1
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Lockwood TD. Coordination chemistry suggests that independently observed benefits of metformin and Zn 2+ against COVID-19 are not independent. Biometals 2024; 37:983-1022. [PMID: 38578560 PMCID: PMC11255062 DOI: 10.1007/s10534-024-00590-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/12/2024] [Indexed: 04/06/2024]
Abstract
Independent trials indicate that either oral Zn2+ or metformin can separately improve COVID-19 outcomes by approximately 40%. Coordination chemistry predicts a mechanistic relationship and therapeutic synergy. Zn2+ deficit is a known risk factor for both COVID-19 and non-infectious inflammation. Most dietary Zn2+ is not absorbed. Metformin is a naked ligand that presumably increases intestinal Zn2+ bioavailability and active absorption by cation transporters known to transport metformin. Intracellular Zn2+ provides a natural buffer of many protease reactions; the variable "set point" is determined by Zn2+ regulation or availability. A Zn2+-interactive protease network is suggested here. The two viral cysteine proteases are therapeutic targets against COVID-19. Viral and many host proteases are submaximally inhibited by exchangeable cell Zn2+. Inhibition of cysteine proteases can improve COVID-19 outcomes and non-infectious inflammation. Metformin reportedly enhances the natural moderating effect of Zn2+ on bioassayed proteome degradation. Firstly, the dissociable metformin-Zn2+ complex could be actively transported by intestinal cation transporters; thereby creating artificial pathways of absorption and increased body Zn2+ content. Secondly, metformin Zn2+ coordination can create a non-natural protease inhibitor independent of cell Zn2+ content. Moderation of peptidolytic reactions by either or both mechanisms could slow (a) viral multiplication (b) viral invasion and (c) the pathogenic host inflammatory response. These combined actions could allow development of acquired immunity to clear the infection before life-threatening inflammation. Nirmatrelvir (Paxlovid®) opposes COVID-19 by selective inhibition the viral main protease by a Zn2+-independent mechanism. Pending safety evaluation, predictable synergistic benefits of metformin and Zn2+, and perhaps metformin/Zn2+/Paxlovid® co-administration should be investigated.
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Affiliation(s)
- Thomas D Lockwood
- Department Pharmacology and Toxicology, School of Medicine, Wright State University, Dayton, OH, 45435, USA.
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2
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Jiang H, Lin C, Chang J, Zou X, Zhang J, Li J. Crystal structures of the 3C proteases from Coxsackievirus B3 and B4. Acta Crystallogr F Struct Biol Commun 2024; 80:183-190. [PMID: 39052022 PMCID: PMC11299732 DOI: 10.1107/s2053230x24006915] [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: 03/06/2024] [Accepted: 07/15/2024] [Indexed: 07/27/2024] Open
Abstract
Enteroviruses cause a wide range of disorders with varying presentations and severities, and some enteroviruses have emerged as serious public health concerns. These include Coxsackievirus B3 (CVB3), an active causative agent of viral myocarditis, and Coxsackievirus B4 (CVB4), which may accelerate the progression of type 1 diabetes. The 3C proteases from CVB3 and CVB4 play important roles in the propagation of these viruses. In this study, the 3C proteases from CVB3 and CVB4 were expressed in Escherichia coli and purified by affinity chromatography and gel-filtration chromatography. The crystals of the CVB3 and CVB4 3C proteases diffracted to 2.10 and 2.01 Å resolution, respectively. The crystal structures were solved by the molecular-replacement method and contained a typical chymotrypsin-like fold and a conserved His40-Glu71-Cys147 catalytic triad. Comparison with the structures of 3C proteases from other enteroviruses revealed high similarity with minor differences, which will guide the design of 3C-targeting inhibitors with broad-spectrum properties.
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Affiliation(s)
- Haihai Jiang
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang UniversityNanchang330031People’s Republic of China
| | - Cheng Lin
- College of Pharmaceutical Sciences, Gannan Medical UniversityGanzhou341000People’s Republic of China
| | - Jingyi Chang
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang UniversityNanchang330031People’s Republic of China
| | - Xiaofang Zou
- College of Pharmaceutical Sciences, Gannan Medical UniversityGanzhou341000People’s Republic of China
| | - Jin Zhang
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang UniversityNanchang330031People’s Republic of China
| | - Jian Li
- College of Pharmaceutical Sciences, Gannan Medical UniversityGanzhou341000People’s Republic of China
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3
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Song N, Zheng W, Song B, Zheng J. Allosteric Regulation and Inhibition of Coronavirus 3CLpro Revealed by HDX-MS. Chembiochem 2024; 25:e202400001. [PMID: 38720172 DOI: 10.1002/cbic.202400001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 05/03/2024] [Indexed: 07/03/2024]
Abstract
Coronavirus (CoV) infections have caused contagious and fatal respiratory diseases in humans worldwide. CoV 3-chymotrypsin-like proteases (3CLpro or Mpro) play an important role in viral maturation, and maintenance of their dimeric conformation is crucial for viral activity. Therefore, allosterically regulated dimerization of 3CLpro can be employed as a drug development target. Here, we investigated the allosteric regulatory mechanism of 3CLpro dimerization by using hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS) technology. We found that the FLAG tag directly coupled to the N-finger of 3CLpro significantly increased HDX kinetics at the dimer interface, and 3CLpro transformed from a dimer to a monomer. The 3CLpro mutants of SARS-CoV-2, which are monomeric, also exhibited increased deuterium exchange. Binding of the allosteric inhibitor Gastrodenol to most betacoronavirus 3CLpros led to increased allosteric deuterium exchange, resulting in the monomeric conformation of the CoV 3CLpro upon binding. Molecular dynamics (MD) simulation analysis further indicated the molecular mechanism of action of Gastrodenol on CoV 3CLpro: binding of Gastrodenol to SARS-CoV-2 3CLpro destroyed the hydrogen bond in the dimer interface. These results suggest that Gastrodenol may be a potential broad-spectrum anti-betacoronavirus drug.
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Affiliation(s)
- Ning Song
- Immunological Disease Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, 201203, Shanghai, PR China
- University of Chinese Academy of Sciences, No. 1 Yanqihu East Rd, Huairou District, 101408, Beijing, PR China
| | - Wen Zheng
- CADD computer-aided protein Design Simulator, Hubei Yuanda Biotechnology Co., Ltd., Building B6, Optics Valley Biological City, Hongshan District, 430000, Wuhan, Hubei, PR China
| | - Bin Song
- Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, 200025, Shanghai, PR China
| | - Jie Zheng
- Immunological Disease Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, 201203, Shanghai, PR China
- University of Chinese Academy of Sciences, No. 1 Yanqihu East Rd, Huairou District, 101408, Beijing, PR China
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4
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Grifagni D, Lenci E, De Santis A, Orsetti A, Barracchia CG, Tedesco F, Bellini Puglielli R, Lucarelli F, Lauriola A, Assfalg M, Cantini F, Calderone V, Guardavaccaro D, Trabocchi A, D’Onofrio M, Ciofi-Baffoni S. Development of a GC-376 Based Peptidomimetic PROTAC as a Degrader of 3-Chymotrypsin-like Protease of SARS-CoV-2. ACS Med Chem Lett 2024; 15:250-257. [PMID: 38352832 PMCID: PMC10860180 DOI: 10.1021/acsmedchemlett.3c00498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/26/2023] [Accepted: 01/03/2024] [Indexed: 02/16/2024] Open
Abstract
We have applied a proteolysis targeting chimera (PROTAC) technology to obtain a peptidomimetic molecule able to trigger the degradation of SARS-CoV-2 3-chymotrypsin-like protease (3CLPro). The PROTAC molecule was designed by conjugating a GC-376 based dipeptidyl 3CLPro ligand to a pomalidomide moiety through a piperazine-piperidine linker. NMR and crystallographic data complemented with enzymatic and cellular studies showed that (i) the dipeptidyl moiety of PROTAC binds to the active site of the dimeric state of SARS-CoV-2 3CLPro forming a reversible covalent bond with the sulfur atom of catalytic Cys145, (ii) the linker and the pomalidomide cereblon-ligand of PROTAC protrude from the protein, displaying a high degree of flexibility and no interactions with other regions of the protein, and (iii) PROTAC reduces the protein levels of SARS-CoV-2 3CLPro in cultured cells. This study paves the way for the future applicability of peptidomimetic PROTACs to tackle 3CLPro-dependent viral infections.
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Affiliation(s)
- Deborah Grifagni
- Magnetic
Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Elena Lenci
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Alessia De Santis
- Magnetic
Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Andrea Orsetti
- Magnetic
Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | | | - Filomena Tedesco
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Raffaele Bellini Puglielli
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Francesca Lucarelli
- Magnetic
Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Angela Lauriola
- Department
of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Michael Assfalg
- Department
of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Francesca Cantini
- Magnetic
Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Vito Calderone
- Magnetic
Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Daniele Guardavaccaro
- Department
of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Andrea Trabocchi
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Mariapina D’Onofrio
- Department
of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Simone Ciofi-Baffoni
- Magnetic
Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
- Consorzio
Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
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5
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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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6
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Mondal S, Sarvari G, Boehr DD. Picornavirus 3C Proteins Intervene in Host Cell Processes through Proteolysis and Interactions with RNA. Viruses 2023; 15:2413. [PMID: 38140654 PMCID: PMC10747604 DOI: 10.3390/v15122413] [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: 10/15/2023] [Revised: 12/07/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
The Picornaviridae family comprises a large group of non-enveloped viruses with enormous impact on human and animal health. The picornaviral genome contains one open reading frame encoding a single polyprotein that can be processed by viral proteases. The picornaviral 3C proteases share similar three-dimensional structures and play a significant role in the viral life cycle and virus-host interactions. Picornaviral 3C proteins also have conserved RNA-binding activities that contribute to the assembly of the viral RNA replication complex. The 3C protease is important for regulating the host cell response through the cleavage of critical host cell proteins, acting to selectively 'hijack' host factors involved in gene expression, promoting picornavirus replication, and inactivating key factors in innate immunity signaling pathways. The protease and RNA-binding activities of 3C are involved in viral polyprotein processing and the initiation of viral RNA synthesis. Most importantly, 3C modifies critical molecules in host organelles and maintains virus infection by subtly subverting host cell death through the blocking of transcription, translation, and nucleocytoplasmic trafficking to modulate cell physiology for viral replication. Here, we discuss the molecular mechanisms through which 3C mediates physiological processes involved in promoting virus infection, replication, and release.
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Affiliation(s)
| | | | - David D. Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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7
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Trivedi A, Kardam V, Inampudi KK, Vrati S, Gupta D, Singh A, Kayampeta SR, Appaiahgari MB, Sehgal D. Identification of a novel inhibitor of SARS-CoV-2 main protease: an in silico, biochemical, and cell-based approach. FEBS J 2023; 290:5496-5513. [PMID: 37657928 DOI: 10.1111/febs.16947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/06/2023] [Accepted: 08/31/2023] [Indexed: 09/03/2023]
Abstract
The recurrent nature of coronavirus outbreaks, severity of the COVID-19 pandemic, rapid emergence of novel variants, and concerns over the effectiveness of existing vaccines against novel variants have highlighted the need to develop therapeutic interventions. Targeted efforts to identify inhibitors of crucial viral proteins are the preferred strategy. In this study, we screened FDA-approved and natural product libraries using in silico approach for potential hits against the SARS-CoV-2 main protease (Mpro) and experimentally validated their potency using in vitro biochemical and cell-based assays. Seven potential hits were identified through in silico screening and were subsequently evaluated in SARS-CoV-2-based cell-free assays, followed by testing in the HCoV-229E-based culture system. Of the tested compounds, 4-(3,4-dihydroxyphenyl)-6,7-dihydroxy-1-isopropyl-1H-benzofuro[3,2-b]pyrazolo[4,3-e]pyridin-3(2H)-one (PubChem CID:71755304, hereafter referred to as STL522228) exhibited significant antiviral activity. Subsequently, its potential as a novel COVID therapeutic molecule was validated in the SARS-CoV-2-culture system, where STL522228 demonstrated superior antiviral activity (EC50 = 0.44 μm) compared to Remdesivir (EC50 = 0.62 μm). Based on these findings, we report the strong anti-coronavirus activity of STL522228, and propose that it as a promising pan-coronavirus Mpro inhibitor for further experimental and preclinical validation.
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Affiliation(s)
- Aditya Trivedi
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence, Greater Noida, Uttar Pradesh, India
| | - Vandana Kardam
- Department of Chemistry, School of Natural Sciences, Shiv Nadar Institution of Eminence, Greater Noida, Uttar Pradesh, India
| | | | - Sudhanshu Vrati
- Laboratory of Virology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Dharmender Gupta
- Laboratory of Virology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Aekagra Singh
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence, Greater Noida, Uttar Pradesh, India
| | - Sarala Rani Kayampeta
- Research and Development Division, Srikara Biologicals Private Limited, Tirupati, India
| | | | - Deepak Sehgal
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence, Greater Noida, Uttar Pradesh, India
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8
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Forrestall K, Pringle ES, Sands D, Duguay BA, Farewell B, Woldemariam T, Falzarano D, Pottie I, McCormick C, Darvesh S. A phenothiazine urea derivative broadly inhibits coronavirus replication via viral protease inhibition. Antiviral Res 2023; 220:105758. [PMID: 38008194 DOI: 10.1016/j.antiviral.2023.105758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/02/2023] [Accepted: 11/15/2023] [Indexed: 11/28/2023]
Abstract
Coronavirus (CoV) replication requires efficient cleavage of viral polyproteins into an array of non-structural proteins involved in viral replication, organelle formation, viral RNA synthesis, and host shutoff. Human CoVs (HCoVs) encode two viral cysteine proteases, main protease (Mpro) and papain-like protease (PLpro), that mediate polyprotein cleavage. Using a structure-guided approach, a phenothiazine urea derivative that inhibits both SARS-CoV-2 Mpro and PLpro protease activity was identified. In silico docking studies also predicted the binding of the phenothiazine urea to the active sites of structurally similar Mpro and PLpro proteases from distantly related alphacoronavirus, HCoV-229 E (229 E), and the betacoronavirus, HCoV-OC43 (OC43). The lead phenothiazine urea derivative displayed broad antiviral activity against all three HCoVs tested in cellulo. It was further demonstrated that the compound inhibited 229 E and OC43 at an early stage of viral replication, with diminished formation of viral replication organelles, and the RNAs that are made within them, as expected following viral protease inhibition. These observations suggest that the phenothiazine urea derivative readily inhibits viral replication and may broadly inhibit proteases of diverse coronaviruses.
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Affiliation(s)
- Katrina Forrestall
- Department of Medicine (Geriatric Medicine and Neurology) and Medical Neuroscience, Dalhousie University, 5850 College Street, Halifax, NS, Canada, B3H 4R2
| | - Eric S Pringle
- Department of Microbiology & Immunology, Dalhousie University, 5850 College Street, Halifax, NS, Canada, B3H 4R2
| | - Dane Sands
- Department of Medicine (Geriatric Medicine and Neurology) and Medical Neuroscience, Dalhousie University, 5850 College Street, Halifax, NS, Canada, B3H 4R2
| | - Brett A Duguay
- Department of Microbiology & Immunology, Dalhousie University, 5850 College Street, Halifax, NS, Canada, B3H 4R2
| | - Brett Farewell
- Department of Medicine (Geriatric Medicine and Neurology) and Medical Neuroscience, Dalhousie University, 5850 College Street, Halifax, NS, Canada, B3H 4R2
| | | | - Darryl Falzarano
- Vaccine and Infectious Disease Organization (VIDO), 120 Veterinary Road, Saskatoon, SK, Canada, S7N 5E3; Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK, Canada, S7N 5B4
| | - Ian Pottie
- Department of Chemistry & Physics, Mount Saint Vincent University, 166 Bedford Highway, Halifax, NS, Canada, B3M 2J6; Department of Chemistry, Saint Mary's University, 923 Robbie Street, Halifax, NS, Canada, B3H 3C3
| | - Craig McCormick
- Department of Microbiology & Immunology, Dalhousie University, 5850 College Street, Halifax, NS, Canada, B3H 4R2
| | - Sultan Darvesh
- Department of Medicine (Geriatric Medicine and Neurology) and Medical Neuroscience, Dalhousie University, 5850 College Street, Halifax, NS, Canada, B3H 4R2; Department of Chemistry & Physics, Mount Saint Vincent University, 166 Bedford Highway, Halifax, NS, Canada, B3M 2J6.
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9
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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: 31] [Impact Index Per Article: 31.0] [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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10
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Das NK, Hollmann NM, Vogt J, Sevdalis SE, Banna HA, Ojha M, Koirala D. Crystal structure of a highly conserved enteroviral 5' cloverleaf RNA replication element. Nat Commun 2023; 14:1955. [PMID: 37029118 PMCID: PMC10082201 DOI: 10.1038/s41467-023-37658-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 03/23/2023] [Indexed: 04/09/2023] Open
Abstract
The extreme 5'-end of the enterovirus RNA genome contains a conserved cloverleaf-like domain that recruits 3CD and PCBP proteins required for initiating genome replication. Here, we report the crystal structure at 1.9 Å resolution of this domain from the CVB3 genome in complex with an antibody chaperone. The RNA folds into an antiparallel H-type four-way junction comprising four subdomains with co-axially stacked sA-sD and sB-sC helices. Long-range interactions between a conserved A40 in the sC-loop and Py-Py helix within the sD subdomain organize near-parallel orientations of the sA-sB and sC-sD helices. Our NMR studies confirm that these long-range interactions occur in solution and without the chaperone. The phylogenetic analyses indicate that our crystal structure represents a conserved architecture of enteroviral cloverleaf-like domains, including the A40 and Py-Py interactions. The protein binding studies further suggest that the H-shape architecture provides a ready-made platform to recruit 3CD and PCBP2 for viral replication.
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Affiliation(s)
- Naba K Das
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | - Nele M Hollmann
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
- Howard Hughes Medical Institute, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | - Jeff Vogt
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | - Spiridon E Sevdalis
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Hasan A Banna
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | - Manju Ojha
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | - Deepak Koirala
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, 21250, USA.
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11
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Pozzi C, Vanet A, Francesconi V, Tagliazucchi L, Tassone G, Venturelli A, Spyrakis F, Mazzorana M, Costi MP, Tonelli M. Antitarget, Anti-SARS-CoV-2 Leads, Drugs, and the Drug Discovery-Genetics Alliance Perspective. J Med Chem 2023; 66:3664-3702. [PMID: 36857133 PMCID: PMC10005815 DOI: 10.1021/acs.jmedchem.2c01229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
The most advanced antiviral molecules addressing major SARS-CoV-2 targets (Main protease, Spike protein, and RNA polymerase), compared with proteins of other human pathogenic coronaviruses, may have a short-lasting clinical efficacy. Accumulating knowledge on the mechanisms underlying the target structural basis, its mutational progression, and the related biological significance to virus replication allows envisaging the development of better-targeted therapies in the context of COVID-19 epidemic and future coronavirus outbreaks. The identification of evolutionary patterns based solely on sequence information analysis for those targets can provide meaningful insights into the molecular basis of host-pathogen interactions and adaptation, leading to drug resistance phenomena. Herein, we will explore how the study of observed and predicted mutations may offer valuable suggestions for the application of the so-called "synthetic lethal" strategy to SARS-CoV-2 Main protease and Spike protein. The synergy between genetics evidence and drug discovery may prioritize the development of novel long-lasting antiviral agents.
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Affiliation(s)
- Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy,
University of Siena, via Aldo Moro 2, 53100 Siena,
Italy
| | - Anne Vanet
- Université Paris Cité,
CNRS, Institut Jacques Monod, F-75013 Paris,
France
| | - Valeria Francesconi
- Department of Pharmacy, University of
Genoa, viale Benedetto XV n.3, 16132 Genoa, Italy
| | - Lorenzo Tagliazucchi
- Department of Life Science, University of
Modena and Reggio Emilia, via Campi 103, 41125 Modena,
Italy
- Doctorate School in Clinical and Experimental Medicine
(CEM), University of Modena and Reggio Emilia, Via Campi 287,
41125 Modena, Italy
| | - Giusy Tassone
- Department of Biotechnology, Chemistry and Pharmacy,
University of Siena, via Aldo Moro 2, 53100 Siena,
Italy
| | - Alberto Venturelli
- Department of Life Science, University of
Modena and Reggio Emilia, via Campi 103, 41125 Modena,
Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology,
University of Turin, Via Giuria 9, 10125 Turin,
Italy
| | - Marco Mazzorana
- Diamond Light Source, Harwell Science and
Innovation Campus, Didcot, Oxfordshire OX11 0DE,
U.K.
| | - Maria P. Costi
- Department of Life Science, University of
Modena and Reggio Emilia, via Campi 103, 41125 Modena,
Italy
| | - Michele Tonelli
- Department of Pharmacy, University of
Genoa, viale Benedetto XV n.3, 16132 Genoa, Italy
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12
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Wan L, Wang X, Wang T, Yuan X, Liu W, Huang Y, Deng C, Cao S. Comparison of Target Pocket Similarity and Progress into Research on Inhibitors of Picornavirus 3C Proteases. Chem Biodivers 2023; 20:e202201100. [PMID: 36808685 DOI: 10.1002/cbdv.202201100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 02/21/2023]
Abstract
The 3C protease (3C Pro) plays a significant role in the life cycle of picornaviruses from replication to translation, making it an attractive target for structure-based design of drugs against picornaviruses. The structurally related 3C-like protease (3CL Pro) is an important protein involved in the replication of coronaviruses. With the emergence of COVID-19 and consequent intensive research into 3CL Pro, development of 3CL Pro inhibitors has emerged as a popular topic. This article compares the similarities of the target pockets of various 3C and 3CL Pros from numerous pathogenic viruses. This article also reports several types of 3C Pro inhibitors that are currently undergoing extensive studies and introduces various structural modifications of 3C Pro inhibitors to provide a reference for the development of new and more effective inhibitors of 3C Pro and 3CL Pro.
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Affiliation(s)
- Li Wan
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Xiaobo Wang
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, 437100, P. R. China
| | - Tangle Wang
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Xiaolan Yuan
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Wei Liu
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Yan Huang
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Changyong Deng
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Shuang Cao
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
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13
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Discovery of inhibitors against SARS-CoV-2 main protease using fragment-based drug design. Chem Biol Interact 2023; 371:110352. [PMID: 36642317 PMCID: PMC9837207 DOI: 10.1016/j.cbi.2023.110352] [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: 07/21/2022] [Revised: 12/29/2022] [Accepted: 01/12/2023] [Indexed: 01/15/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of coronavirus disease 2019 (COVID-19), in which the main protease (Mpro) plays an important role in the virus's life cycle. In this work, two representative peptide inhibitors (11a and PF-07321332) were selected, and their interaction mechanisms of non-covalently bound with Mpro were firstly investigated by means of molecular dynamical simulation. Then, using the fragment-based drug design method, some fragments from the existing SARS-CoV and SARS-CoV-2 inhibitors were selected to replace the original P2 and P3 fragments, resulting in some new molecules. Among them, two molecules (O-74 and N-98) were confirmed by molecular docking and molecular dynamics simulation, and ADMET properties prediction was employed for further verification. The results shown that they presented excellent activity and physicochemical properties, and had the potential to be new inhibitors for SARS-CoV-2 main protease.
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14
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Chen TH, Tsai MJ, Chang CS, Xu L, Fu YS, Weng CF. The exploration of phytocompounds theoretically combats SARS-CoV-2 pandemic against virus entry, viral replication and immune evasion. J Infect Public Health 2023; 16:42-54. [PMID: 36470006 PMCID: PMC9675089 DOI: 10.1016/j.jiph.2022.11.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The novel coronavirus disease-2019 (COVID-19) that emerged in China, is an extremely contagious and pathogenic viral infection caused by the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) that has sparked a global pandemic. The few and limited availability of approved therapeutic agents or vaccines is of great concern. Urgently, Remdesivir, Nirmatrelvir, Molnupiravir, and some phytochemicals including polyphenol, flavonoid, alkaloid, and triterpenoid are applied to develop as repurposing drugs against the SARS-CoV-2 invasion. METHODS This study was conducted to perform molecular docking and absorption, distribution, metabolism, excretion and toxicity (ADMET) analysis of the potential phytocompounds and repurposing drugs against three targets of SARS-CoV-2 proteins (RNA dependent RNA polymerase, RdRp, Endoribonclease, S-protein of ACE2-RBD). RESULTS The docking data illustrated Arachidonic acid, Rutin, Quercetin, and Curcumin were highly bound with coronavirus polyprotein replicase and Ebolavirus envelope protein. Furthermore, anti- Ebolavirus molecule Remedesivir, anti-HIV molecule Chloroquine, and Darunavir were repurposed with coronavirus polyprotein replicase as well as Ebolavirus envelope protein. The strongest binding interaction of each targets are Rutin with RdRp, Endoribonclease with Amentoflavone, and ACE2-RBD with Epigallocatechin gallate. CONCLUSIONS Taken altogether, these results shed a light on that phytocompounds have a therapeutic potential for the treatment of anti-SARS-CoV-2 may base on multi-target effects or cocktail formulation for blocking viral infection through invasion/activation, transcription/reproduction, and posttranslational cleavage to battle COVID-19 pandemic.
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Affiliation(s)
- Ting-Hsu Chen
- Functional Physiology Section, Department of Basic Medical Science, Xiamen Medical College, Xiamen 361023, Fujian, China
| | - May-Jywan Tsai
- Department of Neurosurgery, Neurological Institute, Neurological Institute, Taipei 11217, Taiwan
| | - Chun-Sheng Chang
- Department of biotechnology and food technology, Southern Taiwan University of Science and Technology, Yungkang City 701, Taiwan
| | - Linxi Xu
- Functional Physiology Section, Department of Basic Medical Science, Xiamen Medical College, Xiamen 361023, Fujian, China
| | - Yaw-Syan Fu
- Functional Physiology Section, Department of Basic Medical Science, Xiamen Medical College, Xiamen 361023, Fujian, China,Institute of Respiratory Disease, Department of Basic Medical Science, Xiamen Medical College, Xiamen 361023, Fujian, China,Corresponding author
| | - Ching-Feng Weng
- Functional Physiology Section, Department of Basic Medical Science, Xiamen Medical College, Xiamen 361023, Fujian, China,Institute of Respiratory Disease, Department of Basic Medical Science, Xiamen Medical College, Xiamen 361023, Fujian, China,Corresponding author
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15
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Lau B, Emani PS, Chapman J, Yao L, Lam T, Merrill P, Warrell J, Gerstein MB, Lam HYK. Insights from incorporating quantum computing into drug design workflows. Bioinformatics 2023; 39:6881079. [PMID: 36477833 PMCID: PMC9825754 DOI: 10.1093/bioinformatics/btac789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 10/14/2022] [Accepted: 12/06/2022] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION While many quantum computing (QC) methods promise theoretical advantages over classical counterparts, quantum hardware remains limited. Exploiting near-term QC in computer-aided drug design (CADD) thus requires judicious partitioning between classical and quantum calculations. RESULTS We present HypaCADD, a hybrid classical-quantum workflow for finding ligands binding to proteins, while accounting for genetic mutations. We explicitly identify modules of our drug-design workflow currently amenable to replacement by QC: non-intuitively, we identify the mutation-impact predictor as the best candidate. HypaCADD thus combines classical docking and molecular dynamics with quantum machine learning (QML) to infer the impact of mutations. We present a case study with the coronavirus (SARS-CoV-2) protease and associated mutants. We map a classical machine-learning module onto QC, using a neural network constructed from qubit-rotation gates. We have implemented this in simulation and on two commercial quantum computers. We find that the QML models can perform on par with, if not better than, classical baselines. In summary, HypaCADD offers a successful strategy for leveraging QC for CADD. AVAILABILITY AND IMPLEMENTATION Jupyter Notebooks with Python code are freely available for academic use on GitHub: https://www.github.com/hypahub/hypacadd_notebook. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | | | - Lijing Yao
- HypaHealth, HypaHub Inc., San Jose, CA 95128, USA
| | - Tarsus Lam
- HypaHealth, HypaHub Inc., San Jose, CA 95128, USA
| | - Paul Merrill
- HypaHealth, HypaHub Inc., San Jose, CA 95128, USA
| | - Jonathan Warrell
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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16
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Recent advances in anti-coxsackievirus A16 viral drug research. Future Med Chem 2023; 15:97-117. [PMID: 36538291 DOI: 10.4155/fmc-2022-0195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Hand, foot and mouth disease, a childhood disorder caused by enteroviruses, is intermittently endemic in the Asia-Pacific region and endangers the lives of many infants and young children. Coxsackievirus A16 (CV-A16) is one of the major pathogens causing hand, foot, and mouth disease on occasion, resulting in catastrophic neurological sequelae and patient death. Currently, no clinical interventions are available that completely block the CV-A16 infection. Therefore, research on anti-CV-A16 treatment continues to be a significant focus of interest. This report provides a detailed background on and an introduction to CV-A16; a description of the viral gene and protein structures and a summary of the current advances in pharmaceutical targets, drug research and other related areas.
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17
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Green Synthesized Zinc Oxide Nanoparticles Based on Cestrum diurnum L. of Potential Antiviral Activity against Human Corona 229-E Virus. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010266. [PMID: 36615461 PMCID: PMC9822259 DOI: 10.3390/molecules28010266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/16/2022] [Accepted: 12/18/2022] [Indexed: 12/30/2022]
Abstract
SARS-CoV-2 has caused more than 596 million infections and 6 million fatalities globally. Looking for urgent medication for prevention, treatment, and rehabilitation is obligatory. Plant extracts and green synthesized nanoparticles have numerous biological activities, including antiviral activity. HPLC analysis of C. dirnum L. leaf extract showed that catechin, ferulic acid, chlorogenic acid, and syringic acid were the most major compounds, with concentrations of 1425.16, 1004.68, 207.46, and 158.95 µg/g, respectively. Zinc nanoparticles were biosynthesized using zinc acetate and C. dirnum extract. TEM analysis revealed that the particle size of ZnO-NPs varied between 3.406 and 4.857 nm. An XRD study showed the existence of hexagonal crystals of ZnO-NPs with an average size of 12.11 nm. Both ZnO-NPs (IC50 = 7.01 and CC50 = 145.77) and C. dirnum L. extract (IC50 = 61.15 and CC50 = 145.87 µg/mL) showed antiviral activity against HCOV-229E, but their combination (IC50 = 2.41 and CC50 = 179.23) showed higher activity than both. Molecular docking was used to investigate the affinity of some metabolites against the HCOV-229E main protease. Chlorogenic acid, solanidine, and catchin showed high affinity (-7.13, -6.95, and -6.52), compared to the ligand MDP (-5.66 Kcal/mol). Cestrum dinurum extract and ZnO-NPs combination should be subjected to further studies to be used as an antiviral drug.
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18
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Discovery and mechanism of action of Thonzonium bromide from an FDA-approved drug library with potent and broad-spectrum inhibitory activity against main proteases of human coronaviruses. Bioorg Chem 2022; 130:106264. [PMCID: PMC9643332 DOI: 10.1016/j.bioorg.2022.106264] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 10/28/2022] [Accepted: 11/04/2022] [Indexed: 11/10/2022]
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19
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Bafna K, Cioffi CL, Krug RM, Montelione GT. Structural similarities between SARS-CoV2 3CL pro and other viral proteases suggest potential lead molecules for developing broad spectrum antivirals. Front Chem 2022; 10:948553. [PMID: 36353143 PMCID: PMC9638714 DOI: 10.3389/fchem.2022.948553] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/08/2022] [Indexed: 09/01/2023] Open
Abstract
Considering the significant impact of the recent COVID-19 outbreak, development of broad-spectrum antivirals is a high priority goal to prevent future global pandemics. Antiviral development processes generally emphasize targeting a specific protein from a particular virus. However, some antiviral agents developed for specific viral protein targets may exhibit broad spectrum antiviral activity, or at least provide useful lead molecules for broad spectrum drug development. There is significant potential for repurposing a wide range of existing viral protease inhibitors to inhibit the SARS-CoV2 3C-like protease (3CLpro). If effective even as relatively weak inhibitors of 3CLpro, these molecules can provide a diverse and novel set of scaffolds for new drug discovery campaigns. In this study, we compared the sequence- and structure-based similarity of SARS-CoV2 3CLpro with proteases from other viruses, and identified 22 proteases with similar active-site structures. This structural similarity, characterized by secondary-structure topology diagrams, is evolutionarily divergent within taxonomically related viruses, but appears to result from evolutionary convergence of protease enzymes between virus families. Inhibitors of these proteases that are structurally similar to the SARS-CoV2 3CLpro protease were identified and assessed as potential inhibitors of SARS-CoV2 3CLpro protease by virtual docking. Several of these molecules have docking scores that are significantly better than known SARS-CoV2 3CLpro inhibitors, suggesting that these molecules are also potential inhibitors of the SARS-CoV2 3CLpro protease. Some have been previously reported to inhibit SARS-CoV2 3CLpro. The results also suggest that established inhibitors of SARS-CoV2 3CLpro may be considered as potential inhibitors of other viral 3C-like proteases.
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Affiliation(s)
- Khushboo Bafna
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, United States
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Christopher L. Cioffi
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Robert M. Krug
- Department of Molecular Biosciences, John Ring LaMontagne Center for Infectious Disease, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, United States
| | - Gaetano T. Montelione
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, United States
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
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20
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Hu Q, Xiong Y, Zhu G, Zhang Y, Zhang Y, Huang P, Ge G. The SARS-CoV-2 main protease (M pro): Structure, function, and emerging therapies for COVID-19. MedComm (Beijing) 2022; 3:e151. [PMID: 35845352 PMCID: PMC9283855 DOI: 10.1002/mco2.151] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/06/2022] [Accepted: 06/06/2022] [Indexed: 12/21/2022] Open
Abstract
The main proteases (Mpro), also termed 3-chymotrypsin-like proteases (3CLpro), are a class of highly conserved cysteine hydrolases in β-coronaviruses. Increasing evidence has demonstrated that 3CLpros play an indispensable role in viral replication and have been recognized as key targets for preventing and treating coronavirus-caused infectious diseases, including COVID-19. This review is focused on the structural features and biological function of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease Mpro (also known as 3CLpro), as well as recent advances in discovering and developing SARS-CoV-2 3CLpro inhibitors. To better understand the characteristics of SARS-CoV-2 3CLpro inhibitors, the inhibition activities, inhibitory mechanisms, and key structural features of various 3CLpro inhibitors (including marketed drugs, peptidomimetic, and non-peptidomimetic synthetic compounds, as well as natural compounds and their derivatives) are summarized comprehensively. Meanwhile, the challenges in this field are highlighted, while future directions for designing and developing efficacious 3CLpro inhibitors as novel anti-coronavirus therapies are also proposed. Collectively, all information and knowledge presented here are very helpful for understanding the structural features and inhibitory mechanisms of SARS-CoV-2 3CLpro inhibitors, which offers new insights or inspiration to medicinal chemists for designing and developing more efficacious 3CLpro inhibitors as novel anti-coronavirus agents.
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Affiliation(s)
- Qing Hu
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
- Clinical Pharmacy CenterCancer CenterDepartment of PharmacyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical College, HangzhouZhejiangChina
| | - Yuan Xiong
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Guang‐Hao Zhu
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Ya‐Ni Zhang
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Yi‐Wen Zhang
- Clinical Pharmacy CenterCancer CenterDepartment of PharmacyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical College, HangzhouZhejiangChina
| | - Ping Huang
- Clinical Pharmacy CenterCancer CenterDepartment of PharmacyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical College, HangzhouZhejiangChina
| | - Guang‐Bo Ge
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
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21
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Yuan X, Kadowaki T. DWV 3C Protease Uncovers the Diverse Catalytic Triad in Insect RNA Viruses. Microbiol Spectr 2022; 10:e0006822. [PMID: 35575593 PMCID: PMC9241925 DOI: 10.1128/spectrum.00068-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/22/2022] [Indexed: 11/20/2022] Open
Abstract
Deformed wing virus (DWV) is the most prevalent Iflavirus that is infecting honey bees worldwide. However, the mechanisms of its infection and replication in host cells are poorly understood. In this study, we analyzed the structure and function of DWV 3C protease (3Cpro), which is necessary for the cleavage of the polyprotein to synthesize mature viral proteins. Thus, it is one of the nonstructural viral proteins essential for the replication. We found that the 3Cpros of DWV and picornaviruses share common enzymatic properties, including sensitivity to the same inhibitors, such as rupintrivir. The predicted structure of DWV 3Cpro by AlphaFold2, the predicted rupintrivir binding domain, and the protease activities of mutant proteins revealed that it has a Cys-His-Asn catalytic triad. Moreover, 3Cpros of other Iflaviruses and Dicistrovirus appear to contain Asn, Ser, Asp, or Glu as the third residue of the catalytic triad, suggesting diversity in insect RNA viruses. Both precursor 3Cpro with RNA-dependent RNA polymerase and mature 3Cpro are present in DWV-infected cells, suggesting that they may have different enzymatic properties and functions. DWV 3Cpro is the first 3Cpro characterized among insect RNA viruses, and our study uncovered both the common and unique characteristics among 3Cpros of Picornavirales. Furthermore, it would be possible to use the specific inhibitors of DWV 3Cpro to control DWV infection in honey bees in future. IMPORTANCE The number of managed honey bee (Apis mellifera) colonies has considerably declined in many developed countries in the recent years. Deformed wing virus (DWV) vectored by the mites is the major threat to honey bee colonies and health. To give insight into the mechanism of DWV replication in the host cells, we studied the structure-function relationship of 3C protease (3Cpro), which is necessary to cleave a viral polyprotein at the specific sites to produce the mature proteins. We found that the overall structure, some inhibitors, and processing of 3Cpro are shared between Picornavirales; however, there is diversity in the catalytic triad. DWV 3Cpro is the first viral protease characterized among insect RNA viruses and reveals the evolutionary history of 3Cpro among Picornavirales. Furthermore, DWV 3Cpro inhibitors identified in our study could also be applied to control DWV in honey bees in future.
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Affiliation(s)
- Xuye Yuan
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Jiangsu Province, China
| | - Tatsuhiko Kadowaki
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Jiangsu Province, China
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22
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Katre SG, Asnani AJ, Pratyush K, Sakharkar NG, Bhope AG, Sawarkar KT, Nimbekar VS. Review on development of potential inhibitors of SARS-CoV-2 main protease (M Pro). FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2022; 8:36. [PMID: 35756354 PMCID: PMC9209839 DOI: 10.1186/s43094-022-00423-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 06/03/2022] [Indexed: 11/10/2022] Open
Abstract
Background The etiological agent for the coronavirus illness outbreak in 2019-2020 is a novel coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (COVID-19), whereas coronavirus disease pandemic of 2019 (COVID-19) has compelled the implementation of novel therapeutic options. Main body of the abstract There are currently no targeted therapeutic medicines for this condition, and effective treatment options are quite restricted; however, new therapeutic candidates targeting the viral replication cycle are being investigated. The primary protease of the severe acute respiratory syndrome coronavirus 2 virus is a major target for therapeutic development (MPro). Severe acute respiratory syndrome coronavirus 2, severe acute respiratory syndrome coronavirus, and Middle East respiratory syndrome coronavirus (MERS-CoV) all seem to have a structurally conserved substrate-binding domain that can be used to develop novel protease inhibitors. Short conclusion With the recent publication of the X-ray crystal structure of the severe acute respiratory syndrome coronavirus 2 Mm, virtual and in vitro screening investigations to find MPro inhibitors are fast progressing. The focus of this review is on recent advancements in the quest for small-molecule inhibitors of the severe acute respiratory syndrome coronavirus 2 main protease.
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Affiliation(s)
- Soumya Gulab Katre
- Department of Pharmaceutical Chemistry, Priyadarshini J L College of Pharmacy, Nagpur, MH 440016 India
| | - Alpana Jagdish Asnani
- Department of Pharmaceutical Chemistry, Priyadarshini J L College of Pharmacy, Nagpur, MH 440016 India
| | - Kumar Pratyush
- Department of Pharmaceutical Chemistry, Priyadarshini J L College of Pharmacy, Nagpur, MH 440016 India
| | | | - Ashwini Gajanan Bhope
- Department of Pharmaceutical Chemistry, Priyadarshini J L College of Pharmacy, Nagpur, MH 440016 India
| | - Kanchan Tekram Sawarkar
- Department of Pharmaceutical Chemistry, Priyadarshini J L College of Pharmacy, Nagpur, MH 440016 India
| | - Vaibhav Santosh Nimbekar
- Department of Pharmaceutical Chemistry, Priyadarshini J L College of Pharmacy, Nagpur, MH 440016 India
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23
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Li H, Yuan S, Wei X, Sun H. Metal-based strategies for the fight against COVID-19. Chem Commun (Camb) 2022; 58:7466-7482. [PMID: 35730442 DOI: 10.1039/d2cc01772e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The emerging COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has claimed over six million lives globally to date. Despite the availability of vaccines, the pandemic still cannot be fully controlled owing to rapid mutation of the virus that renders enhanced transmissibility and antibody evasion. This is thus an unmet need to develop safe and effective therapeutic options for COVID-19, in particular, remedies that can be used at home. Considering the great success of multi-targeted cocktail therapy for the treatment of viral infections, metal-based drugs might represent a unique and new source of antivirals that resemble a cocktail therapy in terms of their mode of actions. In this review, we first summarize the role that metal ions played in SARS-CoV-2 viral replication and pathogenesis, then highlight the chemistry of metal-based strategies in the fight against SARS-CoV-2 infection, including both metal displacement and chelation based approaches. Finally, we outline a perspective and direction on how to design and develop metal-based antivirals for the fight against the current or future coronavirus pandemic.
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Affiliation(s)
- Hongyan Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry and CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | - Shuofeng Yuan
- Department of Microbiology and State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Xueying Wei
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry and CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pokfulam, Hong Kong SAR, China. .,Department of Microbiology and State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Hongzhe Sun
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry and CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
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Structure of Senecavirus A 3C Protease Revealed the Cleavage Pattern of 3C Protease in Picornaviruses. J Virol 2022; 96:e0073622. [PMID: 35727031 DOI: 10.1128/jvi.00736-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Senecavirus A (SVA) is an emerging picornavirus infecting porcine of all age groups and causing foot and mouth disease (FMD)-like symptoms. One of its key enzymes is the 3C protease (3Cpro), which is similar to other picornaviruses and essential for virus maturation by controlling polyprotein cleavage and RNA replication. In this study, we reported the crystal structure of SVA 3Cpro at a resolution of 1.9 Å and a thorough structural comparison against all published picornavirus 3Cpro structures. Using statistical and graphical visualization techniques, we also investigated the sequence specificity of the 3Cpro. The structure revealed that SVA 3Cpro adopted a typical chymotrypsin-like fold with the S1 subsite as the most conservative site among picornavirus 3Cpro. The surface loop, A1-B1 hairpin, adopted a novel conformation in SVA 3Cpro and formed a positively charged protrusion around S' subsites. Correspondingly, SVA scissile bonds preferred Asp rather than neutral amino acids at P3' and P4'. Moreover, SVA 3Cpro showed a wide range tolerance to P4 residue volume (acceptable range: 67 Å3 to 141 Å3), such as aromatic side chain, in contrast to other picornaviruses. In summary, our results provided valuable information for understanding the cleavage pattern of 3Cpro. IMPORTANCE Picornaviridae is a group of RNA viruses that harm both humans and livestock. 3Cpro is an essential enzyme for picornavirus maturation, which makes it a promising target for antiviral drug development and a critical component for virus-like particle (VLP) production. However, the current challenge in the development of antiviral drugs and VLP vaccines includes the limited knowledge of how subsite structure determines the 3Cpro cleavage pattern. Thus, an extensive comparative study of various picornaviral 3Cpro was required. Here, we showed the 1.9 Å crystal structure of SVA 3Cpro. The structure revealed similarities and differences in the substrate-binding groove among picornaviruses, providing new insights into the development of inhibitors and VLP.
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25
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Zhu Y, Scholle F, Kisthardt SC, Xie DY. Flavonols and dihydroflavonols inhibit the main protease activity of SARS-CoV-2 and the replication of human coronavirus 229E. Virology 2022; 571:21-33. [PMID: 35439707 PMCID: PMC9002334 DOI: 10.1016/j.virol.2022.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/07/2022] [Accepted: 04/07/2022] [Indexed: 12/14/2022]
Abstract
Since December 2019, the deadly novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the current COVID-19 pandemic. To date, vaccines are available in the developed countries to prevent the infection of this virus; however, medicines are necessary to help control COVID-19. Human coronavirus 229E (HCoV-229E) causes the common cold. The main protease (Mpro) is an essential enzyme required for the multiplication of these two viruses in the host cells, and thus is an appropriate candidate to screen potential medicinal compounds. Flavonols and dihydroflavonols are two groups of plant flavonoids. In this study, we report docking simulation with two Mpro enzymes and five flavonols and three dihydroflavonols, in vitro inhibition of the SARS-CoV-2 Mpro, and in vitro inhibition of the HCoV 229E replication. The docking simulation results predicted that (+)-dihydrokaempferol, (+)- dihydroquercetin, (+)-dihydromyricetin, kaempferol, quercetin, myricentin, isoquercitrin, and rutin could bind to at least two subsites (S1, S1’, S2, and S4) in the binding pocket and inhibit the activity of SARS-CoV-2 Mpro. Their affinity scores ranged from −8.8 to −7.4 (kcal/mol). Likewise, these compounds were predicted to bind and inhibit the HCoV-229E Mpro activity with affinity scores ranging from −7.1 to −7.8 (kcal/mol). In vitro inhibition assays showed that seven available compounds effectively inhibited the SARS-CoV-2 Mpro activity and their IC50 values ranged from 0.125 to 12.9 μM. Five compounds inhibited the replication of HCoV-229E in Huh-7 cells. These findings indicate that these antioxidative flavonols and dihydroflavonols are promising candidates for curbing the two viruses.
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Affiliation(s)
- Yue Zhu
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Frank Scholle
- Department of Biology, North Carolina State University, Raleigh, NC, USA
| | | | - De-Yu Xie
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA.
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26
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de Jesus JR, Galazzi RM, Lopes Júnior CA, Arruda MAZ. Trace element homeostasis in the neurological system after SARS-CoV-2 infection: Insight into potential biochemical mechanisms. J Trace Elem Med Biol 2022; 71:126964. [PMID: 35240553 PMCID: PMC8881805 DOI: 10.1016/j.jtemb.2022.126964] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 02/10/2022] [Accepted: 02/23/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Several studies have suggested that COVID-19 is a systemic disease that can affect several organs, including the brain. In the brain, specifically, viral infection can cause dyshomeostasis of some trace elements that promote complex biochemical reactions in specialized neurological functions. OBJECTIVE Understand the neurovirulence of SARS-CoV-2 and the relationship between trace elements and neurological disorders after infection, and provide new insights on the drug development for the treatment of SARS-CoV-2 infections. METHODS The main databases were used to search studies published up September 2021, focusing on the role of trace elements during viral infection and on the correct functioning of the brain. RESULTS The imbalance of important trace elements can accelerate SARS-CoV-2 neurovirulence and increase the neurotoxicity since many neurological processes can be associated with the homeostasis of metal and metalloproteins. Some studies involving animals and humans have suggested the synapse as a vulnerable region of the brain to neurological disorders after viral infection. Considering the combined evidence, some mechanisms have been suggested to understand the relationship between neurological disorders and imbalance of trace elements in the brain after viral infection. CONCLUSION Trace elements play important roles in viral infections, such as helping to activate immune cells, produce antibodies, and inhibit virus replication. However, the relationship between trace elements and virus infections is complex since the specific functions of several elements remain largely undefined. Therefore, there is still a lot to be explored to understand the biochemical mechanisms involved between trace elements and viral infections, especially in the brain.
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Affiliation(s)
- Jemmyson Romário de Jesus
- Research Laboratory in Bionanomaterials, LPbio, Brazil; Chemistry Department, Federal University of Viçosa, UFV, Viçosa, Minas Gerais, Brazil.
| | - Rodrigo Moretto Galazzi
- Analytical Instrumentation Division, Analytik Jena GmbH, an Endress & Hauser Company, São Paulo, SP 04029-901, Brazil.
| | - Cícero Alves Lopes Júnior
- Grupo de Estudos em Bioanalítica - GEBIO, Department of Chemistry, Federal University of Piauí, 64049-550 Teresina, PI, Brazil.
| | - Marco Aurélio Zezzi Arruda
- Spectrometry, Sample Preparation and Mechanization Group, GEPAM, Institute of Chemistry, University of Campinas, UNICAMP, Campinas, Brazil; National Institute of Science and Technology for Bioanalytics, Brazil.
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Wang F, Chen C, Wang Z, Han X, Shi P, Zhou K, Liu X, Xiao Y, Cai Y, Huang J, Zhang L, Yang H. The Structure of the Porcine Deltacoronavirus Main Protease Reveals a Conserved Target for the Design of Antivirals. Viruses 2022; 14:v14030486. [PMID: 35336895 PMCID: PMC8949103 DOI: 10.3390/v14030486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 11/17/2022] Open
Abstract
The existing zoonotic coronaviruses (CoVs) and viral genetic variants are important microbiological pathogens that cause severe disease in humans and animals. Currently, no effective broad-spectrum antiviral drugs against existing and emerging CoVs are available. The CoV main protease (Mpro) plays an essential role in viral replication, making it an ideal target for drug development. However, the structure of the Deltacoronavirus Mpro is still unavailable. Porcine deltacoronavirus (PDCoV) is a novel CoV that belongs to the genus Deltacoronavirus and causes atrophic enteritis, severe diarrhea, vomiting and dehydration in pigs. Here, we determined the structure of PDCoV Mpro complexed with a Michael acceptor inhibitor. Structural comparison showed that the backbone of PDCoV Mpro is similar to those of alpha-, beta- and gamma-CoV Mpros. The substrate-binding pocket of Mpro is well conserved in the subfamily Coronavirinae. In addition, we also observed that Mpros from the same genus adopted a similar conformation. Furthermore, the structure of PDCoV Mpro in complex with a Michael acceptor inhibitor revealed the mechanism of its inhibition of PDCoV Mpro. Our results provide a basis for the development of broad-spectrum antivirals against PDCoV and other CoVs.
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Affiliation(s)
- Fenghua Wang
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (F.W.); (C.C.); (Z.W.); (X.H.); (P.S.); (Y.X.); (J.H.)
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China; (K.Z.); (X.L.); (Y.C.)
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Cheng Chen
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (F.W.); (C.C.); (Z.W.); (X.H.); (P.S.); (Y.X.); (J.H.)
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China; (K.Z.); (X.L.); (Y.C.)
| | - Zefang Wang
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (F.W.); (C.C.); (Z.W.); (X.H.); (P.S.); (Y.X.); (J.H.)
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China; (K.Z.); (X.L.); (Y.C.)
| | - Xu Han
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (F.W.); (C.C.); (Z.W.); (X.H.); (P.S.); (Y.X.); (J.H.)
| | - Peidian Shi
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (F.W.); (C.C.); (Z.W.); (X.H.); (P.S.); (Y.X.); (J.H.)
| | - Kaixuan Zhou
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China; (K.Z.); (X.L.); (Y.C.)
| | - Xiaomei Liu
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China; (K.Z.); (X.L.); (Y.C.)
| | - Yunjie Xiao
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (F.W.); (C.C.); (Z.W.); (X.H.); (P.S.); (Y.X.); (J.H.)
| | - Yan Cai
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China; (K.Z.); (X.L.); (Y.C.)
| | - Jinhai Huang
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (F.W.); (C.C.); (Z.W.); (X.H.); (P.S.); (Y.X.); (J.H.)
| | - Lei Zhang
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (F.W.); (C.C.); (Z.W.); (X.H.); (P.S.); (Y.X.); (J.H.)
- Correspondence: (L.Z.); (H.Y.)
| | - Haitao Yang
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (F.W.); (C.C.); (Z.W.); (X.H.); (P.S.); (Y.X.); (J.H.)
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China; (K.Z.); (X.L.); (Y.C.)
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
- Correspondence: (L.Z.); (H.Y.)
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Chia CSB, Xu W, Shuyi Ng P. A Patent Review on SARS Coronavirus Main Protease (3CL pro ) Inhibitors. ChemMedChem 2022; 17:e202100576. [PMID: 34651447 PMCID: PMC8653044 DOI: 10.1002/cmdc.202100576] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/11/2021] [Indexed: 12/23/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is an unprecedented global health emergency causing more than 4.2 million fatalities as of 30 July 2021. Only three antiviral therapies have been approved or granted emergency use authorization by the FDA. The SARS-CoV-2 3CL protease (3CLpro ) is deemed an attractive drug target as it plays an essential role in viral polyprotein processing and pathogenesis, although no inhibitors have been approved. This patent review discusses SARS coronavirus 3CLpro inhibitors that have been filed up to 30 July 2021, giving an overview on the types of inhibitors that have generated commercial interest, especially amongst drug companies. Insights into the common structural motifs required for active site binding is also discussed.
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Affiliation(s)
- C. S. Brian Chia
- Experimental Drug Development Centre10 Biopolis Road138670Chromos #08-01Singapore
| | - Weijun Xu
- Experimental Drug Development Centre10 Biopolis Road138670Chromos #08-01Singapore
| | - Pearly Shuyi Ng
- Experimental Drug Development Centre10 Biopolis Road138670Chromos #08-01Singapore
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29
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Discovery of C-12 dithiocarbamate andrographolide analogues as inhibitors of SARS-CoV-2 main protease: In vitro and in silico studies. Comput Struct Biotechnol J 2022; 20:2784-2797. [PMID: 35677603 PMCID: PMC9167041 DOI: 10.1016/j.csbj.2022.05.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 05/27/2022] [Accepted: 05/27/2022] [Indexed: 11/27/2022] Open
Abstract
Andrographolide analogues were found to inhibit SARS-CoV-2 main protease. The compounds 3k, 3l, 3m and 3t showed promising in vitro inhibitory activity. Most of the candidates could bind well to the SARS-CoV-2 main protease active site.
A global crisis of coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has impacted millions of people’s lives throughout the world. In parallel to vaccine development, identifying potential antiviral agents against SARS-CoV-2 has become an urgent need to combat COVID-19. One of the most attractive drug targets for discovering anti-SARS-CoV-2 agents is the main protease (Mpro), which plays a pivotal role in the viral life cycle. This study aimed to elucidate a series of twenty-one 12-dithiocarbamate-14-deoxyandrographolide analogues as SARS-CoV-2 Mpro inhibitors using in vitro and in silico studies. These compounds were initially screened for the inhibitory activity toward SARS-CoV-2 Mpro by in vitro enzyme-based assay. We found that compounds 3k, 3l, 3m and 3t showed promising inhibitory activity against SARS-CoV-2 Mpro with >50% inhibition at 10 μM. Afterward, the binding mode of each compound in the active site of SARS-CoV-2 Mpro was explored by molecular docking. The optimum docked complexes were then chosen and subjected to molecular dynamic (MD) simulations. The MD results suggested that all studied complexes were stable along the simulation time, and most of the compounds could fit well with the SARS-CoV-2 Mpro active site, particularly at S1, S2 and S4 subsites. The per-residue decomposition free energy calculations indicated that the hot-spot residues essential for ligand binding were T25, H41, C44, S46, M49, C145, H163, M165, E166, L167, D187, R188, Q189 and T190. Therefore, the obtained information from the combined experimental and computational techniques could lead to further optimization of more specific and potent andrographolide analogues toward SARS-CoV-2 Mpro.
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30
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Jawarkar R, Bakal RL, Zaki ME, Al-Hussain S, Ghosh A, Gandhi A, Mukerjee N, Samad A, Masand VH, Lewaa I. QSAR based virtual screening derived identification of a novel hit as a SARS CoV-229E 3CL pro Inhibitor: GA-MLR QSAR modeling supported by molecular Docking, molecular dynamics simulation and MMGBSA calculation approaches. ARAB J CHEM 2022; 15:103499. [PMID: 34909066 PMCID: PMC8524701 DOI: 10.1016/j.arabjc.2021.103499] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 10/10/2021] [Indexed: 12/26/2022] Open
Abstract
Congruous coronavirus drug targets and analogous lead molecules must be identified as quickly as possible to produce antiviral therapeutics against human coronavirus (HCoV SARS 3CLpro) infections. In the present communication, we bear recognized a HIT candidate for HCoV SARS 3CLpro inhibition. Four Parametric GA-MLR primarily based QSAR model (R2:0.84, R2adj:0.82, Q2loo: 0.78) was once promoted using a dataset over 37 structurally diverse molecules along QSAR based virtual screening (QSAR-VS), molecular docking (MD) then molecular dynamic simulation (MDS) analysis and MMGBSA calculations. The QSAR-based virtual screening was utilized to find novel lead molecules from an in-house database of 100 molecules. The QSAR-vS successfully offered a hit molecule with an improved PEC50 value from 5.88 to 6.08. The benzene ring, phenyl ring, amide oxygen and nitrogen, and other important pharmacophoric sites are revealed via MD and MDS studies. Ile164, Pro188, Leu190, Thr25, His41, Asn46, Thr47, Ser49, Asn189, Gln191, Thr47, and Asn141 are among the key amino acid residues in the S1 and S2 pocket. A stable complex of a lead molecule with the HCoV SARS 3CLpro was discovered using MDS. MM-GBSA calculations resulted from MD simulation results well supported with the binding energies calculated from the docking results. The results of this study can be exploited to develop a novel antiviral target, such as an HCoV SARS 3CLpro Inhibitor.
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Key Words
- 3CLpro, 3C like Protease
- FDA, Food and Drug Administration
- GA-MLR
- GA-MLR, Genetic Algorithm Multilinear Regression
- HCoV SARS 3CLpro
- HCoV-HKU1, Human coronavirus HKU1
- HCoV-NL63, Human coronavirus NL63
- HCoVs, human coronaviruses
- Lead
- MD, Molecular Docking
- MDS, molecular dynamic simulation
- MERS, Middle East Respiratory Syndrome
- MMGBSA calculations
- MMGBSA, Molecular Mechanics Generalized Born and Surface Area
- Molecular docking and MD simulation
- OECD, Organization for Economic Corporation and Development
- QSAR based virtual screening
- QSAR, Quantitative Structure Activity Relationship
- RNA, Ribo-nucleic acid
- SARS, severe acute respiratory sign
- VS, Virtual Screening
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Affiliation(s)
- R.D. Jawarkar
- Department of Medicinal Chemistry, Dr. Rajendra Gode Institute of Pharmacy, University-Mardi Road, Amravati, Maharashtra, 444603, India,Corresponding authors at: Department of Medicinal Chemistry, Dr. Rajendra Gode College of Pharmacy, Mardi Road, Amravati, Maharashtra, India and (Rahul D. Jawarkar). Department of Chemistry, Faculty of Science, Al-Imam Mohammad Ibn Saud Islamic university, Riyadh 13318, Saudi Arabia (Magdi E.A. Zaki)
| | - Ravindrakumar L. Bakal
- Department of Medicinal Chemistry, Dr. Rajendra Gode Institute of Pharmacy, University-Mardi Road, Amravati, Maharashtra, 444603, India
| | - Magdi E.A. Zaki
- Department of Chemistry, Faculty of Science, Al-Imam Mohammad Ibn Saud Islamic university, Riyadh 13318, Saudi Arabia
| | - Sami Al-Hussain
- Department of Chemistry, Faculty of Science, Al-Imam Mohammad Ibn Saud Islamic university, Riyadh 13318, Saudi Arabia,Corresponding authors at: Department of Medicinal Chemistry, Dr. Rajendra Gode College of Pharmacy, Mardi Road, Amravati, Maharashtra, India and (Rahul D. Jawarkar). Department of Chemistry, Faculty of Science, Al-Imam Mohammad Ibn Saud Islamic university, Riyadh 13318, Saudi Arabia (Magdi E.A. Zaki)
| | - Arabinda Ghosh
- Microbiology Division, Department of Botany, Gauhati University, Guwahati, Assam 781014, India
| | - Ajaykumar Gandhi
- Department of Chemistry, Government College of Arts and Science, Aurangabad, Maharashtra 431 004, India
| | - Nobendu Mukerjee
- Department of Microbiology; Ramakrishna Mission Vivekananda Centenary College, Akhil Mukherjee Rd, Chowdhary Para, Rahara, Khardaha, Kolkata, West Bengal 700118, India
| | - Abdul Samad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tishk International University, Erbil, Kurdistan Region, Iraq
| | - Vijay H. Masand
- Department of Chemistry, Vidyabharti Mahavidyalaya, Camp Road, Amravati Maharashtra, India
| | - Israa Lewaa
- Department of Business Administration, Faculty of Business Administration, Economics & Political Science, The British University in Egypt (BUE), Cairo, Egypt
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Abstract
The main protease (Mpro) plays a crucial role in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication and is highly conserved, rendering it one of the most attractive therapeutic targets for SARS-CoV-2 inhibition. Currently, although two drug candidates targeting SARS-CoV-2 Mpro designed by Pfizer are under clinical trials, no SARS-CoV-2 medication is approved due to the long period of drug development. Here, we collect a comprehensive list of 817 available SARS-CoV-2 and SARS-CoV Mpro inhibitors from the literature or databases and analyze their molecular mechanisms of action. The structure-activity relationships (SARs) among each series of inhibitors are discussed. Additionally, we broadly examine available antiviral activity, ADMET (absorption, distribution, metabolism, excretion, and toxicity), and animal tests of these inhibitors. We comment on their druggability or drawbacks that prevent them from becoming drugs. This Perspective sheds light on the future development of Mpro inhibitors for SARS-CoV-2 and future coronavirus diseases.
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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
| | - Jetze J Tepe
- Department of Chemistry and Pharmacology & Toxicology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Faqing Huang
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Guo-Wei Wei
- Department of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
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32
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Panchariya L, Khan WA, Kuila S, Sonkar K, Sahoo S, Ghoshal A, Kumar A, Verma DK, Hasan A, Khan MA, Jain N, Mohapatra AK, Das S, Thakur JK, Maiti S, Nanda RK, Halder R, Sunil S, Arockiasamy A. Zinc 2+ ion inhibits SARS-CoV-2 main protease and viral replication in vitro. Chem Commun (Camb) 2021; 57:10083-10086. [PMID: 34514483 DOI: 10.1039/d1cc03563k] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Zinc deficiency is linked to poor prognosis in COVID-19 patients while clinical trials with zinc demonstrate better clinical outcomes. The molecular targets and mechanistic details of the anti-coronaviral activity of zinc remain obscure. We show that zinc not only inhibits the SARS-CoV-2 main protease (Mpro) with nanomolar affinity, but also viral replication. We present the first crystal structure of the Mpro-Zn2+ complex at 1.9 Å and provide the structural basis of viral replication inhibition. We show that Zn2+ coordinates with the catalytic dyad at the enzyme active site along with two previously unknown water molecules in a tetrahedral geometry to form a stable inhibited Mpro-Zn2+ complex. Further, the natural ionophore quercetin increases the anti-viral potency of Zn2+. As the catalytic dyad is highly conserved across SARS-CoV, MERS-CoV and all variants of SARS-CoV-2, Zn2+ mediated inhibition of Mpro may have wider implications.
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Affiliation(s)
- Love Panchariya
- Membrane Protein Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India.
| | - Wajahat Ali Khan
- Membrane Protein Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India.
| | - Shobhan Kuila
- Membrane Protein Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India.
| | - Kirtishila Sonkar
- Membrane Protein Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India.
| | - Sibasis Sahoo
- Membrane Protein Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India.
| | - Archita Ghoshal
- Membrane Protein Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India.
| | - Ankit Kumar
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Dileep Kumar Verma
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Abdul Hasan
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Mohd Azeem Khan
- Membrane Protein Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India.
| | - Niyati Jain
- CSIR-Institute of Genomics and Integrative Biology, Near Jubilee Hall, Mall Road, Delhi-110007, India
| | - Amit Kumar Mohapatra
- Translational Health Group, International Centre for Genetic Engineering and Biotechnology, New Delhi-110067, India
| | - Shubhashis Das
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110 067, India
| | - Jitendra K Thakur
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110 067, India
| | - Souvik Maiti
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ranjan Kumar Nanda
- Translational Health Group, International Centre for Genetic Engineering and Biotechnology, New Delhi-110067, India
| | - Rajkumar Halder
- Ruhvenile Biomedical OPC PVT LTD, Plot No-8, OCF Pocket Institution, Sarita Vihar, New Delhi-110070, India
| | - Sujatha Sunil
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Arulandu Arockiasamy
- Membrane Protein Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India.
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33
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Grifagni D, Calderone V, Giuntini S, Cantini F, Fragai M, Banci L. SARS-CoV-2 M pro inhibition by a zinc ion: structural features and hints for drug design. Chem Commun (Camb) 2021; 57:7910-7913. [PMID: 34278402 DOI: 10.1039/d1cc02956h] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Structural data on the SARS-CoV-2 main protease in complex with a zinc-containing organic inhibitor are already present in the literature and gave hints on the presence of a zinc binding site involving the catalytically relevant cysteine and histidine residues. In this paper, the structural basis of ionic zinc binding to the SARS-CoV-2 main protease has been elucidated by X-ray crystallography. The zinc binding affinity and its ability to inhibit the SARS-CoV-2 main protease have been investigated. These findings provide solid ground for the design of potent and selective metal-conjugated inhibitors of the SARS-CoV-2 main protease.
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Affiliation(s)
- Deborah Grifagni
- Magnetic Resonance Center (CERM), University of Florence, via Sacconi 6, Sesto Fiorentino, 50019, Italy.
| | - Vito Calderone
- Magnetic Resonance Center (CERM), University of Florence, via Sacconi 6, Sesto Fiorentino, 50019, Italy. and Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, 50019, Italy and Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, 50019, Italy
| | - Stefano Giuntini
- Magnetic Resonance Center (CERM), University of Florence, via Sacconi 6, Sesto Fiorentino, 50019, Italy.
| | - Francesca Cantini
- Magnetic Resonance Center (CERM), University of Florence, via Sacconi 6, Sesto Fiorentino, 50019, Italy. and Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, 50019, Italy and Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, 50019, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, via Sacconi 6, Sesto Fiorentino, 50019, Italy. and Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, 50019, Italy and Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, 50019, Italy
| | - Lucia Banci
- Magnetic Resonance Center (CERM), University of Florence, via Sacconi 6, Sesto Fiorentino, 50019, Italy. and Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, 50019, Italy and Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, 50019, Italy
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34
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Marjomäki V, Kalander K, Hellman M, Permi P. Enteroviruses and coronaviruses: similarities and therapeutic targets. Expert Opin Ther Targets 2021; 25:479-489. [PMID: 34253126 PMCID: PMC8330013 DOI: 10.1080/14728222.2021.1952985] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Introduction: Enteroviruses are common viruses causing a huge number of acute and chronic infections and producing towering economic costs. Similarly, coronaviruses cause seasonal mild infections, epidemics, and even pandemics and can lead to severe respiratory symptoms. It is important to develop broadly acting antiviral molecules to efficiently tackle the infections caused by thes.Areas covered: This review illuminates the differences and similarities between enteroviruses and coronaviruses and examines the most appealing therapeutic targets to combat both virus groups. Publications of both virus groups and deposited structures discovered through PubMed to March 2021 for viral proteases have been evaluated.Expert opinion: The main protease of coronaviruses and enteroviruses share similarities in their structure and function. These proteases process their viral polyproteins and thus drugs that bind to the active site have potential to target both virus groups. It is important to develop drugs that target more evolutionarily conserved processes and proteins. Moreover, it is a wise strategy to concentrate on processes that are similar between several virus families.
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Affiliation(s)
- Varpu Marjomäki
- Department of Biological and Environmental Science/Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Kerttu Kalander
- Department of Biological and Environmental Science/Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Maarit Hellman
- Department of Biological and Environmental Science/Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Perttu Permi
- Department of Biological and Environmental Science/Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
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35
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Drayman N, DeMarco JK, Jones KA, Azizi SA, Froggatt HM, Tan K, Maltseva NI, Chen S, Nicolaescu V, Dvorkin S, Furlong K, Kathayat RS, Firpo MR, Mastrodomenico V, Bruce EA, Schmidt MM, Jedrzejczak R, Muñoz-Alía MÁ, Schuster B, Nair V, Han KY, O’Brien A, Tomatsidou A, Meyer B, Vignuzzi M, Missiakas D, Botten JW, Brooke CB, Lee H, Baker SC, Mounce BC, Heaton NS, Severson WE, Palmer KE, Dickinson BC, Joachimiak A, Randall G, Tay S. Masitinib is a broad coronavirus 3CL inhibitor that blocks replication of SARS-CoV-2. Science 2021; 373:931-936. [PMID: 34285133 PMCID: PMC8809056 DOI: 10.1126/science.abg5827] [Citation(s) in RCA: 169] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 07/14/2021] [Indexed: 01/16/2023]
Abstract
There is an urgent need for antiviral agents that treat severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We screened a library of 1900 clinically safe drugs against OC43, a human beta coronavirus that causes the common cold, and evaluated the top hits against SARS-CoV-2. Twenty drugs significantly inhibited replication of both viruses in cultured human cells. Eight of these drugs inhibited the activity of the SARS-CoV-2 main protease, 3CLpro, with the most potent being masitinib, an orally bioavailable tyrosine kinase inhibitor. X-ray crystallography and biochemistry show that masitinib acts as a competitive inhibitor of 3CLpro. Mice infected with SARS-CoV-2 and then treated with masitinib showed >200-fold reduction in viral titers in the lungs and nose, as well as reduced lung inflammation. Masitinib was also effective in vitro against all tested variants of concern (B.1.1.7, B.1.351, and P.1).
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Affiliation(s)
- Nir Drayman
- Pritzker School for Molecular Engineering, The University of Chicago, Chicago, IL, USA.,Corresponding author. (S.T.); (N.D.)
| | - Jennifer K. DeMarco
- Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Krysten A. Jones
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA
| | - Saara-Anne Azizi
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Heather M. Froggatt
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.,Institut Pasteur, Viral Populations and Pathogenesis Unit, Centre National de la Recherche Scientifique UMR 3569, Paris, France
| | - Kemin Tan
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.,Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA.,Department of Medicine, Division of Immunobiology, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Natalia Ivanovna Maltseva
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.,Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA.,Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA
| | - Siquan Chen
- Cellular Screening Center, The University of Chicago, Chicago, IL, USA.,Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA
| | - Vlad Nicolaescu
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA
| | - Steve Dvorkin
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA
| | - Kevin Furlong
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA
| | - Rahul S. Kathayat
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA
| | - Mason R. Firpo
- Pritzker School for Molecular Engineering, The University of Chicago, Chicago, IL, USA.,Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Vincent Mastrodomenico
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Emily A. Bruce
- Cellular Screening Center, The University of Chicago, Chicago, IL, USA.,Department of Medicine, Division of Immunobiology, Larner College of Medicine, University of Vermont, Burlington, VT, USA.,Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Madaline M. Schmidt
- Department of Medicine, Division of Immunobiology, Larner College of Medicine, University of Vermont, Burlington, VT, USA.,Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Robert Jedrzejczak
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.,Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA
| | | | - Brooke Schuster
- Pritzker School for Molecular Engineering, The University of Chicago, Chicago, IL, USA.,Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA
| | - Vishnu Nair
- Pritzker School for Molecular Engineering, The University of Chicago, Chicago, IL, USA.,Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA
| | - Kyu-yeon Han
- Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, USA.,Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Amornrat O’Brien
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, Biophysics Core at Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA
| | - Anastasia Tomatsidou
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA.,Department of Medicine, Division of Immunobiology, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Bjoern Meyer
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Centre National de la Recherche Scientifique UMR 3569, Paris, France
| | - Marco Vignuzzi
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA.,Institut Pasteur, Viral Populations and Pathogenesis Unit, Centre National de la Recherche Scientifique UMR 3569, Paris, France
| | - Dominique Missiakas
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA
| | - Jason W. Botten
- Cellular Screening Center, The University of Chicago, Chicago, IL, USA.,Department of Medicine, Division of Immunobiology, Larner College of Medicine, University of Vermont, Burlington, VT, USA.,Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT, USA.,Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Christopher B. Brooke
- Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hyun Lee
- Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, VT, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, Biophysics Core at Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA
| | - Susan C. Baker
- Pritzker School for Molecular Engineering, The University of Chicago, Chicago, IL, USA.,Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA.,Institut Pasteur, Viral Populations and Pathogenesis Unit, Centre National de la Recherche Scientifique UMR 3569, Paris, France
| | - Bryan C. Mounce
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA.,Institut Pasteur, Viral Populations and Pathogenesis Unit, Centre National de la Recherche Scientifique UMR 3569, Paris, France.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Nicholas S. Heaton
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.,Institut Pasteur, Viral Populations and Pathogenesis Unit, Centre National de la Recherche Scientifique UMR 3569, Paris, France
| | - William E. Severson
- Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, USA.,Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Kenneth E. Palmer
- Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Bryan C. Dickinson
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA
| | - Andrzej Joachimiak
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.,Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Glenn Randall
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Savaş Tay
- Pritzker School for Molecular Engineering, The University of Chicago, Chicago, IL, USA.,Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA.,Corresponding author. (S.T.); (N.D.)
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36
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Günther S, Reinke PYA, Fernández-García Y, Lieske J, Lane TJ, Ginn HM, Koua FHM, Ehrt C, Ewert W, Oberthuer D, Yefanov O, Meier S, Lorenzen K, Krichel B, Kopicki JD, Gelisio L, Brehm W, Dunkel I, Seychell B, Gieseler H, Norton-Baker B, Escudero-Pérez B, Domaracky M, Saouane S, Tolstikova A, White TA, Hänle A, Groessler M, Fleckenstein H, Trost F, Galchenkova M, Gevorkov Y, Li C, Awel S, Peck A, Barthelmess M, Schlünzen F, Lourdu Xavier P, Werner N, Andaleeb H, Ullah N, Falke S, Srinivasan V, França BA, Schwinzer M, Brognaro H, Rogers C, Melo D, Zaitseva-Kinneberg JI, Knoska J, Peña-Murillo GE, Mashhour AR, Hennicke V, Fischer P, Hakanpää J, Meyer J, Gribbon P, Ellinger B, Kuzikov M, Wolf M, Beccari AR, Bourenkov G, von Stetten D, Pompidor G, Bento I, Panneerselvam S, Karpics I, Schneider TR, Garcia-Alai MM, Niebling S, Günther C, Schmidt C, Schubert R, Han H, Boger J, Monteiro DCF, Zhang L, Sun X, Pletzer-Zelgert J, Wollenhaupt J, Feiler CG, Weiss MS, Schulz EC, Mehrabi P, Karničar K, Usenik A, Loboda J, Tidow H, Chari A, Hilgenfeld R, Uetrecht C, Cox R, Zaliani A, Beck T, Rarey M, Günther S, Turk D, Hinrichs W, Chapman HN, Pearson AR, Betzel C, Meents A. X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease. Science 2021; 372:642-646. [PMID: 33811162 PMCID: PMC8224385 DOI: 10.1126/science.abf7945] [Citation(s) in RCA: 219] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/29/2021] [Indexed: 12/17/2022]
Abstract
The coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous human suffering. To date, no effective drug is available to directly treat the disease. In a search for a drug against COVID-19, we have performed a high-throughput x-ray crystallographic screen of two repurposing drug libraries against the SARS-CoV-2 main protease (Mpro), which is essential for viral replication. In contrast to commonly applied x-ray fragment screening experiments with molecules of low complexity, our screen tested already-approved drugs and drugs in clinical trials. From the three-dimensional protein structures, we identified 37 compounds that bind to Mpro In subsequent cell-based viral reduction assays, one peptidomimetic and six nonpeptidic compounds showed antiviral activity at nontoxic concentrations. We identified two allosteric binding sites representing attractive targets for drug development against SARS-CoV-2.
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Affiliation(s)
- Sebastian Günther
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
| | - Patrick Y A Reinke
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Yaiza Fernández-García
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Str. 74, 20359 Hamburg, Germany
| | - Julia Lieske
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Thomas J Lane
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Helen M Ginn
- Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Faisal H M Koua
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Christiane Ehrt
- Universität Hamburg, Center for Bioinformatics, Bundesstr. 43, 20146 Hamburg, Germany
| | - Wiebke Ewert
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Susanne Meier
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | | | - Boris Krichel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistr. 52, 20251 Hamburg, Germany
| | - Janine-Denise Kopicki
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistr. 52, 20251 Hamburg, Germany
| | - Luca Gelisio
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Wolfgang Brehm
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Ilona Dunkel
- Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Brandon Seychell
- Universität Hamburg, Department of Chemistry, Institute of Physical Chemistry, Grindelallee 117, 20146 Hamburg, Germany
| | - Henry Gieseler
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Brenna Norton-Baker
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Chemistry, UC Irvine, Irvine, CA 92697-2025, USA
| | - Beatriz Escudero-Pérez
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Str. 74, 20359 Hamburg, Germany
| | - Martin Domaracky
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Sofiane Saouane
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Alexandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Anna Hänle
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Michael Groessler
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Holger Fleckenstein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Fabian Trost
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Marina Galchenkova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Yaroslav Gevorkov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Vision Systems, Hamburg University of Technology, 21071 Hamburg, Germany
| | - Chufeng Li
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Salah Awel
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Ariana Peck
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Miriam Barthelmess
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Frank Schlünzen
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - P Lourdu Xavier
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Nadine Werner
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Hina Andaleeb
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Najeeb Ullah
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Sven Falke
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Vasundara Srinivasan
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Bruno Alves França
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Martin Schwinzer
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Hévila Brognaro
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Cromarte Rogers
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Diogo Melo
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Joanna Irina Zaitseva-Kinneberg
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Gisel E Peña-Murillo
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Aida Rahmani Mashhour
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Vincent Hennicke
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Pontus Fischer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Johanna Hakanpää
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Jan Meyer
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Bernhard Ellinger
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Maria Kuzikov
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Markus Wolf
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, Germany
| | | | - Gleb Bourenkov
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - David von Stetten
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | - Isabel Bento
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | - Ivars Karpics
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | | | - Stephan Niebling
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Christian Günther
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | - Robin Schubert
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Huijong Han
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Juliane Boger
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
| | - Diana C F Monteiro
- Hauptmann Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Linlin Zhang
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562 Lübeck, Germany
| | - Xinyuanyuan Sun
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562 Lübeck, Germany
| | | | - Jan Wollenhaupt
- Helmholtz Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Christian G Feiler
- Helmholtz Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Manfred S Weiss
- Helmholtz Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Eike-Christian Schulz
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Pedram Mehrabi
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Katarina Karničar
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Aleksandra Usenik
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Jure Loboda
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Henning Tidow
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Ashwin Chari
- Research Group for Structural Biochemistry and Mechanisms, Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Rolf Hilgenfeld
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562 Lübeck, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistr. 52, 20251 Hamburg, Germany
| | - Russell Cox
- Institute for Organic Chemistry and BMWZ, Leibniz University of Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Tobias Beck
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Department of Chemistry, Institute of Physical Chemistry, Grindelallee 117, 20146 Hamburg, Germany
| | - Matthias Rarey
- Universität Hamburg, Center for Bioinformatics, Bundesstr. 43, 20146 Hamburg, Germany
| | - Stephan Günther
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Str. 74, 20359 Hamburg, Germany
| | - Dusan Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Winfried Hinrichs
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
- Universität Greifswald, Institute of Biochemistry, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Department of Physics, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Arwen R Pearson
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Christian Betzel
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Alke Meents
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
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Yi J, Peng J, Yang W, Zhu G, Ren J, Li D, Zheng H. Picornavirus 3C - a protease ensuring virus replication and subverting host responses. J Cell Sci 2021; 134:134/5/jcs253237. [PMID: 33692152 DOI: 10.1242/jcs.253237] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The protease 3C is encoded by all known picornaviruses, and the structural features related to its protease and RNA-binding activities are conserved; these contribute to the cleavage of viral polyproteins and the assembly of the viral RNA replication complex during virus replication. Furthermore, 3C performs functions in the host cell through its interaction with host proteins. For instance, 3C has been shown to selectively 'hijack' host factors involved in gene expression, promoting picornavirus replication, and to inactivate key factors in innate immunity signaling pathways, inhibiting the production of interferon and inflammatory cytokines. Importantly, 3C maintains virus infection by subtly subverting host cell death and modifying critical molecules in host organelles. This Review focuses on the molecular mechanisms through which 3C mediates physiological processes involved in virus-host interaction, thus highlighting the picornavirus-mediated pathogenesis caused by 3C.
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Affiliation(s)
- Jiamin Yi
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China
| | - Jiangling Peng
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China
| | - Wenping Yang
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China
| | - Guoqiang Zhu
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China
| | - Jingjing Ren
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China
| | - Dan Li
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China
| | - Haixue Zheng
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China
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Denesyuk AI, Permyakov SE, Johnson MS, Permyakov EA, Uversky VN, Denessiouk K. Structural leitmotif and functional variations of the structural catalytic core in (chymo)trypsin-like serine/cysteine fold proteinases. Int J Biol Macromol 2021; 179:601-609. [PMID: 33713772 DOI: 10.1016/j.ijbiomac.2021.03.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/03/2021] [Accepted: 03/09/2021] [Indexed: 11/29/2022]
Abstract
Proteinases with the (chymo)trypsin-like serine/cysteine fold comprise a large superfamily performing their function through the Acid - Base - Nucleophile catalytic triad. In our previous work (Denesyuk AI, Johnson MS, Salo-Ahen OMH, Uversky VN, Denessiouk K. Int J Biol Macromol. 2020;153:399-411), we described a universal three-dimensional (3D) structural motif, NBCZone, that contains eleven amino acids: dipeptide 42 T-43 T, pentapeptide 54 T-55 T-56 T-57 T(base)-58 T, tripeptide 195 T(nucleophile)-196 T-197 T and residue 213 T (T - numeration of amino acids in trypsin). The comparison of the NBCZones among the members of the (chymo)trypsin-like protease family suggested the existence of 15 distinct groups. Within each group, the NBCZones incorporate an identical set of conserved interactions and bonds. In the present work, the structural environment of the catalytic acid at the position 102 T and the fourth member of the "catalytic tetrad" at the position 214 T was analyzed in 169 3D structures of proteinases with the (chymo)trypsin-like serine/cysteine fold. We have identified a complete Structural Catalytic Core (SCC) consisting of two classes and four groups. The proteinases belonging to different classes and groups differ from each other by the nature of the interaction between their N- and C-terminal β-barrels. Comparative analysis of the 3CLpro(s) from SARS-CoV-2 and SARS-CoV, used as an example, showed that the amino acids at positions 103 T and 179 T affect the nature of the interaction of the "catalytic acid" core (102 T-Core, N-terminal β-barrel) with the "supplementary" core (S-Core, C-terminal β-barrel), which ultimately results in the modulation of the enzymatic activity. The reported analysis represents an important standalone contribution to the analysis and systematization of the 3D structures of (chymo)trypsin-like serine/cysteine fold proteinases. The use of the developed approach for the comparison of 3D structures will allow, in the event of the appearance of new representatives of a given fold in the PDB, to quickly determine their structural homologues with the identification of possible differences.
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Affiliation(s)
- Alexander I Denesyuk
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow region 142290, Russia; Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku 20520, Finland.
| | - Sergei E Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow region 142290, Russia
| | - Mark S Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku 20520, Finland
| | - Eugene A Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow region 142290, Russia
| | - Vladimir N Uversky
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow region 142290, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku 20520, Finland
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Roe MK, Junod NA, Young AR, Beachboard DC, Stobart CC. Targeting novel structural and functional features of coronavirus protease nsp5 (3CL pro, M pro) in the age of COVID-19. J Gen Virol 2021; 102:001558. [PMID: 33507143 PMCID: PMC8515871 DOI: 10.1099/jgv.0.001558] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 01/08/2021] [Indexed: 01/18/2023] Open
Abstract
Coronavirus protease nsp5 (Mpro, 3CLpro) remains a primary target for coronavirus therapeutics due to its indispensable and conserved role in the proteolytic processing of the viral replicase polyproteins. In this review, we discuss the diversity of known coronaviruses, the role of nsp5 in coronavirus biology, and the structure and function of this protease across the diversity of known coronaviruses, and evaluate past and present efforts to develop inhibitors to the nsp5 protease with a particular emphasis on new and mostly unexplored potential targets of inhibition. With the recent emergence of pandemic SARS-CoV-2, this review provides novel and potentially innovative strategies and directions to develop effective therapeutics against the coronavirus protease nsp5.
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Affiliation(s)
- Molly K. Roe
- Department of Biological Sciences, Butler University, Indianapolis, IN, USA
| | - Nathan A. Junod
- Department of Biological Sciences, Butler University, Indianapolis, IN, USA
| | - Audrey R. Young
- Department of Biological Sciences, Butler University, Indianapolis, IN, USA
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Banerjee R, Perera L, Tillekeratne LMV. Potential SARS-CoV-2 main protease inhibitors. Drug Discov Today 2021; 26:804-816. [PMID: 33309533 PMCID: PMC7724992 DOI: 10.1016/j.drudis.2020.12.005] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/16/2020] [Accepted: 12/03/2020] [Indexed: 01/12/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has prompted an urgent need for new treatment strategies. No target-specific drugs are currently available for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but new drug candidates targeting the viral replication cycle are being explored. A prime target of drug-discovery efforts is the SARS-CoV-2 main protease (Mpro). The main proteases of different coronaviruses, including SARS-CoV-2, SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV), share a structurally conserved substrate-binding region that can be exploited to design new protease inhibitors. With the recent reporting of the X-ray crystal structure of the SARS-CoV-2 Mpro, studies to discover Mpro inhibitors using both virtual and in vitro screening are progressing rapidly. This review focusses on the recent developments in the search for small-molecule inhibitors targeting the SARS-CoV-2 Mpro.
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Affiliation(s)
- Riddhidev Banerjee
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH 43606, USA
| | - Lalith Perera
- Laboratory of Genome Integrity and Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA.
| | - L M Viranga Tillekeratne
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH 43606, USA.
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Servidio C, Stellacci F. Therapeutic approaches against coronaviruses acute respiratory syndrome. Pharmacol Res Perspect 2021; 9:e00691. [PMID: 33378565 PMCID: PMC7773137 DOI: 10.1002/prp2.691] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 10/13/2020] [Accepted: 10/25/2020] [Indexed: 01/08/2023] Open
Abstract
Coronaviruses represent global health threat. In this century, they have already caused two epidemics and one serious pandemic. Although, at present, there are no approved drugs and therapies for the treatment and prevention of human coronaviruses, several agents, FDA-approved, and preclinical, have shown in vitro and/or in vivo antiviral activity. An in-depth analysis of the current situation leads to the identification of several potential drugs that could have an impact on the fight against coronaviruses infections. In this review, we discuss the virology of human coronaviruses highlighting the main biological targets and summarize the current state-of-the-art of possible therapeutic options to inhibit coronaviruses infections. We mostly focus on FDA-approved and preclinical drugs targeting viral conserved elements.
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Affiliation(s)
- Camilla Servidio
- Department of Pharmacy, Health and Nutrition SciencesUniversity of CalabriaRendeItaly
- Institute of MaterialsEcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Francesco Stellacci
- Institute of MaterialsEcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
- Bioengineering Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
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Jin Z, Wang H, Duan Y, Yang H. The main protease and RNA-dependent RNA polymerase are two prime targets for SARS-CoV-2. Biochem Biophys Res Commun 2021; 538:63-71. [PMID: 33288200 PMCID: PMC7680044 DOI: 10.1016/j.bbrc.2020.10.091] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 10/20/2020] [Indexed: 01/18/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), poses an unprecedented global health crisis. It is particularly urgent to develop clinically effective therapies to contain the pandemic. The main protease (Mpro) and the RNA-dependent RNA polymerase (RdRP), which are responsible for the viral polyprotein proteolytic process and viral genome replication and transcription, respectively, are two attractive drug targets for SARS-CoV-2. This review summarizes up-to-date progress in the structural and pharmacological aspects of those two key targets above. Different classes of inhibitors individually targeting Mpro and RdRP are discussed, which could promote drug development to treat SARS-CoV-2 infection.
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Affiliation(s)
- Zhenming Jin
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China,School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China
| | - Haofeng Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China,School of Life Sciences, Tianjin University, Tianjin, China,Corresponding author. Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Yinkai Duan
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China,Corresponding author
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Behnam MAM. Protein structural heterogeneity: A hypothesis for the basis of proteolytic recognition by the main protease of SARS-CoV and SARS-CoV-2. Biochimie 2021; 182:177-184. [PMID: 33484784 PMCID: PMC7817518 DOI: 10.1016/j.biochi.2021.01.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 01/15/2021] [Accepted: 01/15/2021] [Indexed: 02/06/2023]
Abstract
The main protease (Mpro) of SARS-CoV and SARS-CoV-2 is a key enzyme in viral replication and a promising target for the development of antiviral therapeutics. The understanding of this protein is based on a number of observations derived from earlier x-ray structures, which mostly consider substrates or ligands as the main reason behind modulation of the active site. This lead to the concept of substrate-induced subsite cooperativity as an initial attempt to explain the dual binding specificity of this enzyme in recognizing the cleavage sequences at its N- and C-termini, which are important processing steps in obtaining the mature protease. The presented hypothesis proposes that structural heterogeneity is a property of the enzyme, independent of the presence of a substrate or ligand. Indeed, the analysis of Mpro structures of SARS-CoV and SARS-CoV-2 reveals a conformational diversity for the catalytically competent state in ligand-free structures. Variation in the binding site appears to result from flexibility at residues lining the S1 subpocket and segments incorporating methionine 49 and glutamine 189. The structural evidence introduces “structure-based recognition” as a new paradigm in substrate proteolysis by Mpro. In this concept, the binding space in subpockets of the enzyme varies in a non-cooperative manner, causing distinct conformations, which recognize and process different cleavage sites, as the N- and C-termini. Insights into the recognition basis of the protease provide explanation to the ordered processing of cleavage sites. The hypothesis expands the conformational space of the enzyme and consequently opportunities for drug development and repurposing efforts.
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Affiliation(s)
- Mira A M Behnam
- Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany.
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Xiong M, Su H, Zhao W, Xie H, Shao Q, Xu Y. What coronavirus 3C-like protease tells us: From structure, substrate selectivity, to inhibitor design. Med Res Rev 2021; 41:1965-1998. [PMID: 33460213 PMCID: PMC8014231 DOI: 10.1002/med.21783] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 12/17/2020] [Accepted: 01/05/2021] [Indexed: 12/13/2022]
Abstract
The emergence of a variety of coronaviruses (CoVs) in the last decades has posed huge threats to human health. Especially, the ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to more than 70 million infections and over 1.6 million of deaths worldwide in the past few months. None of the efficacious antiviral agents against human CoVs have been approved yet. 3C-like protease (3CLpro ) is an attractive target for antiviral intervention due to its essential role in processing polyproteins translated from viral RNA, and its conserved structural feature and substrate specificity among CoVs in spite of the sequence variation. This review focuses on all available crystal structures of 12 CoV 3CLpro s and their inhibitors, and intends to provide a comprehensive understanding of this protease from multiple aspects including its structural features, substrate specificity, inhibitor binding modes, and more importantly, to recapitulate the similarity and diversity among different CoV 3CLpro s and the structure-activity relationship of various types of inhibitors. Such an attempt could gain a deep insight into the inhibition mechanisms and drive future structure-based drug discovery targeting 3CLpro s.
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Affiliation(s)
- Muya Xiong
- CAS Key Laboratory of Receptor Research
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Haixia Su
- CAS Key Laboratory of Receptor Research
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenfeng Zhao
- CAS Key Laboratory of Receptor Research
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Hang Xie
- CAS Key Laboratory of Receptor Research
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Qiang Shao
- CAS Key Laboratory of Receptor Research
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yechun Xu
- CAS Key Laboratory of Receptor Research
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
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Isgrò C, Sardanelli AM, Palese LL. Systematic Search for SARS-CoV-2 Main Protease Inhibitors for Drug Repurposing: Ethacrynic Acid as a Potential Drug. Viruses 2021; 13:v13010106. [PMID: 33451132 PMCID: PMC7828626 DOI: 10.3390/v13010106] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/04/2021] [Accepted: 01/08/2021] [Indexed: 12/24/2022] Open
Abstract
In 2019 an outbreak occurred which resulted in a global pandemic. The causative agent has been identified in a virus belonging to the Coronaviridae family, similar to the agent of SARS, referred to as SARS-CoV-2. This epidemic spread rapidly globally with high morbidity and mortality. Although vaccine development is at a very advanced stage, there are currently no truly effective antiviral drugs to treat SARS-CoV-2 infection. In this study we present systematic and integrative antiviral drug repurposing effort aimed at identifying, among the drugs already authorized for clinical use, some active inhibitors of the SARS-CoV-2 main protease. The most important result of this analysis is the demonstration that ethacrynic acid, a powerful diuretic, is revealed to be an effective inhibitor of SARS-CoV-2 main protease. Even with all the necessary cautions, given the particular nature of this drug, these data can be the starting point for the development of an effective therapeutic strategy against SARS-CoV-2.
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Affiliation(s)
- Camilla Isgrò
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy;
- Department of Medicine, University Campus Bio-Medico of Rome, Via Alvaro del Portillo 21, 00128 Rome, Italy
| | - Anna Maria Sardanelli
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy;
- Department of Medicine, University Campus Bio-Medico of Rome, Via Alvaro del Portillo 21, 00128 Rome, Italy
- Correspondence: or (A.M.S.); (L.L.P.)
| | - Luigi Leonardo Palese
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy;
- Correspondence: or (A.M.S.); (L.L.P.)
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Pormohammad A, Monych NK, Turner RJ. Zinc and SARS‑CoV‑2: A molecular modeling study of Zn interactions with RNA‑dependent RNA‑polymerase and 3C‑like proteinase enzymes. Int J Mol Med 2021; 47:326-334. [PMID: 33236142 PMCID: PMC7723401 DOI: 10.3892/ijmm.2020.4790] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 10/13/2020] [Indexed: 11/09/2022] Open
Abstract
RNA‑dependent RNA‑polymerase (RdRp) and 3C‑like proteinase (3CLpro) are two main enzymes that play a key role in the replication of SARS‑CoV‑2. Zinc (Zn) has strong immunogenic properties and is known to bind to a number of proteins, modulating their activities. Zn also has a history of use in viral infection control. Thus, the present study models potential Zn binding to RdRp and the 3CLpro. Through molecular modeling, the Zn binding sites in the aforementioned two important enzymes of viral replication were found to be conserved between severe acute respiratory syndrome (SARS)‑coronavirus (CoV) and SARS‑CoV‑2. The location of these sites may influence the enzymatic activity of 3CLpro and RdRp in coronavirus disease 2019 (COVID‑19). Since Zn has established immune health benefits, is readily available, non‑expensive and a safe food supplement, with the comparisons presented here between SARS‑CoV and COVID‑19, the present study proposes that Zn could help ameliorate the disease process of COVID‑19 infection.
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Affiliation(s)
- Ali Pormohammad
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N4V8, Canada
| | - Nadia K. Monych
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N4V8, Canada
| | - Raymond J. Turner
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N4V8, Canada
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47
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Konno H, Akaji K. Preparation of SARS-CoV 3CL Protease and Synthesis of its Inhibitors. J SYN ORG CHEM JPN 2021. [DOI: 10.5059/yukigoseikyokaishi.79.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hiroyuki Konno
- Graduate School of Science and Engineering, Yamagata University
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Gioia M, Ciaccio C, Calligari P, De Simone G, Sbardella D, Tundo G, Fasciglione GF, Di Masi A, Di Pierro D, Bocedi A, Ascenzi P, Coletta M. Role of proteolytic enzymes in the COVID-19 infection and promising therapeutic approaches. Biochem Pharmacol 2020; 182:114225. [PMID: 32956643 PMCID: PMC7501082 DOI: 10.1016/j.bcp.2020.114225] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/11/2020] [Accepted: 09/16/2020] [Indexed: 02/07/2023]
Abstract
In the Fall of 2019 a sudden and dramatic outbreak of a pulmonary disease (Coronavirus Disease COVID-19), due to a new Coronavirus strain (i.e., SARS-CoV-2), emerged in the continental Chinese area of Wuhan and quickly diffused throughout the world, causing up to now several hundreds of thousand deaths. As for common viral infections, the crucial event for the viral life cycle is the entry of genetic material inside the host cell, realized by the spike protein of the virus through its binding to host receptors and its activation by host proteases; this is followed by translation of the viral RNA into a polyprotein, exploiting the host cell machinery. The production of individual mature viral proteins is pivotal for replication and release of new virions. Several proteolytic enzymes either of the host and of the virus act in a concerted fashion to regulate and coordinate specific steps of the viral replication and assembly, such as (i) the entry of the virus, (ii) the maturation of the polyprotein and (iii) the assembly of the secreted virions for further diffusion. Therefore, proteases involved in these three steps are important targets, envisaging that molecules which interfere with their activity are promising therapeutic compounds. In this review, we will survey what is known up to now on the role of specific proteolytic enzymes in these three steps and of most promising compounds designed to impair this vicious cycle.
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Key Words
- covid-19, coronavirus disease – 19
- sars-cov, severe acute respiratory syndrome coronavirus
- sars-cov-2, severe acute respiratory syndrome – 2
- mers-cov, middle east respiratory syndrome coronavirus
- orf, open reading frame
- plpro, papain-like protease
- mpro, main protease
- pp, polyprotein
- nsp, non structural protein
- rdrp, rna dependent rna polymerase
- hel, helicase
- s protein, spike protein
- tmprss2, trans-membrane protease serine protease-2
- tmprss4, trans-membrane protease serine protease-4
- hat, human airway trypsin-like protease
- tgn, trans-golgi network
- ace2, angiotensin-converting enzyme receptor-2
- rbd, receptor binding domain
- pc, pro-protein convertase
- hcov-oc43, human coronavirus-oc43
- mhv-a59, murine hepatitis virus – a59
- hiv, human immunodeficiency virus
- cmk, chloro-methyl-ketone
- dec, decanoyl
- phac, phenyl-acetyl
- ttsp, type ii transmembrane serine proteases family
- hpv, human papillomavirus
- hbv, hepatitis b virus
- evd, ebola virus disease
- zikv, zika virus
- jev, japanese encephalitis virus
- fpv, feline panleukopenia virus
- hpaiv, highly pathogenic avian influenza virus
- cdv, canine distemper virus
- rsv, respiratory syncytial virus (rsv)
- a1at, alpha-1-anti trypsin
- aebsf, 4-(2-aminomethyl)-benzene sulphonyl fluoride
- bhh, bromhexine hydrochloride
- pcsk, pro-protein convertase subtilisin/kexin
- ampk, adenosine monophosphate-activated protein kinase
- hcov-nl63, human coronavirus – nl63
- hcov-229e, human coronavirus – 229e
- hcov-hku1, human coronavirus – hku1
- 3cpro, 3chymotrypsin protease of rhinoviruses
- 3d-qsar, three-dimensional quantitative structure-activity relationships
- fda, food and drug agency
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Affiliation(s)
- Magda Gioia
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy.
| | - Chiara Ciaccio
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy.
| | - Paolo Calligari
- Department of Chemical and Technological Sciences, University of Roma Tor Vergata, Roma, Italy
| | | | | | | | | | | | - Donato Di Pierro
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy
| | - Alessio Bocedi
- Department of Chemical and Technological Sciences, University of Roma Tor Vergata, Roma, Italy
| | - Paolo Ascenzi
- Department of Sciences, Roma Tre University, Roma, Italy,Interdepartmental Laboratory for Electron Microscopy, Roma Tre University, Roma, Italy
| | - Massimo Coletta
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy.
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Shitrit A, Zaidman D, Kalid O, Bloch I, Doron D, Yarnizky T, Buch I, Segev I, Ben-Zeev E, Segev E, Kobiler O. Conserved interactions required for inhibition of the main protease of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Sci Rep 2020; 10:20808. [PMID: 33257760 PMCID: PMC7704658 DOI: 10.1038/s41598-020-77794-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/17/2020] [Indexed: 12/13/2022] Open
Abstract
The COVID-19 pandemic caused by the SARS-CoV-2 requires a fast development of antiviral drugs. SARS-CoV-2 viral main protease (Mpro, also called 3C-like protease, 3CLpro) is a potential target for drug design. Crystal and co-crystal structures of the SARS-CoV-2 Mpro have been solved, enabling the rational design of inhibitory compounds. In this study we analyzed the available SARS-CoV-2 and the highly similar SARS-CoV-1 crystal structures. We identified within the active site of the Mpro, in addition to the inhibitory ligands' interaction with the catalytic C145, two key H-bond interactions with the conserved H163 and E166 residues. Both H-bond interactions are present in almost all co-crystals and are likely to occur also during the viral polypeptide cleavage process as suggested from docking of the Mpro cleavage recognition sequence. We screened in silico a library of 6900 FDA-approved drugs (ChEMBL) and filtered using these key interactions and selected 29 non-covalent compounds predicted to bind to the protease. Additional screen, using DOCKovalent was carried out on DrugBank library (11,414 experimental and approved drugs) and resulted in 6 covalent compounds. The selected compounds from both screens were tested in vitro by a protease activity inhibition assay. Two compounds showed activity at the 50 µM concentration range. Our analysis and findings can facilitate and focus the development of highly potent inhibitors against SARS-CoV-2 infection.
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Affiliation(s)
- Alina Shitrit
- The Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel-Aviv University, 69978, Tel Aviv, Israel
| | - Daniel Zaidman
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | | | - Itai Bloch
- Biotechnology Department, Migal - Galilee Research Institute, Kiryat-Shmona, Israel
| | - Dvir Doron
- Chemical & Computational Toxicology, Non-Clinical Development, Global R&D, Teva Pharmaceutical Industries Ltd., Netanya, Israel
| | - Tali Yarnizky
- Tali Yarnizky Scientific Consulting, Maccabim-Reut, Israel
| | - Idit Buch
- Emendo Biotherapeutics Ltd., Ness Ziona, Israel
| | | | - Efrat Ben-Zeev
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Elad Segev
- Department of Applied Mathematics, Faculty of Science, Holon Institute of Technology, Holon, Israel
| | - Oren Kobiler
- The Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel-Aviv University, 69978, Tel Aviv, Israel.
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50
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Rodrigues GCS, Dos Santos Maia M, de Menezes RPB, Cavalcanti ABS, de Sousa NF, de Moura ÉP, Monteiro AFM, Scotti L, Scotti MT. Ligand and Structure-based Virtual Screening of Lamiaceae Diterpenes with Potential Activity against a Novel Coronavirus (2019-nCoV). Curr Top Med Chem 2020; 20:2126-2145. [PMID: 32674732 DOI: 10.2174/1568026620666200716114546] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/15/2020] [Accepted: 04/20/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND The emergence of a new coronavirus (CoV), named 2019-nCoV, as an outbreak originated in the city of Wuhan, China, has resulted in the death of more than 3,400 people this year alone and has caused worldwide an alarming situation, particularly following previous CoV epidemics, including the Severe Acute Respiratory Syndrome (SARS) in 2003 and the Middle East Respiratory Syndrome (MERS) in 2012. Currently, no exists for infections caused by CoVs; however, some natural products may represent potential treatment resources, such as those that contain diterpenes. OBJECTIVE This study aimed to use computational methods to perform a virtual screening (VS) of candidate diterpenes with the potential to act as CoV inhibitors. METHODS 1,955 diterpenes, derived from the Nepetoideae subfamily (Lamiaceae), were selected using the SistematX tool (https://sistematx.ufpb.br), which were used to make predictions. From the ChEMBL database, 3 sets of chemical structures were selected for the construction of predictive models. RESULTS The chemical structures of molecules with known activity against SARS CoV, two of which were tested for activity against specific viral proteins and one of which was tested for activity against the virus itself, were classified according to their pIC50 values [-log IC50 (mol/l)]. CONCLUSION In the consensus analysis approach, combining both ligand- and structure-based VSs, 19 compounds were selected as potential CoV inhibitors, including isotanshinone IIA (01), tanshinlactone (02), isocryptotanshinone (03), and tanshinketolactone (04), which did not present toxicity within the evaluated parameters.
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Affiliation(s)
- Gabriela Cristina Soares Rodrigues
- Laboratory of Cheminformatics, Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraiba, Joao Pessoa-PB, Brazil
| | - Mayara Dos Santos Maia
- Laboratory of Cheminformatics, Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraiba, Joao Pessoa-PB, Brazil
| | - Renata Priscila Barros de Menezes
- Laboratory of Cheminformatics, Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraiba, Joao Pessoa-PB, Brazil
| | - Andreza Barbosa Silva Cavalcanti
- Laboratory of Cheminformatics, Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraiba, Joao Pessoa-PB, Brazil
| | - Natália Ferreira de Sousa
- Laboratory of Cheminformatics, Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraiba, Joao Pessoa-PB, Brazil
| | - Érika Paiva de Moura
- Laboratory of Cheminformatics, Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraiba, Joao Pessoa-PB, Brazil
| | - Alex France Messias Monteiro
- Laboratory of Cheminformatics, Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraiba, Joao Pessoa-PB, Brazil
| | - Luciana Scotti
- Laboratory of Cheminformatics, Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraiba, Joao Pessoa-PB, Brazil
| | - Marcus Tullius Scotti
- Laboratory of Cheminformatics, Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraiba, Joao Pessoa-PB, Brazil
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