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Polge C, Cabantous S, Taillandier D. Tripartite Split-GFP for High Throughput Screening of Small Molecules: A Powerful Strategy for Targeting Transient/Labile Interactors like E2-E3 Ubiquitination Enzymes. Chembiochem 2024; 25:e202300723. [PMID: 38088048 DOI: 10.1002/cbic.202300723] [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: 10/20/2023] [Revised: 12/05/2023] [Indexed: 01/13/2024]
Abstract
The search for inhibitors of the Ubiquitin Proteasome System (UPS) is an expanding area, due to the crucial role of UPS enzymes in several diseases. The complexity of the UPS and the multiple protein-protein interactions (PPIs) involved, either between UPS proteins themselves or between UPS components and theirs targets, offer an incredibly wide field for the development of chemical compounds for specifically modulating or inhibiting metabolic pathways. However, numerous UPS PPIs are transient/labile, due the processivity of the system (Ubiquitin [Ub] chain elongation, Ub transfer, etc.). Among the different strategies that can be used either for deciphering UPS PPI or for identifying/characterizing small compounds inhibitors, the split-GFP approach offers several advantages notably for high throughput screening of drugs. Split-GFP is based on the principle of protein-fragment complementation assay (PCA). PCA allows addressing PPIs by coupling each protein of interest (POI) to fragments of a reporter protein whose reconstitution is linked to the interaction of the POI. Here, we review the evolution of the split-GFP approach from bipartite to tripartite Split-GFP and its recent applicability for screening chemical compounds targeting the UPS.
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Affiliation(s)
- Cécile Polge
- Université Clermont Auvergne INRAE, UNH, Unité de Nutrition Humaine, F-63000, Clermont-Ferrand, France
| | - Stéphanie Cabantous
- Cancer Research Center of Toulouse INSERM UMR 1037, Université de Toulouse, F-31037, Toulouse, France
| | - Daniel Taillandier
- Université Clermont Auvergne INRAE, UNH, Unité de Nutrition Humaine, F-63000, Clermont-Ferrand, France
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2
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Nunes C, Anckaert J, De Vloed F, De Wyn J, Durinck K, Vandesompele J, Speleman F, Vermeirssen V. HTSplotter: An end-to-end data processing, analysis and visualisation tool for chemical and genetic in vitro perturbation screening. PLoS One 2024; 19:e0296322. [PMID: 38181013 PMCID: PMC10769073 DOI: 10.1371/journal.pone.0296322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 12/11/2023] [Indexed: 01/07/2024] Open
Abstract
In biomedical research, high-throughput screening is often applied as it comes with automatization, higher-efficiency, and more and faster results. High-throughput screening experiments encompass drug, drug combination, genetic perturbagen or a combination of genetic and chemical perturbagen screens. These experiments are conducted in real-time assays over time or in an endpoint assay. The data analysis consists of data cleaning and structuring, as well as further data processing and visualisation, which, due to the amount of data, can easily become laborious, time-consuming and error-prone. Therefore, several tools have been developed to aid researchers in this process, but these typically focus on specific experimental set-ups and are unable to process data of several time points and genetic-chemical perturbagen screens. To meet these needs, we developed HTSplotter, a web tool and Python module that performs automatic data analysis and visualization of visualization of eitherendpoint or real-time assays from different high-throughput screening experiments: drug, drug combination, genetic perturbagen and genetic-chemical perturbagen screens. HTSplotter implements an algorithm based on conditional statements to identify experiment types and controls. After appropriate data normalization, including growth rate normalization, HTSplotter executes downstream analyses such as dose-response relationship and drug synergism assessment by the Bliss independence (BI), Zero Interaction Potency (ZIP) and Highest Single Agent (HSA) methods. All results are exported as a text file and plots are saved in a PDF file. The main advantage of HTSplotter over other available tools is the automatic analysis of genetic-chemical perturbagen screens and real-time assays where growth rate and perturbagen effect results are plotted over time. In conclusion, HTSplotter allows for the automatic end-to-end data processing, analysis and visualisation of various high-throughput in vitro cell culture screens, offering major improvements in terms of versatility, efficiency and time over existing tools.
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Affiliation(s)
- Carolina Nunes
- Lab for Computational Biology, Integromics and Gene Regulation (CBIGR), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Pediatric Precision Oncology Lab (PPOL), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Jasper Anckaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Fanny De Vloed
- Pediatric Precision Oncology Lab (PPOL), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Jolien De Wyn
- Pediatric Precision Oncology Lab (PPOL), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Kaat Durinck
- Pediatric Precision Oncology Lab (PPOL), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Frank Speleman
- Pediatric Precision Oncology Lab (PPOL), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Vanessa Vermeirssen
- Lab for Computational Biology, Integromics and Gene Regulation (CBIGR), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Pediatric Precision Oncology Lab (PPOL), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
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3
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Song L, Gao S, Ye B, Yang M, Cheng Y, Kang D, Yi F, Sun JP, Menéndez-Arias L, Neyts J, Liu X, Zhan P. Medicinal chemistry strategies towards the development of non-covalent SARS-CoV-2 M pro inhibitors. Acta Pharm Sin B 2024; 14:87-109. [PMID: 38239241 PMCID: PMC10792984 DOI: 10.1016/j.apsb.2023.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/10/2023] [Accepted: 08/02/2023] [Indexed: 01/22/2024] Open
Abstract
The main protease (Mpro) of SARS-CoV-2 is an attractive target in anti-COVID-19 therapy for its high conservation and major role in the virus life cycle. The covalent Mpro inhibitor nirmatrelvir (in combination with ritonavir, a pharmacokinetic enhancer) and the non-covalent inhibitor ensitrelvir have shown efficacy in clinical trials and have been approved for therapeutic use. Effective antiviral drugs are needed to fight the pandemic, while non-covalent Mpro inhibitors could be promising alternatives due to their high selectivity and favorable druggability. Numerous non-covalent Mpro inhibitors with desirable properties have been developed based on available crystal structures of Mpro. In this article, we describe medicinal chemistry strategies applied for the discovery and optimization of non-covalent Mpro inhibitors, followed by a general overview and critical analysis of the available information. Prospective viewpoints and insights into current strategies for the development of non-covalent Mpro inhibitors are also discussed.
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Affiliation(s)
- Letian Song
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Shenghua Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Shenzhen Research Institute of Shandong University, Shenzhen 518057, China
| | - Bing Ye
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Mianling Yang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Yusen Cheng
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Fan Yi
- The Key Laboratory of Infection and Immunity of Shandong Province, Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan 250012, China
| | - Jin-Peng Sun
- Key Laboratory Experimental Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Luis Menéndez-Arias
- Centro de Biología Molecular “Severo Ochoa” (Consejo Superior de Investigaciones Científicas & Autonomous University of Madrid), Madrid 28049, Spain
| | - Johan Neyts
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven 3000, Belgium
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
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4
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Shi YJ, Li JQ, Zhang HQ, Deng CL, Zhu QX, Zhang B, Li XD. A high throughput antiviral screening platform for alphaviruses based on Semliki Forest virus expressing eGFP reporter gene. Virol Sin 2023; 38:585-594. [PMID: 37390870 PMCID: PMC10436050 DOI: 10.1016/j.virs.2023.06.007] [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: 02/03/2023] [Accepted: 06/20/2023] [Indexed: 07/02/2023] Open
Abstract
Alphaviruses, which contain a variety of mosquito-borne pathogens, are important pathogens of emerging/re-emerging infectious diseases and potential biological weapons. Currently, no specific antiviral drugs are available for the treatment of alphaviruses infection. For most highly pathogenic alphaviruses are classified as risk group-3 agents, the requirement of biosafety level 3 (BSL-3) facilities limits the live virus-based antiviral study. To facilitate the antiviral development of alphaviruses, we developed a high throughput screening (HTS) platform based on a recombinant Semliki Forest virus (SFV) which can be manipulated in BSL-2 laboratory. Using the reverse genetics approach, the recombinant SFV and SFV reporter virus expressing eGFP (SFV-eGFP) were successfully rescued. The SFV-eGFP reporter virus exhibited robust eGFP expression and remained relatively stable after four passages in BHK-21 cells. Using a broad-spectrum alphavirus inhibitor ribavirin, we demonstrated that the SFV-eGFP can be used as an effective tool for antiviral study. The SFV-eGFP reporter virus-based HTS assay in a 96-well format was then established and optimized with a robust Z' score. A section of reference compounds that inhibit highly pathogenic alphaviruses were used to validate that the SFV-eGFP reporter virus-based HTS assay enables rapid screening of potent broad-spectrum inhibitors of alphaviruses. This assay provides a safe and convenient platform for antiviral study of alphaviruses.
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Affiliation(s)
- Yu-Jia Shi
- Hunan Normal University, School of Medicine, Changsha, 410081, China
| | - Jia-Qi Li
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong-Qing Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cheng-Lin Deng
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qin-Xuan Zhu
- Hunan Normal University, School of Medicine, Changsha, 410081, China
| | - Bo Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiao-Dan Li
- Hunan Normal University, School of Medicine, Changsha, 410081, China.
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5
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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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6
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Smith E, Davis-Gardner ME, Garcia-Ordonez RD, Nguyen TT, Hull M, Chen E, Yu X, Bannister TD, Baillargeon P, Scampavia L, Griffin P, Farzan M, Spicer TP. High throughput screening for drugs that inhibit 3C-like protease in SARS-CoV-2. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:95-101. [PMID: 36646172 PMCID: PMC9839384 DOI: 10.1016/j.slasd.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/14/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023]
Abstract
The SARS coronavirus 2 (SARS-CoV-2) pandemic remains a major problem in many parts of the world and infection rates remain at extremely high levels. This high prevalence drives the continued emergence of new variants, and possibly ones that are more vaccine-resistant and that can drive infections even in highly vaccinated populations. The high rate of variant evolution makes clear the need for new therapeutics that can be clinically applied to minimize or eliminate the effects of COVID-19. With a hurdle of 10 years, on average, for first in class small molecule therapeutics to achieve FDA approval, the fastest way to identify therapeutics is by drug repurposing. To this end, we developed a high throughput cell-based screen that incorporates the essential viral 3C-like protease and its peptide cleavage site into a luciferase complementation assay to evaluate the efficacy of known drugs encompassing approximately 15,000 clinical-stage or FDA-approved small molecules. Confirmed inhibitors were also tested to determine their cytotoxic properties. Medicinal chemistry efforts to optimize the hits identified Tranilast as a potential lead. Here, we report the rapid screening and identification of potentially relevant drugs that exhibit selective inhibition of the SARS-CoV-2 viral 3C-like protease.
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Affiliation(s)
- Emery Smith
- Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, FL 33458, United States
| | | | - Ruben D Garcia-Ordonez
- Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, FL 33458, United States
| | - Tu-Trinh Nguyen
- Calibr at Scripps Research, La Jolla, CA 92037, United States
| | - Mitchell Hull
- Calibr at Scripps Research, La Jolla, CA 92037, United States
| | - Emily Chen
- Calibr at Scripps Research, La Jolla, CA 92037, United States
| | - Xuerong Yu
- Department of Chemistry, UF Scripps Biomedical Research, Jupiter, FL 33458, United States
| | - Thomas D Bannister
- Department of Chemistry, UF Scripps Biomedical Research, Jupiter, FL 33458, United States
| | - Pierre Baillargeon
- Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, FL 33458, United States
| | - Louis Scampavia
- Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, FL 33458, United States
| | - Patrick Griffin
- Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, FL 33458, United States
| | - Michael Farzan
- Immunology and Microbiology, UF Scripps Biomedical Research, Jupiter, FL 33458, United States
| | - Timothy P Spicer
- Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, FL 33458, United States.
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7
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Yang Z, Cai X, Ye Q, Zhao Y, Li X, Zhang S, Zhang L. High-Throughput Screening for the Potential Inhibitors of SARS-CoV-2 with Essential Dynamic Behavior. Curr Drug Targets 2023; 24:532-545. [PMID: 36876836 DOI: 10.2174/1389450124666230306141725] [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: 06/18/2022] [Revised: 11/09/2022] [Accepted: 01/11/2023] [Indexed: 03/07/2023]
Abstract
Global health security has been challenged by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic. Due to the lengthy process of generating vaccinations, it is vital to reposition currently available drugs in order to relieve anti-epidemic tensions and accelerate the development of therapies for Coronavirus Disease 2019 (COVID-19), the public threat caused by SARS-CoV-2. High throughput screening techniques have established their roles in the evaluation of already available medications and the search for novel potential agents with desirable chemical space and more cost-effectiveness. Here, we present the architectural aspects of highthroughput screening for SARS-CoV-2 inhibitors, especially three generations of virtual screening methodologies with structural dynamics: ligand-based screening, receptor-based screening, and machine learning (ML)-based scoring functions (SFs). By outlining the benefits and drawbacks, we hope that researchers will be motivated to adopt these methods in the development of novel anti- SARS-CoV-2 agents.
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Affiliation(s)
- Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Xinhui Cai
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Qiushi Ye
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Yizhen Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Xuhua Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
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8
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Discovery of Novel Thioquinazoline- N-aryl-acetamide/ N-arylacetohydrazide Hybrids as Anti-SARS-CoV-2 Agents: Synthesis, in vitro Biological Evaluation, and Molecular Docking Studies. J Mol Struct 2022; 1276:134690. [PMCID: PMC9709698 DOI: 10.1016/j.molstruc.2022.134690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/10/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022]
Abstract
In the current investigation, two novel series of (tetrahydro)thioquinazoline-N-arylacetamides and (tetrahydro)thioquinazoline-N-arylacetohydrazides were designed, synthesized and investigated for their antiviral activity against SARS-CoV-2. The thioquinazoline-N-arylacetamide 17g as well as the tetrahydrothioquinazoline-N-arylacetohydrazides 18c and 18f showed potent antiviral activity with IC50 of 21.4, 38.45 and 26.4 µM, respectively. In addition, 18c and 18f demonstrated potential selectivity toward the SARS-CoV-2 over the host cells with SI of 10.67 and 16.04, respectively. Further evaluation of the mechanism of action of the three derivatives 17g, 18c, and 18f displayed that they can inhibit the virus at the adsorption as well as at the replication stages, in addition to their virucidal properties. In addition, 17g, 18c, and 18f demonstrated satisfactory physicochemical properties as well as drug-likeness properties to be further optimized for the discovery of novel antiviral agents. The docking simulation predicted the binding pattern of the target compounds rationalizing their differential activity based on their hydrophobic interaction and fitting in the hydrophobic S2 subsite of the binding site
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9
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Discovery and structural characterization of chicoric acid as a SARS-CoV-2 nucleocapsid protein ligand and RNA binding disruptor. Sci Rep 2022; 12:18500. [PMID: 36323732 PMCID: PMC9628480 DOI: 10.1038/s41598-022-22576-4] [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: 06/03/2022] [Accepted: 10/17/2022] [Indexed: 01/06/2023] Open
Abstract
The nucleocapsid (N) protein plays critical roles in coronavirus genome transcription and packaging, representing a key target for the development of novel antivirals, and for which structural information on ligand binding is scarce. We used a novel fluorescence polarization assay to identify small molecules that disrupt the binding of the N protein to a target RNA derived from the SARS-CoV-2 genome packaging signal. Several phenolic compounds, including L-chicoric acid (CA), were identified as high-affinity N-protein ligands. The binding of CA to the N protein was confirmed by isothermal titration calorimetry, 1H-STD and 15N-HSQC NMR, and by the crystal structure of CA bound to the N protein C-terminal domain (CTD), further revealing a new modulatory site in the SARS-CoV-2 N protein. Moreover, CA reduced SARS-CoV-2 replication in cell cultures. These data thus open venues for the development of new antivirals targeting the N protein, an essential and yet underexplored coronavirus target.
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10
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Puhl AC, Mottin M, Sacramento CQ, Tavella TA, Dias GG, Fintelman-Rodrigues N, Temerozo JR, Dias SSG, Ramos PRPS, Merten EM, Pearce KH, Costa FT, Premkumar L, Souza TML, Andrade CH, Ekins S. Computational and Experimental Approaches Identify Beta-Blockers as Potential SARS-CoV-2 Spike Inhibitors. ACS OMEGA 2022; 7:27950-27958. [PMID: 35983371 PMCID: PMC9380819 DOI: 10.1021/acsomega.2c01707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Finding antivirals for SARS-CoV-2 is still a major challenge, and many computational and experimental approaches have been employed to find a solution to this problem. While the global vaccination campaigns are the primary driver of controlling the current pandemic, orally bioavailable small-molecule drugs and biologics are critical to overcome this global issue. Improved therapeutics and prophylactics are required to treat people with circulating and emerging new variants, addressing severe infection, and people with underlying or immunocompromised conditions. The SARS-CoV-2 envelope spike is a challenging target for viral entry inhibitors. Pindolol presented a good docking score in a previous virtual screening using computational docking calculations after screening a Food and Drug Administration (FDA)-approved drug library of 2400 molecules as potential candidates to block the SARS-CoV-2 spike protein interaction with the angiotensin-converting enzyme 2 (ACE-2). Here, we expanded the computational evaluation to identify five beta-blockers against SARS-CoV-2 using several techniques, such as microscale thermophoresis, NanoDSF, and in vitro assays in different cell lines. These data identified carvedilol with a K d of 364 ± 22 nM for the SARS-CoV-2 spike and in vitro activity (EC50 of 7.57 μM, CC50 of 18.07 μM) against SARS-CoV-2 in Calu-3 cells. We have shown how we can apply multiple computational and experimental approaches to find molecules that can be further optimized to improve anti-SARS-CoV-2 activity.
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Affiliation(s)
- Ana C. Puhl
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Melina Mottin
- LabMol
- Laboratory of Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia 74605-170, GO, Brazil
- Pathogen-Host
Interface Laboratory, Department of Cell Biology, University of Brasilia, Brasilia 70910-900, Brazil
| | - Carolina Q. Sacramento
- Laboratory
of Immunopharmacology, Oswaldo Cruz Institute—Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil
- Center
of Technological Development in Health (CDTS)/National Institute of
Science and Technology for Innovation on Neglected Population Diseases
(INCT-IDPN), Rio de Janeiro 21040-900, RJ, Brazil
| | - Tatyana Almeida Tavella
- Laboratory
of Tropical Diseases—Prof. Dr. Luiz Jacinto da Silva, Department
of Genetics, Evolution, Microbiology and Immunology, University of Campinas-UNICAMP, Campinas 13083-970, SP, Brazil
| | - Gabriel Gonçalves Dias
- LabMol
- Laboratory of Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia 74605-170, GO, Brazil
| | - Natalia Fintelman-Rodrigues
- Laboratory
of Immunopharmacology, Oswaldo Cruz Institute—Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil
- Center
of Technological Development in Health (CDTS)/National Institute of
Science and Technology for Innovation on Neglected Population Diseases
(INCT-IDPN), Rio de Janeiro 21040-900, RJ, Brazil
| | - Jairo R. Temerozo
- Laboratory
on Thymus Research, Oswaldo Cruz Institute—Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil
- National
Institute for Science and Technology on Neuroimmunomodulation (INCT/NIM), Oswaldo Cruz Institute—Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil
| | - Suelen S. G. Dias
- Laboratory
of Immunopharmacology, Oswaldo Cruz Institute—Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil
| | | | - Eric M. Merten
- Center
for Integrative Chemical Biology and Drug Discovery, Chemical Biology
and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Kenneth H. Pearce
- Center
for Integrative Chemical Biology and Drug Discovery, Chemical Biology
and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- UNC
Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, United States
| | - Fabio Trindade
Maranhão Costa
- Laboratory
of Tropical Diseases—Prof. Dr. Luiz Jacinto da Silva, Department
of Genetics, Evolution, Microbiology and Immunology, University of Campinas-UNICAMP, Campinas 13083-970, SP, Brazil
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Thiago Moreno L. Souza
- Laboratory
of Immunopharmacology, Oswaldo Cruz Institute—Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil
- Center
of Technological Development in Health (CDTS)/National Institute of
Science and Technology for Innovation on Neglected Population Diseases
(INCT-IDPN), Rio de Janeiro 21040-900, RJ, Brazil
| | - Carolina Horta Andrade
- LabMol
- Laboratory of Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia 74605-170, GO, Brazil
| | - Sean Ekins
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
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11
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Li J, Wang JL, Gan CY, Cai XF, Wang YW, Long QX, Sun YX, Wei XF, Cui J, Huang AL, Hu JL. Caspase sensors based on NanoLuc. J Biotechnol 2022; 357:100-107. [PMID: 35963591 DOI: 10.1016/j.jbiotec.2022.08.005] [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: 08/12/2021] [Accepted: 08/09/2022] [Indexed: 11/26/2022]
Abstract
Caspases are a family of evolutionary conserved cysteine proteases that play key roles in programmed cell death and inflammation. Among the methods for the detection of caspase activity, biosensors based on luciferases have advantages in genetical encoding and convenience in assay. In this study, we constructed a new set of caspase biosensors based on NanoLuc luciferase. This kind of sensors, named NanoLock, work in dark-to-bright model, with the help of a NanoLuc quencher peptide (HiBiT-R/D) mutated from HiBiT. Optimized NanoLock responded to proteases with high signal to noise ratio (S/N), 1233-fold activation by tobacco etch virus protease in HEK293 cells and > 500-fold induction to caspase 3 in vitro. We constructed NanoLocks for the detection of caspase 1, 3, 6, 7, 8, 9, and 10, and assays in HEK293 cells demonstrated that these sensors performed better than commercial kits in the aspect of S/N and convenience. We further established a cell line stably expressing NanoLock-casp 6 and provided a proof-of-concept for the usage of this cell line in the high throughput screening of caspase 6 modulator.
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Affiliation(s)
- Jie Li
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Jin-Lan Wang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Chun-Yang Gan
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Xue-Fei Cai
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China; Department of Laboratory Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China; Laboratory for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Yu-Wei Wang
- Department of Laboratory Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China; Laboratory for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Quan-Xin Long
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Yu-Xue Sun
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Xia-Fei Wei
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Jing Cui
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Ai-Long Huang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China.
| | - Jie-Li Hu
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China.
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12
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Deroubaix A, Kramvis A. Imaging Techniques: Essential Tools for the Study of SARS-CoV-2 Infection. Front Cell Infect Microbiol 2022; 12:794264. [PMID: 35937687 PMCID: PMC9355083 DOI: 10.3389/fcimb.2022.794264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 06/21/2022] [Indexed: 01/08/2023] Open
Abstract
The world has seen the emergence of a new virus in 2019, SARS-CoV-2, causing the COVID-19 pandemic and millions of deaths worldwide. Microscopy can be much more informative than conventional detection methods such as RT-PCR. This review aims to present the up-to-date microscopy observations in patients, the in vitro studies of the virus and viral proteins and their interaction with their host, discuss the microscopy techniques for detection and study of SARS-CoV-2, and summarize the reagents used for SARS-CoV-2 detection. From basic fluorescence microscopy to high resolution techniques and combined technologies, this article shows the power and the potential of microscopy techniques, especially in the field of virology.
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Affiliation(s)
- Aurélie Deroubaix
- Hepatitis Virus Diversity Research Unit, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Life Sciences Imaging Facility, University of the Witwatersrand, Johannesburg, South Africa
| | - Anna Kramvis
- Hepatitis Virus Diversity Research Unit, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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13
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Chen K, Krischuns T, Varga L, Harigua-Souiai E, Paisant S, Zettor A, Chiaravalli J, Delpal A, Courtney D, O'Brien A, Baker S, Decroly E, Isel C, Agou F, Jacob Y, Blondel A, Naffakh N. A highly sensitive cell-based luciferase assay for high-throughput automated screening of SARS-CoV-2 nsp5/3CLpro inhibitors. Antiviral Res 2022; 201:105272. [PMID: 35278581 PMCID: PMC8906008 DOI: 10.1016/j.antiviral.2022.105272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/19/2022] [Accepted: 02/23/2022] [Indexed: 12/15/2022]
Abstract
Effective drugs against SARS-CoV-2 are urgently needed to treat severe cases of infection and for prophylactic use. The main viral protease (nsp5 or 3CLpro) represents an attractive and possibly broad-spectrum target for drug development as it is essential to the virus life cycle and highly conserved among betacoronaviruses. Sensitive and efficient high-throughput screening methods are key for drug discovery. Here we report the development of a gain-of-signal, highly sensitive cell-based luciferase assay to monitor SARS-CoV-2 nsp5 activity and show that it is suitable for the screening of compounds in a 384-well format. A benefit of miniaturisation and automation is that screening can be performed in parallel on a wild-type and a catalytically inactive nsp5, which improves the selectivity of the assay. We performed molecular docking-based screening on a set of 14,468 compounds from an in-house chemical database, selected 359 candidate nsp5 inhibitors and tested them experimentally. We identified two molecules which show anti-nsp5 activity, both in our cell-based assay and in vitro on purified nsp5 protein, and inhibit SARS-CoV-2 replication in A549-ACE2 cells with EC50 values in the 4–8 μM range. The here described high-throughput-compatible assay will allow the screening of large-scale compound libraries for SARS-CoV-2 nsp5 inhibitors. Moreover, we provide evidence that this assay can be adapted to other coronaviruses and viruses which rely on a viral protease.
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14
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Narayanan A, Narwal M, Majowicz SA, Varricchio C, Toner SA, Ballatore C, Brancale A, Murakami KS, Jose J. Identification of SARS-CoV-2 inhibitors targeting Mpro and PLpro using in-cell-protease assay. Commun Biol 2022; 5:169. [PMID: 35217718 PMCID: PMC8881501 DOI: 10.1038/s42003-022-03090-9] [Citation(s) in RCA: 96] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 02/01/2022] [Indexed: 01/08/2023] Open
Abstract
SARS-CoV-2 proteases Mpro and PLpro are promising targets for antiviral drug development. In this study, we present an antiviral screening strategy involving a novel in-cell protease assay, antiviral and biochemical activity assessments, as well as structural determinations for rapid identification of protease inhibitors with low cytotoxicity. We identified eight compounds with anti-SARS-CoV-2 activity from a library of 64 repurposed drugs and modeled at protease active sites by in silico docking. We demonstrate that Sitagliptin and Daclatasvir inhibit PLpro, and MG-101, Lycorine HCl, and Nelfinavir mesylate inhibit Mpro of SARS-CoV-2. The X-ray crystal structure of Mpro in complex with MG-101 shows a covalent bond formation between the inhibitor and the active site Cys145 residue indicating its mechanism of inhibition is by blocking the substrate binding at the active site. Thus, we provide methods for rapid and effective screening and development of inhibitors for blocking virus polyprotein processing as SARS-CoV-2 antivirals. Additionally, we show that the combined inhibition of Mpro and PLpro is more effective in inhibiting SARS-CoV-2 and the delta variant.
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Affiliation(s)
- Anoop Narayanan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Manju Narwal
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Sydney A Majowicz
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Carmine Varricchio
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, CF10 3NB, Cardiff, UK
| | - Shay A Toner
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Carlo Ballatore
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Andrea Brancale
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, CF10 3NB, Cardiff, UK
| | - Katsuhiko S Murakami
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Joyce Jose
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.
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15
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Structure-based inhibitor design and repurposing clinical drugs to target SARS-CoV-2 proteases. Biochem Soc Trans 2022; 50:151-165. [PMID: 35015073 DOI: 10.1042/bst20211180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 01/01/2023]
Abstract
SARS-CoV-2, the coronavirus responsible for the current COVID-19 pandemic, encodes two proteases, 3CLpro and PLpro, two of the main antiviral research targets. Here we provide an overview of the structures and functions of 3CLpro and PLpro and examine strategies of structure-based drug designing and drug repurposing against these proteases. Rational structure-based drug design enables the generation of potent and target-specific antivirals. Drug repurposing offers an attractive prospect with an accelerated turnaround. Thus far, several protease inhibitors have been identified, and some candidates are undergoing trials that may well prove to be effective antivirals against SARS-CoV-2.
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16
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Chen KY, Krischuns T, Ortega Varga L, Harigua-Souiai E, Paisant S, Zettor A, Chiaravalli J, Courtney D, O’Brien A, Baker SC, Isel C, Agou F, Jacob Y, Blondel A, Naffakh N. A highly sensitive cell-based luciferase assay for high-throughput automated screening of SARS-CoV-2 nsp5/3CLpro inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.12.18.473303. [PMID: 34981051 PMCID: PMC8722588 DOI: 10.1101/2021.12.18.473303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Effective drugs against SARS-CoV-2 are urgently needed to treat severe cases of infection and for prophylactic use. The main viral protease (nsp5 or 3CLpro) represents an attractive and possibly broad-spectrum target for drug development as it is essential to the virus life cycle and highly conserved among betacoronaviruses. Sensitive and efficient high-throughput screening methods are key for drug discovery. Here we report the development of a gain-of-signal, highly sensitive cell-based luciferase assay to monitor SARS-CoV-2 nsp5 activity and show that it is suitable for high-throughput screening of compounds in a 384-well format. A benefit of miniaturisation and automation is that screening can be performed in parallel on a wild-type and a catalytically inactive nsp5, which improves the selectivity of the assay. We performed molecular docking-based screening on a set of 14,468 compounds from an in-house chemical database, selected 359 candidate nsp5 inhibitors and tested them experimentally. We identified four molecules, including the broad-spectrum antiviral merimepodib/VX-497, which show anti-nsp5 activity and inhibit SARS-CoV-2 replication in A549-ACE2 cells with IC 50 values in the 4-21 µM range. The here described assay will allow the screening of large-scale compound libraries for SARS-CoV-2 nsp5 inhibitors. Moreover, we provide evidence that this assay can be adapted to other coronaviruses and viruses which rely on a viral protease.
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Affiliation(s)
- KY Chen
- RNA Biology and Influenza Virus Unit, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
| | - T Krischuns
- RNA Biology and Influenza Virus Unit, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
| | - L Ortega Varga
- Structural Bioinformatics Unit, Institut Pasteur, Université de Paris, Paris, France
| | - E Harigua-Souiai
- Laboratory of Molecular Epidemiology and Experimental Pathology – LR16IPT04, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - S Paisant
- RNA Biology and Influenza Virus Unit, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
| | - A Zettor
- Chemogenomic and Biological Screening Platform, Institut Pasteur, Université de Paris, Paris, France
| | - J Chiaravalli
- Chemogenomic and Biological Screening Platform, Institut Pasteur, Université de Paris, Paris, France
| | - D Courtney
- RNA Biology and Influenza Virus Unit, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
| | - A O’Brien
- Department of Microbiology and Immunology, Loyola University Chicago, Stritch School of Medicine, Maywood, IL, USA
| | - SC Baker
- Department of Microbiology and Immunology, Loyola University Chicago, Stritch School of Medicine, Maywood, IL, USA
| | - C Isel
- RNA Biology and Influenza Virus Unit, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
| | - F Agou
- Chemogenomic and Biological Screening Platform, Institut Pasteur, Université de Paris, Paris, France
| | - Y Jacob
- Molecular Genetics of RNA Viruses, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
| | - A Blondel
- Structural Bioinformatics Unit, Institut Pasteur, Université de Paris, Paris, France
| | - N Naffakh
- RNA Biology and Influenza Virus Unit, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
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17
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Kato Y, Higashiyama A, Takaoka E, Nishikawa M, Ikushiro S. Food phytochemicals, epigallocatechin gallate and myricetin, covalently bind to the active site of the coronavirus main protease in vitro. ADVANCES IN REDOX RESEARCH : AN OFFICIAL JOURNAL OF THE SOCIETY FOR REDOX BIOLOGY AND MEDICINE AND THE SOCIETY FOR FREE RADICAL RESEARCH-EUROPE 2021; 3:100021. [PMID: 35425933 PMCID: PMC8498006 DOI: 10.1016/j.arres.2021.100021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/02/2021] [Accepted: 10/03/2021] [Indexed: 12/30/2022]
Abstract
SARS-CoV-2 main protease is a possible target for protection against viral infection. This study examined the inhibitory effect of food phytochemicals on the main protease of SARS-CoV-2 by determining a cleaved product after chromatographic separation. First, 37 phytochemicals, including glycosides and metabolites, were screened at 20 µM; epigallocatechin gallate, myricetin, theaflavin, herbacetin, piceatannol, myricitrin, and isothiocyanates inhibited the enzyme in varying degrees. The IC50 values were estimated from 0.4 to 33.3 µM against the 0.5-µM enzyme. The dose-dependent adduction of epigallocatechin gallate and myricetin was confirmed by quinone staining of protein blotted onto a membrane. The enzyme activity was decreased by increasing the concentration of the two phytochemicals, accompanied by increasing the respective adducted molecule estimated by intact mass spectrometry. Reduced glutathione canceled the formation of conjugate and the inhibitory effect of epigallocatechin gallate or myricetin on the enzyme, suggesting that the formation of the quinone moiety in the phytochemicals is critical for the inhibition. The covalent binding of epigallocatechin gallate or myricetin to the cysteine residue at the active site was confirmed by analyzing peptides from the chymotrypsin-digested main protease.
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Affiliation(s)
- Yoji Kato
- School of Human Science and Environment
- Research Institute for Food and Nutritional Sciences, University of Hyogo, Himeji, Hyogo, 670-0092, Japan
| | | | | | - Miyu Nishikawa
- Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, Imizu, Toyama, 939-0398, Japan
| | - Shinichi Ikushiro
- Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, Imizu, Toyama, 939-0398, Japan
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18
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Oktay L, Erdemoğlu E, Tolu İ, Yumak Y, Özcan A, Acar E, Büyükkiliç Ş, Olkan A, Durdaği S. Binary-QSAR guided virtual screening of FDA approved drugs and compounds in clinical investigation against SARS-CoV-2 main protease. Turk J Biol 2021; 45:459-468. [PMID: 34803447 PMCID: PMC8573836 DOI: 10.3906/biy-2106-61] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/06/2021] [Indexed: 12/20/2022] Open
Abstract
With the emergence of the new SARS-CoV-2 virus, drug repurposing studies have gained substantial importance. Combined with the efficacy of recent improvements in ligand- and target-based virtual screening approaches, virtual screening has become faster and more productive than ever. In the current study, an FDA library of approved drugs and compounds under clinical investigation were screened for their antiviral activity using the antiviral therapeutic activity binary QSAR model of the MetaCore/MetaDrug platform. Among 6733-compound collection, we found 370 compounds with a normalized therapeutic activity value greater than a cutoff of 0.75. Only these selected compounds were used for molecular docking studies against the SARS-CoV-2 main protease (Mpro). After initial short (10 ns) molecular dynamics (MD) simulations with the top-50 docking scored compounds and following molecular mechanics generalized born surface area (MM/GBSA) calculations, top-10 compounds were subjected to longer (100 ns) MD simulations and end-point MM/GBSA estimations. Our virtual screening protocol yielded Cefuroxime pivoxetil, an ester prodrug of second-generation cephalosporin antibiotic Cefuroxime, as being a considerable molecule for drug repurposing against the SARS-CoV-2 Mpro.
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Affiliation(s)
- Lalehan Oktay
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, İstanbul Turkey
| | - Ece Erdemoğlu
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, İstanbul Turkey.,School of Medicine, Mersin University, Mersin Turkey
| | - İlayda Tolu
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, İstanbul Turkey
| | - Yeşim Yumak
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, İstanbul Turkey.,Faculty of Science and Letters, Tokat Gaziosmanpaşa University, Tokat Turkey
| | - Ayşenur Özcan
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, İstanbul Turkey.,Faculty of Medicine, İstanbul Medeniyet University, İstanbul Turkey
| | - Elif Acar
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, İstanbul Turkey.,Faculty of Medicine, İstanbul Medeniyet University, İstanbul Turkey
| | - Şehriban Büyükkiliç
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, İstanbul Turkey.,Faculty of Science, Necmettin Erbakan University, Konya Turkey
| | - Alpsu Olkan
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, İstanbul Turkey.,School of Medicine, Bahçeşehir University, İstanbul Turkey
| | - Serdar Durdaği
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, İstanbul Turkey
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19
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Mathieu C, Touret F, Jacquemin C, Janin YL, Nougairède A, Brailly M, Mazelier M, Décimo D, Vasseur V, Hans A, Valle-Casuso JC, de Lamballerie X, Horvat B, André P, Si-Tahar M, Lotteau V, Vidalain PO. A Bioluminescent 3CL Pro Activity Assay to Monitor SARS-CoV-2 Replication and Identify Inhibitors. Viruses 2021; 13:1814. [PMID: 34578395 PMCID: PMC8473059 DOI: 10.3390/v13091814] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/04/2021] [Accepted: 09/06/2021] [Indexed: 02/07/2023] Open
Abstract
Our therapeutic arsenal against viruses is very limited and the current pandemic of SARS-CoV-2 highlights the critical need for effective antivirals against emerging coronaviruses. Cellular assays allowing a precise quantification of viral replication in high-throughput experimental settings are essential to the screening of chemical libraries and the selection of best antiviral chemical structures. To develop a reporting system for SARS-CoV-2 infection, we generated cell lines expressing a firefly luciferase maintained in an inactive form by a consensus cleavage site for the viral protease 3CLPro of coronaviruses, so that the luminescent biosensor is turned on upon 3CLPro expression or SARS-CoV-2 infection. This cellular assay was used to screen a metabolism-oriented library of 492 compounds to identify metabolic vulnerabilities of coronaviruses for developing innovative therapeutic strategies. In agreement with recent reports, inhibitors of pyrimidine biosynthesis were found to prevent SARS-CoV-2 replication. Among the top hits, we also identified the NADPH oxidase (NOX) inhibitor Setanaxib. The anti-SARS-CoV-2 activity of Setanaxib was further confirmed using ACE2-expressing human pulmonary cells Beas2B as well as human primary nasal epithelial cells. Altogether, these results validate our cell-based functional assay and the interest of screening libraries of different origins to identify inhibitors of SARS-CoV-2 for drug repurposing or development.
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Affiliation(s)
- Cyrille Mathieu
- CIRI, Centre International de Recherche en Infectiologie, Team Immunobiology of the Viral Infections, Univ Lyon, Institut National de la Santé et de la Recherche Médicale (Inserm), U1111, Centre National de la Recherche Scientifique (CNRS), UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 69007 Lyon, France; (C.M.); (M.B.); (M.M.); (D.D.); (B.H.)
| | - Franck Touret
- Unité des Virus Emergents (UVE), Aix Marseille Univ, Institut de Recherche pour le Développement (IRD) 190, Institut National de la Santé et de la Recherche Médicale (Inserm) U1207, IHU Méditerranée Infection, 13005 Marseille, France; (F.T.); (A.N.); (X.d.L.)
| | - Clémence Jacquemin
- CIRI, Centre International de Recherche en Infectiologie, Team Viral Infection, Metabolism and Immunity, Univ Lyon, Institut National de la Santé et de la Recherche Médicale (Inserm), U1111, Centre National de la Recherche Scientifique (CNRS), UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 69007 Lyon, France; (C.J.); (P.A.)
| | - Yves L. Janin
- Unité de Chimie et Biocatalyse, Institut Pasteur, Centre National de la Recherche Scientifique (CNRS), UMR 3523, 28 rue du Dr. Roux, CEDEX 15, 75724 Paris, France;
| | - Antoine Nougairède
- Unité des Virus Emergents (UVE), Aix Marseille Univ, Institut de Recherche pour le Développement (IRD) 190, Institut National de la Santé et de la Recherche Médicale (Inserm) U1207, IHU Méditerranée Infection, 13005 Marseille, France; (F.T.); (A.N.); (X.d.L.)
| | - Manon Brailly
- CIRI, Centre International de Recherche en Infectiologie, Team Immunobiology of the Viral Infections, Univ Lyon, Institut National de la Santé et de la Recherche Médicale (Inserm), U1111, Centre National de la Recherche Scientifique (CNRS), UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 69007 Lyon, France; (C.M.); (M.B.); (M.M.); (D.D.); (B.H.)
| | - Magalie Mazelier
- CIRI, Centre International de Recherche en Infectiologie, Team Immunobiology of the Viral Infections, Univ Lyon, Institut National de la Santé et de la Recherche Médicale (Inserm), U1111, Centre National de la Recherche Scientifique (CNRS), UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 69007 Lyon, France; (C.M.); (M.B.); (M.M.); (D.D.); (B.H.)
| | - Didier Décimo
- CIRI, Centre International de Recherche en Infectiologie, Team Immunobiology of the Viral Infections, Univ Lyon, Institut National de la Santé et de la Recherche Médicale (Inserm), U1111, Centre National de la Recherche Scientifique (CNRS), UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 69007 Lyon, France; (C.M.); (M.B.); (M.M.); (D.D.); (B.H.)
| | - Virginie Vasseur
- Centre d’Etude des Pathologies Respiratoires (CEPR), Institut National de la Santé et de la Recherche Médicale (Inserm), U1100, Faculty of Medecine, University of Tours, 37000 Tours, France; (V.V.); (M.S.-T.)
| | - Aymeric Hans
- Laboratoire de Santé Animale, Site de Normandie de l’Agence nationale de sécurité sanitaire de l’alimentation, de l’environnement et du travail (ANSES), Physiopathologie et épidémiologie des maladies équines (PhEED) Unit, 14430 Goustranville, France; (A.H.); (J.-C.V.-C.)
| | - José-Carlos Valle-Casuso
- Laboratoire de Santé Animale, Site de Normandie de l’Agence nationale de sécurité sanitaire de l’alimentation, de l’environnement et du travail (ANSES), Physiopathologie et épidémiologie des maladies équines (PhEED) Unit, 14430 Goustranville, France; (A.H.); (J.-C.V.-C.)
| | - Xavier de Lamballerie
- Unité des Virus Emergents (UVE), Aix Marseille Univ, Institut de Recherche pour le Développement (IRD) 190, Institut National de la Santé et de la Recherche Médicale (Inserm) U1207, IHU Méditerranée Infection, 13005 Marseille, France; (F.T.); (A.N.); (X.d.L.)
| | - Branka Horvat
- CIRI, Centre International de Recherche en Infectiologie, Team Immunobiology of the Viral Infections, Univ Lyon, Institut National de la Santé et de la Recherche Médicale (Inserm), U1111, Centre National de la Recherche Scientifique (CNRS), UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 69007 Lyon, France; (C.M.); (M.B.); (M.M.); (D.D.); (B.H.)
| | - Patrice André
- CIRI, Centre International de Recherche en Infectiologie, Team Viral Infection, Metabolism and Immunity, Univ Lyon, Institut National de la Santé et de la Recherche Médicale (Inserm), U1111, Centre National de la Recherche Scientifique (CNRS), UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 69007 Lyon, France; (C.J.); (P.A.)
| | - Mustapha Si-Tahar
- Centre d’Etude des Pathologies Respiratoires (CEPR), Institut National de la Santé et de la Recherche Médicale (Inserm), U1100, Faculty of Medecine, University of Tours, 37000 Tours, France; (V.V.); (M.S.-T.)
| | - Vincent Lotteau
- CIRI, Centre International de Recherche en Infectiologie, Team Viral Infection, Metabolism and Immunity, Univ Lyon, Institut National de la Santé et de la Recherche Médicale (Inserm), U1111, Centre National de la Recherche Scientifique (CNRS), UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 69007 Lyon, France; (C.J.); (P.A.)
| | - Pierre-Olivier Vidalain
- CIRI, Centre International de Recherche en Infectiologie, Team Viral Infection, Metabolism and Immunity, Univ Lyon, Institut National de la Santé et de la Recherche Médicale (Inserm), U1111, Centre National de la Recherche Scientifique (CNRS), UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 69007 Lyon, France; (C.J.); (P.A.)
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20
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Recent advances in drug repurposing using machine learning. Curr Opin Chem Biol 2021; 65:74-84. [PMID: 34274565 DOI: 10.1016/j.cbpa.2021.06.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 12/11/2022]
Abstract
Drug repurposing aims to find new uses for already existing and approved drugs. We now provide a brief overview of recent developments in drug repurposing using machine learning alongside other computational approaches for comparison. We also highlight several applications for cancer using kinase inhibitors, Alzheimer's disease as well as COVID-19.
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21
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Nour I, Alenazi IO, Hanif A, Eifan S. Molecular adaptive evolution of SARS-COV-2 spike protein in Saudi Arabia. Saudi J Biol Sci 2021; 28:3325-3332. [PMID: 33679194 PMCID: PMC7923870 DOI: 10.1016/j.sjbs.2021.02.077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 02/06/2023] Open
Abstract
The sequences of SARS-CoV-2 spike (S) from Saudi Arabia along with SARS-CoV and bat SARS-like CoVs were obtained. Positive selection analysis and secondary structure investigation of spike sequences were performed. Adaptive molecular evolution was observed in SARS-CoV-2 displayed by positive selection pressure at N-terminal domain (NTD; codons 41, 163, 174 and 218), Receptor binding domain (RBD; codons 378 and 404) and S1/S2 Cleavage site (codon 690). Furthermore, the spike protein secondary structure depicted by the homo-trimer structure showed a high similarity between Saudi SARS-CoV-2 isolate and the parental strain (bat SL-COVZC45). Despite the high similarity depicted in the spike sequence model alignment, it displayed a significant difference when each chain was treated solely owing to 7 motif differences in the three composing chains. In addition, SARS-CoV-2 S trimer model uncovered the presence of N-acetyl glucosamine ligands. Eventually, 3C-like proteinase cleavage site was observed in S2 domain could be used as a site for drug discovery. Genetics and molecular evolutionary facts are useful for assessment of evolution, host adaptation and epidemic patterns ultimately helpful for adaptation of control strategies.
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Affiliation(s)
- Islam Nour
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ibrahim O. Alenazi
- National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Atif Hanif
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saleh Eifan
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
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22
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Cheng J, Li X. Development and Application of Activity-based Fluorescent Probes for High-Throughput Screening. Curr Med Chem 2021; 29:1739-1756. [PMID: 34036907 DOI: 10.2174/0929867328666210525141728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 11/22/2022]
Abstract
High-throughput screening facilitates the rapid identification of novel hit compounds; however, it remains challenging to design effective high-throughput assays, partially due to the difficulty of achieving sensitivity in the assay techniques. Among the various analytical methods that are used, fluorescence-based assays dominate owing to their high sensitivity and ease of operation. Recent advances in activity-based sensing/imaging have further expanded the availability of fluorescent probes as monitors for high-throughput screening of result outputs. In this study, we have reviewed various activity-based fluorescent probes used in high-throughput screening assays, emphasizing their structure-related working mechanisms. Moreover, we have explored the possibility of the development of additional and better probes to boost hit identification and drug development against various targets.
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Affiliation(s)
- Juan Cheng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Xin Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
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