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Janin YL. On the origins of SARS-CoV-2 main protease inhibitors. RSC Med Chem 2024; 15:81-118. [PMID: 38283212 PMCID: PMC10809347 DOI: 10.1039/d3md00493g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/13/2023] [Indexed: 01/30/2024] Open
Abstract
In order to address the world-wide health challenge caused by the COVID-19 pandemic, the 3CL protease/SARS-CoV-2 main protease (SARS-CoV-2-Mpro) coded by its nsp5 gene became one of the biochemical targets for the design of antiviral drugs. In less than 3 years of research, 4 inhibitors of SARS-CoV-2-Mpro have actually been authorized for COVID-19 treatment (nirmatrelvir, ensitrelvir, leritrelvir and simnotrelvir) and more such as EDP-235, FB-2001 and STI-1558/Olgotrelvir or five undisclosed compounds (CDI-988, ASC11, ALG-097558, QLS1128 and H-10517) are undergoing clinical trials. This review is an attempt to picture this quite unprecedented medicinal chemistry feat and provide insights on how these cysteine protease inhibitors were discovered. Since many series of covalent SARS-CoV-2-Mpro inhibitors owe some of their origins to previous work on other proteases, we first provided a description of various inhibitors of cysteine-bearing human caspase-1 or cathepsin K, as well as inhibitors of serine proteases such as human dipeptidyl peptidase-4 or the hepatitis C protein complex NS3/4A. This is then followed by a description of the results of the approaches adopted (repurposing, structure-based and high throughput screening) to discover coronavirus main protease inhibitors.
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Affiliation(s)
- Yves L Janin
- Structure et Instabilité des Génomes (StrInG), Muséum National d'Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université 75005 Paris France
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2
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Li X, Song Y. Structure and function of SARS-CoV and SARS-CoV-2 main proteases and their inhibition: A comprehensive review. Eur J Med Chem 2023; 260:115772. [PMID: 37659195 PMCID: PMC10529944 DOI: 10.1016/j.ejmech.2023.115772] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 09/04/2023]
Abstract
Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) identified in 2003 infected ∼8000 people in 26 countries with 800 deaths, which was soon contained and eradicated by syndromic surveillance and enhanced quarantine. A closely related coronavirus SARS-CoV-2, the causative agent of COVID-19 identified in 2019, has been dramatically more contagious and catastrophic. It has infected and caused various flu-like symptoms of billions of people in >200 countries, including >6 million people died of or with the virus. Despite the availability of several vaccines and antiviral drugs against SARS-CoV-2, finding new therapeutics is needed because of viral evolution and a possible emerging coronavirus in the future. The main protease (Mpro) of these coronaviruses plays important roles in their life cycle and is essential for the viral replication. This article represents a comprehensive review of the function, structure and inhibition of SARS-CoV and -CoV-2 Mpro, including structure-activity relationships, protein-inhibitor interactions and clinical trial status.
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Affiliation(s)
- Xin Li
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
| | - Yongcheng Song
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
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3
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Ruatta SM, Prada Gori DN, Fló Díaz M, Lorenzelli F, Perelmuter K, Alberca LN, Bellera CL, Medeiros A, López GV, Ingold M, Porcal W, Dibello E, Ihnatenko I, Kunick C, Incerti M, Luzardo M, Colobbio M, Ramos JC, Manta E, Minini L, Lavaggi ML, Hernández P, Šarlauskas J, Huerta García CS, Castillo R, Hernández-Campos A, Ribaudo G, Zagotto G, Carlucci R, Medrán NS, Labadie GR, Martinez-Amezaga M, Delpiccolo CML, Mata EG, Scarone L, Posada L, Serra G, Calogeropoulou T, Prousis K, Detsi A, Cabrera M, Alvarez G, Aicardo A, Araújo V, Chavarría C, Mašič LP, Gantner ME, Llanos MA, Rodríguez S, Gavernet L, Park S, Heo J, Lee H, Paul Park KH, Bollati-Fogolín M, Pritsch O, Shum D, Talevi A, Comini MA. Garbage in, garbage out: how reliable training data improved a virtual screening approach against SARS-CoV-2 MPro. Front Pharmacol 2023; 14:1193282. [PMID: 37426813 PMCID: PMC10323144 DOI: 10.3389/fphar.2023.1193282] [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: 03/24/2023] [Accepted: 05/31/2023] [Indexed: 07/11/2023] Open
Abstract
Introduction: The identification of chemical compounds that interfere with SARS-CoV-2 replication continues to be a priority in several academic and pharmaceutical laboratories. Computational tools and approaches have the power to integrate, process and analyze multiple data in a short time. However, these initiatives may yield unrealistic results if the applied models are not inferred from reliable data and the resulting predictions are not confirmed by experimental evidence. Methods: We undertook a drug discovery campaign against the essential major protease (MPro) from SARS-CoV-2, which relied on an in silico search strategy -performed in a large and diverse chemolibrary- complemented by experimental validation. The computational method comprises a recently reported ligand-based approach developed upon refinement/learning cycles, and structure-based approximations. Search models were applied to both retrospective (in silico) and prospective (experimentally confirmed) screening. Results: The first generation of ligand-based models were fed by data, which to a great extent, had not been published in peer-reviewed articles. The first screening campaign performed with 188 compounds (46 in silico hits and 100 analogues, and 40 unrelated compounds: flavonols and pyrazoles) yielded three hits against MPro (IC50 ≤ 25 μM): two analogues of in silico hits (one glycoside and one benzo-thiazol) and one flavonol. A second generation of ligand-based models was developed based on this negative information and newly published peer-reviewed data for MPro inhibitors. This led to 43 new hit candidates belonging to different chemical families. From 45 compounds (28 in silico hits and 17 related analogues) tested in the second screening campaign, eight inhibited MPro with IC50 = 0.12-20 μM and five of them also impaired the proliferation of SARS-CoV-2 in Vero cells (EC50 7-45 μM). Discussion: Our study provides an example of a virtuous loop between computational and experimental approaches applied to target-focused drug discovery against a major and global pathogen, reaffirming the well-known "garbage in, garbage out" machine learning principle.
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Affiliation(s)
- Santiago M. Ruatta
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Denis N. Prada Gori
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
| | - Martín Fló Díaz
- Laboratory of Immunovirology, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Inmunobiología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Franca Lorenzelli
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Karen Perelmuter
- Cell Biology Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Lucas N. Alberca
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Carolina L. Bellera
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Andrea Medeiros
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Gloria V. López
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Vascular Biology and Drug Discovery Lab, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Mariana Ingold
- Vascular Biology and Drug Discovery Lab, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Williams Porcal
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Vascular Biology and Drug Discovery Lab, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Estefanía Dibello
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Irina Ihnatenko
- PVZ—Center of Pharmaceutical Engineering, Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Conrad Kunick
- PVZ—Center of Pharmaceutical Engineering, Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Marcelo Incerti
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Martín Luzardo
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Maximiliano Colobbio
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Química Fina, Facultad de Química, Instituto Polo Tecnológico de Pando, Universidad de la República, Montevideo, Uruguay
| | - Juan Carlos Ramos
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Química Fina, Facultad de Química, Instituto Polo Tecnológico de Pando, Universidad de la República, Montevideo, Uruguay
| | - Eduardo Manta
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Química Fina, Facultad de Química, Instituto Polo Tecnológico de Pando, Universidad de la República, Montevideo, Uruguay
| | - Lucía Minini
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - María Laura Lavaggi
- Laboratorio de Química Biológica Ambiental, Sede Rivera, Centro Universitario Regional Noreste, Universidad de la República, Montevideo, Uruguay
| | - Paola Hernández
- Departamento de Genética, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Jonas Šarlauskas
- Life Sciences Centre, Department of Xenobiotic Biochemistry, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | | | - Rafael Castillo
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de Mexico, Mexico
| | - Alicia Hernández-Campos
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de Mexico, Mexico
| | - Giovanni Ribaudo
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Giuseppe Zagotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Renzo Carlucci
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química Rosario (IQUIR) UNR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Noelia S. Medrán
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química Rosario (IQUIR) UNR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Guillermo R. Labadie
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química Rosario (IQUIR) UNR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Maitena Martinez-Amezaga
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química Rosario (IQUIR) UNR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Carina M. L. Delpiccolo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química Rosario (IQUIR) UNR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Ernesto G. Mata
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química Rosario (IQUIR) UNR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Laura Scarone
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Laura Posada
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Gloria Serra
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | | | - Kyriakos Prousis
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Anastasia Detsi
- Laboratory of Organic Chemistry, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Mauricio Cabrera
- Laboratorio de Moléculas Bioactivas, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Paysandú, Uruguay
| | - Guzmán Alvarez
- Laboratorio de Moléculas Bioactivas, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Paysandú, Uruguay
| | - Adrián Aicardo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
- Departamento de Nutrición Clínica, Escuela de Nutrición, Universidad de la República, Montevideo, Uruguay
| | - Verena Araújo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
- Departamento de Alimentos, Escuela de Nutrición, Universidad de la República, Montevideo, Uruguay
| | - Cecilia Chavarría
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | | | - Melisa E. Gantner
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Manuel A. Llanos
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Santiago Rodríguez
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
| | - Luciana Gavernet
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Soonju Park
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam, Republic of Korea
| | - Jinyeong Heo
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam, Republic of Korea
| | - Honggun Lee
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam, Republic of Korea
| | - Kyu-Ho Paul Park
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam, Republic of Korea
| | | | - Otto Pritsch
- Laboratory of Immunovirology, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Inmunobiología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - David Shum
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam, Republic of Korea
| | - Alan Talevi
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Marcelo A. Comini
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
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4
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Anton DB, Galvez Bulhões Pedreira J, Zvirtes ML, Laufer SA, Ducati RG, Goettert M, Saraiva Macedo Timmers LF. Targeting SARS-CoV-2 Main Protease (MPro) with Kinase Inhibitors: A Promising Approach for Discovering Antiviral and Anti-inflammatory Molecules against SARS-CoV-2. J Chem Inf Model 2023. [PMID: 37329322 DOI: 10.1021/acs.jcim.3c00324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus infected over 688 million people worldwide, causing public health concern and approximately 6.8 million deaths due to COVID-19. COVID-19, especially severe cases, is characterized by exacerbated lung inflammation with an increase of pro-inflammatory cytokines. In addition to antiviral drugs, there is a need for anti-inflammatory therapies to treat all phases of COVID-19. One of the most attractive drug targets for COVID-19 is the SARS-CoV-2 main protease (MPro), an enzyme responsible for cleaving polyproteins formed after the translation of viral RNA, which is essential for viral replication. MPro inhibitors, therefore, have the potential to stop viral replication and act as antiviral drugs. Considering that several kinase inhibitors are known for their action in inflammatory pathways, this could also be investigated toward a potential anti-inflammatory treatment for COVID-19. Therefore, the use of kinase inhibitors against SARS-CoV-2 MPro may be a promising strategy to find molecules with dual activity─antiviral and anti-inflammatory. Considering this, the potential of six kinase inhibitors against SARS-CoV-2 MPro were evaluated in silico and in vitro, including Baricitinib, Tofacitinib, Ruxolitinib, BIRB-796, Skepinone-L, and Sorafenib. To assess the inhibitory potential of the kinase inhibitors, a continuous fluorescent-based enzyme activity assay was optimized with SARS-CoV-2 MPro and MCA-AVLQSGFR-K(Dnp)-K-NH2 (substrate). BIRB-796 and Baricitinib were identified as inhibitors of SARS-CoV-2 MPro, presenting IC50 values of 7.99 and 25.31 μM, respectively. As they are also known for their anti-inflammatory action, both are prototype compounds with the potential to present antiviral and anti-inflammatory activity against SARS-CoV-2 infection.
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Affiliation(s)
- Débora Bublitz Anton
- Biotechnology Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado CEP 95914-014, Brazil
| | - Júlia Galvez Bulhões Pedreira
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen 72076, Germany
| | - Maria Luiza Zvirtes
- Department of Medicine, Universidade do Vale do Taquari (Univates), Lajeado CEP 95914-014, Brazil
| | - Stefan A Laufer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen 72076, Germany
| | - Rodrigo Gay Ducati
- Biotechnology Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado CEP 95914-014, Brazil
- Department of Medicine, Universidade do Vale do Taquari (Univates), Lajeado CEP 95914-014, Brazil
| | - Márcia Goettert
- Biotechnology Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado CEP 95914-014, Brazil
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen 72076, Germany
- Medical Science Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado CEP 95914-014, Brazil
| | - Luis Fernando Saraiva Macedo Timmers
- Biotechnology Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado CEP 95914-014, Brazil
- Department of Medicine, Universidade do Vale do Taquari (Univates), Lajeado CEP 95914-014, Brazil
- Medical Science Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado CEP 95914-014, Brazil
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5
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Santos LH, Kronenberger T, Almeida RG, Silva EB, Rocha REO, Oliveira JC, Barreto LV, Skinner D, Fajtová P, Giardini MA, Woodworth B, Bardine C, Lourenço AL, Craik CS, Poso A, Podust LM, McKerrow JH, Siqueira-Neto JL, O’Donoghue AJ, da Silva
Júnior EN, Ferreira RS. Structure-Based Identification of Naphthoquinones and Derivatives as Novel Inhibitors of Main Protease M pro and Papain-like Protease PL pro of SARS-CoV-2. J Chem Inf Model 2022; 62:6553-6573. [PMID: 35960688 PMCID: PMC9397563 DOI: 10.1021/acs.jcim.2c00693] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Indexed: 01/07/2023]
Abstract
The worldwide COVID-19 pandemic caused by the coronavirus SARS-CoV-2 urgently demands novel direct antiviral treatments. The main protease (Mpro) and papain-like protease (PLpro) are attractive drug targets among coronaviruses due to their essential role in processing the polyproteins translated from the viral RNA. In this study, we virtually screened 688 naphthoquinoidal compounds and derivatives against Mpro of SARS-CoV-2. Twenty-four derivatives were selected and evaluated in biochemical assays against Mpro using a novel fluorogenic substrate. In parallel, these compounds were also assayed with SARS-CoV-2 PLpro. Four compounds inhibited Mpro with half-maximal inhibitory concentration (IC50) values between 0.41 μM and 9.0 μM. In addition, three compounds inhibited PLpro with IC50 ranging from 1.9 μM to 3.3 μM. To verify the specificity of Mpro and PLpro inhibitors, our experiments included an assessment of common causes of false positives such as aggregation, high compound fluorescence, and inhibition by enzyme oxidation. Altogether, we confirmed novel classes of specific Mpro and PLpro inhibitors. Molecular dynamics simulations suggest stable binding modes for Mpro inhibitors with frequent interactions with residues in the S1 and S2 pockets of the active site. For two PLpro inhibitors, interactions occur in the S3 and S4 pockets. In summary, our structure-based computational and biochemical approach identified novel naphthoquinonal scaffolds that can be further explored as SARS-CoV-2 antivirals.
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Affiliation(s)
- Lucianna H. Santos
- Department of Biochemistry and Immunology,
Federal University of Minas Gerais, Belo Horizonte, Minas
Gerais 31270-901, Brazil
| | - Thales Kronenberger
- Department of Oncology and Pneumonology, Internal
Medicine VIII, University Hospital Tübingen,
Otfried-Müller-Straße 10, DE72076 Tübingen,
Germany
- School of Pharmacy, Faculty of Health Sciences,
University of Eastern Finland, 70211 Kuopio,
Finland
- Institute of Pharmacy, Pharmaceutical/Medicinal
Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2),
Eberhard Karls University Tübingen, Auf der
Morgenstelle 8, 72076 Tübingen, Germany
| | - Renata G. Almeida
- Institute of Exact Sciences, Department of Chemistry,
Federal University of Minas Gerais, Belo Horizonte, Minas
Gerais 31270-901, Brazil
| | - Elany B. Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, 9500 Gilman Drive, La
Jolla, California 92093-0657, United States
| | - Rafael E. O. Rocha
- Department of Biochemistry and Immunology,
Federal University of Minas Gerais, Belo Horizonte, Minas
Gerais 31270-901, Brazil
| | - Joyce C. Oliveira
- Institute of Exact Sciences, Department of Chemistry,
Federal University of Minas Gerais, Belo Horizonte, Minas
Gerais 31270-901, Brazil
| | - Luiza V. Barreto
- Department of Biochemistry and Immunology,
Federal University of Minas Gerais, Belo Horizonte, Minas
Gerais 31270-901, Brazil
| | - Danielle Skinner
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, 9500 Gilman Drive, La
Jolla, California 92093-0657, United States
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, 9500 Gilman Drive, La
Jolla, California 92093-0657, United States
- Institute of Organic Chemistry and Biochemistry,
Academy of Sciences of the Czech Republic, 16610 Prague,
Czech Republic
| | - Miriam A. Giardini
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, 9500 Gilman Drive, La
Jolla, California 92093-0657, United States
| | - Brendon Woodworth
- Department of Medicine, Division of Infectious
Diseases, University of California San Diego, La Jolla,
California 92093, United States
| | - Conner Bardine
- Department of Pharmaceutical Chemistry,
University of California San Francisco, San Francisco,
California 94143, United States
| | - André L. Lourenço
- Department of Pharmaceutical Chemistry,
University of California San Francisco, San Francisco,
California 94143, United States
| | - Charles S. Craik
- Department of Pharmaceutical Chemistry,
University of California San Francisco, San Francisco,
California 94143, United States
| | - Antti Poso
- Department of Oncology and Pneumonology, Internal
Medicine VIII, University Hospital Tübingen,
Otfried-Müller-Straße 10, DE72076 Tübingen,
Germany
- School of Pharmacy, Faculty of Health Sciences,
University of Eastern Finland, 70211 Kuopio,
Finland
| | - Larissa M. Podust
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, 9500 Gilman Drive, La
Jolla, California 92093-0657, United States
| | - James H. McKerrow
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, 9500 Gilman Drive, La
Jolla, California 92093-0657, United States
| | - Jair L. Siqueira-Neto
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, 9500 Gilman Drive, La
Jolla, California 92093-0657, United States
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, 9500 Gilman Drive, La
Jolla, California 92093-0657, United States
| | - Eufrânio N. da Silva
Júnior
- Institute of Exact Sciences, Department of Chemistry,
Federal University of Minas Gerais, Belo Horizonte, Minas
Gerais 31270-901, Brazil
| | - Rafaela S. Ferreira
- Department of Biochemistry and Immunology,
Federal University of Minas Gerais, Belo Horizonte, Minas
Gerais 31270-901, Brazil
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6
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Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
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Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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7
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Manzer HS, Villarreal RI, Doran KS. Targeting the BspC-vimentin interaction to develop anti-virulence therapies during Group B streptococcal meningitis. PLoS Pathog 2022; 18:e1010397. [PMID: 35316308 PMCID: PMC8939794 DOI: 10.1371/journal.ppat.1010397] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/25/2022] [Indexed: 12/21/2022] Open
Abstract
Bacterial infections are a major cause of morbidity and mortality worldwide and the rise of antibiotic resistance necessitates development of alternative treatments. Pathogen adhesins that bind to host cells initiate disease pathogenesis and represent potential therapeutic targets. We have shown previously that the BspC adhesin in Group B Streptococcus (GBS), the leading cause of bacterial neonatal meningitis, interacts with host vimentin to promote attachment to brain endothelium and disease development. Here we determined that the BspC variable (V-) domain contains the vimentin binding site and promotes GBS adherence to brain endothelium. Site directed mutagenesis identified a binding pocket necessary for GBS host cell interaction and development of meningitis. Using a virtual structure-based drug screen we identified compounds that targeted the V-domain binding pocket, which blocked GBS adherence and entry into the brain in vivo. These data indicate the utility of targeting the pathogen-host interface to develop anti-virulence therapeutics.
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Affiliation(s)
- Haider S. Manzer
- University of Colorado Anschutz Medical Campus, Department of Immunology and Microbiology, Aurora, Colorado, United States of America
| | - Ricardo I. Villarreal
- University of Colorado Anschutz Medical Campus, Department of Immunology and Microbiology, Aurora, Colorado, United States of America
| | - Kelly S. Doran
- University of Colorado Anschutz Medical Campus, Department of Immunology and Microbiology, Aurora, Colorado, United States of America
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8
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Santos LH, Kronenberger T, Almeida RG, Silva EB, Rocha REO, Oliveira JC, Barreto LV, Skinner D, Fajtová P, Giardini MA, Woodworth B, Bardine C, Lourenço AL, Craik CS, Poso A, Podust LM, McKerrow JH, Siqueira-Neto JL, O'Donoghue AJ, da Silva Júnior EN, Ferreira RS. Structure-based identification of naphthoquinones and derivatives as novel inhibitors of main protease Mpro and papain-like protease PLpro of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.01.05.475095. [PMID: 35018373 PMCID: PMC8750648 DOI: 10.1101/2022.01.05.475095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The worldwide COVID-19 pandemic caused by the coronavirus SARS-CoV-2 urgently demands novel direct antiviral treatments. The main protease (Mpro) and papain-like protease (PLpro) are attractive drug targets among coronaviruses due to their essential role in processing the polyproteins translated from the viral RNA. In the present work, we virtually screened 688 naphthoquinoidal compounds and derivatives against Mpro of SARS-CoV-2. Twenty-four derivatives were selected and evaluated in biochemical assays against Mpro using a novel fluorogenic substrate. In parallel, these compounds were also assayed with SARS-CoV-2 PLpro. Four compounds inhibited Mpro with half-maximal inhibitory concentration (IC 50 ) values between 0.41 µM and 66 µM. In addition, eight compounds inhibited PLpro with IC 50 ranging from 1.7 µM to 46 µM. Molecular dynamics simulations suggest stable binding modes for Mpro inhibitors with frequent interactions with residues in the S1 and S2 pockets of the active site. For two PLpro inhibitors, interactions occur in the S3 and S4 pockets. In summary, our structure-based computational and biochemical approach identified novel naphthoquinonal scaffolds that can be further explored as SARS-CoV-2 antivirals.
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9
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Gentile F, Fernandez M, Ban F, Ton AT, Mslati H, Perez CF, Leblanc E, Yaacoub JC, Gleave J, Stern A, Wong B, Jean F, Strynadka N, Cherkasov A. Automated discovery of noncovalent inhibitors of SARS-CoV-2 main protease by consensus Deep Docking of 40 billion small molecules. Chem Sci 2021; 12:15960-15974. [PMID: 35024120 PMCID: PMC8672713 DOI: 10.1039/d1sc05579h] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 11/12/2021] [Indexed: 12/24/2022] Open
Abstract
Recent explosive growth of 'make-on-demand' chemical libraries brought unprecedented opportunities but also significant challenges to the field of computer-aided drug discovery. To address this expansion of the accessible chemical universe, molecular docking needs to accurately rank billions of chemical structures, calling for the development of automated hit-selecting protocols to minimize human intervention and error. Herein, we report the development of an artificial intelligence-driven virtual screening pipeline that utilizes Deep Docking with Autodock GPU, Glide SP, FRED, ICM and QuickVina2 programs to screen 40 billion molecules against SARS-CoV-2 main protease (Mpro). This campaign returned a significant number of experimentally confirmed inhibitors of Mpro enzyme, and also enabled to benchmark the performance of twenty-eight hit-selecting strategies of various degrees of stringency and automation. These findings provide new starting scaffolds for hit-to-lead optimization campaigns against Mpro and encourage the development of fully automated end-to-end drug discovery protocols integrating machine learning and human expertise.
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Affiliation(s)
- Francesco Gentile
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia 2660 Oak Street Vancouver BC V6H3Z6 Canada
| | - Michael Fernandez
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia 2660 Oak Street Vancouver BC V6H3Z6 Canada
| | - Fuqiang Ban
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia 2660 Oak Street Vancouver BC V6H3Z6 Canada
| | - Anh-Tien Ton
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia 2660 Oak Street Vancouver BC V6H3Z6 Canada
| | - Hazem Mslati
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia 2660 Oak Street Vancouver BC V6H3Z6 Canada
| | - Carl F Perez
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia 2660 Oak Street Vancouver BC V6H3Z6 Canada
| | - Eric Leblanc
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia 2660 Oak Street Vancouver BC V6H3Z6 Canada
| | - Jean Charle Yaacoub
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia 2660 Oak Street Vancouver BC V6H3Z6 Canada
| | - James Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia 2660 Oak Street Vancouver BC V6H3Z6 Canada
| | | | | | - François Jean
- Department of Microbiology and Immunology, The University of British Columbia Vancouver BC Canada
| | - Natalie Strynadka
- Department of Biochemistry and Molecular Biology, The University of British Columbia Vancouver BC Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia 2660 Oak Street Vancouver BC V6H3Z6 Canada
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10
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Yan F, Gao F. An overview of potential inhibitors targeting non-structural proteins 3 (PL pro and Mac1) and 5 (3CL pro/M pro) of SARS-CoV-2. Comput Struct Biotechnol J 2021; 19:4868-4883. [PMID: 34457214 PMCID: PMC8382591 DOI: 10.1016/j.csbj.2021.08.036] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 08/02/2021] [Accepted: 08/21/2021] [Indexed: 12/11/2022] Open
Abstract
There is an urgent need to develop effective treatments for coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The rapid spread of SARS-CoV-2 has resulted in a global pandemic that has not only affected the daily lives of individuals but also had a significant impact on the global economy and public health. Although extensive research has been conducted to identify inhibitors targeting SARS-CoV-2, there are still no effective treatment strategies to combat COVID-19. SARS-CoV-2 comprises two important proteolytic enzymes, namely, the papain-like proteinase, located within non-structural protein 3 (nsp3), and nsp5, both of which cleave large replicase polypeptides into multiple fragments that are required for viral replication. Moreover, a domain within nsp3, known as the macrodomain (Mac1), also plays an important role in viral replication. Inhibition of their functions should be able to significantly interfere with the replication cycle of the virus, and therefore these key proteins may serve as potential therapeutic targets. The functions of the above viral targets and their corresponding inhibitors have been summarized in the current review. This review provides comprehensive updates of nsp3 and nsp5 inhibitor development and would help advance the discovery of novel anti-viral therapeutics against SARS-CoV-2.
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Affiliation(s)
- Fangfang Yan
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
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11
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Amendola G, Ettari R, Previti S, Di Chio C, Messere A, Di Maro S, Hammerschmidt SJ, Zimmer C, Zimmermann RA, Schirmeister T, Zappalà M, Cosconati S. Lead Discovery of SARS-CoV-2 Main Protease Inhibitors through Covalent Docking-Based Virtual Screening. J Chem Inf Model 2021; 61:2062-2073. [PMID: 33784094 PMCID: PMC8029447 DOI: 10.1021/acs.jcim.1c00184] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Indexed: 12/13/2022]
Abstract
During almost all 2020, coronavirus disease 2019 (COVID-19) pandemic has constituted the major risk for the worldwide health and economy, propelling unprecedented efforts to discover drugs for its prevention and cure. At the end of the year, these efforts have culminated with the approval of vaccines by the American Food and Drug Administration (FDA) and the European Medicines Agency (EMA) giving new hope for the future. On the other hand, clinical data underscore the urgent need for effective drugs to treat COVID-19 patients. In this work, we embarked on a virtual screening campaign against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Mpro chymotrypsin-like cysteine protease employing our in-house database of peptide and non-peptide ligands characterized by different types of warheads acting as Michael acceptors. To this end, we employed the AutoDock4 docking software customized to predict the formation of a covalent adduct with the target protein. In vitro verification of the inhibition properties of the most promising candidates allowed us to identify two new lead inhibitors that will deserve further optimization. From the computational point of view, this work demonstrates the predictive power of AutoDock4 and suggests its application for the in silico screening of large chemical libraries of potential covalent binders against the SARS-CoV-2 Mpro enzyme.
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Affiliation(s)
- Giorgio Amendola
- DiSTABiF, University of Campania Luigi
Vanvitelli, Via Vivaldi 43, Caserta 81100, Italy
| | - Roberta Ettari
- Department of Chemical, Biological, Pharmaceutical,
and Environmental Sciences, University of Messina, Viale
Annunziata, Messina 98168, Italy
| | - Santo Previti
- Department of Chemical, Biological, Pharmaceutical,
and Environmental Sciences, University of Messina, Viale
Annunziata, Messina 98168, Italy
| | - Carla Di Chio
- Department of Chemical, Biological, Pharmaceutical,
and Environmental Sciences, University of Messina, Viale
Annunziata, Messina 98168, Italy
| | - Anna Messere
- DiSTABiF, University of Campania Luigi
Vanvitelli, Via Vivaldi 43, Caserta 81100, Italy
| | - Salvatore Di Maro
- DiSTABiF, University of Campania Luigi
Vanvitelli, Via Vivaldi 43, Caserta 81100, Italy
| | - Stefan J. Hammerschmidt
- Institute of Pharmaceutical and Biomedical Sciences,
University of Mainz, Staudingerweg 5, Mainz 55128,
Germany
| | - Collin Zimmer
- Institute of Pharmaceutical and Biomedical Sciences,
University of Mainz, Staudingerweg 5, Mainz 55128,
Germany
| | - Robert A. Zimmermann
- Institute of Pharmaceutical and Biomedical Sciences,
University of Mainz, Staudingerweg 5, Mainz 55128,
Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences,
University of Mainz, Staudingerweg 5, Mainz 55128,
Germany
| | - Maria Zappalà
- Department of Chemical, Biological, Pharmaceutical,
and Environmental Sciences, University of Messina, Viale
Annunziata, Messina 98168, Italy
| | - Sandro Cosconati
- DiSTABiF, University of Campania Luigi
Vanvitelli, Via Vivaldi 43, Caserta 81100, Italy
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12
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Mengist HM, Dilnessa T, Jin T. Structural Basis of Potential Inhibitors Targeting SARS-CoV-2 Main Protease. Front Chem 2021; 9:622898. [PMID: 33889562 PMCID: PMC8056153 DOI: 10.3389/fchem.2021.622898] [Citation(s) in RCA: 173] [Impact Index Per Article: 57.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/04/2021] [Indexed: 12/23/2022] Open
Abstract
The Coronavirus disease-19 (COVID-19) pandemic is still devastating the world causing significant social, economic, and political chaos. Corresponding to the absence of globally approved antiviral drugs for treatment and vaccines for controlling the pandemic, the number of cases and/or mortalities are still rising. Current patient management relies on supportive treatment and the use of repurposed drugs as an indispensable option. Of a crucial role in the viral life cycle, ongoing studies are looking for potential inhibitors to the main protease (Mpro) of severe acute respiratory syndrome Coronavirus -2 (SARS-CoV-2) to tackle the pandemic. Although promising results have been achieved in searching for drugs inhibiting the Mpro, work remains to be done on designing structure-based improved drugs. This review discusses the structural basis of potential inhibitors targeting SARS-CoV-2 Mpro, identifies gaps, and provides future directions. Further, compounds with potential Mpro based antiviral activity are highlighted.
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Affiliation(s)
- Hylemariam Mihiretie Mengist
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of innate immunity and chronic disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Department of Medical Laboratory Science, College of Health Science, Debre Markos University, Debre Markos, Ethiopia
| | - Tebelay Dilnessa
- Department of Medical Laboratory Science, College of Health Science, Debre Markos University, Debre Markos, Ethiopia
| | - Tengchuan Jin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of innate immunity and chronic disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Science, Shanghai, China
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