - Nasim Fawad
- Poultry Research Institute, Rawalpindi, Pakistan
| | - Waheed Alam
- National Institute of Health, Islamabad, Pakistan
| | - Arif Ali
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
- Centre for Research in Molecular Modeling, Concordia University, Québec, Canada
| |
Collapse
|
8
|
Sasikumar DSN, Thiruselvam P, Sundararajan V, Ravindran R, Gunasekaran S, Madathil D, Kaliamurthi S, Peslherbe GH, Selvaraj G, Sudhakaran SL. Insights into dietary phytochemicals targeting Parkinson's disease key genes and pathways: A network pharmacology approach. Comput Biol Med 2024; 172:108195. [PMID: 38460310 DOI: 10.1016/j.compbiomed.2024.108195] [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: 09/03/2023] [Revised: 01/26/2024] [Accepted: 02/18/2024] [Indexed: 03/11/2024]
Abstract
Parkinson's disease (PD) is a complex neurological disease associated with the degeneration of dopaminergic neurons. Oxidative stress is a key player in instigating apoptosis in dopaminergic neurons. To improve the survival of neurons many dietary phytochemicals have gathered significant attention recently. Thus, the present study implements a comprehensive network pharmacology approach to unravel the mechanisms of action of dietary phytochemicals that benefit disease management. A literature search was performed to identify ligands (i.e., comprising dietary phytochemicals and Food and Drug Administration pre-approved PD drugs) in the PubMed database. Targets associated with selected ligands were extracted from the search tool for interactions of chemicals (STITCH) database. Then, the construction of a gene-gene interaction (GGI) network, analysis of hub-gene, functional and pathway enrichment, associated transcription factors, miRNAs, ligand-target interaction network, docking were performed using various bioinformatics tools together with molecular dynamics (MD) simulations. The database search resulted in 69 ligands and 144 unique targets. GGI and subsequent topological measures indicate histone acetyltransferase p300 (EP300), mitogen-activated protein kinase 1 (MAPK1) or extracellular signal-regulated kinase (ERK)2, and CREB-binding protein (CREBBP) as hub genes. Neurodegeneration, MAPK signaling, apoptosis, and zinc binding are key pathways and gene ontology terms. hsa-miR-5692a and SCNA gene-associated transcription factors interact with all the 3 hub genes. Ligand-target interaction (LTI) network analysis suggest rasagiline and baicalein as candidate ligands targeting MAPK1. Rasagiline and baicalein form stable complexes with the Y205, K330, and V173 residues of MAPK1. Computational molecular insights suggest that baicalein and rasagiline are promising preclinical candidates for PD management.
Collapse
Affiliation(s)
- Devi Soorya Narayana Sasikumar
- Integrative Multiomics Lab, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, TN, 632014, India
| | - Premkumar Thiruselvam
- Integrative Multiomics Lab, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, TN, 632014, India
| | - Vino Sundararajan
- Integrative Multiomics Lab, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, TN, 632014, India
| | - Radhika Ravindran
- Department of Biotechnology, Indian Institute of Technology (Madras), Chennai, TN, 600036, India
| | - Shoba Gunasekaran
- Department of Biotechnology, Dwaraka Doss Goverdhan Doss Vaishnav College, Chennai, TN, 600106, India
| | - Deepa Madathil
- Jindal Institute of Behavioral Sciences, O.P Jindal Global University, Sonipat, Haryana, 131001, India
| | - Satyavani Kaliamurthi
- Centre for Research in Molecular Modeling (CERMM), Department of Chemistry and Biochemistry, Concordia University, Loyola Campus, Montreal, QC, H4B 1R6, Canada
| | - Gilles H Peslherbe
- Centre for Research in Molecular Modeling (CERMM), Department of Chemistry and Biochemistry, Concordia University, Loyola Campus, Montreal, QC, H4B 1R6, Canada
| | - Gurudeeban Selvaraj
- Centre for Research in Molecular Modeling (CERMM), Department of Chemistry and Biochemistry, Concordia University, Loyola Campus, Montreal, QC, H4B 1R6, Canada; Bioinformatics Unit, Department of Biomaterials, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS) University, Chennai, TN, 600077, India.
| | - Sajitha Lulu Sudhakaran
- Integrative Multiomics Lab, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, TN, 632014, India.
| |
Collapse
|
9
|
Nguyen TH, Thai QM, Pham MQ, Minh PTH, Phung HTT. Machine learning combines atomistic simulations to predict SARS-CoV-2 Mpro inhibitors from natural compounds. Mol Divers 2024; 28:553-561. [PMID: 36823394 PMCID: PMC9950021 DOI: 10.1007/s11030-023-10601-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/04/2023] [Indexed: 02/25/2023]
Abstract
To date, the COVID-19 pandemic has still been infectious around the world, continuously causing social and economic damage on a global scale. One of the most important therapeutic targets for the treatment of COVID-19 is the main protease (Mpro) of SARS-CoV-2. In this study, we combined machine-learning (ML) model with atomistic simulations to computationally search for highly promising SARS-CoV-2 Mpro inhibitors from the representative natural compounds of the National Cancer Institute (NCI) Database. First, the trained ML model was used to scan the library quickly and reliably for possible Mpro inhibitors. The ML output was then confirmed using atomistic simulations integrating molecular docking and molecular dynamic simulations with the linear interaction energy scheme. The results turned out to show that there was evidently good agreement between ML and atomistic simulations. Ten substances were proposed to be able to inhibit SARS-CoV-2 Mpro. Seven of them have high-nanomolar affinity and are very potential inhibitors. The strategy has been proven to be reliable and appropriate for fast prediction of SARS-CoV-2 Mpro inhibitors, benefiting for new emerging SARS-CoV-2 variants in the future accordingly.
Collapse
Affiliation(s)
- Trung Hai Nguyen
- Laboratory of Theoretical and Computational Biophysics, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Quynh Mai Thai
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Minh Quan Pham
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Pham Thi Hong Minh
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Juárez-Mercado KE, Gómez-Hernández MA, Salinas-Trujano J, Córdova-Bahena L, Espitia C, Pérez-Tapia SM, Medina-Franco JL, Velasco-Velázquez MA. Identification of SARS-CoV-2 Main Protease Inhibitors Using Chemical Similarity Analysis Combined with Machine Learning. Pharmaceuticals (Basel) 2024; 17:240. [PMID: 38399455 PMCID: PMC10892746 DOI: 10.3390/ph17020240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/05/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
SARS-CoV-2 Main Protease (Mpro) is an enzyme that cleaves viral polyproteins translated from the viral genome, which is critical for viral replication. Mpro is a target for anti-SARS-CoV-2 drug development. Herein, we performed a large-scale virtual screening by comparing multiple structural descriptors of reference molecules with reported anti-coronavirus activity against a library with >17 million compounds. Further filtering, performed by applying two machine learning algorithms, identified eighteen computational hits as anti-SARS-CoV-2 compounds with high structural diversity and drug-like properties. The activities of twelve compounds on Mpro's enzymatic activity were evaluated by fluorescence resonance energy transfer (FRET) assays. Compound 13 (ZINC13878776) significantly inhibited SARS-CoV-2 Mpro activity and was employed as a reference for an experimentally hit expansion. The structural analogues 13a (ZINC4248385), 13b (ZNC13523222), and 13c (ZINC4248365) were tested as Mpro inhibitors, reducing the enzymatic activity of recombinant Mpro with potency as follows: 13c > 13 > 13b > 13a. Then, their anti-SARS-CoV-2 activities were evaluated in plaque reduction assays using Vero CCL81 cells. Subtoxic concentrations of compounds 13a, 13c, and 13b displayed in vitro antiviral activity with IC50 in the mid micromolar range. Compounds 13a-c could become lead compounds for the development of new Mpro inhibitors with improved activity against anti-SARS-CoV-2.
Collapse
Affiliation(s)
| | - Milton Abraham Gómez-Hernández
- School of Medicine, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- Graduate Program in Biomedical Sciences, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Juana Salinas-Trujano
- Research and Development in Biotherapeutics Unit (UDIBI), National School of Biological Sciences, Instituto Politécnico Nacional, Mexico City 11350, Mexico
- National Laboratory for Specialized Services of Investigation, Development and Innovation (I+D+i) for Pharma Chemicals and Biotechnological Products, LANSEIDI-FarBiotech-CONACHyT, Mexico City 11350, Mexico
| | - Luis Córdova-Bahena
- School of Medicine, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- National Council of Humanities, Science and Technology (CONAHCYT), Mexico City 03940, Mexico
| | - Clara Espitia
- Immunology Department, Institute for Biomedical Research, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Sonia Mayra Pérez-Tapia
- Research and Development in Biotherapeutics Unit (UDIBI), National School of Biological Sciences, Instituto Politécnico Nacional, Mexico City 11350, Mexico
- National Laboratory for Specialized Services of Investigation, Development and Innovation (I+D+i) for Pharma Chemicals and Biotechnological Products, LANSEIDI-FarBiotech-CONACHyT, Mexico City 11350, Mexico
- Immunology Department, National School of Biological Sciences, Instituto Politécnico Nacional, Mexico City 11350, Mexico
| | - José L. Medina-Franco
- DIFACQUIM Research Group, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | | |
Collapse
|
12
|
Chan HTH, Brewitz L, Lukacik P, Strain-Damerell C, Walsh MA, Schofield CJ, Duarte F. Studies on the selectivity of the SARS-CoV-2 papain-like protease reveal the importance of the P2' proline of the viral polyprotein. RSC Chem Biol 2024; 5:117-130. [PMID: 38333195 PMCID: PMC10849127 DOI: 10.1039/d3cb00128h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/13/2023] [Indexed: 02/10/2024] Open
Abstract
The SARS-CoV-2 papain-like protease (PLpro) is an antiviral drug target that catalyzes the hydrolysis of the viral polyproteins pp1a/1ab, so releasing the non-structural proteins (nsps) 1-3 that are essential for the coronavirus lifecycle. The LXGG↓X motif in pp1a/1ab is crucial for recognition and cleavage by PLpro. We describe molecular dynamics, docking, and quantum mechanics/molecular mechanics (QM/MM) calculations to investigate how oligopeptide substrates derived from the viral polyprotein bind to PLpro. The results reveal how the substrate sequence affects the efficiency of PLpro-catalyzed hydrolysis. In particular, a proline at the P2' position promotes catalysis, as validated by residue substitutions and mass spectrometry-based analyses. Analysis of PLpro catalyzed hydrolysis of LXGG motif-containing oligopeptides derived from human proteins suggests that factors beyond the LXGG motif and the presence of a proline residue at P2' contribute to catalytic efficiency, possibly reflecting the promiscuity of PLpro. The results will help in identifying PLpro substrates and guiding inhibitor design.
Collapse
Affiliation(s)
- H T Henry Chan
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Petra Lukacik
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Claire Strain-Damerell
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Martin A Walsh
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Fernanda Duarte
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| |
Collapse
|
13
|
Allayeh AK, El-boghdady AH, Said MA, Saleh MGA, Abdel-Aal MT, Abouelenein MG. Discovery of Pyrano[2,3- c]pyrazole Derivatives as Novel Potential Human Coronavirus Inhibitors: Design, Synthesis, In Silico, In Vitro, and ADME Studies. Pharmaceuticals (Basel) 2024; 17:198. [PMID: 38399412 PMCID: PMC10892497 DOI: 10.3390/ph17020198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 02/25/2024] Open
Abstract
The SARS-CoV-2 pandemic at the end of 2019 had major worldwide health and economic consequences. Until effective vaccination approaches were created, the healthcare sectors endured a shortage of operative treatments that might prevent the infection's spread. As a result, academia and the pharmaceutical industry prioritized the development of SARS-CoV2 antiviral medication. Pyranopyrazoles have been shown to play a prominent function in pharmaceutical chemistry and drug sighting because of their significant bioactive properties. We provide herein a novel sequence of pyranopyrazoles and their annulated systems whose antiviral efficacy and cytotoxicity were explored versus human coronavirus 229E (HCoV-229E) Vero-E6 cell lines as a model for the Coronaviridae family. Fifteen synthetic congeners pointed out miscellaneous antiviral efficacies against HCoV-229E with variable inhibition degrees. Compound 18 showed a high selectivity index (SI = 12.6) that established spectacular inhibitory capacity against human coronavirus 229E. Compounds 6, 7, and 14 exposed moderate efficacies. Compounds 6, 7, 14, and 18 exhibited substantial antiviral action through the replication phase with reduction percentages extending from 53.6%, 60.7%, and 55% to 82.2%, correspondingly. Likewise, when assessed to the positive control tipranavir (88.6%), the inhibitory efficiency of compounds 6, 7, 14, and 18 versus the SARS-CoV2 Mpro provided high percentages of 80.4%, 73.1%, 81.4% and up to 84.5%, respectively. In silico studies were performed to investigate further the biological activity and the target compounds' physical and chemical features, including molecular dynamic (MD) simulations, protein-ligand docking, ADME studies, and density functional theory (DFT) calculations. These inquiries demonstrated that this series of metabolically stable pyranopyrazoles and their annulated systems are effective human coronavirus inhibitors that inhibit the viral Mpro protein and may have emerged as a novel COVID-19 curative option.
Collapse
Affiliation(s)
- Abdou K. Allayeh
- Environmental Virology Laboratory 176, Water Pollution Research Department, Environment and Climate Change Institute, National Research Centre (NRC), 33 El-Behouth St., Dokki, Giza 12622, Egypt;
| | - Aliaa H. El-boghdady
- Chemistry Department, Faculty of Science, Menofia University, Shebin El-Kom 32511, Egypt; (A.H.E.-b.); (M.T.A.-A.); (M.G.A.)
| | - Mohamed A. Said
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Egyptian Russian University, Cairo 11829, Egypt;
| | - Mahmoud G. A. Saleh
- Department of Chemistry, College of Science, Northern Border University, Arar 91431, Saudi Arabia
| | - Mohammed T. Abdel-Aal
- Chemistry Department, Faculty of Science, Menofia University, Shebin El-Kom 32511, Egypt; (A.H.E.-b.); (M.T.A.-A.); (M.G.A.)
| | - Mohamed G. Abouelenein
- Chemistry Department, Faculty of Science, Menofia University, Shebin El-Kom 32511, Egypt; (A.H.E.-b.); (M.T.A.-A.); (M.G.A.)
| |
Collapse
|
14
|
Waseem W, Zafar R, Jan MS, Alomar TS, Almasoud N, Rauf A, Khattak H. Drug repurposing of FDA-approved anti-viral drugs via computational screening against novel 6M03 SARS-COVID-19. Ir J Med Sci 2024; 193:73-83. [PMID: 37515684 DOI: 10.1007/s11845-023-03473-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/23/2023] [Indexed: 07/31/2023]
Abstract
OBJECTIVE The COVID-19 pandemic has been recognized as severe acute respiratory syndrome, one of the worst and disastrous infectious diseases in human history. Until now, there is no cure to this contagious infection although some multinational pharmaceutical companies have synthesized the vaccines and injecting them into humans, but a drug treatment regimen is yet to come. AIM Among the multiple areas of SARS-CoV-2 that can be targeted, protease protein has significant values due to its essential role in viral replication and life. The repurposing of FDA-approved drugs for the treatment of COVID-19 has been a critical strategy during the pandemic due to the urgency of effective therapies. The novelty in this work refers to the innovative use of existing drugs with greater safety, speed, cost-effectiveness, broad availability, and diversity in the mechanism of action that have been approved and developed for other medical conditions. METHODS In this research work, we have engaged drug reprofiling or drug repurposing to recognize possible inhibitors of protease protein 6M03 in an instantaneous approach through computational docking studies. RESULTS We screened 16 FDA-approved anti-viral drugs that were known for different viral infections to be tested against this contagious novel strain. Through these reprofiling studies, we come up with 5 drugs, namely, Delavirdine, Fosamprenavir, Imiquimod, Stavudine, and Zanamivir, showing excellent results with the negative binding energies in Kcal/mol as - 8.5, - 7.0, - 6.8, - 6.8, and - 6.6, respectively, in the best binding posture. In silico studies allowed us to demonstrate the potential role of these drugs against COVID-19. CONCLUSION In our study, we also observed the nucleotide sequence of protease protein consisting of 316 amino acid residues and the influence of these pronouncing drugs over these sequences. The outcome of this research work provides researchers with a track record for carrying out further investigational procedures by applying docking simulations and in vitro and in vivo experimentation with these reprofile drugs so that a better drug can be formulated against coronavirus.
Collapse
Affiliation(s)
- Wajeeha Waseem
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Lahore Campus, Lahore, 54000, Pakistan
| | - Rehman Zafar
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Riphah International University, Islamabad, 44000, Pakistan
| | - Muhammad Saeed Jan
- Department of Pharmacy, Bacha Khan University Charsadda, Charsadda, 24420, KP, Pakistan.
| | - Taghrid S Alomar
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84427, 11671, Riyadh, Saudi Arabia.
| | - Najla Almasoud
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84427, 11671, Riyadh, Saudi Arabia
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Swabi, 23430, Anbar, Pakistan.
| | - Humayoon Khattak
- Department of Pharmacy, Bacha Khan University Charsadda, Charsadda, 24420, KP, Pakistan
| |
Collapse
|
15
|
Algaissi A, Khan E, Tabassum H, Samreen S, Khamjan NA, Lohani M, Khan S, Kameli N, Madkhali F, Ahmad IZ. Campesterol and dithymoquinone as a potent inhibitors of SARS cov-2 main proteases-promising drug candidates for targeting its novel variants. J Biomol Struct Dyn 2024:1-15. [PMID: 38288958 DOI: 10.1080/07391102.2023.2301684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 09/13/2023] [Indexed: 02/16/2024]
Abstract
The sudden outbreak of the COVID-19 pandemic has currently taken approximately 2.4 million lives, with no specific medication and fast-tracked tested vaccines for prevention. These vaccines have their own adverse effects, which have severely affected the global healthcare system. The discovery of the main protease structure of coronavirus (Mpro/Clpro) has resulted in the identification of compounds having antiviral potential, especially from the herbal system. In this study, the computer-associated drug design tools were utilised to analyze the reported phytoconstituents of Nigella sativa for their antiviral activity against the main protease. Fifty-eight compounds were subjected to pharmacological parameter analysis to determine their lead likeness in comparison to the standard drugs (chloroquine and nirmatrelvir) used in the treatment of SARS-CoV-2. Nearly 31 compounds were docked against five different SARS-CoV-2 main proteases, and all compounds showed better binding affinity and inhibition constant against the proteases. However, dithymoquinone and campesterol displayed the best binding scores and hence were further subjected to dynamics and MMPBSA study for 100 ns. The stability analysis shows that dithymoquinone and campesterol show less variation in fluctuation in residues compared to standard complexes. Moreover, dithymoquinone exhibited higher binding affinity and favorable interaction followed by campesterol as compared to the standard drug. The in silico computational analysis provides a promising hit for regulating the main proteases activity.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Abdullah Algaissi
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
- Emerging and Epidemic Infectious Diseases Research Unit, Medical Research Center, Jazan University, Jazan, Saudi Arabia
| | - Elhan Khan
- Natural Products Laboratory, Department of Bioengineering, Integral University, Lucknow, Uttar Pradesh, India
| | - Heena Tabassum
- Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, India
| | - Sadiyah Samreen
- Natural Products Laboratory, Department of Bioengineering, Integral University, Lucknow, Uttar Pradesh, India
| | - Nizar A Khamjan
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Mohtashim Lohani
- Medical Research Centre, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Saif Khan
- Department of Basic Dental and Medical Sciences, College of Dentistry, Ha'il University, Ha'il, Saudi Arabia
| | - Nader Kameli
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Faisal Madkhali
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Iffat Zareen Ahmad
- Natural Products Laboratory, Department of Bioengineering, Integral University, Lucknow, Uttar Pradesh, India
| |
Collapse
|
16
|
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.
Collapse
Affiliation(s)
- Yves L Janin
- Structure et Instabilité des Génomes (StrInG), Muséum National d'Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université 75005 Paris France
| |
Collapse
|
17
|
Yi Y, Yu R, Xue H, Jin Z, Zhang M, Bao YO, Wang Z, Wei H, Qiao X, Yang H. Chrysin 7-O-β-D-glucuronide, a dual inhibitor of SARS-CoV-2 3CL pro and PL pro, for the prevention and treatment of COVID-19. Int J Antimicrob Agents 2024; 63:107039. [PMID: 37981073 DOI: 10.1016/j.ijantimicag.2023.107039] [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: 02/20/2023] [Revised: 09/08/2023] [Accepted: 11/14/2023] [Indexed: 11/21/2023]
Abstract
The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) resulted in the coronavirus disease 2019 (COVID-19) pandemic. Given the advent of subvariants, there is an urgent need to develop novel drugs. The aim of this study was to find SARS-CoV-2 inhibitors from Scutellaria baicalensis Georgi targeting the proteases 3CLpro and PLpro. After screening 25 flavonoids, chrysin 7-O-β-D-glucuronide was found to be a potent inhibitor of SARS-CoV-2 on Vero E6 cells, with half-maximal effective concentration of 8.72 µM. Surface plasmon resonance assay, site-directed mutagenesis and enzymatic activity measurements indicated that chrysin-7-O-β-D-glucuronide inhibits SARS-CoV-2 by binding to H41 of 3CLpro, and K157 and E167 of PLpro. Hydrogen-deuterium exchange mass spectrometry analysis showed that chrysin-7-O-β-D-glucuronide changes the conformation of PLpro. Finally, chrysin 7-O-β-D-glucuronide was shown to have anti-inflammatory activity, mainly due to reduction of the levels of the pro-inflammatory cytokines interleukin (IL)-1β and IL-6.
Collapse
Affiliation(s)
- Yang Yi
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China; Yunnan Baiyao International Medical Research Centre, Peking University, Beijing, China.
| | - Rong Yu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Heng Xue
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Zhengtong Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Meng Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Yang-Oujie Bao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Zilong Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xue Qiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Hang Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China; Hubei Jiangxia Laboratory, Wuhan, China.
| |
Collapse
|
18
|
De SK. Discovery of Novel Cysteine Protease Inhibitors for the Treatment of Coronavirus (COVID-19). Curr Med Chem 2024; 31:1165-1169. [PMID: 37211851 DOI: 10.2174/0929867330666230519163305] [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: 02/11/2023] [Revised: 04/09/2023] [Accepted: 04/19/2023] [Indexed: 05/23/2023]
Abstract
The application describes compounds, such as compounds of general Formula, with warheads and their use in treating medical diseases or disorders, such as viral infections. Pharmaceutical compositions and synthetic methods of various compounds with warheads are included. The compounds are inhibitors of proteases, such as the 3C, CL- or 3CL-like protease.
Collapse
Affiliation(s)
- Surya K De
- Department of Chemistry, Conju-Probe, San Diego, California, USA
- Department of Chemistry, Bharath University, Chennai, Tamil Nadu, 600126, India
| |
Collapse
|
19
|
Choi K. Structure-property Relationships Reported for the New Drugs Approved in 2022. Mini Rev Med Chem 2024; 24:330-340. [PMID: 37211842 DOI: 10.2174/1389557523666230519162803] [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: 01/20/2023] [Revised: 02/20/2023] [Accepted: 03/15/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND The structure-property relationship illustrates how modifying the chemical structure of a pharmaceutical compound influences its absorption, distribution, metabolism, excretion, and other related properties. Understanding structure-property relationships of clinically approved drugs could provide useful information for drug design and optimization strategies. METHOD Among new drugs approved around the world in 2022, including 37 in the US, structure- property relationships of seven drugs were compiled from medicinal chemistry literature, in which detailed pharmacokinetic and/or physicochemical properties were disclosed not only for the final drug but also for its key analogues generated during drug development. RESULTS The discovery campaigns for these seven drugs demonstrate extensive design and optimization efforts to identify suitable candidates for clinical development. Several strategies have been successfully employed, such as attaching a solubilizing group, bioisosteric replacement, and deuterium incorporation, resulting in new compounds with enhanced physicochemical and pharmacokinetic properties. CONCLUSION The structure-property relationships hereby summarized illustrate how proper structural modifications could successfully improve the overall drug-like properties. The structure-property relationships of clinically approved drugs are expected to continue to provide valuable references and guides for the development of future drugs.
Collapse
Affiliation(s)
- Kihang Choi
- Department of Chemistry, Korea University, Seoul, 02841, Korea (ROK)
| |
Collapse
|
20
|
Zhou S, Wang K, Hu Z, Chen T, Dong Y, Gao R, Wu M, Li Y, Ji X. Design, synthesis, and structure-activity relationships of a novel class of quinazoline derivatives as coronavirus inhibitors. Eur J Med Chem 2023; 261:115831. [PMID: 37813064 DOI: 10.1016/j.ejmech.2023.115831] [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: 07/31/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/11/2023]
Abstract
There remain great unmet needs to treat coronavirus infections in clinic, and the development of novel antiviral agents is highly demanded. In this work, a phenotypic screening against our in-house compound library identified several cajanine derivatives with moderate antiviral activity against HCoV-OC43. Based on the scaffold of cajanine, a series of quinazoline derivatives were designed employing a scaffold-hopping strategy. After an iterative structural optimization campaign, several quinazoline derivatives with potent antiviral efficacy (EC50: ∼0.1 μM) and high selectivity (SI > 1000) were successfully identified. The preliminary mechanism of action study indicated that such quinazoline derivatives functioned at the early stage of infection. In aggregate, this work delivered a new chemical type of coronavirus inhibitors, which could be employed not only for further development of antiviral drugs but also as important chemical tools to delineate the target of action.
Collapse
Affiliation(s)
- Shengchao Zhou
- College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu, 15021, China
| | - Kun Wang
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ziwei Hu
- College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu, 15021, China
| | - Tao Chen
- College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu, 15021, China
| | - Yao Dong
- College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu, 15021, China
| | - Rongmei Gao
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mengyuan Wu
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuhuan Li
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Xingyue Ji
- College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu, 15021, China.
| |
Collapse
|
21
|
Feral A, Martin AR, Desfoux A, Amblard M, Vezenkov LL. Covalent-reversible peptide-based protease inhibitors. Design, synthesis, and clinical success stories. Amino Acids 2023; 55:1775-1800. [PMID: 37330416 DOI: 10.1007/s00726-023-03286-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/22/2023] [Indexed: 06/19/2023]
Abstract
Dysregulated human peptidases are implicated in a large variety of diseases such as cancer, hypertension, and neurodegeneration. Viral proteases for their part are crucial for the pathogens' maturation and assembly. Several decades of research were devoted to exploring these precious therapeutic targets, often addressing them with synthetic substrate-based inhibitors to elucidate their biological roles and develop medications. The rational design of peptide-based inhibitors offered a rapid pathway to obtain a variety of research tools and drug candidates. Non-covalent modifiers were historically the first choice for protease inhibition due to their reversible enzyme binding mode and thus presumably safer profile. However, in recent years, covalent-irreversible inhibitors are having a resurgence with dramatic increase of their related publications, preclinical and clinical trials, and FDA-approved drugs. Depending on the context, covalent modifiers could provide more effective and selective drug candidates, hence requiring lower doses, thereby limiting off-target effects. Additionally, such molecules seem more suitable to tackle the crucial issue of cancer and viral drug resistances. At the frontier of reversible and irreversible based inhibitors, a new drug class, the covalent-reversible peptide-based inhibitors, has emerged with the FDA approval of Bortezomib in 2003, shortly followed by 4 other listings to date. The highlight in the field is the breathtakingly fast development of the first oral COVID-19 medication, Nirmatrelvir. Covalent-reversible inhibitors can hipothetically provide the safety of the reversible modifiers combined with the high potency and specificity of their irreversible counterparts. Herein, we will present the main groups of covalent-reversible peptide-based inhibitors, focusing on their design, synthesis, and successful drug development programs.
Collapse
Affiliation(s)
- Anthony Feral
- IBMM, University Montpellier, CNRS, ENSCM, Montpellier, France
| | | | | | - Muriel Amblard
- IBMM, University Montpellier, CNRS, ENSCM, Montpellier, France
| | | |
Collapse
|
22
|
Tan H, Wang Z, Hu G. GAABind: a geometry-aware attention-based network for accurate protein-ligand binding pose and binding affinity prediction. Brief Bioinform 2023; 25:bbad462. [PMID: 38102069 PMCID: PMC10724026 DOI: 10.1093/bib/bbad462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 11/19/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023] Open
Abstract
Protein-ligand interactions are increasingly profiled at high-throughput, playing a vital role in lead compound discovery and drug optimization. Accurate prediction of binding pose and binding affinity constitutes a pivotal challenge in advancing our computational understanding of protein-ligand interactions. However, inherent limitations still exist, including high computational cost for conformational search sampling in traditional molecular docking tools, and the unsatisfactory molecular representation learning and intermolecular interaction modeling in deep learning-based methods. Here we propose a geometry-aware attention-based deep learning model, GAABind, which effectively predicts the pocket-ligand binding pose and binding affinity within a multi-task learning framework. Specifically, GAABind comprehensively captures the geometric and topological properties of both binding pockets and ligands, and employs expressive molecular representation learning to model intramolecular interactions. Moreover, GAABind proficiently learns the intermolecular many-body interactions and simulates the dynamic conformational adaptations of the ligand during its interaction with the protein through meticulously designed networks. We trained GAABind on the PDBbindv2020 and evaluated it on the CASF2016 dataset; the results indicate that GAABind achieves state-of-the-art performance in binding pose prediction and shows comparable binding affinity prediction performance. Notably, GAABind achieves a success rate of 82.8% in binding pose prediction, and the Pearson correlation between predicted and experimental binding affinities reaches up to 0.803. Additionally, we assessed GAABind's performance on the severe acute respiratory syndrome coronavirus 2 main protease cross-docking dataset. In this evaluation, GAABind demonstrates a notable success rate of 76.5% in binding pose prediction and achieves the highest Pearson correlation coefficient in binding affinity prediction compared with all baseline methods.
Collapse
Affiliation(s)
- Huishuang Tan
- Key Laboratory of Ministry of Education for Protein Science, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhixin Wang
- Key Laboratory of Ministry of Education for Protein Science, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute of Molecular Enzymology, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China
| | - Guang Hu
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Key Laboratory of Pathogen Bioscience and Anti-infective Medicine, Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou 215123, China
| |
Collapse
|
23
|
Zhou K, Chen D. Conventional Understanding of SARS-CoV-2 M pro and Common Strategies for Developing Its Inhibitors. Chembiochem 2023; 24:e202300301. [PMID: 37577869 DOI: 10.1002/cbic.202300301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/15/2023]
Abstract
The Coronavirus Disease 2019 (COVID-19) pandemic has brought a widespread influence on the world, especially in the face of sudden coronavirus infections, and there is still an urgent need for specific small molecule therapies to cope with possible future pandemics. The pathogen responsible for this pandemic is Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and understanding its structure and lifecycle is beneficial for designing specific drugs of treatment for COVID-19. The main protease (Mpro ) which has conservative and specific advantages is essential for viral replication and transcription. It is regarded as one of the most potential targets for anti-SARS-CoV-2 drug development. This review introduces the popular knowledge of SARS-CoV-2 Mpro in drug development and lists a series of design principles and relevant activities of advanced Mpro inhibitors, hoping to provide some new directions and ideas for researchers.
Collapse
Affiliation(s)
- Kun Zhou
- School of Pharmacy, Yantai University, Yantai, Shandong, RT 264005, P. R. China
| | - Daquan Chen
- School of Pharmacy, Yantai University, Yantai, Shandong, RT 264005, P. R. China
| |
Collapse
|
24
|
Kushwaha ND, Mohan J, Kushwaha B, Ghazi T, Nwabuife JC, Koorbanally N, Chuturgoon AA. A comprehensive review on the global efforts on vaccines and repurposed drugs for combating COVID-19. Eur J Med Chem 2023; 260:115719. [PMID: 37597435 DOI: 10.1016/j.ejmech.2023.115719] [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: 05/15/2023] [Revised: 07/31/2023] [Accepted: 08/09/2023] [Indexed: 08/21/2023]
Abstract
The recently discovered coronavirus, known as SARS-CoV-2, is a highly contagious and potentially lethal viral infection that was declared a pandemic by the World Health Organization on March 11, 2020. Since the beginning of the pandemic, an unprecedented number of COVID-19 vaccine candidates have been investigated for their potential to manage the pandemic. Herein, we reviewed vaccine development and the associated research effort, both traditional and forward-looking, to demonstrate the advantages and disadvantages of their technology, in addition to their efficacy limitations against mutant SARS-CoV-2. Moreover, we report repurposed drug discovery, which mainly focuses on virus-based and host-based targets, as well as their inhibitors. SARS-CoV-2 targets include the main protease (Mpro), and RNA-dependent RNA-polymerase (RdRp), which are the most well-studied and conserved across coronaviruses, enabling the development of broad-spectrum inhibitors of these enzymes.
Collapse
Affiliation(s)
- Narva Deshwar Kushwaha
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, 48201, USA.
| | - Jivanka Mohan
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Babita Kushwaha
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Terisha Ghazi
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Joshua C Nwabuife
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Neil Koorbanally
- School of Chemistry, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Anil A Chuturgoon
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
| |
Collapse
|
25
|
Brewitz L, Henry Chan HT, Lukacik P, Strain-Damerell C, Walsh MA, Duarte F, Schofield CJ. Mass spectrometric assays monitoring the deubiquitinase activity of the SARS-CoV-2 papain-like protease inform on the basis of substrate selectivity and have utility for substrate identification. Bioorg Med Chem 2023; 95:117498. [PMID: 37857256 PMCID: PMC10933793 DOI: 10.1016/j.bmc.2023.117498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/07/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023]
Abstract
The SARS-CoV-2 papain-like protease (PLpro) and main protease (Mpro) are nucleophilic cysteine enzymes that catalyze hydrolysis of the viral polyproteins pp1a/1ab. By contrast with Mpro, PLpro is also a deubiquitinase (DUB) that accepts post-translationally modified human proteins as substrates. Here we report studies on the DUB activity of PLpro using synthetic Nε-lysine-branched oligopeptides as substrates that mimic post-translational protein modifications by ubiquitin (Ub) or Ub-like modifiers (UBLs), such as interferon stimulated gene 15 (ISG15). Mass spectrometry (MS)-based assays confirm the DUB activity of isolated recombinant PLpro. They reveal that the sequence of both the peptide fragment derived from the post-translationally modified protein and that derived from the UBL affects PLpro catalysis; the nature of substrate binding in the S sites appears to be more important for catalytic efficiency than binding in the S' sites. Importantly, the results reflect the reported cellular substrate selectivity of PLpro, i.e. human proteins conjugated to ISG15 are better substrates than those conjugated to Ub or other UBLs. The combined experimental and modelling results imply that PLpro catalysis is affected not only by the identity of the substrate residues binding in the S and S' sites, but also by the substrate fold and the conformational dynamics of the blocking loop 2 of the PLpro:substrate complex. Nε-Lysine-branched oligopeptides thus have potential to help the identification of PLpro substrates. More generally, the results imply that MS-based assays with Nε-lysine-branched oligopeptides have potential to monitor catalysis by human DUBs and hence to inform on their substrate preferences.
Collapse
Affiliation(s)
- Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom; The Ineos Oxford Institute for Antimicrobial Research, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom.
| | - H T Henry Chan
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Petra Lukacik
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom; Research Complex at Harwell, Harwell Science and Innovation Campus, OX11 0FA Didcot, United Kingdom
| | - Claire Strain-Damerell
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom; Research Complex at Harwell, Harwell Science and Innovation Campus, OX11 0FA Didcot, United Kingdom
| | - Martin A Walsh
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom; Research Complex at Harwell, Harwell Science and Innovation Campus, OX11 0FA Didcot, United Kingdom
| | - Fernanda Duarte
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom; The Ineos Oxford Institute for Antimicrobial Research, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom.
| |
Collapse
|
26
|
Zhang FM, Huang T, Wang F, Zhang GS, Liu D, Dai J, Zhang JW, Li QH, Lin GQ, Gao D, Zhao J, Tian P. Discovery of highly potent covalent SARS-CoV-2 3CL pro inhibitors bearing 2-sulfoxyl-1,3,4-oxadiazole scaffold for combating COVID-19. Eur J Med Chem 2023; 260:115721. [PMID: 37598484 DOI: 10.1016/j.ejmech.2023.115721] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/22/2023]
Abstract
The coronavirus disease (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has emerged as a major public health crisis, posing a significant threat to human well-being. Despite the availability of vaccines, COVID-19 continues to spread owing to the emergence of SARS-CoV-2 mutants. This highlights the urgent need for the discovery of more effective drugs to combat COVID-19. As an important target for COVID-19 treatment, 3C-like protease (3CLpro) plays a crucial role in the replication of SARS-CoV-2. In our previous research, we demonstrated the potent inhibitory activities of compound A1, which contains a 2-sulfonyl-1,3,4-oxadiazole scaffold, against SARS-CoV-2 3CLpro. Herein, we present a detailed investigation of structural optimization of A1 and conduct a study on the structure-activity relationship. Among the various compounds tested, sulfoxide D6 demonstrates a potent irreversible inhibitory activity (IC50 = 0.030 μM) against SARS-CoV-2 3CLpro, as well as a favorable selectivity towards host cysteine proteases such as cathepsin B and cathepsin L. Utilizing mass spectrometry-based peptide profiling, we found that D6 covalently binds to Cys145 of SARS-CoV-2 3CLpro. Some representative compounds, namely C11, D9 and D10 also demonstrates antiviral activity against SARS-CoV-2 in Vero E6 cells. Overall, the investigation of the 2-sulfoxyl-1,3,4-oxadiazole scaffold as a novel cysteine reactive warhead would provide valuable insights into the design of potent covalent 3CLpro inhibitors for COVID-19 treatment.
Collapse
Affiliation(s)
- Fu-Mao Zhang
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Ting Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510182, China
| | - Feng Wang
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Gui-Shan Zhang
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Donglan Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510182, China
| | - Jun Dai
- Guangzhou Customs District Technology Center, Guangzhou, 510700, China
| | - Jian-Wei Zhang
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Qing-Hua Li
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Guo-Qiang Lin
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Dingding Gao
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510182, China.
| | - Ping Tian
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| |
Collapse
|
27
|
Liu W, Wang J, Wang S, Yue K, Hu Y, Liu X, Wang L, Wan S, Xu X. Discovery of new non-covalent and covalent inhibitors targeting SARS-CoV-2 papain-like protease and main protease. Bioorg Chem 2023; 140:106830. [PMID: 37683544 DOI: 10.1016/j.bioorg.2023.106830] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/04/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023]
Abstract
Global coronavirus disease 2019 (COVID-19) pandemic still threatens human health and public safety, and the development of effective antiviral agent is urgently needed. The SARS-CoV-2 main protease (Mpro) and papain-like protease (PLpro) are vital proteins in viral replication and promising therapeutic targets. Additionally, PLpro also modulates host immune response by cleaving ubiquitin and interferon-stimulated gene product 15 (ISG15) from ISGylated host proteins. In this report, we identified [1,2]selenazolo[5,4-c]pyridin-3(2H)-one and benzo[d]isothiazol-3(2H)-one as attractive scaffolds of PLpro and Mpro inhibitors. The representative compounds 6c and 7e exhibited excellent PLpro inhibition with percent inhibition of 42.9% and 44.9% at 50 nM, respectively. The preliminary enzyme kinetics experiment and fluorescent labelling experiment results determined that 6c was identified as a covalent PLpro inhibitor, while 7e was a non-covalent inhibitor. Molecular docking and dynamics simulations revealed that 6c and 7e bound to Zn-finger domain of PLpro. Compounds 6c and 7e were also identified to potent Mpro inhibitors, and they exhibited potent antiviral activities in SARS-CoV-2 infected Vero E6 cells, with EC50 value of 3.9 μM and 7.4 μM, respectively. In addition, the rat liver homogenate half-life of 6c and 7e exceeded 24 h. These findings suggest that 6c and 7e are promising led compounds for further development of PLpro/Mpro dual-target antiviral drugs.
Collapse
Affiliation(s)
- Wandong Liu
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 266003 Qingdao, China
| | - Juan Wang
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 266003 Qingdao, China
| | - Suyun Wang
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, 430071 Wuhan, China
| | - Kairui Yue
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 266003 Qingdao, China
| | - Yu Hu
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 266003 Qingdao, China
| | - Xiaochun Liu
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 266003 Qingdao, China
| | - Lihao Wang
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 266003 Qingdao, China
| | - Shengbiao Wan
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 266003 Qingdao, China.
| | - Ximing Xu
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 266003 Qingdao, China.
| |
Collapse
|
28
|
Ren H, Wang J, Tang H, Qian X, Xia B, Luo Z, Xu Z, Qi Z, Zhao P. Tiratricol inhibits yellow fever virus replication through targeting viral RNA-dependent RNA polymerase of NS5. Antiviral Res 2023; 219:105737. [PMID: 37879570 DOI: 10.1016/j.antiviral.2023.105737] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/06/2023] [Accepted: 10/18/2023] [Indexed: 10/27/2023]
Abstract
Yellow fever virus (YFV) infection is a major public concern that threatens a large population in South America and Africa. No specific antiviral drugs are available for treating yellow fever. Here, we report that tiratricol (triiodothyroacetic acid, TRIAC), a clinically approved drug used to treat thyroid hormone resistance syndrome (THRS), is a potent YFV inhibitor both in host cells and in animal models.An in vitro study demonstrates that TRIAC remarkably suppresses viral RNA synthesis and protein expression in a dose-dependent manner in human hepatoma cell lines (Huh-7) with an EC50 value of 2.07 μM and a CC50 value of 385.77 μM respectively. The surface plasmon resonance assay and molecular docking analysis indicate that TRIAC hinders viral replication by binding to the RNA-dependent RNA polymerase (RdRp) domain of viral nonstructural protein NS5, probably through interacting with the active sites of RdRp.The inhibitory effect of TRIAC in vivo is also confirmed in 3-week old C57BL/6 mice challenged with YFV infection, from which the survival of the mice as well as lesions and infection in their tissues and serum issignificantly promoted following oral administration of TRIAC (0.2 mg/kg/day). Additionally, TRIAC shows a broad-spectrum antiviral activity against multiple flaviviruses such as TBEV, WNV,ZIKV, andJEV in vitro. Our data demonstrate that the TH analogue TRIAC is an effective anti-YFV compound and may act as a potential therapeutic candidate for the treatment of YFV infection if its clinical importance is determined in patients in future.
Collapse
Affiliation(s)
- Hao Ren
- Department of Microbiology, Faculty of Naval Medicine, Shanghai Key Laboratory of Medical Biodefense, Naval Medical University, Shanghai, China
| | - Jiaqi Wang
- Department of Microbiology, Faculty of Naval Medicine, Shanghai Key Laboratory of Medical Biodefense, Naval Medical University, Shanghai, China
| | - Hailin Tang
- Department of Microbiology, Faculty of Naval Medicine, Shanghai Key Laboratory of Medical Biodefense, Naval Medical University, Shanghai, China
| | - Xijing Qian
- Department of Microbiology, Faculty of Naval Medicine, Shanghai Key Laboratory of Medical Biodefense, Naval Medical University, Shanghai, China
| | - Binghui Xia
- Department of Microbiology, Faculty of Naval Medicine, Shanghai Key Laboratory of Medical Biodefense, Naval Medical University, Shanghai, China
| | - Zhenghan Luo
- Department of Microbiology, Faculty of Naval Medicine, Shanghai Key Laboratory of Medical Biodefense, Naval Medical University, Shanghai, China
| | - Zhenghao Xu
- Department of Microbiology, Faculty of Naval Medicine, Shanghai Key Laboratory of Medical Biodefense, Naval Medical University, Shanghai, China
| | - Zhongtian Qi
- Department of Microbiology, Faculty of Naval Medicine, Shanghai Key Laboratory of Medical Biodefense, Naval Medical University, Shanghai, China.
| | - Ping Zhao
- Department of Microbiology, Faculty of Naval Medicine, Shanghai Key Laboratory of Medical Biodefense, Naval Medical University, Shanghai, China.
| |
Collapse
|
29
|
Tam NM, Nguyen TH, Pham MQ, Hong ND, Tung NT, Vu VV, Quang DT, Ngo ST. Upgrading nirmatrelvir to inhibit SARS-CoV-2 Mpro via DeepFrag and free energy calculations. J Mol Graph Model 2023; 124:108535. [PMID: 37295158 PMCID: PMC10233213 DOI: 10.1016/j.jmgm.2023.108535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/23/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023]
Abstract
The first oral drug for the treatment of COVID-19, Paxlovid, has been authorized; however, nirmatrelvir, a major component of the drug, is reported to be associated with some side effects. Moreover, the appearance of many novel variants raises concerns about drug resistance, and designing new potent inhibitors to prevent viral replication is thus urgent. In this context, using a hybrid approach combining machine learning (ML) and free energy simulations, 6 compounds obtained by modifying nirmatrelvir were proposed to bind strongly to SARS-CoV-2 Mpro. The structural modification of nirmatrelvir significantly enhances the electrostatic interaction free energy between the protein and ligand and slightly decreases the vdW term. However, the vdW term is the most important factor in controlling the ligand-binding affinity. In addition, the modified nirmatrelvir might be less toxic to the human body than the original inhibitor.
Collapse
Affiliation(s)
- Nguyen Minh Tam
- Faculty of Basic Sciences, University of Phan Thiet, Phan Thiet City, Binh Thuan, Viet Nam
| | - Trung Hai Nguyen
- Laboratory of Biophysics, Institute for Advanced Study in Technology, Ton Duc Thang University, Ho Chi Minh City, Viet Nam; Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Viet Nam
| | - Minh Quan Pham
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Viet Nam
| | - Nam Dao Hong
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Viet Nam
| | - Nguyen Thanh Tung
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Viet Nam; Institute of Materials Science, Vietnam Academy of Science and Technology, Hanoi, Viet Nam.
| | - Van V Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Viet Nam
| | - Duong Tuan Quang
- Department of Chemistry, Hue University, Thua Thien Hue Province, Hue City, Viet Nam.
| | - Son Tung Ngo
- Laboratory of Biophysics, Institute for Advanced Study in Technology, Ton Duc Thang University, Ho Chi Minh City, Viet Nam; Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Viet Nam.
| |
Collapse
|
30
|
Jiang X, Su H, Shang W, Zhou F, Zhang Y, Zhao W, Zhang Q, Xie H, Jiang L, Nie T, Yang F, Xiong M, Huang X, Li M, Chen P, Peng S, Xiao G, Jiang H, Tang R, Zhang L, Shen J, Xu Y. Structure-based development and preclinical evaluation of the SARS-CoV-2 3C-like protease inhibitor simnotrelvir. Nat Commun 2023; 14:6463. [PMID: 37833261 PMCID: PMC10575921 DOI: 10.1038/s41467-023-42102-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
The persistent pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants accentuates the great demand for developing effective therapeutic agents. Here, we report the development of an orally bioavailable SARS-CoV-2 3C-like protease (3CLpro) inhibitor, namely simnotrelvir, and its preclinical evaluation, which lay the foundation for clinical trials studies as well as the conditional approval of simnotrelvir in combination with ritonavir for the treatment of COVID-19. The structure-based optimization of boceprevir, an approved HCV protease inhibitor, leads to identification of simnotrelvir that covalently inhibits SARS-CoV-2 3CLpro with an enthalpy-driven thermodynamic binding signature. Multiple enzymatic assays reveal that simnotrelvir is a potent pan-CoV 3CLpro inhibitor but has high selectivity. It effectively blocks replications of SARS-CoV-2 variants in cell-based assays and exhibits good pharmacokinetic and safety profiles in male and female rats and monkeys, leading to robust oral efficacy in a male mouse model of SARS-CoV-2 Delta infection in which it not only significantly reduces lung viral loads but also eliminates the virus from brains. The discovery of simnotrelvir thereby highlights the utility of structure-based development of marked protease inhibitors for providing a small molecule therapeutic effectively combatting human coronaviruses.
Collapse
Affiliation(s)
- Xiangrui Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Haixia Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Weijuan Shang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, 430071, Wuhan, China
| | - Feng Zhou
- State Key Laboratory of Neurology and Oncology Drug Development, 210023, Nanjing, China
- Simcere Zaiming Pharmaceutical Co., Ltd, 200000, Shanghai, China
| | - Yan Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Wenfeng Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Qiumeng Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Hang Xie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 210023, Nanjing, China
| | - Lei Jiang
- Simcere Zaiming Pharmaceutical Co., Ltd, 200000, Shanghai, China
| | - Tianqing Nie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 210023, Nanjing, China
| | - Feipu Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Muya Xiong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xiaoxing Huang
- Simcere Zaiming Pharmaceutical Co., Ltd, 200000, Shanghai, China
| | - Minjun Li
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, 201210, Shanghai, China
| | - Ping Chen
- Jiangsu Simcere Pharmaceutical Co., Ltd, 210023, Nanjing, China
| | - Shaoping Peng
- State Key Laboratory of Neurology and Oncology Drug Development, 210023, Nanjing, China
- Jiangsu Simcere Pharmaceutical Co., Ltd, 210023, Nanjing, China
| | - Gengfu Xiao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, 430071, Wuhan, China
| | - Hualiang Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Renhong Tang
- State Key Laboratory of Neurology and Oncology Drug Development, 210023, Nanjing, China.
- Simcere Zaiming Pharmaceutical Co., Ltd, 200000, Shanghai, China.
| | - Leike Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, 430071, Wuhan, China.
- Hubei jiangxia Laboratory, 430200, Wuhan, China.
| | - Jingshan Shen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
| | - Yechun Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 310024, Hangzhou, China.
| |
Collapse
|
31
|
Leusciatti M, Macchi B, Marino-Merlo F, Mastino A, Morra G, Quadrelli P. Inhibition of the RNA-Dependent RNA-Polymerase from SARS-CoV-2 by 6-Chloropurine Isoxazoline-Carbocyclic Monophosphate Nucleotides. ACS OMEGA 2023; 8:36311-36320. [PMID: 37810686 PMCID: PMC10552509 DOI: 10.1021/acsomega.3c04918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023]
Abstract
Isoxazoline-carbocyclic monophosphate nucleotides were designed and synthesized through the chemistry of nitrosocarbonyl intermediates and stable anthracenenitrile oxide. Docking and molecular dynamics studies were first conducted for determining the best candidate for polymerase SARS-CoV-2 inhibition. The setup phosphorylation protocol afforded the nucleotides available for the biological tests. Preliminary inhibition and cytotoxicity assays were then performed, and the results showed a moderate activity of the nucleotides accompanied by cytotoxicity.
Collapse
Affiliation(s)
- Marco Leusciatti
- Department
of Chemistry, University of Pavia, Viale Taramelli 12, 27100 Pavia,Italy
| | - Beatrice Macchi
- Department
of Chemical Science and Technology, University
of Rome Tor Vergata, Via della ricerca scientifica 1, 00133 Roma, Italy
| | - Francesca Marino-Merlo
- Department
of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres, 31, 98166 Messina, Italy
| | - Antonio Mastino
- The
Institute of Translational Pharmacology, CNR, Via Fosso del Cavaliere 100, 00133 Roma, Italy
| | - Giulia Morra
- Biocomputing
Lab, SCITEC-Istituto di Scienze e Tecnologie
Chimiche CNR, Via Mario
Bianco 9, 20131 Milano, Italy
| | - Paolo Quadrelli
- Department
of Chemistry, University of Pavia, Viale Taramelli 12, 27100 Pavia,Italy
| |
Collapse
|
32
|
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.
Collapse
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
| |
Collapse
|
33
|
Preschel HD, Otte RT, Zhuo Y, Ruscoe RE, Burke AJ, Kellerhals R, Horst B, Hennig S, Janssen E, Green AP, Turner NJ, Ruijter E. Multicomponent Synthesis of the SARS-CoV-2 Main Protease Inhibitor Nirmatrelvir. J Org Chem 2023; 88:12565-12571. [PMID: 37607396 PMCID: PMC10476182 DOI: 10.1021/acs.joc.3c01274] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Indexed: 08/24/2023]
Abstract
In the wake of the Covid-19 pandemic, it has become clear that global access to efficacious antiviral drugs will be critical to combat future outbreaks of SARS-CoV-2 or related viruses. The orally available SARS-CoV-2 main protease inhibitor nirmatrelvir has proven an effective treatment option for Covid-19, especially in compromised patients. We report a new synthesis of nirmatrelvir featuring a highly enantioselective biocatalytic desymmetrization (>99% ee) and a highly diastereoselective multicomponent reaction (>25:1 dr) as the key steps. Our route avoids the use of transition metals and peptide coupling reagents, resulting in an overall highly efficient and atom-economic process.
Collapse
Affiliation(s)
- H. Daniel Preschel
- Department
of Chemistry & Pharmaceutical Sciences, Amsterdam Institute of
Molecular & Life Sciences (AIMMS), Vrije
Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Ruben T. Otte
- Department
of Chemistry & Pharmaceutical Sciences, Amsterdam Institute of
Molecular & Life Sciences (AIMMS), Vrije
Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Ying Zhuo
- Department
of Chemistry, The University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United
Kingdom
| | - Rebecca E. Ruscoe
- Department
of Chemistry, The University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United
Kingdom
| | - Ashleigh J. Burke
- Department
of Chemistry, The University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United
Kingdom
| | - Rachel Kellerhals
- Department
of Chemistry & Pharmaceutical Sciences, Amsterdam Institute of
Molecular & Life Sciences (AIMMS), Vrije
Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Brendan Horst
- Department
of Chemistry & Pharmaceutical Sciences, Amsterdam Institute of
Molecular & Life Sciences (AIMMS), Vrije
Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Sven Hennig
- Department
of Chemistry & Pharmaceutical Sciences, Amsterdam Institute of
Molecular & Life Sciences (AIMMS), Vrije
Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Elwin Janssen
- Department
of Chemistry & Pharmaceutical Sciences, Amsterdam Institute of
Molecular & Life Sciences (AIMMS), Vrije
Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Anthony P. Green
- Department
of Chemistry, The University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United
Kingdom
| | - Nicholas J. Turner
- Department
of Chemistry, The University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United
Kingdom
| | - Eelco Ruijter
- Department
of Chemistry & Pharmaceutical Sciences, Amsterdam Institute of
Molecular & Life Sciences (AIMMS), Vrije
Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| |
Collapse
|
34
|
Chenna A, Khan WH, Dash R, Saraswat S, Chugh A, Rathore AS, Goel G. An efficient computational protocol for template-based design of peptides that inhibit interactions involving SARS-CoV-2 proteins. Proteins 2023; 91:1222-1234. [PMID: 37283297 DOI: 10.1002/prot.26511] [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: 10/07/2022] [Revised: 02/17/2023] [Accepted: 04/25/2023] [Indexed: 06/08/2023]
Abstract
The RNA-dependent RNA polymerase (RdRp) complex of SARS-CoV-2 lies at the core of its replication and transcription processes. The interfaces between holo-RdRp subunits are highly conserved, facilitating the design of inhibitors with high affinity for the interaction interface hotspots. We, therefore, take this as a model protein complex for the application of a structural bioinformatics protocol to design peptides that inhibit RdRp complexation by preferential binding at the interface of its core subunit nonstructural protein, nsp12, with accessory factor nsp7. Here, the interaction hotspots of the nsp7-nsp12 subunit of RdRp, determined from a long molecular dynamics trajectory, are used as a template. A large library of peptide sequences constructed from multiple hotspot motifs of nsp12 is screened in-silico to determine sequences with high geometric complementarity and interaction specificity for the binding interface of nsp7 (target) in the complex. Two lead designed peptides are extensively characterized using orthogonal bioanalytical methods to determine their suitability for inhibition of RdRp complexation. Binding affinity of these peptides to accessory factor nsp7, determined using a surface plasmon resonance (SPR) assay, is slightly better than that of nsp12: dissociation constant of 133nM and 167nM, respectively, compared to 473nM for nsp12. A competitive ELISA is used to quantify inhibition of nsp7-nsp12 complexation, with one of the lead peptides giving an IC50 of 25μM . Cell penetrability and cytotoxicity are characterized using a cargo delivery assay and MTT cytotoxicity assay, respectively. Overall, this work presents a proof-of-concept of an approach for rational discovery of peptide inhibitors of SARS-CoV-2 protein-protein interactions.
Collapse
Affiliation(s)
- Akshay Chenna
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Wajihul Hasan Khan
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
- Virology Unit, Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Rozaleen Dash
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Saurabh Saraswat
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Archana Chugh
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Anurag S Rathore
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Gaurav Goel
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| |
Collapse
|
35
|
Leonard RA, Rao VN, Bartlett A, Froggatt HM, Luftig MA, Heaton BE, Heaton NS. A low-background, fluorescent assay to evaluate inhibitors of diverse viral proteases. J Virol 2023; 97:e0059723. [PMID: 37578235 PMCID: PMC10506478 DOI: 10.1128/jvi.00597-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/11/2023] [Indexed: 08/15/2023] Open
Abstract
Multiple coronaviruses (CoVs) can cause respiratory diseases in humans. While prophylactic vaccines designed to prevent infection are available for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), incomplete vaccine efficacy, vaccine hesitancy, and the threat of other pathogenic CoVs for which vaccines do not exist have highlighted the need for effective antiviral therapies. While antiviral compounds targeting the viral polymerase and protease are already in clinical use, their sensitivity to potential resistance mutations as well as their breadth against the full range of human and preemergent CoVs remain incompletely defined. To begin to fill that gap in knowledge, we report here the development of an improved, noninfectious, cell-based fluorescent assay with high sensitivity and low background that reports on the activity of viral proteases, which are key drug targets. We demonstrate that the assay is compatible with not only the SARS-CoV-2 Mpro protein but also orthologues from a range of human and nonhuman CoVs as well as clinically reported SARS-CoV-2 drug-resistant Mpro variants. We then use this assay to define the breadth of activity of two clinically used protease inhibitors, nirmatrelvir and ensitrelvir. Continued use of this assay will help define the strengths and limitations of current therapies and may also facilitate the development of next-generation protease inhibitors that are broadly active against both currently circulating and preemergent CoVs. IMPORTANCE Coronaviruses (CoVs) are important human pathogens with the ability to cause global pandemics. Working in concert with vaccines, antivirals specifically limit viral disease in people who are actively infected. Antiviral compounds that target CoV proteases are already in clinical use; their efficacy against variant proteases and preemergent zoonotic CoVs, however, remains incompletely defined. Here, we report an improved, noninfectious, and highly sensitive fluorescent method of defining the sensitivity of CoV proteases to small molecule inhibitors. We use this approach to assay the activity of current antiviral therapies against clinically reported SARS-CoV-2 protease mutants and a panel of highly diverse CoV proteases. Additionally, we show this system is adaptable to other structurally nonrelated viral proteases. In the future, this assay can be used to not only better define the strengths and limitations of current therapies but also help develop new, broadly acting inhibitors that more broadly target viral families.
Collapse
Affiliation(s)
- Rebecca A. Leonard
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Vishwas N. Rao
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Medical Scientist Training Program, Duke University School of Medicine, Durham, North Carolina, USA
| | - Alexandria Bartlett
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Heather M. Froggatt
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Micah A. Luftig
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Center for Virology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Brook E. Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Nicholas S. Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Center for Virology, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| |
Collapse
|
36
|
Takashita E, Fujisaki S, Morita H, Nagata S, Miura H, Nagashima M, Watanabe S, Takeda M, Kawaoka Y, Hasegawa H. Assessment of the frequency of SARS-CoV-2 Omicron variant escape from RNA-dependent RNA polymerase inhibitors and 3C-like protease inhibitors. Antiviral Res 2023:105671. [PMID: 37451629 DOI: 10.1016/j.antiviral.2023.105671] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
The emergence and spread of antiviral-resistant SARS-CoV-2 is of great concern. In this study, we evaluated the propensity of Omicron variants to escape from RNA-dependent RNA polymerase (RdRP) inhibitors and 3C-like protease (3CLpro) inhibitors. SARS-CoV-2 Delta and Omicron variants were serially passaged in vitro in the presence of RdRP inhibitors (remdesivir and molnupiravir) and 3CLpro inhibitors (nirmatrelvir and lufotrelvir) to detect SARS-CoV-2 escape mutants. After five passages with 3CLpro inhibitors, mutant viruses that escaped from 3CLpro inhibitors emerged; however, in the presence of RdRP inhibitors all variants disappeared within 2-4 passages. Our findings suggest that the frequency of SARS-CoV-2 mutant escape from RdRP inhibitors is lower than that from 3CLpro inhibitors. We also found that Delta variants were more likely to acquire amino acid substitutions associated with resistance to 3CLpro inhibitors under the selective pressure of this drug compared with Omicron variants.
Collapse
Affiliation(s)
- Emi Takashita
- Research Center for Influenza and Respiratory Viruses, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo, 208-0011, Japan.
| | - Seiichiro Fujisaki
- Research Center for Influenza and Respiratory Viruses, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo, 208-0011, Japan
| | - Hiroko Morita
- Research Center for Influenza and Respiratory Viruses, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo, 208-0011, Japan
| | - Shiho Nagata
- Research Center for Influenza and Respiratory Viruses, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo, 208-0011, Japan
| | - Hideka Miura
- Research Center for Influenza and Respiratory Viruses, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo, 208-0011, Japan
| | - Mami Nagashima
- Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunin-cho, Shinjuku-ku, Tokyo, 169-0073, Japan
| | - Shinji Watanabe
- Research Center for Influenza and Respiratory Viruses, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo, 208-0011, Japan
| | - Makoto Takeda
- Department of Virology Ⅲ, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo, 208-0011, Japan; Department of Microbiology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan; Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, 1-21-1 Toyama, Shinjuku-ku, Tokyo, 162-8655, Japan; Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, 575 Science Drive, Madison, WI, 53711, USA; The University of Tokyo, Pandemic Preparedness, Infection, and Advanced Research Center, 4-6-1 Shirokanedai, Minato-ku, Tokyo, Japan
| | - Hideki Hasegawa
- Research Center for Influenza and Respiratory Viruses, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo, 208-0011, Japan
| |
Collapse
|
37
|
Luo J, Wang W, Jiang H, Li W, Zeng P, Wang J, Zhou X, Zou X, Chen S, Wang Q, Zhang J, Li J. Crystal structures of main proteases of SARS-CoV-2 variants bound to a benzothiazole-based inhibitor. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1257-1264. [PMID: 37357528 PMCID: PMC10448042 DOI: 10.3724/abbs.2023053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/20/2023] [Indexed: 06/27/2023] Open
Abstract
Main protease (M pro) serves as an indispensable factor in the life cycle of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as well as its constantly emerging variants and is therefore considered an attractive target for antiviral drug development. Benzothiazole-based inhibitors targeting M pro have recently been investigated by several groups and proven to be promising leads for coronaviral drug development. In the present study, we determine the crystal structures of a benzothiazole-based inhibitor, YH-53, bound to M pro mutants from SARS-CoV-2 variants of concern (VOCs) or variants of interest (VOIs), including K90R (Beta, B.1.351), G15S (Lambda, C.37), Y54C (Delta, AY.4), M49I (Omicron, BA.5) and P132H (Omicron, B.1.1.529). The structures show that the benzothiazole group in YH-53 forms a C-S covalent bond with the sulfur atom of catalytic residue Cys145 in SARS-CoV-2 M pro mutants. Structural analysis reveals the key molecular determinants necessary for interaction and illustrates the binding mode of YH-53 to these mutant M pros. In conclusion, structural insights from this study offer more information to develop benzothiazole-based drugs that are broader spectrum, more effective and safer.
Collapse
Affiliation(s)
- Jiqing Luo
- College of Pharmaceutical SciencesGannan Medical UniversityGanzhou341000China
| | - Weiwei Wang
- Shanghai Advanced Research InstituteChinese Academy of SciencesShanghai201204China
| | - Haihai Jiang
- School of Basic Medical SciencesNanchang UniversityNanchang330031China
| | - Wenwen Li
- Shenzhen Crystalo Biopharmaceutical Co.Ltd.Shenzhen518118China
- Jiangxi Jmerry Biopharmaceutical Co.Ltd.Ganzhou341000China
| | - Pei Zeng
- Jiangxi Jmerry Biopharmaceutical Co.Ltd.Ganzhou341000China
| | - Jie Wang
- Jiangxi Jmerry Biopharmaceutical Co.Ltd.Ganzhou341000China
| | - Xuelan Zhou
- Jiangxi Jmerry Biopharmaceutical Co.Ltd.Ganzhou341000China
| | - Xiaofang Zou
- Jiangxi Jmerry Biopharmaceutical Co.Ltd.Ganzhou341000China
| | | | - Qisheng Wang
- Shanghai Advanced Research InstituteChinese Academy of SciencesShanghai201204China
| | - Jin Zhang
- School of Basic Medical SciencesNanchang UniversityNanchang330031China
| | - Jian Li
- College of Pharmaceutical SciencesGannan Medical UniversityGanzhou341000China
| |
Collapse
|
38
|
Castillo-Campos L, Velázquez-Libera JL, Caballero J. Computational study of the binding orientation and affinity of noncovalent inhibitors of the papain-like protease (PLpro) from SARS-CoV-1 considering the protein flexibility by using molecular dynamics and cross-docking. Front Mol Biosci 2023; 10:1215499. [PMID: 37426421 PMCID: PMC10326900 DOI: 10.3389/fmolb.2023.1215499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023] Open
Abstract
The papain-like protease (PLpro) from zoonotic coronaviruses (CoVs) has been identified as a target with an essential role in viral respiratory diseases caused by Severe Acute Respiratory Syndrome-associated coronaviruses (SARS-CoVs). The design of PLpro inhibitors has been proposed as an alternative to developing potential drugs against this disease. In this work, 67 naphthalene-derived compounds as noncovalent PLpro inhibitors were studied using molecular modeling methods. Structural characteristics of the bioactive conformations of these inhibitors and their interactions at the SARS-CoV-1 PLpro binding site were reported here in detail, taking into account the flexibility of the protein residues. Firstly, a molecular docking protocol was used to obtain the orientations of the inhibitors. After this, the orientations were compared, and the recurrent interactions between the PLpro residues and ligand chemical groups were described (with LigRMSD and interaction fingerprints methods). In addition, efforts were made to find correlations between docking energy values and experimentally determined binding affinities. For this, the PLpro was sampled by using Gaussian Accelerated Molecular Dynamics (GaMD), generating multiple conformations of the binding site. Diverse protein conformations were selected and a cross-docking experiment was performed, yielding models of the 67 naphthalene-derived compounds adopting different binding modes. Representative complexes for each ligand were selected to obtain the highest correlation between docking energies and activities. A good correlation (R 2 = 0.948) was found when this flexible docking protocol was performed.
Collapse
|
39
|
Grigorenko BL, Polyakov IV, Khrenova MG, Giudetti G, Faraji S, Krylov AI, Nemukhin AV. Multiscale Simulations of the Covalent Inhibition of the SARS-CoV-2 Main Protease: Four Compounds and Three Reaction Mechanisms. J Am Chem Soc 2023; 145:13204-13214. [PMID: 37294056 DOI: 10.1021/jacs.3c02229] [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: 06/10/2023]
Abstract
We report the results of computational modeling of the reactions of the SARS-CoV-2 main protease (MPro) with four potential covalent inhibitors. Two of them, carmofur and nirmatrelvir, have shown experimentally the ability to inhibit MPro. Two other compounds, X77A and X77C, were designed computationally in this work. They were derived from the structure of X77, a non-covalent inhibitor forming a tight surface complex with MPro. We modified the X77 structure by introducing warheads capable of reacting with the catalytic cysteine residue in the MPro active site. The reaction mechanisms of the four molecules with MPro were investigated by quantum mechanics/molecular mechanics (QM/MM) simulations. The results show that all four compounds form covalent adducts with the catalytic cysteine Cys 145 of MPro. From the chemical perspective, the reactions of these four molecules with MPro follow three distinct mechanisms. The reactions are initiated by a nucleophilic attack of the thiolate group of the deprotonated cysteine residue from the catalytic dyad Cys145-His41 of MPro. In the case of carmofur and X77A, the covalent binding of the thiolate to the ligand is accompanied by the formation of the fluoro-uracil leaving group. The reaction with X77C follows the nucleophilic aromatic substitution SNAr mechanism. The reaction of MPro with nirmatrelvir (which has a reactive nitrile group) leads to the formation of a covalent thioimidate adduct with the thiolate of the Cys145 residue in the enzyme active site. Our results contribute to the ongoing search for efficient inhibitors of the SARS-CoV-2 enzymes.
Collapse
Affiliation(s)
- Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Igor V Polyakov
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Maria G Khrenova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow 119071, Russia
| | - Goran Giudetti
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Shirin Faraji
- Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| |
Collapse
|
40
|
Singh P, Hernandez‐Rauda R, Peña‐Rodas O. Preventative and therapeutic potential of animal milk components against COVID-19: A comprehensive review. Food Sci Nutr 2023; 11:2547-2579. [PMID: 37324885 PMCID: PMC10261805 DOI: 10.1002/fsn3.3314] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/07/2023] [Accepted: 02/24/2023] [Indexed: 06/17/2023] Open
Abstract
The global pandemic of COVID-19 is considered one of the most catastrophic events on earth. During the pandemic, food ingredients may play crucial roles in preventing infectious diseases and sustaining people's general health and well-being. Animal milk acts as a super food since it has the capacity to minimize the occurrence of viral infections due to inherent antiviral properties of its ingredients. SARS-CoV-2 virus infection can be prevented by immune-enhancing and antiviral properties of caseins, α-lactalbumin, β-lactoglobulin, mucin, lactoferrin, lysozyme, lactoperoxidase, oligosaccharides, glycosaminoglycans, and glycerol monolaurate. Some of the milk proteins (i.e., lactoferrin) may work synergistically with antiviral medications (e.g., remdesivir), and enhance the effectiveness of treatment in this disease. Cytokine storm during COVID-19 can be managed by casein hydrolyzates, lactoferrin, lysozyme, and lactoperoxidase. Thrombus formation can be prevented by casoplatelins as these can inhibit human platelet aggregation. Milk vitamins (i.e., A, D, E, and B complexes) and minerals (i.e., Ca, P, Mg, Zn, and Se) can have significantly positive effects on boosting the immunity and health status of individuals. In addition, certain vitamins and minerals can also act as antioxidants, anti-inflammatory, and antivirals. Thus, the overall effect of milk might be a result of synergistic antiviral effects and host immunomodulator activities from multiple components. Due to multiple overlapping functions of milk ingredients, they can play vital and synergistic roles in prevention as well as supportive agents during principle therapy of COVID-19.
Collapse
Affiliation(s)
- Parminder Singh
- Department of Animal Husbandry AmritsarGovernment of PunjabAmritsarIndia
| | - Roberto Hernandez‐Rauda
- Laboratorio de Inocuidad de AlimentosUniversidad Doctor Andres BelloSan SalvadorEl Salvador, América Central
| | - Oscar Peña‐Rodas
- Laboratorio de Inocuidad de AlimentosUniversidad Doctor Andres BelloSan SalvadorEl Salvador, América Central
| |
Collapse
|
41
|
Zhang K, Wang T, Li M, Liu M, Tang H, Wang L, Ye K, Yang J, Jiang S, Xiao Y, Xie Y, Lu M, Zhang X. Discovery of quinazolin-4-one-based non-covalent inhibitors targeting the severe acute respiratory syndrome coronavirus 2 main protease (SARS-CoV-2 M pro). Eur J Med Chem 2023; 257:115487. [PMID: 37257212 DOI: 10.1016/j.ejmech.2023.115487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/30/2023] [Accepted: 05/13/2023] [Indexed: 06/02/2023]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 continues to pose a great threat to public health while various vaccines are available worldwide. Main protease (Mpro) has been validated as an effective anti-COVID-19 drug target. Using medicinal chemistry and rational drug design strategies, we identified a quinazolin-4-one series of nonpeptidic, noncovalent SARS-CoV-2 Mpro inhibitors based on baicalein, 5,6,7-trihydroxy-2-phenyl-4H-chromen-4-one. In particular, compound C7 exhibits superior inhibitory activity against SARS-CoV-2 Mpro relative to baicalein (IC50 = 0.085 ± 0.006 and 0.966 ± 0.065 μM, respectively), as well as improved physicochemical and drug metabolism and pharmacokinetics (DMPK) properties. In addition, C7 inhibits viral replication in SARS-CoV-2-infected Vero E6 cells more effectively than baicalein (EC50 = 1.10 ± 0.12 and 5.15 ± 1.64 μM, respectively) with low cytotoxicity (CC50 > 50 μM). An X-ray co-crystal structure reveals a non-covalent mechanism of action, and a noncanonical binding mode not observed by baicalein. These results suggest that C7 represents a promising lead for development of more effective SARS-CoV-2 Mpro inhibitors and anti-COVID-19 drugs.
Collapse
Affiliation(s)
- Kuojun Zhang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Tianyu Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Maotian Li
- Department of Pharmacology, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China
| | - Mu Liu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Diseases and Biosecurity, School of Basic Medical Sciences, Fudan University, 200032, Shanghai, China
| | - He Tang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Lin Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Ke Ye
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Jiamei Yang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Sheng Jiang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Yibei Xiao
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Youhua Xie
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Diseases and Biosecurity, School of Basic Medical Sciences, Fudan University, 200032, Shanghai, China.
| | - Meiling Lu
- Department of Pharmacology, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China.
| | - Xiangyu Zhang
- Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, Nanjing, 210009, China.
| |
Collapse
|
42
|
Yang H, You M, Shu X, Zhen J, Zhu M, Fu T, Zhang Y, Jiang X, Zhang L, Xu Y, Zhang Y, Su H, Zhang Q, Shen J. Design, synthesis and biological evaluation of peptidomimetic benzothiazolyl ketones as 3CL pro inhibitors against SARS-CoV-2. Eur J Med Chem 2023; 257:115512. [PMID: 37253309 DOI: 10.1016/j.ejmech.2023.115512] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 05/01/2023] [Accepted: 05/22/2023] [Indexed: 06/01/2023]
Abstract
A series of peptidomimetic compounds containing benzothiazolyl ketone and [2.2.1] azabicyclic ring was designed, synthesized and evaluated in the hope of obtaining potent oral 3CLpro inhibitors with improved pharmacokinetic properties. Among the target compounds, 11b had the best enzymatic potency (IC50 = 0.110 μM) and 11e had the best microsomal stability (t1/2 > 120 min) and good enzyme activity (IC50 = 0.868 μM). Therefore, compounds 11b and 11e were chosen for further evaluation of pharmacokinetics in ICR mice. The results exhibited that the AUC(0-t) of 11e was 5143 h*ng/mL following single-dose oral administration of 20 mg/kg, and the F was 67.98%. Further structural modification was made to obtain compounds 11g-11j based on 11e. Among them, 11j exhibited the best enzyme inhibition activity against SARS-CoV-2 3CLpro (IC50 = 1.646 μM), the AUC(0-t) was 32473 h*ng/mL (20 mg/kg, po), and the F was 48.1%. In addition, 11j displayed significant anti-SARS-CoV-2 activity (EC50 = 0.18 μM) and low cytotoxicity (CC50 > 50 μM) in Vero E6 cells. All of the above results suggested that compound 11j was a promising lead compound in the development of oral 3CLpro inhibitors and deserved further research.
Collapse
Affiliation(s)
- Hanxi Yang
- College of Chemistry, Zhengzhou University, 100 Kexuedadao Road, Zhengzhou, 450001, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Mengyuan You
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xiaoyang Shu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Jingyao Zhen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, PR China
| | - Mengwei Zhu
- College of Pharmacy, An Hui University of Traditional Chinese Medicine, Hefei, 230012, China; Yangtze Delta Drug Advanced Research Institute and Yangtze Delta Pharmaceutical College, Nantong, 226133, China
| | - Tiantian Fu
- College of Pharmacy, An Hui University of Traditional Chinese Medicine, Hefei, 230012, China; Yangtze Delta Drug Advanced Research Institute and Yangtze Delta Pharmaceutical College, Nantong, 226133, China
| | - Yan Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xiangrui Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, PR China
| | - Leike Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China; Hubei Jiangxia Laboratory, Wuhan, 430200, China
| | - Yechun Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yumin Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China.
| | - Haixia Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Qiumeng Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Jingshan Shen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| |
Collapse
|
43
|
Fumagalli V, Di Lucia P, Ravà M, Marotta D, Bono E, Grassi S, Donnici L, Cannalire R, Stefanelli I, Ferraro A, Esposito F, Pariani E, Inverso D, Montesano C, Delbue S, Perlman S, Tramontano E, De Francesco R, Summa V, Guidotti LG, Iannacone M. Nirmatrelvir treatment of SARS-CoV-2-infected mice blunts antiviral adaptive immune responses. EMBO Mol Med 2023; 15:e17580. [PMID: 36946379 PMCID: PMC10165354 DOI: 10.15252/emmm.202317580] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 03/23/2023] Open
Abstract
Alongside vaccines, antiviral drugs are becoming an integral part of our response to the SARS-CoV-2 pandemic. Nirmatrelvir-an orally available inhibitor of the 3-chymotrypsin-like cysteine protease-has been shown to reduce the risk of progression to severe COVID-19. However, the impact of nirmatrelvir treatment on the development of SARS-CoV-2-specific adaptive immune responses is unknown. Here, by using mouse models of SARS-CoV-2 infection, we show that nirmatrelvir administration blunts the development of SARS-CoV-2-specific antibody and T cell responses. Accordingly, upon secondary challenge, nirmatrelvir-treated mice recruited significantly fewer memory T and B cells to the infected lungs and mediastinal lymph nodes, respectively. Together, the data highlight a potential negative impact of nirmatrelvir treatment with important implications for clinical management and might help explain the virological and/or symptomatic relapse after treatment completion reported in some individuals.
Collapse
Affiliation(s)
- Valeria Fumagalli
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
| | - Pietro Di Lucia
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
| | - Micol Ravà
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
| | - Davide Marotta
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
| | - Elisa Bono
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Stefano Grassi
- Pathology UnitIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Lorena Donnici
- INGM ‐ Istituto Nazionale di Genetica Molecolare “Romeo ed Erica Invernizzi”MilanItaly
| | - Rolando Cannalire
- Department of Pharmacy, School of Medicine and SurgeryUniversity of Naples Federico IINaplesItaly
| | - Irina Stefanelli
- Department of Pharmacy, School of Medicine and SurgeryUniversity of Naples Federico IINaplesItaly
| | - Anastasia Ferraro
- Department of Pharmacy, School of Medicine and SurgeryUniversity of Naples Federico IINaplesItaly
| | - Francesca Esposito
- Dipartimento di Scienze della Vita e dell'AmbienteCittadella Universitaria di MonserratoCagliariItaly
| | - Elena Pariani
- Department of Biomedical Sciences for HealthUniversity of MilanMilanItaly
| | - Donato Inverso
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
| | | | - Serena Delbue
- Department of Biomedical, Surgical and Dental SciencesUniversity of MilanMilanItaly
| | - Stanley Perlman
- Department of Microbiology and ImmunologyUniversity of IowaIowa CityIAUSA
- Department of PediatricsUniversity of IowaIowa CityIAUSA
| | - Enzo Tramontano
- Dipartimento di Scienze della Vita e dell'AmbienteCittadella Universitaria di MonserratoCagliariItaly
| | - Raffaele De Francesco
- INGM ‐ Istituto Nazionale di Genetica Molecolare “Romeo ed Erica Invernizzi”MilanItaly
- Department of Pharmacological and Biomolecular SciencesUniversity of MilanMilanItaly
| | - Vincenzo Summa
- Department of Pharmacy, School of Medicine and SurgeryUniversity of Naples Federico IINaplesItaly
| | - Luca G Guidotti
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
| | - Matteo Iannacone
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
- Experimental Imaging CenterIRCCS San Raffaele Scientific InstituteMilanItaly
| |
Collapse
|
44
|
Su P, Wu Y, Xie F, Zheng Q, Chen L, Liu Z, Meng X, Zhou F, Zhang L. A Review of Extracellular Vesicles in COVID-19 Diagnosis, Treatment, and Prevention. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023:e2206095. [PMID: 37144543 DOI: 10.1002/advs.202206095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 04/15/2023] [Indexed: 05/06/2023]
Abstract
The 2019 novel coronavirus disease (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is ongoing, and has necessitated scientific efforts in disease diagnosis, treatment, and prevention. Interestingly, extracellular vesicles (EVs) have been crucial in these developments. EVs are a collection of various nanovesicles which are delimited by a lipid bilayer. They are enriched in proteins, nucleic acids, lipids, and metabolites, and naturally released from different cells. Their natural material transport properties, inherent long-term recycling ability, excellent biocompatibility, editable targeting, and inheritance of parental cell properties make EVs one of the most promising next-generation drug delivery nanocarriers and active biologics. During the COVID-19 pandemic, many efforts have been made to exploit the payload of natural EVs for the treatment of COVID-19. Furthermore, strategies that use engineered EVs to manufacture vaccines and neutralization traps have produced excellent efficacy in animal experiments and clinical trials. Here, the recent literature on the application of EVs in COVID-19 diagnosis, treatment, damage repair, and prevention is reviewed. And the therapeutic value, application strategies, safety, and biotoxicity in the production and clinical applications of EV agents for COVID-19 treatment, as well as inspiration for using EVs to block and eliminate novel viruses are discussed.
Collapse
Affiliation(s)
- Peng Su
- Department of Breast Surgery, Zhejiang Provincial People's Hospital, Hangzhou, 310014, P. R. China
- Institutes of Biology and Medical Science, Soochow University, Suzhou, 215123, P. R. China
| | - Yuchen Wu
- Department of Clinical Medicine, The First School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, P. R. China
| | - Feng Xie
- Institutes of Biology and Medical Science, Soochow University, Suzhou, 215123, P. R. China
| | - Qinghui Zheng
- Department of Breast Surgery, Zhejiang Provincial People's Hospital, Hangzhou, 310014, P. R. China
| | - Long Chen
- Center for Translational Medicine, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang, Jiangsu, 215600, China
| | - Zhuang Liu
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Xuli Meng
- Department of Breast Surgery, Zhejiang Provincial People's Hospital, Hangzhou, 310014, P. R. China
| | - Fangfang Zhou
- Institutes of Biology and Medical Science, Soochow University, Suzhou, 215123, P. R. China
| | - Long Zhang
- Department of Breast Surgery, Zhejiang Provincial People's Hospital, Hangzhou, 310014, P. R. China
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, P. R. China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, P. R. China
| |
Collapse
|
45
|
Hersi F, Sebastian A, Tarazi H, Srinivasulu V, Mostafa A, Allayeh AK, Zeng C, Hachim IY, Liu SL, Abu-Yousef IA, Majdalawieh AF, Zaher DM, Omar HA, Al-Tel TH. Discovery of novel papain-like protease inhibitors for potential treatment of COVID-19. Eur J Med Chem 2023; 254:115380. [PMID: 37075625 PMCID: PMC10106510 DOI: 10.1016/j.ejmech.2023.115380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/09/2023] [Accepted: 04/12/2023] [Indexed: 04/21/2023]
Abstract
The recent emergence of different SARS-CoV-2 variants creates an urgent need to develop more effective therapeutic agents to prevent COVID-19 outbreaks. Among SARS-CoV-2 essential proteases is papain-like protease (SARS-CoV-2 PLpro), which plays multiple roles in regulating SARS-CoV-2 viral spread and innate immunity such as deubiquitinating and deISG15ylating (interferon-induced gene 15) activities. Many studies are currently focused on targeting this protease to tackle SARS-CoV-2 infection. In this context, we performed a phenotypic screening using an in-house pilot compounds collection possessing a diverse skeleta against SARS-CoV-2 PLpro. This screen identified SIMR3030 as a potent inhibitor of SARS-CoV-2. SIMR3030 has been shown to exhibit deubiquitinating activity and inhibition of SARS-CoV-2 specific gene expression (ORF1b and Spike) in infected host cells and possessing virucidal activity. Moreover, SIMR3030 was demonstrated to inhibit the expression of inflammatory markers, including IFN-α, IL-6, and OAS1, which are reported to mediate the development of cytokine storms and aggressive immune responses. In vitro absorption, distribution, metabolism, and excretion (ADME) assessment of the drug-likeness properties of SIMR3030 demonstrated good microsomal stability in liver microsomes. Furthermore, SIMR3030 demonstrated very low potency as an inhibitor of CYP450, CYP3A4, CYP2D6 and CYP2C9 which rules out any potential drug-drug interactions. In addition, SIMR3030 showed moderate permeability in Caco2-cells. Critically, SIMR3030 has maintained a high in vivo safety profile at different concentrations. Molecular modeling studies of SIMR3030 in the active sites of SARS-CoV-2 and MERS-CoV PLpro were performed to shed light on the binding modes of this inhibitor. This study demonstrates that SIMR3030 is a potent inhibitor of SARS-CoV-2 PLpro that forms the foundation for developing new drugs to tackle the COVID-19 pandemic and may pave the way for the development of novel therapeutics for a possible future outbreak of new SARS-CoV-2 variants or other Coronavirus species.
Collapse
Affiliation(s)
- Fatema Hersi
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates; College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Anusha Sebastian
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Hamadeh Tarazi
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Vunnam Srinivasulu
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, Environment and Climate Change Institute, National Research Centre, Giza, 12622, Egypt
| | - Abdou Kamal Allayeh
- Virology Lab 176, Water Pollution Research Department, Environment and Climate Change Institute, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Cong Zeng
- Center for Retrovirus Research, The Ohio State University, Columbus, OH, 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Ibrahim Y Hachim
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates; College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH, 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Imad A Abu-Yousef
- Department of Biology, Chemistry and Environmental Sciences, College of Arts and Sciences, American University of Sharjah, P.O. Box 26666, Sharjah, United Arab Emirates
| | - Amin F Majdalawieh
- Department of Biology, Chemistry and Environmental Sciences, College of Arts and Sciences, American University of Sharjah, P.O. Box 26666, Sharjah, United Arab Emirates
| | - Dana M Zaher
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates; College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Hany A Omar
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates; College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates; Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt.
| | - Taleb H Al-Tel
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates; College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates.
| |
Collapse
|
46
|
Pozzi C, Vanet A, Francesconi V, Tagliazucchi L, Tassone G, Venturelli A, Spyrakis F, Mazzorana M, Costi MP, Tonelli M. Antitarget, Anti-SARS-CoV-2 Leads, Drugs, and the Drug Discovery-Genetics Alliance Perspective. J Med Chem 2023; 66:3664-3702. [PMID: 36857133 PMCID: PMC10005815 DOI: 10.1021/acs.jmedchem.2c01229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
The most advanced antiviral molecules addressing major SARS-CoV-2 targets (Main protease, Spike protein, and RNA polymerase), compared with proteins of other human pathogenic coronaviruses, may have a short-lasting clinical efficacy. Accumulating knowledge on the mechanisms underlying the target structural basis, its mutational progression, and the related biological significance to virus replication allows envisaging the development of better-targeted therapies in the context of COVID-19 epidemic and future coronavirus outbreaks. The identification of evolutionary patterns based solely on sequence information analysis for those targets can provide meaningful insights into the molecular basis of host-pathogen interactions and adaptation, leading to drug resistance phenomena. Herein, we will explore how the study of observed and predicted mutations may offer valuable suggestions for the application of the so-called "synthetic lethal" strategy to SARS-CoV-2 Main protease and Spike protein. The synergy between genetics evidence and drug discovery may prioritize the development of novel long-lasting antiviral agents.
Collapse
Affiliation(s)
- Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy,
University of Siena, via Aldo Moro 2, 53100 Siena,
Italy
| | - Anne Vanet
- Université Paris Cité,
CNRS, Institut Jacques Monod, F-75013 Paris,
France
| | - Valeria Francesconi
- Department of Pharmacy, University of
Genoa, viale Benedetto XV n.3, 16132 Genoa, Italy
| | - Lorenzo Tagliazucchi
- Department of Life Science, University of
Modena and Reggio Emilia, via Campi 103, 41125 Modena,
Italy
- Doctorate School in Clinical and Experimental Medicine
(CEM), University of Modena and Reggio Emilia, Via Campi 287,
41125 Modena, Italy
| | - Giusy Tassone
- Department of Biotechnology, Chemistry and Pharmacy,
University of Siena, via Aldo Moro 2, 53100 Siena,
Italy
| | - Alberto Venturelli
- Department of Life Science, University of
Modena and Reggio Emilia, via Campi 103, 41125 Modena,
Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology,
University of Turin, Via Giuria 9, 10125 Turin,
Italy
| | - Marco Mazzorana
- Diamond Light Source, Harwell Science and
Innovation Campus, Didcot, Oxfordshire OX11 0DE,
U.K.
| | - Maria P. Costi
- Department of Life Science, University of
Modena and Reggio Emilia, via Campi 103, 41125 Modena,
Italy
| | - Michele Tonelli
- Department of Pharmacy, University of
Genoa, viale Benedetto XV n.3, 16132 Genoa, Italy
| |
Collapse
|
47
|
Brier L, Hassan H, Hanoulle X, Landry V, Moschidi D, Desmarets L, Rouillé Y, Dumont J, Herledan A, Warenghem S, Piveteau C, Carré P, Ikherbane S, Cantrelle FX, Dupré E, Dubuisson J, Belouzard S, Leroux F, Deprez B, Charton J. Novel dithiocarbamates selectively inhibit 3CL protease of SARS-CoV-2 and other coronaviruses. Eur J Med Chem 2023; 250:115186. [PMID: 36796300 PMCID: PMC9901219 DOI: 10.1016/j.ejmech.2023.115186] [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: 12/05/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023]
Abstract
Since end of 2019, the global and unprecedented outbreak caused by the coronavirus SARS-CoV-2 led to dramatic numbers of infections and deaths worldwide. SARS-CoV-2 produces two large viral polyproteins which are cleaved by two cysteine proteases encoded by the virus, the 3CL protease (3CLpro) and the papain-like protease, to generate non-structural proteins essential for the virus life cycle. Both proteases are recognized as promising drug targets for the development of anti-coronavirus chemotherapy. Aiming at identifying broad spectrum agents for the treatment of COVID-19 but also to fight emergent coronaviruses, we focused on 3CLpro that is well conserved within this viral family. Here we present a high-throughput screening of more than 89,000 small molecules that led to the identification of a new chemotype, potent inhibitor of the SARS-CoV-2 3CLpro. The mechanism of inhibition, the interaction with the protease using NMR and X-Ray, the specificity against host cysteine proteases and promising antiviral properties in cells are reported.
Collapse
Affiliation(s)
- Lucile Brier
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Haitham Hassan
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Xavier Hanoulle
- CNRS, EMR9002 - BSI - Integrative Structural Biology, F-59000, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000, Lille, France
| | - Valerie Landry
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Danai Moschidi
- CNRS, EMR9002 - BSI - Integrative Structural Biology, F-59000, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000, Lille, France
| | - Lowiese Desmarets
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Yves Rouillé
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Julie Dumont
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Adrien Herledan
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Sandrine Warenghem
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Catherine Piveteau
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Paul Carré
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Sarah Ikherbane
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - François-Xavier Cantrelle
- CNRS, EMR9002 - BSI - Integrative Structural Biology, F-59000, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000, Lille, France
| | - Elian Dupré
- CNRS, EMR9002 - BSI - Integrative Structural Biology, F-59000, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000, Lille, France
| | - Jean Dubuisson
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Sandrine Belouzard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Florence Leroux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, EGID, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Benoit Deprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, EGID, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France.
| | - Julie Charton
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, EGID, F-59000, Lille, France
| |
Collapse
|
48
|
Stefanelli I, Corona A, Cerchia C, Cassese E, Improta S, Costanzi E, Pelliccia S, Morasso S, Esposito F, Paulis A, Scognamiglio S, Di Leva FS, Storici P, Brindisi M, Tramontano E, Cannalire R, Summa V. Broad-spectrum coronavirus 3C-like protease peptidomimetic inhibitors effectively block SARS-CoV-2 replication in cells: Design, synthesis, biological evaluation, and X-ray structure determination. Eur J Med Chem 2023; 253:115311. [PMID: 37043904 PMCID: PMC10068823 DOI: 10.1016/j.ejmech.2023.115311] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/23/2023] [Accepted: 03/26/2023] [Indexed: 04/03/2023]
Abstract
Despite the approval of vaccines, monoclonal antibodies and restrictions during the pandemic, the demand for new efficacious and safe antivirals is compelling to boost the therapeutic arsenal against the COVID-19. The viral 3-chymotrypsin-like protease (3CLpro) is an essential enzyme for replication with high homology in the active site across CoVs and variants showing an almost unique specificity for Leu-Gln as P2-P1 residues, allowing the development of broad-spectrum inhibitors. The design, synthesis, biological activity, and cocrystal structural information of newly conceived peptidomimetic covalent reversible inhibitors are herein described. The inhibitors display an aldehyde warhead, a Gln mimetic at P1 and modified P2-P3 residues. Particularly, functionalized proline residues were inserted at P2 to stabilize the β-turn like bioactive conformation, modulating the affinity. The most potent compounds displayed low/sub-nM potency against the 3CLpro of SARS-CoV-2 and MERS-CoV and inhibited viral replication of three human CoVs, i.e. SARS-CoV-2, MERS-CoV, and HCoV 229 in different cell lines. Particularly, derivative 12 exhibited nM-low μM antiviral activity depending on the virus, and the highest selectivity index. Some compounds were co-crystallized with SARS-CoV-2 3CLpro validating our design. Altogether, these results foster future work toward broad-spectrum 3CLpro inhibitors to challenge CoVs related pandemics.
Collapse
|
49
|
Hamad M, AlKhamach DMH, Alsayadi LM, Sarhan SA, Saeed BQ, Sokovic M, Ben Hadda T, Soliman SSM. Alpha to Omicron (Variants of Concern): Mutation Journey, Vaccines, and Therapy. Viral Immunol 2023; 36:83-100. [PMID: 36695729 DOI: 10.1089/vim.2022.0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) initially emerged in December 2019 and has subsequently expanded globally, leading to the ongoing pandemic. The extensive spread of various SARS-CoV-2 variants possesses a serious public health threat. An extensive literature search along with deep analysis was performed to describe and evaluate the characteristics of SARS-CoV-2 variants of concern in relation to the effectiveness of the current vaccines and therapeutics. The obtained results showed that several significant mutations have evolved during the COVID-19 pandemic. The developed variants and their various structural mutations can compromise the effectiveness of several vaccines, escape the neutralizing antibodies, and limit the efficiency of available therapeutics. Furthermore, deep analysis of the available data enables the prediction of the future impact of virus mutations on the ongoing pandemic along with the selection of appropriate vaccines and therapeutics.
Collapse
Affiliation(s)
- Mohamad Hamad
- College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Dana M H AlKhamach
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
| | | | | | | | - Marina Sokovic
- Institute for Biological Research "Siniša Stanković," National Institute of the Republic of Serbia, University of Belgrade, Beograd, Serbia
| | - Taibi Ben Hadda
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, Oujda, Morocco
| | - Sameh S M Soliman
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
| |
Collapse
|
50
|
Brewitz L, Dumjahn L, Zhao Y, Owen CD, Laidlaw SM, Malla TR, Nguyen D, Lukacik P, Salah E, Crawshaw AD, Warren AJ, Trincao J, Strain-Damerell C, Carroll MW, Walsh MA, Schofield CJ. Alkyne Derivatives of SARS-CoV-2 Main Protease Inhibitors Including Nirmatrelvir Inhibit by Reacting Covalently with the Nucleophilic Cysteine. J Med Chem 2023; 66:2663-2680. [PMID: 36757959 PMCID: PMC9924091 DOI: 10.1021/acs.jmedchem.2c01627] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Indexed: 02/10/2023]
Abstract
Nirmatrelvir (PF-07321332) is a nitrile-bearing small-molecule inhibitor that, in combination with ritonavir, is used to treat infections by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Nirmatrelvir interrupts the viral life cycle by inhibiting the SARS-CoV-2 main protease (Mpro), which is essential for processing viral polyproteins into functional nonstructural proteins. We report studies which reveal that derivatives of nirmatrelvir and other Mpro inhibitors with a nonactivated terminal alkyne group positioned similarly to the electrophilic nitrile of nirmatrelvir can efficiently inhibit isolated Mpro and SARS-CoV-2 replication in cells. Mass spectrometric and crystallographic evidence shows that the alkyne derivatives inhibit Mpro by apparent irreversible covalent reactions with the active site cysteine (Cys145), while the analogous nitriles react reversibly. The results highlight the potential for irreversible covalent inhibition of Mpro and other nucleophilic cysteine proteases by alkynes, which, in contrast to nitriles, can be functionalized at their terminal position to optimize inhibition and selectivity, as well as pharmacodynamic and pharmacokinetic properties.
Collapse
Affiliation(s)
- Lennart Brewitz
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Leo Dumjahn
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Yilin Zhao
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - C. David Owen
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research
Complex at Harwell, Harwell Science and
Innovation Campus, Didcot OX11 0FA, United
Kingdom
| | - Stephen M. Laidlaw
- Wellcome
Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Tika R. Malla
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Dung Nguyen
- Wellcome
Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Petra Lukacik
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research
Complex at Harwell, Harwell Science and
Innovation Campus, Didcot OX11 0FA, United
Kingdom
| | - Eidarus Salah
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Adam D. Crawshaw
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Anna J. Warren
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Jose Trincao
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Claire Strain-Damerell
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research
Complex at Harwell, Harwell Science and
Innovation Campus, Didcot OX11 0FA, United
Kingdom
| | - Miles W. Carroll
- Wellcome
Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Martin A. Walsh
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research
Complex at Harwell, Harwell Science and
Innovation Campus, Didcot OX11 0FA, United
Kingdom
| | - Christopher J. Schofield
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| |
Collapse
|