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Castillo F, Ramírez D, Ramos MC, Martinez-Arribas B, Domingo-Contreras E, Mackenzie TA, Peña-Varas C, Lindemann S, Montero F, Annang F, Vicente F, Genilloud O, González-Pacanowska D, Fernandez-Godino R. Repurposing the Open Global Health Library for the discovery of novel Mpro destabilizers with scope as broad-spectrum antivirals. Front Pharmacol 2024; 15:1390705. [PMID: 39050758 PMCID: PMC11267763 DOI: 10.3389/fphar.2024.1390705] [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: 02/23/2024] [Accepted: 05/29/2024] [Indexed: 07/27/2024] Open
Abstract
The SARS coronavirus 2 (SARS-CoV-2) epidemic remains globally active. The emergence of new variants of interest and variants of concern (VoCs), which are potentially more vaccine-resistant and less sensitive to existing treatments, is evident due to their high prevalence. The prospective spread of such variants and other coronaviruses with epidemic potential demands preparedness that can be met by developing fast-track workflows to find new candidates that target viral proteins with a clear in vitro and in vivo phenotype. Mpro (or 3CLpro) is directly involved in the viral replication cycle and the production and function of viral polyproteins, which makes it an ideal target. The biological relevance of Mpro is highly conserved among betacoronaviruses like HCoV-OC43 and SARS-CoV-2, which makes the identification of new chemical scaffolds targeting them a good starting point for designing broad-spectrum antivirals. We report an optimized methodology based on orthogonal cell-free assays to identify small molecules that inhibit the binding pockets of both SARS-CoV-2-Mpro and HCoV-OC43-Mpro; this blockade correlates with antiviral activities in HCoV-OC43 cellular models. By using such a fast-tracking approach against the Open Global Health Library (Merck KGaA), we have found evidence of the antiviral activity of compound OGHL98. In silico studies dissecting intermolecular interactions between OGHL98 and both proteases and comprising docking and molecular dynamics simulations (MDSs) concluded that the binding mode was primarily governed by conserved H-bonds with their C-terminal amino acids and that the rational design of OGHL98 has potential against VoCs proteases resistant to current therapeutics.
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Affiliation(s)
| | - David Ramírez
- Departamento de Farmacología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | | | - Blanca Martinez-Arribas
- Instituto de Parasitología y Biomedicina Lopez-Neyra, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | | | | | - Carlos Peña-Varas
- Departamento de Farmacología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Doctorado en Biotecnología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Sven Lindemann
- Strategic Innovation, Merck Healthcare KGaA, Darmstadt, Germany
| | - Fernando Montero
- Fundación MEDINA, Granada, Spain
- Department of Physical Chemistry and Institute of Biotechnology, Universidad de Granada, Granada, Spain
| | | | | | | | - Dolores González-Pacanowska
- Instituto de Parasitología y Biomedicina Lopez-Neyra, Consejo Superior de Investigaciones Científicas, Granada, Spain
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2
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Menendez CA, Mohamed A, Perez-Lemus GR, Weiss AM, Rawe BW, Liu G, Crolais AE, Kenna E, Byléhn F, Alvarado W, Mendels D, Rowan SJ, Tay S, de Pablo JJ. Development of Masitinib Derivatives with Enhanced M pro Ligand Efficiency and Reduced Cytotoxicity. Molecules 2023; 28:6643. [PMID: 37764425 PMCID: PMC10536273 DOI: 10.3390/molecules28186643] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Recently, a high-throughput screen of 1900 clinically used drugs identified masitinib, an orally bioavailable tyrosine kinase inhibitor, as a potential treatment for COVID-19. Masitinib acts as a broad-spectrum inhibitor for human coronaviruses, including SARS-CoV-2 and several of its variants. In this work, we rely on atomistic molecular dynamics simulations with advanced sampling methods to develop a deeper understanding of masitinib's mechanism of Mpro inhibition. To improve the inhibitory efficiency and to increase the ligand selectivity for the viral target, we determined the minimal portion of the molecule (fragment) that is responsible for most of the interactions that arise within the masitinib-Mpro complex. We found that masitinib forms highly stable and specific H-bond interactions with Mpro through its pyridine and aminothiazole rings. Importantly, the interaction with His163 is a key anchoring point of the inhibitor, and its perturbation leads to ligand unbinding within nanoseconds. Based on these observations, a small library of rationally designed masitinib derivatives (M1-M5) was proposed. Our results show increased inhibitory efficiency and highly reduced cytotoxicity for the M3 and M4 derivatives compared to masitinib.
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Affiliation(s)
- Cintia A. Menendez
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
| | - Adil Mohamed
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
| | - Gustavo R. Perez-Lemus
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
| | - Adam M. Weiss
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA (G.L.); (A.E.C.)
| | - Benjamin W. Rawe
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
| | - Guancen Liu
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA (G.L.); (A.E.C.)
| | - Alex E. Crolais
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA (G.L.); (A.E.C.)
| | - Emma Kenna
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
| | - Fabian Byléhn
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
| | - Walter Alvarado
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
| | - Dan Mendels
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
| | - Stuart J. Rowan
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA (G.L.); (A.E.C.)
| | - Savaş Tay
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
| | - Juan J. de Pablo
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
- Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
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3
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Li J, Wang Y, Rajpoot S, Lavrijsen M, Pan Q, Li P, Baig MS. Investigating theobromine as a potential anti-human coronaviral agent. Microbiol Immunol 2023; 67:404-412. [PMID: 37415325 DOI: 10.1111/1348-0421.13086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/08/2023] [Accepted: 06/08/2023] [Indexed: 07/08/2023]
Abstract
Coronaviruses (CoVs) have long been known to infect humans, mainly alpha-CoV and beta-CoV. The vaccines developed for SARS-CoV-2 are likely not effective against other coronavirus species, whereas the risk of the emergence of new strains that may cause the next epidemic/pandemic is high. The development of antiviral drugs that are effective across different CoVs represents a viable strategy for improving pandemic preparedness. In this study, we aim to identify pan-coronaviral agents by targeting the conserved main protease (Mpro). For drug screening, the catalytic dyad of four human CoVs (HCoVs: SARS-CoV-2, and seasonal CoV NL63, OC43, and 229E) was targeted by molecular docking. The identified leading candidate theobromine, a xanthine derivative, was further tested in cell culture models of coronavirus infection. Theobromine binds strongly with the catalytic dyad (His41 and Cys144/145) of SARS-CoV-2 and HCoV-NL63 Mpro, mildly with HCoV-OC43, but not with HCoV-229E. However, theobromine only shows dose-dependent inhibition in Calu3 cells inoculated with SARS-CoV-2, but not in cells inoculated with seasonal CoVs. Theobromine exerts antiviral activity against coronavirus infections potentially through targeting Mpro. However, the antiviral potency is distinct among different CoVs.
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Affiliation(s)
- Jiajing Li
- Department of Gastroenterology & Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Yining Wang
- Department of Gastroenterology & Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Sajjan Rajpoot
- Department of Biosciences & Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India
| | - Marla Lavrijsen
- Department of Gastroenterology & Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Qiuwei Pan
- Department of Gastroenterology & Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Pengfei Li
- Department of Gastroenterology & Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Mirza S Baig
- Department of Biosciences & Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India
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4
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Kuang Y, Ma X, Shen W, Rao Q, Yang S. Discovery of 3CLpro inhibitor of SARS-CoV-2 main protease. Future Sci OA 2023; 9:FSO853. [PMID: 37090493 PMCID: PMC10116374 DOI: 10.2144/fsoa-2023-0020] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 03/20/2023] [Indexed: 04/08/2023] Open
Abstract
Coronavirus main protease (3CLpro), a special cysteine protease in coronavirus family, is highly desirable in the life cycle of coronavirus. Here, molecular docking, ADMET pharmacokinetic profiles and molecular dynamics (MD) simulation were performed to develop specific 3CLpro inhibitor. The results showed that the 137 compounds originated from Chinese herbal have good binding affinity to 3CLpro. Among these, Cleomiscosin C, (+)-Norchelidonine, Protopine, Turkiyenine, Isochelidonine and Mallotucin A possessed prominent drug-likeness properties. Cleomiscosin C and Turkiyenine exhibited excellent pharmacokinetic profiles. Furthermore, the complex of Cleomiscosin C with SARS-CoV-2 main protease presented high stability. The findings in this work indicated that Cleomiscosin C is highly promising as a potential 3CLpro inhibitor, thus facilitating the development of effective drugs for COVID-19.
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Affiliation(s)
- Yi Kuang
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, Zhejiang, 311300, PR China
| | - Xiaodong Ma
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, Zhejiang, 311300, PR China
| | - Wenjing Shen
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, Zhejiang, 311300, PR China
| | - Qingqing Rao
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, Zhejiang, 311300, PR China
| | - Shengxiang Yang
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, Zhejiang, 311300, PR China
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5
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Repurposing dyphylline as a pan-coronavirus antiviral therapy. Future Med Chem 2022; 14:685-699. [PMID: 35387498 PMCID: PMC9048854 DOI: 10.4155/fmc-2021-0311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background: In the last two decades, the world has witnessed the emergence of zoonotic corona viruses (CoVs), which cause mild to severe respiratory diseases in humans. Human coronaviruses (HCoVs), mainly from the alpha-CoV and beta-CoV genera, have evolved to be highly pathogenic, such as SARS-CoV-2 causing the COVID-19 pandemic. These coronaviruses carry functional enzymes necessary for the virus life cycle, which represent attractive antiviral targets. Methods & Results: We aimed to therapeutically target the main protease (Mpro) of HCoV-NL63 and HCoV-229E (from alpha-CoV genus) and HCoV-OC43 and SARS-CoV-2 (from beta-CoV genus). Through virtual screening, we identified an FDA-approved drug dyphylline, a xanthine derivate, that binds to the catalytic dyad residues; histidine and cystine of the Mpro structures. Importantly, dyphylline dose-dependently inhibited the viral replication in cell culture models infected with the viruses. Conclusion: Our findings support the repurposing of dyphylline as a pan-coronavirus antiviral agent.
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Chourasia R, Padhi S, Phukon LC, Abedin MM, Sirohi R, Singh SP, Rai AK. Peptide candidates for the development of therapeutics and vaccines against β-coronavirus infection. Bioengineered 2022; 13:9435-9454. [PMID: 35387556 PMCID: PMC9161909 DOI: 10.1080/21655979.2022.2060453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 01/18/2023] Open
Abstract
Betacoronaviruses (β-CoVs) have caused major viral outbreaks in the last two decades in the world. The mutation and recombination abilities in β-CoVs resulted in zoonotic diseases in humans. Proteins responsible for viral attachment and replication are highly conserved in β-CoVs. These conserved proteins have been extensively studied as targets for preventing infection and the spread of β-CoVs. Peptides are among the most promising candidates for developing vaccines and therapeutics against viral pathogens. The immunostimulatory and viral inhibitory potential of natural and synthetic peptides has been extensively studied since the SARS-CoV outbreak. Food-derived peptides demonstrating high antiviral activity can be used to develop effective therapeutics against β-CoVs. Specificity, tolerability, and customizability of peptides can be explored to develop potent drugs against β-CoVs. However, the proteolytic susceptibility and low bioavailability of peptides pose challenges for the development of therapeutics. This review illustrates the potential role of peptides in eliciting an adaptive immune response and inhibiting different stages of the β-CoV life cycle. Further, the challenges and future directions associated with developing peptide-based therapeutics and vaccines against existing and future β-CoV pathogens have been discussed.
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Affiliation(s)
- Rounak Chourasia
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Tadong- 737102, India
| | - Srichandan Padhi
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Tadong- 737102, India
| | - Loreni Chiring Phukon
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Tadong- 737102, India
| | - Md Minhajul Abedin
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Tadong- 737102, India
| | - Ranjana Sirohi
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, 02841, Republic of Korea
| | - Sudhir P Singh
- Centre of Innovative and Applied Bioprocessing (DBT-CIAB), Sector-81, S.A.S. Nagar, Mohali- 140306, India
| | - Amit Kumar Rai
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Tadong- 737102, India
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Mizoram Node, Aizawl, India
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7
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Inhibitors of Coronavirus 3CL Proteases Protect Cells from Protease-Mediated Cytotoxicity. J Virol 2021; 95:e0237420. [PMID: 33910954 DOI: 10.1128/jvi.02374-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We describe a mammalian cell-based assay to identify coronavirus 3CL protease (3CLpro) inhibitors. This assay is based on rescuing protease-mediated cytotoxicity and does not require live virus. By enabling the facile testing of compounds across a range of 15 distantly related coronavirus 3CLpro enzymes, we identified compounds with broad 3CLpro-inhibitory activity. We also adapted the assay for use in compound screening and in doing so uncovered additional severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) 3CLpro inhibitors. We observed strong concordance between data emerging from this assay and those obtained from live-virus testing. The reported approach democratizes the testing of 3CLpro inhibitors by developing a simplified method for identifying coronavirus 3CLpro inhibitors that can be used by the majority of laboratories, rather than the few with extensive biosafety infrastructure. We identified two lead compounds, GC376 and compound 4, with broad activity against all 3CL proteases tested, including 3CLpro enzymes from understudied zoonotic coronaviruses. IMPORTANCE Multiple coronavirus pandemics have occurred over the last 2 decades. This has highlighted a need to be proactive in the development of therapeutics that can be readily deployed in the case of future coronavirus pandemics. We developed and validated a simplified cell-based assay for the identification of chemical inhibitors of 3CL proteases encoded by a wide range of coronaviruses. This assay is reporter free, does not require specialized biocontainment, and is optimized for performance in high-throughput screening. By testing reported 3CL protease inhibitors against a large collection of 3CL proteases with variable sequence similarity, we identified compounds with broad activity against 3CL proteases and uncovered structural insights into features that contribute to their broad activity. Furthermore, we demonstrated that this assay is suitable for identifying chemical inhibitors of proteases from families other than 3CL proteases.
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8
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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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Chourasia R, Padhi S, Chiring Phukon L, Abedin MM, Singh SP, Rai AK. A Potential Peptide From Soy Cheese Produced Using Lactobacillus delbrueckii WS4 for Effective Inhibition of SARS-CoV-2 Main Protease and S1 Glycoprotein. Front Mol Biosci 2020; 7:601753. [PMID: 33363209 PMCID: PMC7759660 DOI: 10.3389/fmolb.2020.601753] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic caused by novel SARS-CoV-2 has resulted in an unprecedented loss of lives and economy around the world. In this study, search for potential inhibitors against two of the best characterized SARS-CoV-2 drug targets: S1 glycoprotein receptor-binding domain (RBD) and main protease (3CLPro), was carried out using the soy cheese peptides. A total of 1,420 peptides identified from the cheese peptidome produced using Lactobacillus delbrueckii WS4 were screened for antiviral activity by employing the web tools, AVPpred, and meta-iAVP. Molecular docking studies of the selected peptides revealed one potential peptide "KFVPKQPNMIL" that demonstrated strong affinity toward significant amino acid residues responsible for the host cell entry (RBD) and multiplication (3CLpro) of SARS-CoV-2. The peptide was also assessed for its ability to interact with the critical residues of S1 RBD and 3CLpro of other β-coronaviruses. High binding affinity was observed toward critical amino acids of both the targeted proteins in SARS-CoV, MERS-CoV, and HCoV-HKU1. The binding energy of KFVPKQPNMIL against RBD and 3CLpro of the four viruses ranged from -8.45 to -26.8 kcal/mol and -15.22 to -22.85 kcal/mol, respectively. The findings conclude that cheese, produced by using Lb. delbrueckii WS4, could be explored as a prophylactic food for SARS-CoV-2 and related viruses. In addition, the multi-target inhibitor peptide, which effectively inhibited both the viral proteins, could further be used as a terminus a quo for the in vitro and in vivo function against SARS-CoV-2.
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Affiliation(s)
- Rounak Chourasia
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Sikkim, India
| | - Srichandan Padhi
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Sikkim, India
| | - Loreni Chiring Phukon
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Sikkim, India
| | - Md Minhajul Abedin
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Sikkim, India
| | - Sudhir P. Singh
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), Mohali, India
| | - Amit Kumar Rai
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Sikkim, India
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10
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Augustin TL, Hajbabaie R, Harper MT, Rahman T. Novel Small-Molecule Scaffolds as Candidates against the SARS Coronavirus 2 Main Protease: A Fragment-Guided in Silico Approach. Molecules 2020; 25:molecules25235501. [PMID: 33255326 PMCID: PMC7727661 DOI: 10.3390/molecules25235501] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 12/23/2022] Open
Abstract
The ongoing pandemic caused by the novel coronavirus has been the greatest global health crisis since the Spanish flu pandemic of 1918. Thus far, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in over 1 million deaths, and there is no cure or vaccine to date. The recently solved crystal structure of the SARS-CoV-2 main protease has been a major focus for drug-discovery efforts. Here, we present a fragment-guided approach using ZINCPharmer, where 17 active fragments known to bind to the catalytic centre of the SARS-CoV-2 main protease (SARS-CoV-2 Mpro) were used as pharmacophore queries to search the ZINC databases of natural compounds and natural derivatives. This search yielded 134 hits that were then subjected to multiple rounds of in silico analyses, including blind and focused docking against the 3D structure of the main protease. We scrutinised the poses, scores, and protein-ligand interactions of 15 hits and selected 7. The scaffolds of the seven hits were structurally distinct from known inhibitor scaffolds, thus indicating scaffold novelty. Our work presents several novel scaffolds as potential candidates for experimental validation against SARS-CoV-2 Mpro.
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11
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Trovato M, Sartorius R, D’Apice L, Manco R, De Berardinis P. Viral Emerging Diseases: Challenges in Developing Vaccination Strategies. Front Immunol 2020; 11:2130. [PMID: 33013898 PMCID: PMC7494754 DOI: 10.3389/fimmu.2020.02130] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/06/2020] [Indexed: 12/11/2022] Open
Abstract
In the last decades, a number of infectious viruses have emerged from wildlife or re-emerged, generating serious threats to the global health and to the economy worldwide. Ebola and Marburg hemorrhagic fevers, Lassa fever, Dengue fever, Yellow fever, West Nile fever, Zika, and Chikungunya vector-borne diseases, Swine flu, Severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and the recent Coronavirus disease 2019 (COVID-19) are examples of zoonoses that have spread throughout the globe with such a significant impact on public health that the scientific community has been called for a rapid intervention in preventing and treating emerging infections. Vaccination is probably the most effective tool in helping the immune system to activate protective responses against pathogens, reducing morbidity and mortality, as proven by historical records. Under health emergency conditions, new and alternative approaches in vaccine design and development are imperative for a rapid and massive vaccination coverage, to manage a disease outbreak and curtail the epidemic spread. This review gives an update on the current vaccination strategies for some of the emerging/re-emerging viruses, and discusses challenges and hurdles to overcome for developing efficacious vaccines against future pathogens.
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MESH Headings
- Animals
- Antibody-Dependent Enhancement/immunology
- Betacoronavirus/immunology
- COVID-19
- COVID-19 Vaccines
- Communicable Diseases, Emerging/prevention & control
- Communicable Diseases, Emerging/virology
- Coronavirus Infections/immunology
- Coronavirus Infections/prevention & control
- Coronavirus Infections/therapy
- Coronavirus Infections/virology
- Cross Reactions/immunology
- Humans
- Immunization, Passive
- Pandemics/prevention & control
- Pneumonia, Viral/prevention & control
- Pneumonia, Viral/therapy
- Pneumonia, Viral/virology
- SARS-CoV-2
- Vaccination
- Vaccines, Attenuated/immunology
- Vaccines, DNA/immunology
- Vaccines, Inactivated/immunology
- Vaccines, Subunit/immunology
- Viral Vaccines/immunology
- COVID-19 Serotherapy
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Affiliation(s)
- Maria Trovato
- Institute of Biochemistry and Cell Biology, National Research Council, Naples, Italy
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12
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Resnick SJ, Iketani S, Hong SJ, Zask A, Liu H, Kim S, Melore S, Nair MS, Huang Y, Tay NE, Rovis T, Yang HW, Stockwell BR, Ho DD, Chavez A. A simplified cell-based assay to identify coronavirus 3CL protease inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.08.29.272864. [PMID: 32869020 PMCID: PMC7457602 DOI: 10.1101/2020.08.29.272864] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We describe a mammalian cell-based assay capable of identifying coronavirus 3CL protease (3CLpro) inhibitors without requiring the use of live virus. By enabling the facile testing of compounds across a range of coronavirus 3CLpro enzymes, including the one from SARS-CoV-2, we are able to quickly identify compounds with broad or narrow spectra of activity. We further demonstrate the utility of our approach by performing a curated compound screen along with structure-activity profiling of a series of small molecules to identify compounds with antiviral activity. Throughout these studies, we observed concordance between data emerging from this assay and from live virus assays. By democratizing the testing of 3CL inhibitors to enable screening in the majority of laboratories rather than the few with extensive biosafety infrastructure, we hope to expedite the search for coronavirus 3CL protease inhibitors, to address the current epidemic and future ones that will inevitably arise.
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Affiliation(s)
- Samuel J. Resnick
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Seo Jung Hong
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Arie Zask
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Hengrui Liu
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Sungsoo Kim
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Schuyler Melore
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Manoj S. Nair
- Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Nicholas E.S. Tay
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Tomislav Rovis
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Hee Won Yang
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Brent R. Stockwell
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - David D. Ho
- Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
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MERS-CoV: Understanding the Latest Human Coronavirus Threat. Viruses 2018; 10:v10020093. [PMID: 29495250 PMCID: PMC5850400 DOI: 10.3390/v10020093] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/28/2018] [Accepted: 02/02/2018] [Indexed: 12/19/2022] Open
Abstract
Human coronaviruses cause both upper and lower respiratory tract infections in humans. In 2012, a sixth human coronavirus (hCoV) was isolated from a patient presenting with severe respiratory illness. The 60-year-old man died as a result of renal and respiratory failure after admission to a hospital in Jeddah, Saudi Arabia. The aetiological agent was eventually identified as a coronavirus and designated Middle East respiratory syndrome coronavirus (MERS-CoV). MERS-CoV has now been reported in more than 27 countries across the Middle East, Europe, North Africa and Asia. As of July 2017, 2040 MERS-CoV laboratory confirmed cases, resulting in 712 deaths, were reported globally, with a majority of these cases from the Arabian Peninsula. This review summarises the current understanding of MERS-CoV, with special reference to the (i) genome structure; (ii) clinical features; (iii) diagnosis of infection; and (iv) treatment and vaccine development.
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Berry M, Fielding BC, Gamieldien J. Potential Broad Spectrum Inhibitors of the Coronavirus 3CLpro: A Virtual Screening and Structure-Based Drug Design Study. Viruses 2015; 7:6642-60. [PMID: 26694449 PMCID: PMC4690886 DOI: 10.3390/v7122963] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 11/16/2015] [Accepted: 11/30/2015] [Indexed: 01/29/2023] Open
Abstract
Human coronaviruses represent a significant disease burden; however, there is currently no antiviral strategy to combat infection. The outbreak of severe acute respiratory syndrome (SARS) in 2003 and Middle East respiratory syndrome (MERS) less than 10 years later demonstrates the potential of coronaviruses to cross species boundaries and further highlights the importance of identifying novel lead compounds with broad spectrum activity. The coronavirus 3CL(pro) provides a highly validated drug target and as there is a high degree of sequence homology and conservation in main chain architecture the design of broad spectrum inhibitors is viable. The ZINC drugs-now library was screened in a consensus high-throughput pharmacophore modeling and molecular docking approach by Vina, Glide, GOLD and MM-GBSA. Molecular dynamics further confirmed results obtained from structure-based techniques. A highly defined hit-list of 19 compounds was identified by the structure-based drug design methodologies. As these compounds were extensively validated by a consensus approach and by molecular dynamics, the likelihood that at least one of these compounds is bioactive is excellent. Additionally, the compounds segregate into 15 significantly dissimilar (p < 0.05) clusters based on shape and features, which represent valuable scaffolds that can be used as a basis for future anti-coronaviral inhibitor discovery experiments. Importantly though, the enriched subset of 19 compounds identified from the larger library has to be validated experimentally.
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Affiliation(s)
- Michael Berry
- South African Medical Research Council Bioinformatics Capacity Development Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa.
- Molecular Biology and Virology Laboratory, Department of Medical BioSciences, Faculty of Natural Sciences, University of the Western Cape, Western Cape, Bellville 7535, South Africa.
| | - Burtram C Fielding
- Molecular Biology and Virology Laboratory, Department of Medical BioSciences, Faculty of Natural Sciences, University of the Western Cape, Western Cape, Bellville 7535, South Africa.
| | - Junaid Gamieldien
- South African Medical Research Council Bioinformatics Capacity Development Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa.
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