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Jahirul Islam M, Nawal Islam N, Siddik Alom M, Kabir M, Halim MA. A review on structural, non-structural, and accessory proteins of SARS-CoV-2: Highlighting drug target sites. Immunobiology 2023; 228:152302. [PMID: 36434912 PMCID: PMC9663145 DOI: 10.1016/j.imbio.2022.152302] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 10/30/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, is a highly transmittable and pathogenic human coronavirus that first emerged in China in December 2019. The unprecedented outbreak of SARS-CoV-2 devastated human health within a short time leading to a global public health emergency. A detailed understanding of the viral proteins including their structural characteristics and virulence mechanism on human health is very crucial for developing vaccines and therapeutics. To date, over 1800 structures of non-structural, structural, and accessory proteins of SARS-CoV-2 are determined by cryo-electron microscopy, X-ray crystallography, and NMR spectroscopy. Designing therapeutics to target the viral proteins has several benefits since they could be highly specific against the virus while maintaining minimal detrimental effects on humans. However, for ongoing and future research on SARS-CoV-2, summarizing all the viral proteins and their detailed structural information is crucial. In this review, we compile comprehensive information on viral structural, non-structural, and accessory proteins structures with their binding and catalytic sites, different domain and motifs, and potential drug target sites to assist chemists, biologists, and clinicians finding necessary details for fundamental and therapeutic research.
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Affiliation(s)
- Md. Jahirul Islam
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka 1215, Bangladesh
| | - Nafisa Nawal Islam
- Department of Biotechnology and Genetic Engineering, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Md. Siddik Alom
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Mahmuda Kabir
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Mohammad A. Halim
- Department of Chemistry and Biochemistry, Kennesaw State University, 370 Paulding Avenue NW, Kennesaw, GA 30144, USA,Corresponding author
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152
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Sarkar M, Saha S. Modeling of SARS-CoV-2 Virus Proteins: Implications on Its Proteome. Methods Mol Biol 2023; 2627:265-299. [PMID: 36959453 DOI: 10.1007/978-1-0716-2974-1_15] [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: 03/25/2023]
Abstract
COronaVIrus Disease 19 (COVID-19) is a severe acute respiratory syndrome (SARS) caused by a group of beta coronaviruses, SARS-CoV-2. The SARS-CoV-2 virus is similar to previous SARS- and MERS-causing strains and has infected nearly six hundred and fifty million people all over the globe, while the death toll has crossed the six million mark (as of December, 2022). In this chapter, we look at how computational modeling approaches of the viral proteins could help us understand the various processes in the viral life cycle inside the host, an understanding of which might provide key insights in mitigating this and future threats. This understanding helps us identify key targets for the purpose of drug discovery and vaccine development.
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Affiliation(s)
- Manish Sarkar
- Hochschule für Technik und Wirtschaft (HTW) Berlin, Berlin, Germany
- MedInsights SAS, Paris, France
| | - Soham Saha
- MedInsights, Veuilly la Poterie, France.
- MedInsights SAS, Paris, France.
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153
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Sruthi D, Dhanalakshmi M, Rao HCY, Parthasarathy R, Deepanraj SP, Jayabaskaran C. Curative Potential of High-Value Phytochemicals on COVID-19 Infection. BIOCHEMISTRY (MOSCOW) 2023; 88:64-72. [PMID: 37068882 PMCID: PMC9937517 DOI: 10.1134/s0006297923010066] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Medicinal plants and their therapeutically promising chemical compounds belonging to the valued category of 'traditional medicine' are potential remedies for various health problems. Due to their complex structure and enormous health benefits, the high-value plant-derived metabolites collectively termed as 'phytochemicals' have emerged as a crucial source for novel drug discovery and development. Indeed, several medicinal plants from diverse habitats are still in the 'underexplored' category in terms of their bioactive principles and therapeutic potential. COVID-19, infection caused by the SARS-CoV-2, first reported in November 2019, resulted in the alarming number of deaths (6.61 million), was further declared 'pandemic', and spread of the disease has continued till today. Even though the well-established scientific world has successfully implemented vaccines against COVID-19 within the short period of time, the focus on alternative remedies for long-term symptom management and immunity boosting have been increased. At this point, interventions based on traditional medicine, which include medicinal plants, their bioactive metabolites, extracts and formulations, attracted a lot of attention as alternative solutions for COVID-19 management. Here, we reviewed the recent research findings related to the effectiveness of phytochemicals in treatment or prevention of COVID-19. Furthermore, the literature regarding the mechanisms behind the preventive or therapeutic effects of these natural phytochemicals were also discussed. In conclusion, we suggest that the active plant-derived components could be used alone or in combination as an alternative solution for the management of SARS-CoV-2 infection. Moreover, the structure of these natural productomes may lead to the emergence of new prophylactic strategies for SARS-CoV-2-caused infection.
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Affiliation(s)
- Damodaran Sruthi
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India.
| | - Menamadathil Dhanalakshmi
- Research and Development Centre, Bharathiar University, Marudhamalai Road, Coimbatore, Tamil Nadu, 641046, India
| | | | | | - Shashikala Paranthaman Deepanraj
- Department of Biological Sciences, Tata Institute for Genetics and Society, Instem building, National Centre for Biological Sciences Campus, Bengaluru, Karnataka, 560065, India
| | - Chelliah Jayabaskaran
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
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154
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Zapata-Cardona MI, Florez-Alvarez L, Guerra-Sandoval AL, Chvatal-Medina M, Guerra-Almonacid CM, Hincapie-Garcia J, Hernandez JC, Rugeles MT, Zapata-Builes W. In vitro and in silico evaluation of antiretrovirals against SARS-CoV-2: A drug repurposing approach. AIMS Microbiol 2023; 9:20-40. [PMID: 36891537 PMCID: PMC9988408 DOI: 10.3934/microbiol.2023002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/26/2022] [Accepted: 12/13/2022] [Indexed: 01/18/2023] Open
Abstract
Background Drug repurposing is a valuable strategy for rapidly developing drugs for treating COVID-19. This study aimed to evaluate the antiviral effect of six antiretrovirals against SARS-CoV-2 in vitro and in silico. Methods The cytotoxicity of lamivudine, emtricitabine, tenofovir, abacavir, efavirenz and raltegravir on Vero E6 was evaluated by MTT assay. The antiviral activity of each of these compounds was evaluated via a pre-post treatment strategy. The reduction in the viral titer was assessed by plaque assay. In addition, the affinities of the antiretroviral interaction with viral targets RdRp (RNA-dependent RNA polymerase), ExoN-NSP10 (exoribonuclease and its cofactor, the non-structural protein 10) complex and 3CLpro (3-chymotrypsin-like cysteine protease) were evaluated by molecular docking. Results Lamivudine exhibited antiviral activity against SARS-CoV-2 at 200 µM (58.3%) and 100 µM (66.7%), while emtricitabine showed anti-SARS-CoV-2 activity at 100 µM (59.6%), 50 µM (43.4%) and 25 µM (33.3%). Raltegravir inhibited SARS-CoV-2 at 25, 12.5 and 6.3 µM (43.3%, 39.9% and 38.2%, respectively). The interaction between the antiretrovirals and SARS-CoV-2 RdRp, ExoN-NSP10 and 3CLpro yielded favorable binding energies (from -4.9 kcal/mol to -7.7 kcal/mol) using bioinformatics methods. Conclusion Lamivudine, emtricitabine and raltegravir showed in vitro antiviral effects against the D614G strain of SARS-CoV-2. Raltegravir was the compound with the greatest in vitro antiviral potential at low concentrations, and it showed the highest binding affinities with crucial SARS-CoV-2 proteins during the viral replication cycle. However, further studies on the therapeutic utility of raltegravir in patients with COVID-19 are required.
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Affiliation(s)
- Maria I Zapata-Cardona
- Grupo Inmunovirologia, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia
| | - Lizdany Florez-Alvarez
- Grupo Inmunovirologia, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia.,Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Mateo Chvatal-Medina
- Grupo Inmunovirologia, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia
| | | | - Jaime Hincapie-Garcia
- Grupo de investigacion, Promocion y prevencion farmaceutica, Facultad de ciencias farmaceuticas yalimentarias, Universidad de Antioquia UdeA, Medellin, Colombia
| | - Juan C Hernandez
- Grupo Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellin, Colombia
| | - Maria T Rugeles
- Grupo Inmunovirologia, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia
| | - Wildeman Zapata-Builes
- Grupo Inmunovirologia, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia.,Grupo Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellin, Colombia
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155
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Bello SO, Yunusa A, Adamu AA, Imam MU, Bello MB, Shuaibu A, Igumbor EU, Habib ZG, Popoola MA, Ochu CL, Bello AY, Deeni YY, Okoye I. Innovative, rapid, high-throughput method for drug repurposing in a pandemic-A case study of SARS-CoV-2 and COVID-19. Front Pharmacol 2023; 14:1130828. [PMID: 36937851 PMCID: PMC10014809 DOI: 10.3389/fphar.2023.1130828] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/20/2023] [Indexed: 03/05/2023] Open
Abstract
Several efforts to repurpose drugs for COVID-19 treatment have largely either failed to identify a suitable agent or agents identified did not translate to clinical use. Reasons that have been suggested to explain the failures include use of inappropriate doses, that are not clinically achievable, in the screening experiments, and the use of inappropriate pre-clinical laboratory surrogates to predict efficacy. In this study, we used an innovative algorithm, that incorporates dissemination and implementation considerations, to identify potential drugs for COVID-19 using iterative computational and wet laboratory methods. The drugs were screened at doses that are known to be achievable in humans. Furthermore, inhibition of viral induced cytopathic effect (CPE) was used as the laboratory surrogate to predict efficacy. Erythromycin, pyridoxine, folic acid and retapamulin were found to inhibit SARS-CoV-2 induced CPE in Vero cells at concentrations that are clinically achievable. Additional studies may be required to further characterize the inhibitions of CPE and the possible mechanisms.
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Affiliation(s)
- Shaibu Oricha Bello
- Department of Pharmacology and Therapeutics, Faculty of Basic Clinical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
- Nigerian COVID-19 Research Coalition, Nigerian Institute of Medical Research Institute, Abuja, Nigeria
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria
- *Correspondence: Shaibu Oricha Bello,
| | - Abdulmajeed Yunusa
- Department of Pharmacology and Therapeutics, Faculty of Basic Clinical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Adamu Ahmed Adamu
- Department of Pharmacology and Therapeutics, Faculty of Basic Clinical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Mustapha Umar Imam
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria
- Department of Medical Biochemistry, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Muhammad Bashir Bello
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria
- Department of veterinary Microbiology, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Abdulmalik Shuaibu
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria
- Department of veterinary Microbiology, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Ehimario Uche Igumbor
- Nigerian COVID-19 Research Coalition, Nigerian Institute of Medical Research Institute, Abuja, Nigeria
- School of Public Health, University of the Western Cape, Cape Town, South Africa
| | - Zaiyad Garba Habib
- Nigerian COVID-19 Research Coalition, Nigerian Institute of Medical Research Institute, Abuja, Nigeria
- Department of Medicine, University of Abuja Teaching Hospital, Gwagwalada, Abuja, Nigeria
| | - Mustapha Ayodele Popoola
- Nigerian COVID-19 Research Coalition, Nigerian Institute of Medical Research Institute, Abuja, Nigeria
| | - Chinwe Lucia Ochu
- Nigerian COVID-19 Research Coalition, Nigerian Institute of Medical Research Institute, Abuja, Nigeria
- Nigerian Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Aishatu Yahaya Bello
- Department of Clinical pharmacy and Pharmacy Practice, Faculty of Pharmaceutical sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Yusuf Yahaya Deeni
- Nigerian COVID-19 Research Coalition, Nigerian Institute of Medical Research Institute, Abuja, Nigeria
- Department of Microbiology and Biotechnology, Federal University of Dutse, Dutse, Nigeria
- Centre for Environmental and Public Health Research and Development, Kano, Nigeria
| | - Ifeoma Okoye
- University of Nigeria Centre for Clinical Trials, University of Nigeria Teaching Hospital, Enugu, Ituku Ozalla, Nigeria
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156
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Figueiredo-Nunes I, Trigueiro-Louro J, Rebelo-de-Andrade H. Exploring new antiviral targets for influenza and COVID-19: Mapping promising hot spots in viral RNA polymerases. Virology 2023; 578:45-60. [PMID: 36463618 PMCID: PMC9674405 DOI: 10.1016/j.virol.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 11/19/2022]
Abstract
Influenza and COVID-19 are infectious respiratory diseases that represent a major concern to public health with social and economic impact worldwide, for which the available therapeutic options are not satisfactory. The RdRp has a central role in viral replication and thus represents a major target for the development of antiviral approaches. In this study, we focused on Influenza A virus PB1 polymerase protein and the betacoronaviruses nsp12 polymerase protein, considering their functional and structural similarities. We have performed conservation and druggability analysis to map conserved druggable regions, that may have functional or structural importance in these proteins. We disclosed the most promising and new targeting regions for the discovery of new potential polymerase inhibitors. Conserved druggable regions of putative interaction with favipiravir and molnupiravir were also mapped. We have also compared and integrated the current findings with previous research.
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Affiliation(s)
- Inês Figueiredo-Nunes
- Host-Pathogen Interaction Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003, Lisbon, Portugal
| | - João Trigueiro-Louro
- Host-Pathogen Interaction Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003, Lisbon, Portugal; Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016, Lisbon, Portugal.
| | - Helena Rebelo-de-Andrade
- Host-Pathogen Interaction Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003, Lisbon, Portugal; Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016, Lisbon, Portugal.
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157
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Chaube U, Patel BD, Bhatt HG. A hypothesis on designing strategy of effective RdRp inhibitors for the treatment of SARS-CoV-2. 3 Biotech 2023; 13:12. [PMID: 36532857 PMCID: PMC9755803 DOI: 10.1007/s13205-022-03430-w] [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: 07/22/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Vaccines are used as one of the major weapons for the eradication of pandemic. However, the rise of different variants of the SARS-CoV-2 virus is creating doubts regarding the end of the pandemic. Hence, there is an urgent need to develop more drug candidates which can be useful for the treatment of COVID-19. In the present research for the scientific hypothesis, emphasis was given on the direct antiviral therapy available for the treatment of COVID-19. In lieu of this, the available molecular targets which include Severe Acute Respiratory Syndrome Chymotrypsin-like Protease (SARS-3CLpro), Papain-Like Cysteine Protease (PLpro), and RNA-Dependent RNA Polymerase (RdRp) were explored. As per the current scientific reports and literature, among all the available molecular targets, RNA-Dependent RNA Polymerase (RdRp) was found to be a crucial molecular target for the treatment of COVID-19. Most of the inhibitors which are reported against this target consisted of the free amine group and carbonyl group which might be playing an important role in the binding interaction with the RdRp protein. Among all the reported RdRp inhibitors, remdesivir, favipiravir, and molnupiravir were found to be the most promising drugs against COVID-19. Overall, the structural features of this RNA-Dependent RNA Polymerase (RdRp) inhibitors proved the importance of pyrrolo-triazine and pyrimidine scaffolds. Previous computational models of these drug molecules indicated that substitution with the polar functional group, hydrogen bond donor, and electronegative atoms on these scaffolds may increase the activity against the RdRp protein. Hence, in line with the proposed hypothesis, in the present research work for the evaluation of the hypothesis, new molecules were designed from the pyrrolo-triazine and pyrimidine scaffolds. Further, molecular docking and MD simulation studies were performed with these designed molecules. All these designed molecules (DM-1, DM-2, and DM-3) showed the results as per the proposed hypothesis. Among all the designed molecules, DM-1 showed promising results against the RdRp protein of SARS-CoV-2. In the future, these structural features can be used for the development of new RdRp inhibitors with improved activity. Also, in the future lead compound DM-1 can be explored against the RdRp protein for the treatment of COVID-19.
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Affiliation(s)
- Udit Chaube
- grid.412204.10000 0004 1792 2351Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat 382481 India
| | - Bhumika D. Patel
- grid.412204.10000 0004 1792 2351Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat 382481 India
| | - Hardik G. Bhatt
- grid.412204.10000 0004 1792 2351Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat 382481 India
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158
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Baron G, Borella S, della Vedova L, Vittorio S, Vistoli G, Carini M, Aldini G, Altomare A. An integrated metabolomic and proteomic approach for the identification of covalent inhibitors of the main protease (Mpro) of SARS-COV-2 from crude natural extracts. Talanta 2023; 252:123824. [PMID: 36027618 PMCID: PMC9371774 DOI: 10.1016/j.talanta.2022.123824] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/03/2022] [Accepted: 08/05/2022] [Indexed: 11/21/2022]
Abstract
Mpro represents one of the most promising drug targets for SARS-Cov-2, as it plays a crucial role in the maturation of viral polyproteins into functional proteins. HTS methods are currently used to screen Mpro inhibitors, and rely on searching chemical databases and compound libraries, meaning that they only consider previously structurally clarified and isolated molecules. A great advancement in the hit identification strategy would be to set-up an approach aimed at exploring un-deconvoluted mixtures of compounds such as plant extracts. Hence, the aim of the present study is to set-up an analytical platform able to fish-out bioactive molecules from complex natural matrices even where there is no knowledge on the constituents. The proposed approach begins with a metabolomic step aimed at annotating the MW of the matrix constituents. A further metabolomic step is based on identifying those natural electrophilic compounds able to form a Michael adduct with thiols, a peculiar chemical feature of many Mpro inhibitors that covalently bind the catalytic Cys145 in the active site, thus stabilizing the complex. A final step consists of incubating recombinant Mpro with natural extracts and identifying compounds adducted to the residues within the Mpro active site by bottom-up proteomic analysis (nano-LC-HRMS). Data analysis is based on two complementary strategies: (i) a targeted search applied by setting the adducted moieties identified as Michael acceptors of Cys as variable modifications; (ii) an untargeted approach aimed at identifying the whole range of adducted peptides containing Cys145 on the basis of the characteristic b and y fragment ions independent of the adduct. The method was set-up and then successfully tested to fish-out bioactive compounds from the crude extract of Scutellaria baicalensis, a Chinese plant containing the catechol-like flavonoid baicalin and its corresponding aglycone baicalein which are well-established inhibitors of Mpro. Molecular dynamics (MD) simulations were carried out in order to explore the binding mode of baicalin and baicalein, within the SARS-CoV-2 Mpro active site, allowing a better understanding of the role of the nucleophilic residues (i.e. His41, Cys145, His163 and His164) in the protein-ligand recognition process.
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159
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Sharma S, Sharma A, Bhattacharyya D, Chauhan RS. Computational identification of potential inhibitory compounds in Indian medicinal and aromatic plant species against major pathogenicity determinants of SARS-CoV-2. J Biomol Struct Dyn 2022; 40:14096-14114. [PMID: 34766880 DOI: 10.1080/07391102.2021.2000500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
SARS-CoV-2 (COVID-19) viral pandemic has been reported across 223 countries and territories. Globalized vaccination programs alongside administration of repurposed drugs will assumingly confer a stronger and longer individual specific immune protection. However, considering possible recurrence of the disease via new variants, a conveniently deliverable phytopharmaceutical drug might be the best option for COVID-19 treatment. In the current study, the efforts have been made to identify potential leads for inhalation therapy as nasal swabs have been reported to transfer viral load prominently. In that direction, 2363 Essential oil (EOs) compounds from Indian medicinal and aromatic plants were screened through docking analysis and potential candidates were shortlisted that can interfere with viral pathogenicity. The main protease (Mpro) of SARS-CoV-2 interacted closely with jatamansin (JM), 6,7-dehydroferruginol (FG) and beta-sitosterol (BS), while Papain-like Protease (PLpro) with friedelane-3-one (F3O) and lantadene D (LD) independently. Reduced Lantadene A (LAR) exhibited preferable interaction with RNA-dependent-RNA-polymerase (RdRp) whereas Lantadene A (LA) with RdRp and spike-glycoprotein (SG-pro) both target proteins. When compared against highest binding affinity conformations of well-known inhibitors of targets, these prioritized compounds conferred superior or comparable SARS-CoV-2 protein inhibition. Additionally, promising results were noted from pharmacokinetics prediction for all shortlisted compounds. Besides, molecular dynamics simulation for 100 ns in two replicates and binding free energy analysis revealed the stability of complexes with optimum compactness. To the best of our knowledge, the current investigation is a unique initial attempt whereby EO compounds have been computationally screened, irrespective of their known medicinal properties to fight COVID-19 infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shilpa Sharma
- Department of Biotechnology, School of Engineering & Applied Sciences, Bennett University, Uttar Pradesh, India
| | - Ashish Sharma
- Department of Biotechnology, School of Engineering & Applied Sciences, Bennett University, Uttar Pradesh, India
| | - Dipto Bhattacharyya
- Department of Biotechnology, School of Engineering & Applied Sciences, Bennett University, Uttar Pradesh, India
| | - Rajinder S Chauhan
- Department of Biotechnology, School of Engineering & Applied Sciences, Bennett University, Uttar Pradesh, India
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160
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Pundir H, Joshi T, Pant M, Bhat S, Pandey J, Chandra S, Tamta S. Identification of SARS-CoV-2 RNA dependent RNA polymerase inhibitors using pharmacophore modelling, molecular docking and molecular dynamics simulation approaches. J Biomol Struct Dyn 2022; 40:13366-13377. [PMID: 34637693 DOI: 10.1080/07391102.2021.1987329] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The RNA-dependent RNA polymerase (RdRp) is one of the crucial enzymes in severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) catalysing the replication of RNA, therefore acts as a potential target for antiviral drug design. The fixation of a ligand in the active site of RdRp may alter the SARS-CoV-2 life cycle. Present work aimed at identifying novel inhibitors of the SARS-CoV-2 RdRp enzyme by performing pharmacophore-based virtual screening, molecular docking and molecular dynamics simulation (MDS). Initially, the pharmacophore model of SARS-CoV-2 RdRp was constructed and the resulting model was used to screen compounds from ChEMBL, ZINC and PubChem databases. During the investigation, 180 compounds were screened using the above model and subjected to molecular docking with RdRp. Two compounds viz. ChEMBL1276156 and PubChem135548348 showed a strong binding affinity with RdRp than its standard inhibitor, Remdesivir. Toxicity prediction of these two compounds reveals their non-toxic nature. These compounds were further subjected to MDS for 100 ns to check their stability after binding with RdRp. The MDS of RdRp-ChEMBL1276156 and RdRp-PubChem135548348 complexes show enhanced stability in comparison to the RdRp-Remdesivir complex. The average interaction energy calculated after 100 ns of MDS was -146.56 and -172.68 KJ mol-1 for RdRp-CHEMBL1276156 complex and RdRp-PubChem135548348 complex, respectively, while -59.90 KJ mol-1 for RdRp-Remdesivir complex. The current investigation reveals that these two compounds are potent inhibitors of SARS-CoV-2 RdRp and they could be tested in the experimental condition to evaluate their efficacy against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hemlata Pundir
- Department of Botany, D.S.B Campus, Kumaun University, Nainital, Uttarakhand, India
| | - Tanuja Joshi
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
| | - Manish Pant
- Department of Post-Harvest Process and Food Engineering, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - Sunaullah Bhat
- Insect Biosystematics & Insect-Pest Management Laboratory, Department of Zoology, Kumaun University-SSJ Campus, Almora, Uttarakhand, India
| | - Jyoti Pandey
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
| | - Subhash Chandra
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
| | - Sushma Tamta
- Department of Botany, D.S.B Campus, Kumaun University, Nainital, Uttarakhand, India
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161
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Dey SK, Saini M, Dhembla C, Bhatt S, Rajesh AS, Anand V, Das HK, Kundu S. Suramin, penciclovir, and anidulafungin exhibit potential in the treatment of COVID-19 via binding to nsp12 of SARS-CoV-2. J Biomol Struct Dyn 2022; 40:14067-14083. [PMID: 34784490 DOI: 10.1080/07391102.2021.2000498] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
COVID-19, for which no confirmed therapeutic agents are available, has claimed over 48,14,000 lives globally. A feasible and quicker method to resolve this problem may be 'drug repositioning'. We investigated selected FDA and WHO-EML approved drugs based on their previously promising potential as antivirals, antibacterials or antifungals. These drugs were docked onto the nsp12 protein, which reigns the RNA-dependent RNA polymerase activity of SARS-CoV-2, a key therapeutic target for coronaviruses. Docked complexes were reevaluated using MM-GBSA analysis and the top three inhibitor-protein complexes were subjected to 100 ns long molecular dynamics simulation followed by another round of MM-GBSA analysis. The RMSF plots, binding energies and the mode of physicochemical interaction of the active site of the protein with the drugs were evaluated. Suramin, Penciclovir, and Anidulafungin were found to bind to nsp12 with similar binding energies as that of Remdesivir, which has been used as a therapy for COVID-19. In addition, recent experimental evidences indicate that these drugs exhibit antiviral efficacy against SARS-CoV-2. Such evidence, along with the significant and varied physical interactions of these drugs with the key viral enzyme outlined in this investigation, indicates that they might have a prospective therapeutic potential in the treatment of COVID-19 as monotherapy or combination therapy with Remdesivir.
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Affiliation(s)
- Sanjay Kumar Dey
- Center for Advanced Biotechnology and Medicine, Rutgers University, New Brunswick, New Jersey, USA.,Department of Biochemistry, University of Delhi South Campus, New Delhi, India.,Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Manisha Saini
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Chetna Dhembla
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Shruti Bhatt
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - A Sai Rajesh
- Department of Biosciences and Biotechnology, Fakir Mohan University, Odisha, India
| | - Varnita Anand
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | | | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
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162
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Patil SM, Martiz RM, Ramu R, Shirahatti PS, Prakash A, Chandra S J, Ranganatha VL. In silico identification of novel benzophenone-coumarin derivatives as SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) inhibitors. J Biomol Struct Dyn 2022; 40:13032-13048. [PMID: 34632942 DOI: 10.1080/07391102.2021.1978322] [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: 01/18/2023]
Abstract
In this study, we propose our novel benzophenone-coumarin derivatives (BCDs) as potent inhibitors of the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 virus, one of the key targets that are involved in the viral genome replication. We aim to evaluate the in silico antiviral potential of BCDs against this protein target, which involves molecular docking simulations, druglikeliness and pharmacokinetic evaluations, PASS analysis, molecular dynamics simulations, and computing binding free energy. Out of all the BCDs screened through these parameters, BCD-8 was found to be the most efficient and potent inhibitor of SARS-CoV-2 RdRp. During molecular docking simulation, BCD-8 showed an extensive molecular interaction in comparison with that of the standard control used, remdesivir. The druglikeliness and pharmacokinetic analyses also proved the efficiency of BCD-8 as an effective drug without adverse effects. Further, pharmacological potential analysis through PASS depicted the antiviral property of BCD-8. With these findings, we performed molecular dynamics simulations, where BCD-8 edged out remdesivir with its exemplary stable interaction with SARS-CoV-2 RdRp. Furthermore, binding free energy of both BCD-8 and remdesivir was calculated, where BCD-8 showed a lower binding energy and standard deviations in comparison with that of remdesivir. Moreover, being a non-nucleoside analogue, BCD-8 can be used effectively against SARS-CoV-2, whereas nucleoside analogues like remdesivir may become non-functional or less functional due to exonuclease activity of nsp14 of the virus. Therefore, we propose BCD-8 as a SARS-CoV-2 RdRp inhibitor, showing higher predicted efficiency than remdesivir in all the in silico experiments conducted.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shashank M Patil
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Reshma Mary Martiz
- Department of Microbiology, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Ramith Ramu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | | | - Ashwini Prakash
- Department of Microbiology, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Jagadeep Chandra S
- Department of Microbiology, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - V Lakshmi Ranganatha
- Department of Chemistry, The National Institute of Engineering, Mysuru, Karnataka, India
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163
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Bibi N, Farid A, Gul S, Ali J, Amin F, Kalthiya U, Hupp T. Drug repositioning against COVID-19: a first line treatment. J Biomol Struct Dyn 2022; 40:12812-12826. [PMID: 34519259 PMCID: PMC8442756 DOI: 10.1080/07391102.2021.1977698] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
COVID-19 disease caused by the SARS-CoV-2 virus has shaken our health and wealth foundations. Although COVID-19 vaccines will become available allowing for attenuation of disease progression rates, distribution of vaccines can create other challenges and delays. Hence repurposed drugs against SARS-CoV-2 can be an attractive parallel strategy that can be integrated into routine clinical practice even in poorly-resourced countries. The present study was designed using knowledge of viral pathogenesis and pharmacodynamics of broad-spectrum antiviral agents (BSAAs). We carried out the virtual screening of BSAAs against the SARS-CoV-2 spike glycoprotein, RNA dependent RNA polymerase (RdRp), the main protease (Mpro) and the helicase enzyme of SARS-CoV-2. Imatinib (a tyrosine kinase inhibitor), Suramin (an anti-parasitic), Glycyrrhizin (an anti-inflammatory) and Bromocriptine (a dopamine agonist) showed higher binding affinity to multiple targets. Further through molecular dynamics simulation, critical conformational changes in the target protein molecules were revealed upon drug binding which illustrates the favorable binding conformations of antiviral drugs against SARS-CoV-2 target proteins. The resulting drugs from the present study in combination and in cocktails from the arsenal of existing drugs could reduce the translational distance and could offer substantial clinical benefit to decrease the burden of COVID-19 illness. This also creates a roadmap for subsequent viral diseases that emerge.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nousheen Bibi
- Department of Bioinformatics, Shaheed Benazir Bhutto Women University, Peshawar, Pakistan,CONTACT Nousheen Bibi ; Department of Bioinformatics, Shaheed Benazir Bhutto Women University, Peshawar, Pakistan
| | - Ayesha Farid
- Department of Bioinformatics, Shaheed Benazir Bhutto Women University, Peshawar, Pakistan
| | - Sana Gul
- Department of Bioinformatics, Shaheed Benazir Bhutto Women University, Peshawar, Pakistan
| | - Johar Ali
- Center for Genomics Sciences RMI, Peshawar, Pakistan
| | - Farhat Amin
- Department of Bioinformatics, Shaheed Benazir Bhutto Women University, Peshawar, Pakistan
| | - Umesh Kalthiya
- International Center for Cancer Vaccine Science, Gdańsk, Poland
| | - Ted Hupp
- International Center for Cancer Vaccine Science, Gdańsk, Poland,Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
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164
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Guo S, Lei X, Chang Y, Zhao J, Wang J, Dong X, Liu Q, Zhang Z, Wang L, Yi D, Ma L, Li Q, Zhang Y, Ding J, Liang C, Li X, Guo F, Wang J, Cen S. SARS-CoV-2 hijacks cellular kinase CDK2 to promote viral RNA synthesis. Signal Transduct Target Ther 2022; 7:400. [PMID: 36575184 PMCID: PMC9793359 DOI: 10.1038/s41392-022-01239-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 09/30/2022] [Accepted: 10/24/2022] [Indexed: 12/28/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has devastated global health. Identifying key host factors essential for SARS-CoV-2 RNA replication is expected to unravel cellular targets for the development of broad-spectrum antiviral drugs which have been quested for the preparedness of future viral outbreaks. Here, we have identified host proteins that associate with nonstructural protein 12 (nsp12), the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 using a mass spectrometry (MS)-based proteomic approach. Among the candidate factors, CDK2 (Cyclin-dependent kinase 2), a member of cyclin-dependent kinases, interacts with nsp12 and causes its phosphorylation at T20, thus facilitating the assembly of the RdRp complex consisting of nsp12, nsp7 and nsp8 and promoting efficient synthesis of viral RNA. The crucial role of CDK2 in viral RdRp function is further supported by our observation that CDK2 inhibitors potently impair viral RNA synthesis and SARS-CoV-2 infection. Taken together, we have discovered CDK2 as a key host factor of SARS-CoV-2 RdRp complex, thus serving a promising target for the development of SARS-CoV-2 RdRp inhibitors.
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Affiliation(s)
- Saisai Guo
- grid.506261.60000 0001 0706 7839Department of Immunology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiaobo Lei
- grid.506261.60000 0001 0706 7839NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yan Chang
- grid.411609.b0000 0004 1758 4735Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Jianyuan Zhao
- grid.506261.60000 0001 0706 7839Department of Immunology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jing Wang
- grid.506261.60000 0001 0706 7839Department of Immunology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiaojing Dong
- grid.506261.60000 0001 0706 7839NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qian Liu
- grid.506261.60000 0001 0706 7839Department of Immunology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zixiong Zhang
- grid.506261.60000 0001 0706 7839Department of Immunology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Lidan Wang
- grid.506261.60000 0001 0706 7839Department of Immunology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Dongrong Yi
- grid.506261.60000 0001 0706 7839Department of Immunology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ling Ma
- grid.506261.60000 0001 0706 7839Department of Immunology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Quanjie Li
- grid.506261.60000 0001 0706 7839Department of Immunology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yongxin Zhang
- grid.506261.60000 0001 0706 7839Department of Immunology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jiwei Ding
- grid.506261.60000 0001 0706 7839Department of Immunology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Chen Liang
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC Canada
| | - Xiaoyu Li
- grid.506261.60000 0001 0706 7839Department of Immunology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Fei Guo
- grid.506261.60000 0001 0706 7839NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jianwei Wang
- grid.506261.60000 0001 0706 7839NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shan Cen
- grid.506261.60000 0001 0706 7839Department of Immunology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China ,grid.506261.60000 0001 0706 7839CAMS Key Laboratory of Antiviral Drug Research, Chinese Academy of Medical Sciences & Peking Union Medical Sciences, Beijing, China
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165
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Giannetti M, Mazzuca C, Ripani G, Palleschi A. Inspection on the Mechanism of SARS-CoV-2 Inhibition by Penciclovir: A Molecular Dynamic Study. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010191. [PMID: 36615385 PMCID: PMC9821970 DOI: 10.3390/molecules28010191] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/18/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022]
Abstract
In recent years, humanity has had to face a critical pandemic due to SARS-CoV-2. In the rapid search for effective drugs against this RNA-positive virus, the repurposing of already existing nucleotide/nucleoside analogs able to stop RNA replication by inhibiting the RNA-dependent RNA polymerase enzyme has been evaluated. In this process, a valid contribution has been the use of in silico experiments, which allow for a rapid evaluation of the possible effectiveness of the proposed drugs. Here we propose a molecular dynamic study to provide insight into the inhibition mechanism of Penciclovir, a nucleotide analog on the RNA-dependent RNA polymerase enzyme. Besides the presented results, in this article, for the first time, molecular dynamic simulations have been performed considering not only the RNA-dependent RNA polymerase protein, but also its cofactors (fundamental for RNA replication) and double-strand RNA.
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166
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Fayyazi N, Mostashari-Rad T, Ghasemi JB, Ardakani MM, Kobarfard F. Molecular dynamics simulation, 3D-pharmacophore and scaffold hopping analysis in the design of multi-target drugs to inhibit potential targets of COVID-19. J Biomol Struct Dyn 2022; 40:11787-11808. [PMID: 34405765 DOI: 10.1080/07391102.2021.1965914] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
SARS-CoV-2 has posed serious threat to the health and has inflicted huge costs in the world. Discovering potent compounds is a critical step to inhibit coronavirus. 3CLpro and RdRp are the most conserved targets associated with COVID-19. In this study, three-dimensional pharmacophore modeling, scaffold hopping, molecular docking, structure-based virtual screening, QSAR-based ADMET predictions and molecular dynamics analysis were used to identify inhibitors for these targets. Binding free energies estimated by molecular docking for each ligand in different binding sites of RdRp were used to predict the active site. Previously reported active 3CLpro and RdRp inhibitors were used to build a pharmacophore model to develop different scaffolds. Structure-based simulations and pharmacophore modeling based on Hip Hop algorithm converged in a state that suggest hydrogen bond acceptor and donor features have a critical role in the two binding sites. Further validations indicated that the best pharmacophore model has fairly good correlation values compared with approved inhibitors. Structure-based simulation results approved that GLu166 and Gln189 in 3CLpro and Lys551 and Glu811 in RdRp, are critical residues for dual activities. Ten compounds were extracted from pharmacophore-based virtual screening in six databases. The results, gained by repurposing approach, suggest the effectiveness of these ten compounds with different scaffolds as possible inhibitors of the two targets. Some quinoline-based hybrid derivatives also were designed. QSAR descriptors plot predicted that the scaffolds have had accepted pharmacokinetic profiles. Multiple molecular dynamics simulations in 100 ns and MM/PBSA studies of some reference inhibitors and the novel compounds in complex with both targets demonstrated stable complexes and confirmed the interaction modes. Based on different computational methods, COVID-19 multi-target inhibitors are proposed. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Neda Fayyazi
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan, Iran.,Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tahereh Mostashari-Rad
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan, Iran.,Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jahan B Ghasemi
- College of Sciences, Faculty of Chemistry, University of Tehran, Tehran, Iran
| | - Mehran Mirabzadeh Ardakani
- Department of Traditional Pharmacy, Faculty of Pharmacy, Tehran University of Medical Science, Tehran, Iran
| | - Farzad Kobarfard
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Medicinal Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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167
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Mukherjee S, Sharma D, Sharma AK, Jaiswal S, Sharma N, Borah S, Kaur G. Flavan-based phytoconstituents inhibit Mpro, a SARS-COV-2 molecular target, in silico. J Biomol Struct Dyn 2022; 40:11545-11559. [PMID: 34348081 DOI: 10.1080/07391102.2021.1960196] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A well-validated in-silico approach can provide promising drug candidates for the treatment of the ongoing CoVID19 pandemic. In this study, we have screened 32 phytochemical constituents (PCCs) with Mpro binding site (PDB:6W63) based on which we identified three possible candidates that are likely to be effective against CoVID19-viz., licoleafol (binding energy: -8.1 kcal/mol), epicatechin gallate (-8.5 kcal/mol) and silibinin (-8.4 kcal/mol) that result in higher binding affinity than the known inhibitor, X77 (-7.7 kcal/mol). Molecular dynamics (MD) simulations of PCCs-Mpro complex confirmed molecular docking results with high structural and dynamical stability. The selected compounds were found to exhibit low mean squared displacements (licoleafol: 2.25 ± 0.43 Å, epicatechin gallate: 1.93 ± 0.35 Å, and silibinin: 1.39 ± 0.19 Å) and overall low fluctuations of the binding complexes (root mean squared fluctuations below 2 Å). Visualization of the MD trajectories and structural analyses revealed that they remain confined to the initial binding region, with mean fluctuations lower than 3 Å. To access the collective motion of the atoms, we performed principal component analysis demonstrating that the first 10 principal components are the major contributors (approximate contribution of 80%) and are responsible for the overall PCCs motion. Considering that the three selected PCCs share the same flavan backbone and exhibit antiviral activity against hepatitis C, we opine that licoleafol, epi-catechin gallate, and silibinin can be promising anti-CoVID19 drug candidates. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Soham Mukherjee
- School of Pharmaceutical Sciences, Shoolini University, Solan, India.,Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, India
| | - Deepika Sharma
- School of Pharmaceutical Sciences, Shoolini University, Solan, India
| | - Ajay Kumar Sharma
- School of Pharmaceutical Sciences, Shoolini University, Solan, India
| | - Shreya Jaiswal
- School of Pharmaceutical Sciences, Shoolini University, Solan, India
| | - Nancy Sharma
- School of Pharmaceutical Sciences, Shoolini University, Solan, India
| | - Sangkha Borah
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Gurjot Kaur
- School of Pharmaceutical Sciences, Shoolini University, Solan, India
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168
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Ahmed S, Mahtarin R, Islam MS, Das S, Al Mamun A, Ahmed SS, Ali MA. Remdesivir analogs against SARS-CoV-2 RNA-dependent RNA polymerase. J Biomol Struct Dyn 2022; 40:11111-11124. [PMID: 34315339 DOI: 10.1080/07391102.2021.1955743] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The COVID-19 pandemic has already taken many lives but is still continuing its spread and exerting jeopardizing effects. This study is aimed to find the most potent ligands from 703 analogs of remdesivir against RNA-dependent RNA polymerase (RdRp) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus . RdRp is a major part of a multi-subunit transcription complex of the virus, which is essential for viral replication. In clinical trials, it has been found that remdesivir is effective to inhibit viral replication in Ebola and in primary human lung cell cultures; it effectively impedes replication of a broad-spectrum pre-pandemic bat coronaviruses and epidemic human coronaviruses. After virtual screening, 30 most potent ligands and remdesivir were modified with triphosphate. Quantum mechanics-based quantitative structure-activity relationship envisages the binding energy for ligands applying partial least square (PLS) regression. PLS regression remarkably predicts the binding energy of the effective ligands with an accuracy of 80% compared to the value attained from molecular docking. Two ligands (L4:58059550 and L28:126719083), which have more interactions with the target protein than the other ligands including standard remdesivir triphosphate, were selected for further analysis. Molecular dynamics simulation is done to assess the stability and dynamic nature of the drug-protein complex. Binding-free energy results via PRODIGY server and molecular mechanics/Poisson-Boltzmann surface area method depict that the potential and solvation energies play a crucial role. Considering all computational analysis, we recommend the best remdesivir analogs can be utilized for efficacy test through in vitro and in vivo trials against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sinthyia Ahmed
- Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Rumana Mahtarin
- Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Shamiul Islam
- Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Susmita Das
- Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Abdulla Al Mamun
- Key Laboratory of Soft Chemistry and Functional Materials of MOE, School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Sayeda Samina Ahmed
- Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Ackas Ali
- Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
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169
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Genetic Study of SARS-CoV-2 Non Structural Protein 12 in COVID-19 Patients Non Responders to Remdesivir. Microbiol Spectr 2022; 10:e0244822. [PMID: 36354320 PMCID: PMC9769853 DOI: 10.1128/spectrum.02448-22] [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] [Indexed: 11/12/2022] Open
Abstract
Remdesivir (RDV) was the first antiviral drug approved by the FDA to treat severe coronavirus disease-2019 (COVID-19) patients. RDV inhibits SARS-CoV-2 replication by stalling the non structural protein 12 (nsp12) subunit of the RNA-dependent RNA polymerase (RdRp). No evidence of global widespread RDV-resistance mutations has been reported, however, defining genetic pathways to RDV resistance and determining emergent mutations prior and subsequent antiviral therapy in clinical settings is necessary. This study identified 57/149 (38.3%) patients who did not respond to one course (5-days) (n = 36/111, 32.4%) or prolonged (5 to 20 days) (n = 21/38, 55.3%) RDV therapy by subgenomic RNA detection. Genetic variants in the nsp12 gene were detected in 29/49 (59.2%) non responder patients by Illumina sequencing, including the de novo E83D mutation that emerged in an immunosuppressed patient after receiving 10 + 8 days of RDV, and the L838I detected at baseline and/or after prolonged RDV treatment in 9/49 (18.4%) non responder subjects. Although 3D protein modeling predicted no interference with RDV, the amino acid substitutions detected in the nsp12 involved changes on the electrostatic outer surface and in secondary structures that may alter antiviral response. It is important for health surveillance to study potential mutations associated with drug resistance as well as the benefit of RDV retreatment, especially in immunosuppressed patients and in those with persistent replication. IMPORTANCE This study provides clinical and microbiologic data of an extended population of hospitalized patients for COVID-19 pneumonia who experienced treatment failure, detected by the presence of subgenomic RNA (sgRNA). The genetic variants found in the nsp12 pharmacological target of RDV bring into focus the importance of monitoring emergent mutations, one of the objectives of the World Health Organization (WHO) for health surveillance. These mutations become even more crucial as RDV keeps being prescribed and new molecules are being repurposed for the treatment of COVID-19. The present article offers new perspectives for the clinical management of non responder patients treated and retreated with RDV and emphasizes the need of further research of the benefit of combinatorial therapies and RDV retreatment, especially in immunosuppressed patients with persistent replication after therapy.
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170
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Snoussi M, Redissi A, Mosbah A, De Feo V, Adnan M, Aouadi K, Alreshidi M, Patel M, Kadri A, Noumi E. Emetine, a potent alkaloid for the treatment of SARS-CoV-2 targeting papain-like protease and non-structural proteins: pharmacokinetics, molecular docking and dynamic studies. J Biomol Struct Dyn 2022; 40:10122-10135. [PMID: 34254564 DOI: 10.1080/07391102.2021.1946715] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The main objective of this study is to find out the anti-SARS-CoV-2 potential of emetine by using molecular docking and dynamic simulation approaches. Interestingly, molecular docking studies suggest that Emetine showed significant binding affinity toward Nsp15 (-10.8 kcal/mol) followed by Nsp12 (-9.5 kcal/mol), RNA-dependent RNA polymerase, RdRp (-9.5 kcal/mol), Nsp16 (-9.4 kcal/mol), Nsp10 (-9.2 kcal/mol), Papain-like protein (-9.0 kcal/mol), Nsp13 (-9.0 kcal/mol), Nsp14 (-8.9 kcal/mol) and Spike Protein Receptor Domain (-8.8 kcal/mol) and chymotrypsin-like protease, 3CLpro (-8.5 kcal/mol), respectively, which are essential for viral infection and replication. In addition, molecular dynamic simulation (MD) was also performed for 140 ns to explore the stability behavior of the main targets and inhibitor complexes as well as the binding mechanics of the ligand to the target proteins. The obtained MD results followed by absolute binding energy calculation confirm that the binding of emetine at the level of the various receptors is more stable. The complex EmetineNSP15, mechanistically was stabilized as follows: Emetine first binds to the monomer, after, binds to the second inducing the formation of a dimer which in turn leading to the formation of complex that simulation stabilizes it at a value less than 5 Å. Overall, supported by the powerful and good pharmacokinetic data of Emetine, our findings with clinical trials may be helpful to confirm that Emetine could be promoted in the prevention and eradication of COVID-19 by reducing the severity in the infected persons and therefore can open possible new strategies for drug repositioning. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mejdi Snoussi
- Department of Biology, College of Science, University of Hail, Ha'il, Saudi Arabia.,Laboratory of Genetics, Biodiversity and Valorization of Bio-resources, Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir, Tunisia
| | - Alaeddine Redissi
- ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, University of Manouba, Ariana, Tunisia
| | - Amor Mosbah
- ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, University of Manouba, Ariana, Tunisia
| | - Vincenzo De Feo
- Department of Pharmacy, University of Salerno, Salerno, Italy
| | - Mohd Adnan
- Department of Biology, College of Science, University of Hail, Ha'il, Saudi Arabia
| | - Kaïss Aouadi
- Department of Chemistry, College of Science, Qassim University, Buraidah, Saudi Arabia.,Faculty of Science of Monastir, Laboratory of Hetrocyclic Chemistry, Natural Products and Reactivity, University of Monastir, Monastir, Tunisia
| | - Mousa Alreshidi
- Department of Biology, College of Science, University of Hail, Ha'il, Saudi Arabia
| | - Mitesh Patel
- Bapalal Vaidya Botanical Research Centre, Department of Biosciences, Veer Narmad South Gujarat University, Surat, India
| | - Adel Kadri
- Faculty of Science of Sfax, Department of Chemistry, University of Sfax, Sfax, Tunisia.,Faculty of Science and Arts in Baljurashi, Albaha University, Al Bahah, Saudi Arabia
| | - Emira Noumi
- Department of Biology, College of Science, University of Hail, Ha'il, Saudi Arabia.,Laboratory of Bioresources: Integrative Biology and Valorization, (LR14-ES06), University of Monastir, Higher Institute of Biotechnology of Monastir, Monastir, Tunisia
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171
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Singh S, Chauhan P, Sharma V, Rao A, Kumbhar BV, Prajapati VK. Identification of multi-targeting natural antiviral peptides to impede SARS-CoV-2 infection. Struct Chem 2022; 34:1-16. [PMID: 36570051 PMCID: PMC9759041 DOI: 10.1007/s11224-022-02113-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
SARS-CoV-2 and its variants cause serious health concerns throughout the world. The alarming increase in the daily number of cases has become a nightmare in many low-income countries; although some vaccines are available, their high cost and low vaccine production make them unreachable to ordinary people in developing countries. Other treatment strategies are required for novel therapeutic options. The peptide-based drug is one of the alternatives with low toxicity, more specificity, and ease of synthesis. Herein, we have applied structure-based virtual screening to identify potential peptides targeting the critical proteins of SARS-CoV-2. Non-toxic natural antiviral peptides were selected from the enormous number of peptides. Comparative modeling was applied to prepare a 3D structure of selected peptides. 3D models of the peptides were docked using the ClusPro docking server to determine their binding affinity and peptide-protein interaction. The high-scoring peptides were docked with other crucial proteins to analyze multiple targeting peptides. The two best peptides were subjected to MD simulations to validate the structure stability and evaluated RMSD, RMSF, Rg, SASA, and H-bonding from the trajectory analysis of 100 ns. The proposed lead peptides can be used as a broad-spectrum drug and potentially develop as a therapeutic to combat SARS-CoV-2, positively impacting the current pandemic. Supplementary Information The online version contains supplementary material available at 10.1007/s11224-022-02113-9.
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Affiliation(s)
- Satyendra Singh
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan 305817 India
| | - Priya Chauhan
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan 305817 India
| | - Vinita Sharma
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan 305817 India
| | - Abhishek Rao
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan 305817 India
| | - Bajarang Vasant Kumbhar
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS University (Deemed), Vile Parle, Mumbai, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan 305817 India
- Department of Biochemistry, School of Biological Sciences, Central University of Punjab, Bathinda, Punjab India
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172
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Sharma PP, Kumar S, Srivastava S, Srivastava M, Jee B, Gorobets NY, Kumar D, Kumar M, Asthana S, Zhang P, Poonam, Zoltner M, Rathi B. Computational study of novel inhibitory molecule, 1-(4-((2 S,3 S)-3-amino-2-hydroxy-4-phenylbutyl)piperazin-1-yl)-3-phenylurea, with high potential to competitively block ATP binding to the RNA dependent RNA polymerase of SARS-CoV-2 virus. J Biomol Struct Dyn 2022; 40:10162-10180. [PMID: 34151735 DOI: 10.1080/07391102.2021.1940281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
For coronaviruses, RNA-dependent RNA polymerase (RdRp) is an essential enzyme that catalyses the replication from RNA template and therefore remains an attractive therapeutic target for anti-COVID drug discovery. In the present study, we performed a comprehensive in silico screening for 16,776 potential molecules from recently established drug libraries based on two important pharmacophores (3-amino-4-phenylbutan-2-ol and piperazine). Based on initial assessment, 4042 molecules were obtained suitable as drug candidates, which were following Lipinski's rule. Molecular docking implemented for the analysis of molecular interactions narrowed this number of compounds down to 19. Subsequent to screening filtering criteria and considering the critical parameters viz. docking score and MM-GBSA binding free energy, 1-(4-((2S,3S)-3-amino-2-hydroxy-4-phenylbutyl)piperazin-1-yl)-3-phenylurea (compound 1) was accomplished to score highest in comparison to the remaining 18 shortlisted drug candidates. Notably, compound 1 displayed higher docking score (-8.069 kcal/mol) and MM-GBSA binding free energy (-49.56 kcal/mol) than the control drug, remdesivir triphosphate, the active form of remdesivir as well as adenosine triphosphate. Furthermore, a molecular dynamics simulation was carried out (100 ns), which substantiated the candidacy of compound 1 as better inhibitor. Overall, our systematic in silico study predicts the potential of compound 1 to exhibit a more favourable specific activity than remdesivir triphosphate. Hence, we suggest compound 1 as a novel potential drug candidate, which should be considered for further exploration and validation of its potential against SARS-CoV-2 in wet lab experimental studies.Communicated by Ramasawamy H. Sarma.
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Affiliation(s)
- Prem Prakash Sharma
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi, India
| | - Sumit Kumar
- Department of Chemistry, Miranda House, University of Delhi, Delhi, India
| | - Sukrit Srivastava
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi, India.,Infection Biology Group, Indian Foundation for Fundamental Research, Rae Bareli, India
| | - Mitul Srivastava
- Translational Health Science and Technology Institute (THSTI), Haryana, India
| | - Babban Jee
- Department of Health Research, Ministry of Health and Family Welfare Government of India, New Delhi, India
| | - Nikolay Yu Gorobets
- Department of Organic and Bioorganic Chemistry, State Scientific Institution 'Institute for Single Crystals' of National Academy of Science of Ukraine, Kharkiv, Ukraine
| | - Dhruv Kumar
- Amity Institute of Molecular Medicine & Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Noida, India
| | - Mukesh Kumar
- Department of Biology, College of Arts and Sciences, Georgia State University, Atlanta, GA, USA
| | - Shailendra Asthana
- Translational Health Science and Technology Institute (THSTI), Haryana, India
| | - Peng Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, PR China
| | - Poonam
- Department of Chemistry, Miranda House, University of Delhi, Delhi, India
| | - Martin Zoltner
- Drug Discovery and Evaluation Unit, Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Brijesh Rathi
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi, India
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173
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Sun Y, Zhao B, Wang Y, Chen Z, Zhang H, Qu L, Zhao Y, Song J. Optimization of potential non-covalent inhibitors for the SARS-CoV-2 main protease inspected by a descriptor of the subpocket occupancy. Phys Chem Chem Phys 2022; 24:29940-29951. [PMID: 36468652 DOI: 10.1039/d2cp03681a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The main protease is regarded as an essential drug target for treating Coronavirus Disease 2019. In the present study, 13 marketed drugs were investigated to explore the possible binding mechanism, utilizing molecular docking, molecular dynamics simulation, and MM-PB(GB)SA binding energy calculations. Our results suggest that fusidic acid, polydatin, SEN-1269, AZD6482, and UNC-2327 have high binding affinities of more than 23 kcal mol-1. A descriptor was defined for the energetic occupancy of the subpocket, and it was found that S4 had a low occupancy of less than 10% on average. The molecular optimization of ADZ6482 via reinforcement learning algorithms was carried out to screen out three lead compounds, in which slight structural changes give more considerable binding energies and an occupancy of the S4 subpocket of up to 43%. The energetic occupancy could be a useful descriptor for evaluating the local binding affinity for drug design.
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Affiliation(s)
- Yujia Sun
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, Henan, 450001, P. R. China.
| | - Bodi Zhao
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, Henan, 450001, P. R. China.
| | - Yuqi Wang
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, Henan, 450001, P. R. China.
| | - Zitong Chen
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, Henan, 450001, P. R. China.
| | - Huaiyu Zhang
- Institute of Computational Quantum Chemistry, College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, Hebei, 050024, P. R. China
| | - Lingbo Qu
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, Henan, 450001, P. R. China.
| | - Yuan Zhao
- The Key Laboratory of Natural Medicine and Immuno - Engineering, Henan University, Kaifeng, Henan, 475000, P. R. China
| | - Jinshuai Song
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, Henan, 450001, P. R. China.
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174
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Zhang J, He M, Xie Q, Su A, Yang K, Liu L, Liang J, Li Z, Huang X, Hu J, Liu Q, Song B, Hu C, Chen L, Wang Y. Predicting In Vitro and In Vivo Anti-SARS-CoV-2 Activities of Antivirals by Intracellular Bioavailability and Biochemical Activity. ACS OMEGA 2022; 7:45023-45035. [PMID: 36530252 PMCID: PMC9753181 DOI: 10.1021/acsomega.2c05376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 10/26/2022] [Indexed: 06/17/2023]
Abstract
Cellular drug response (concentration required for obtaining 50% of a maximum cellular effect, EC50) can be predicted by the intracellular bioavailability (F ic) and biochemical activity (half-maximal inhibitory concentration, IC50) of drugs. In an ideal model, the cellular negative log of EC50 (pEC50) equals the sum of log F ic and the negative log of IC50 (pIC50). Here, we measured F ic's of remdesivir, favipiravir, and hydroxychloroquine in various cells and calculated their anti-SARS-CoV-2 EC50's. The predicted EC50's are close to the observed EC50's in vitro. When the lung concentrations of antiviral drugs are higher than the predicted EC50's in alveolar type 2 cells, the antiviral drugs inhibit virus replication in vivo, and vice versa. Overall, our results indicate that both in vitro and in vivo antiviral activities of drugs can be predicted by their intracellular bioavailability and biochemical activity without using virus. This virus-free strategy can help medicinal chemists and pharmacologists to screen antivirals during early drug discovery, especially for researchers who are not able to work in the high-level biosafety lab.
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Affiliation(s)
- Jinwen Zhang
- Center
for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
| | - Mingfeng He
- Institute
of Orthopedics and Traumatology, Foshan Hospital of Traditional Chinese
Medicine, Foshan528000, China
| | - Qian Xie
- Center
for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
- Key
Laboratory of Structure-based Drug Design & Discovery (Ministry
of Education), School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang110016, China
| | - Ailing Su
- Center
for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
| | - Kuangyang Yang
- Institute
of Orthopedics and Traumatology, Foshan Hospital of Traditional Chinese
Medicine, Foshan528000, China
| | - Lichu Liu
- Institute
of Orthopedics and Traumatology, Foshan Hospital of Traditional Chinese
Medicine, Foshan528000, China
| | - Jianhui Liang
- Center
for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
- Key
Laboratory of Structure-based Drug Design & Discovery (Ministry
of Education), School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang110016, China
| | - Ziqi Li
- Center
for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
| | - Xiuxin Huang
- The
First Clinical College of Changsha Medical College, Changsha410219, China
| | - Jianshu Hu
- Department
of Pharmacology, University of Oxford, OxfordOX1 3QT, UK
| | - Qian Liu
- Center
for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
| | - Bing Song
- Center
for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
| | - Chun Hu
- Key
Laboratory of Structure-based Drug Design & Discovery (Ministry
of Education), School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang110016, China
| | - Lei Chen
- School of
Life Science and Technology, Key Laboratory of Developmental Genes
and Human Disease, Southeast University, Nanjing210096, China
| | - Yan Wang
- Center
for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
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175
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Machitani M, Takei J, Kaneko MK, Ueki S, Ohashi H, Watashi K, Kato Y, Masutomi K. Development of novel monoclonal antibodies against nsp12 of SARS-CoV-2. Virol J 2022; 19:213. [PMID: 36496472 PMCID: PMC9736705 DOI: 10.1186/s12985-022-01948-2] [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: 03/25/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused a global pandemic of coronavirus disease 19. Coronaviruses, including SARS-CoV-2, use RNA-dependent RNA polymerase (RdRP) for viral replication and transcription. Since RdRP is a promising therapeutic target for infection of SARS-CoV-2, it would be beneficial to develop new experimental tools for analysis of the RdRP reaction of SARS-CoV-2. Here, we succeeded to develop novel mouse monoclonal antibodies (mAbs) that recognize SARS-CoV-2 nsp12, catalytic subunit of the RdRP. These anti-nsp12 mAbs, RdMab-2, -13, and -20, specifically recognize SARS-CoV-2 nsp12 by western blotting analysis, while they exhibit less or no cross-reactivity to SARS-CoV nsp12. In addition, SARS-CoV-2 nsp12 was successfully immunoprecipitated using RdMab-2 from lysates of cells overexpressing SARS-CoV-2 nsp12. RdMab-2 was able to detect SARS-CoV-2 nsp12 transiently expressed in established culture cells such as HEK293T cells by indirect immunofluorescence technique. These novel mAbs against SARS-CoV-2 nsp12 are useful to elucidate the RdRP reaction of SARS-CoV-2 and biological cell response against it.
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Affiliation(s)
- Mitsuhiro Machitani
- grid.272242.30000 0001 2168 5385Division of Cancer Stem Cell, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045 Japan
| | - Junko Takei
- grid.69566.3a0000 0001 2248 6943Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi 980-8575 Japan
| | - Mika K. Kaneko
- grid.69566.3a0000 0001 2248 6943Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi 980-8575 Japan
| | - Saori Ueki
- grid.272242.30000 0001 2168 5385Division of Cancer Stem Cell, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045 Japan
| | - Hirofumi Ohashi
- grid.410795.e0000 0001 2220 1880Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo, 162-8640 Japan ,grid.410795.e0000 0001 2220 1880Department of Virology II, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo, 162-8640 Japan
| | - Koichi Watashi
- grid.410795.e0000 0001 2220 1880Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo, 162-8640 Japan ,grid.410795.e0000 0001 2220 1880Department of Virology II, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo, 162-8640 Japan
| | - Yukinari Kato
- grid.69566.3a0000 0001 2248 6943Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi 980-8575 Japan ,grid.69566.3a0000 0001 2248 6943Department of Molecular Pharmacology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi 980-8575 Japan
| | - Kenkichi Masutomi
- grid.272242.30000 0001 2168 5385Division of Cancer Stem Cell, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045 Japan
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176
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Kusano T, Nishino T, Okamoto K, Hille R, Nishino T. The mechanism and significance of the conversion of xanthine dehydrogenase to xanthine oxidase in mammalian secretory gland cells. Redox Biol 2022; 59:102573. [PMID: 36525890 PMCID: PMC9760657 DOI: 10.1016/j.redox.2022.102573] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
The conversion of xanthine dehydrogenase (XDH) to xanthine oxidase (XO) occurs only in mammalian species. In fresh bovine milk, the enzyme exists predominantly as the oxidase form, in contrast to various normal organs where it is found primarily as the dehydrogenase: the mechanism of conversion to the oxidase in milk remains obscure. A systematic search for the essential factors for conversion from XDH to XO has been performed within fresh bovine milk using the highly purified dehydrogenase form after removal endogenous oxidase form by fractionation analysis. We find that conversion to the oxidase form requires four components under air: lactoperoxidase (LPO), XDH, SCN-, and substrate hypoxanthine or xanthine; the contribution of sulfhydryl oxidase appears to be minor. Disulfide bond formation between Cys-535 and Cys-995 is principally involved in the conversion, consistent with the result obtained from previous work with transgenic mice. In vitro reconstitution of LPO and SCN- results in synergistic conversion of the dehydrogenase to the oxidase the presence of xanthine, indicating the conversion is autocatalytic. Milk from an LPO knockout mouse contains a significantly greater proportion of the dehydrogenase form of the enzyme, although some oxidase form is also present, indicating that LPO contributes principally to the conversion, but that sulfhydryl oxidase (SO) may also be involved to a minor extent. All the components XDH/LPO/SCN- are necessary to inhibit bacterial growth in the presence of xanthine through disulfide bond formation in bacterial protein(s) required for replication, as part of an innate immunity system in mammals. Human GTEx Data suggest that mRNA of XDH and LPO are highly co-expressed in the salivary gland, mammary gland, mucosa of the airway and lung alveoli, and we have confirmed these human GTEx Data experimentally in mice. We discuss the possible roles of these components in the propagation of SARS-CoV-2 in these human cell types.
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Affiliation(s)
- Teruo Kusano
- Department of Biochemistry and Molecular Biology, Nippon Medical School, 1-1-5, Sendagi, Bunkyo-Ku, Tokyo, Japan
| | - Tomoko Nishino
- Department of Biochemistry and Molecular Biology, Nippon Medical School, 1-1-5, Sendagi, Bunkyo-Ku, Tokyo, Japan
| | - Ken Okamoto
- Department of Biochemistry and Molecular Biology, Nippon Medical School, 1-1-5, Sendagi, Bunkyo-Ku, Tokyo, Japan
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, USA
| | - Takeshi Nishino
- Department of Biochemistry and Molecular Biology, Nippon Medical School, 1-1-5, Sendagi, Bunkyo-Ku, Tokyo, Japan.
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177
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Wang Z, Yang L, Song XQ. Oral GS-441524 derivatives: Next-generation inhibitors of SARS-CoV-2 RNA-dependent RNA polymerase. Front Immunol 2022; 13:1015355. [PMID: 36561747 PMCID: PMC9763260 DOI: 10.3389/fimmu.2022.1015355] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
GS-441524, an RNA-dependent RNA polymerase (RdRp) inhibitor, is a 1'-CN-substituted adenine C-nucleoside analog with broad-spectrum antiviral activity. However, the low oral bioavailability of GS-441524 poses a challenge to its anti-SARS-CoV-2 efficacy. Remdesivir, the intravenously administered version (version 1.0) of GS-441524, is the first FDA-approved agent for SARS-CoV-2 treatment. However, clinical trials have presented conflicting evidence on the value of remdesivir in COVID-19. Therefore, oral GS-441524 derivatives (VV116, ATV006, and GS-621763; version 2.0, targeting highly conserved viral RdRp) could be considered as game-changers in treating COVID-19 because oral administration has the potential to maximize clinical benefits, including decreased duration of COVID-19 and reduced post-acute sequelae of SARS-CoV-2 infection, as well as limited side effects such as hepatic accumulation. This review summarizes the current research related to the oral derivatives of GS-441524, and provides important insights into the potential factors underlying the controversial observations regarding the clinical efficacy of remdesivir; overall, it offers an effective launching pad for developing an oral version of GS-441524.
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Affiliation(s)
- Zhonglei Wang
- Key Laboratory of Green Natural Products and Pharmaceutical Intermediates in Colleges and Universities of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, China,School of Pharmaceutical Sciences, Tsinghua University, Beijing, China,*Correspondence: Zhonglei Wang, ; Liyan Yang, ; Xian-qing Song,
| | - Liyan Yang
- Shandong Provincial Key Laboratory of Laser Polarization and Information Technology, School of Physics and Physical Engineering, Qufu Normal University, Qufu, China,*Correspondence: Zhonglei Wang, ; Liyan Yang, ; Xian-qing Song,
| | - Xian-qing Song
- General Surgery Department, Ningbo Fourth Hospital, Xiangshan, China,*Correspondence: Zhonglei Wang, ; Liyan Yang, ; Xian-qing Song,
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178
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Lei S, Chen X, Wu J, Duan X, Men K. Small molecules in the treatment of COVID-19. Signal Transduct Target Ther 2022; 7:387. [PMID: 36464706 PMCID: PMC9719906 DOI: 10.1038/s41392-022-01249-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 12/11/2022] Open
Abstract
The outbreak of COVID-19 has become a global crisis, and brought severe disruptions to societies and economies. Until now, effective therapeutics against COVID-19 are in high demand. Along with our improved understanding of the structure, function, and pathogenic process of SARS-CoV-2, many small molecules with potential anti-COVID-19 effects have been developed. So far, several antiviral strategies were explored. Besides directly inhibition of viral proteins such as RdRp and Mpro, interference of host enzymes including ACE2 and proteases, and blocking relevant immunoregulatory pathways represented by JAK/STAT, BTK, NF-κB, and NLRP3 pathways, are regarded feasible in drug development. The development of small molecules to treat COVID-19 has been achieved by several strategies, including computer-aided lead compound design and screening, natural product discovery, drug repurposing, and combination therapy. Several small molecules representative by remdesivir and paxlovid have been proved or authorized emergency use in many countries. And many candidates have entered clinical-trial stage. Nevertheless, due to the epidemiological features and variability issues of SARS-CoV-2, it is necessary to continue exploring novel strategies against COVID-19. This review discusses the current findings in the development of small molecules for COVID-19 treatment. Moreover, their detailed mechanism of action, chemical structures, and preclinical and clinical efficacies are discussed.
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Affiliation(s)
- Sibei Lei
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
| | - Xiaohua Chen
- grid.54549.390000 0004 0369 4060Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072 China
| | - Jieping Wu
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
| | - Xingmei Duan
- grid.54549.390000 0004 0369 4060Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072 China
| | - Ke Men
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
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179
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Arumugam GS, Damodharan K, Doble M, Thennarasu S. Significant perspectives on various viral infections targeted antiviral drugs and vaccines including COVID-19 pandemicity. MOLECULAR BIOMEDICINE 2022; 3:21. [PMID: 35838929 PMCID: PMC9283561 DOI: 10.1186/s43556-022-00078-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 05/05/2022] [Indexed: 11/10/2022] Open
Abstract
A virus enters a living organism and recruits host metabolism to reproduce its own genome and proteins. The viral infections are intricate and cannot be completely removed through existing antiviral drugs. For example, the herpes, influenza, hepatitis and human immunodeficiency viruses are a few dreadful ones amongst them. Significant studies are needed to understand the viral entry and their growth in host cells to design effective antivirals. This review emphasizes the range of therapeutical antiviral drugs, inhibitors along with vaccines to fight against viral pathogens, especially for combating COVID-19. Moreover, we have provided the basic and in depth information about viral targets, drugs availability, their mechanisms of action, method of prevention of viral diseases and highlighted the significances of anticoagulants, convalescent plasma for COVID-19 treatment, scientific details of airborne transmission, characteristics of antiviral drug delivery using nanoparticles/carriers, nanoemulsions, nanogels, metal based nanoparticles, alike the future nanosystems through nanobubbles, nanofibers, nanodiamonds, nanotraps, nanorobots and eventually, the therapeutic applications of micro- and nanoparticulates, current status for clinical development against COVID-19 together with environmental implications of antivirals, gene therapy etc., which may be useful for repurposing and designing of novel antiviral drugs against various dreadful diseases, especially the SARS-CoV-2 and other associated variants.
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180
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Rani R, Long S, Pareek A, Dhaka P, Singh A, Kumar P, McInerney G, Tomar S. Multi-target direct-acting SARS-CoV-2 antivirals against the nucleotide-binding pockets of virus-specific proteins. Virology 2022; 577:1-15. [PMID: 36244310 PMCID: PMC9539459 DOI: 10.1016/j.virol.2022.08.008] [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] [Received: 06/24/2022] [Revised: 08/20/2022] [Accepted: 08/20/2022] [Indexed: 11/30/2022]
Abstract
The nucleotide-binding pockets (NBPs) in virus-specific proteins have proven to be the most successful antiviral targets for several viral diseases. Functionally important NBPs are found in various structural and non-structural proteins of SARS-CoV-2. In this study, the first successful multi-targeting attempt to identify effective antivirals has been made against NBPs in nsp12, nsp13, nsp14, nsp15, nsp16, and nucleocapsid (N) proteins of SARS-CoV-2. A structure-based drug repurposing in silico screening approach with ADME analysis identified small molecules targeting NBPs in SARS-CoV-2 proteins. Further, isothermal titration calorimetry (ITC) experiments validated the binding of top hit molecules to the purified N-protein. Importantly, cell-based antiviral assays revealed antiviral potency for INCB28060, darglitazone, and columbianadin with EC50 values 15.71 μM, 5.36 μM, and 22.52 μM, respectively. These effective antivirals targeting multiple proteins are envisioned to direct the development of antiviral therapy against SARS-CoV-2 and its emerging variants.
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Affiliation(s)
- Ruchi Rani
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Siwen Long
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Akshay Pareek
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Preeti Dhaka
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Ankur Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Gerald McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India.
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181
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Ma J, Deng Y, Zhang M, Yu J. The role of multi-omics in the diagnosis of COVID-19 and the prediction of new therapeutic targets. Virulence 2022; 13:1101-1110. [PMID: 35801633 PMCID: PMC9272836 DOI: 10.1080/21505594.2022.2092941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
The global pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing COVID-19, has led to more than 170 million confirmed cases in 223 countries and regions, claiming 3,872,457 lives. Some patients with COVID-19 have mild clinical symptoms despite severe respiratory failure, which greatly increases the difficulty of diagnosis and treatment. It is therefore necessary to identify biological characteristics of SARS-CoV-2, screen novel diagnostic and prognostic biomarkers, as well as to explore potential therapeutic targets for COVID-19. In this comprehensive review, we discuss the current published literature on COVID-19. We find that the comprehensive application of genomics, transcriptomics, proteomics and metabolomics is becoming increasingly important in the treatment of COVID-19. Multi-omics analysis platforms are expected to revolutionize the diagnosis and classification of COVID-19. This review aims to provide a reference for diagnosis, surveillance and clinical decision making related to COVID-19.
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Affiliation(s)
- Jianli Ma
- Department of Radiation Oncology, Shandong University Cancer Center, Jinan, Shandong Province, People's Republic of China
| | - Yuwei Deng
- Department of Breast Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province, People's Republic of China
| | - Minghui Zhang
- Department of Respiratory Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province, People's Republic of China
| | - Jinming Yu
- Department of Radiation Oncology, Shandong University Cancer Center, Jinan, Shandong Province, People's Republic of China
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182
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Ji X, Meng X, Zhu X, He Q, Cui Y. Research and development of Chinese anti-COVID-19 drugs. Acta Pharm Sin B 2022; 12:4271-4286. [PMID: 36119967 PMCID: PMC9472487 DOI: 10.1016/j.apsb.2022.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/06/2022] [Accepted: 08/18/2022] [Indexed: 12/14/2022] Open
Abstract
The outbreak and spread of coronavirus disease 2019 (COVID-19) highlighted the importance and urgency of the research and development of therapeutic drugs. Very early into the COVID-19 pandemic, China has begun developing drugs, with some notable progress. Herein, we summarizes the anti-COVID-19 drugs and promising drug candidates originally developed and researched in China. Furthermore, we discussed the developmental prospects, mechanisms of action, and advantages and disadvantages of the anti-COVID-19 drugs in development, with the aim to contribute to the rational use of drugs in COVID-19 treatment and more effective development of new drugs against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the variants. Neutralizing antibody is an effective approach to overcome COVID-19. However, drug resistance induced by rapid virus mutation will likely to challenge neutralizing antibodies. Taking into account current epidemic trends, small molecule drugs have a crucial role in fighting COVID-19 due to their significant advantage of convenient administration and affordable and broad-spectrum. Traditional Chinese medicines, including natural products and traditional Chinese medicine prescriptions, contribute to the treatment of COVID-19 due to their unique mechanism of action. Currently, the research and development of Chinese anti-COVID-19 drugs have led to some promising achievements, thus prompting us to expect even more rapidly available solutions.
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Affiliation(s)
- Xiwei Ji
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing 100034, China
| | - Xiangrui Meng
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China
| | - Xiao Zhu
- Department of Clinical Pharmacy and Pharmacy Administration, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Qingfeng He
- Department of Clinical Pharmacy and Pharmacy Administration, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Yimin Cui
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing 100034, China
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183
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Mun CS, Hui LY, Sing LC, Karunakaran R, Ravichandran V. Multi-targeted molecular docking, pharmacokinetics, and drug-likeness evaluation of coumarin based compounds targeting proteins involved in development of COVID-19. Saudi J Biol Sci 2022; 29:103458. [PMID: 36187455 PMCID: PMC9512525 DOI: 10.1016/j.sjbs.2022.103458] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 09/16/2022] [Accepted: 09/21/2022] [Indexed: 11/25/2022] Open
Abstract
COVID-19 is a progressing pandemic of coronavirus disease-2019, which had drowned the whole world in a deep sorrow sea. Uncountable deaths were extending the list of deaths every single day. The present research was aimed to study the multi-target interaction of coumarins against COVID-19 using molecular docking analysis. The structure of coumarin compounds was checked for ADME and Lipinski rule of five by using SwissADME, an online tool. SARS-CoV-2 proteins such as RdRp, PLpro, Mpro and spike protein were collected from the Protein Data Bank. The molecular docking study was performed in the PyRx tool, and the molecular interactions were visualised by Discovery Studio Visualizer. All the coumarin compounds used in the study were obeyed Lipinski’s rule of 5 without any violations. All the three designed derivatives of phenprocoumon, hymecromone, and psoralen were showed high binding affinity and prominent interactions with the drug target. The presence of –OH groups in the compound, His41, a catalytic dyad in Mpro, number of and the distance of hydrogen bond interactions with SARS-CoV-2 targets was accountable for the high binding attractions. The modified drug structures possess better binding efficacy towards at least three targets compared to their parent compounds. Further, molecular dynamic studies can be suggested to find the ligand–protein complex stability. The present study outcome reveals that the designed coumarins can be synthesised and examined as a potent inhibitory drug of SARS-CoV-2.
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Affiliation(s)
- Chan Sook Mun
- Pharmaceutical Chemistry Unit, Faculty of Pharmacy, AIMST University, Semeling 08100, Malaysia
| | - Lok Yong Hui
- Pharmaceutical Chemistry Unit, Faculty of Pharmacy, AIMST University, Semeling 08100, Malaysia
| | - Lai Cong Sing
- Pharmaceutical Chemistry Unit, Faculty of Pharmacy, AIMST University, Semeling 08100, Malaysia
| | - Rohini Karunakaran
- Unit of Biochemistry, Faculty of Medicine, AIMST University, Semeling 08100, Kedah, Malaysia.,Centre of Excellence for Biomaterial Science, AIMST University, Semeling 08100, Kedah, Malaysia
| | - Veerasamy Ravichandran
- Pharmaceutical Chemistry Unit, Faculty of Pharmacy, AIMST University, Semeling 08100, Malaysia.,Centre of Excellence for Biomaterial Science, AIMST University, Semeling 08100, Kedah, Malaysia.,Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India
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184
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Portilla-Martínez A, Ortiz-Flores M, Hidalgo I, Gonzalez-Ruiz C, Meaney E, Ceballos G, Nájera N. In silico evaluation of flavonoids as potential inhibitors of SARS-CoV-2 main nonstructural proteins (Nsps)—amentoflavone as a multitarget candidate. J Mol Model 2022; 28:404. [PMCID: PMC9707096 DOI: 10.1007/s00894-022-05391-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 11/11/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Andrés Portilla-Martínez
- Sección de Posgrado, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis Y Diaz Mirón S/N, Col Santo Tomás, 11340 Mexico City, Mexico
| | - Miguel Ortiz-Flores
- Sección de Posgrado, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis Y Diaz Mirón S/N, Col Santo Tomás, 11340 Mexico City, Mexico
| | - Isabel Hidalgo
- Laboratorio de Investigación en Inmunología Y Salud Pública, Facultad de Estudios Superiores Cuautitlán, Unidad de Investigación Multidisciplinaria Universidad Nacional Autónoma de México, Estado de México, Mexico City, Mexico
| | - Cristian Gonzalez-Ruiz
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Eduardo Meaney
- Sección de Posgrado, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis Y Diaz Mirón S/N, Col Santo Tomás, 11340 Mexico City, Mexico
| | - Guillermo Ceballos
- Sección de Posgrado, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis Y Diaz Mirón S/N, Col Santo Tomás, 11340 Mexico City, Mexico
| | - Nayelli Nájera
- Sección de Posgrado, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis Y Diaz Mirón S/N, Col Santo Tomás, 11340 Mexico City, Mexico
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185
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Sanusi ZK, Lobb KA. Insights into the Dynamics and Binding of Two Polyprotein Substrate Cleavage Points in the Context of the SARS-CoV-2 Main and Papain-like Proteases. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238251. [PMID: 36500348 PMCID: PMC9740519 DOI: 10.3390/molecules27238251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/25/2022] [Accepted: 11/03/2022] [Indexed: 11/29/2022]
Abstract
It is well known that vital enzymes in the replication process of the coronavirus are the SARS-CoV-2 PLpro and SARS-CoV-2 3CLpro, both of which are important targets in the search for anti-coronavirus agents. These two enzymes are responsible for cleavage at various polyprotein sites in the SARS-CoV-2 lifecycle. Herein, the dynamics of the polyprotein cleavage sequences for the boundary between non-structural proteins Nsp1 and Nsp2 (CS1) and between Nsp2 and Nsp3 (CS2) in complex with both the papain-like protein PLpro and the main protease 3CLpro were explored using computational methods. The post dynamics analysis reveals that CS1 and CS2 both have greater stability when complexed with PLpro. Of these two, greater stability is observed for the CS1-PLpro complex, while destabilization resulting in loss of CS2 from the PLpro active site is observed for CS2-PLpro, suggesting the rate of exchange by the papain-like protease is faster for CS2 compared to CS1. On the other hand, the 3CLpro main protease also reveals stability for CS1 suggesting that the main protease could also play a potential role in the cleavage at point CS1. However, destabilization occurs early in the simulation for the complex CLpro-CS2 suggesting a poor interaction and non-plausible protease cleavage of the polyprotein at CS2 by the main protease. These findings could be used as a guide in the development and design of potent COVID-19 antiviral inhibitors that mimic the CS1 cleavage site.
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Affiliation(s)
| | - Kevin Alan Lobb
- Department of Chemistry, Rhodes University, Makhanda 6140, South Africa
- Research Unit in Bioinformatics (RUBi), Rhodes University, Makhanda 6140, South Africa
- Correspondence:
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186
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Di Matteo F, Frumenzio G, Chandramouli B, Grottesi A, Emerson A, Musiani F. Computational Study of Helicase from SARS-CoV-2 in RNA-Free and Engaged Form. Int J Mol Sci 2022; 23:ijms232314721. [PMID: 36499049 PMCID: PMC9738952 DOI: 10.3390/ijms232314721] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/16/2022] [Accepted: 11/22/2022] [Indexed: 11/27/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the pandemic that broke out in 2020 and continues to be the cause of massive global upheaval. Coronaviruses are positive-strand RNA viruses with a genome of ~30 kb. The genome is replicated and transcribed by RNA-dependent RNA polymerase together with accessory factors. One of the latter is the protein helicase (NSP13), which is essential for viral replication. The recently solved helicase structure revealed a tertiary structure composed of five domains. Here, we investigated NSP13 from a structural point of view, comparing its RNA-free form with the RNA-engaged form by using atomistic molecular dynamics (MD) simulations at the microsecond timescale. Structural analyses revealed conformational changes that provide insights into the contribution of the different domains, identifying the residues responsible for domain-domain interactions in both observed forms. The RNA-free system appears to be more flexible than the RNA-engaged form. This result underlies the stabilizing role of the nucleic acid and the functional core role of these domains.
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Affiliation(s)
- Francesca Di Matteo
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy
| | - Giorgia Frumenzio
- Super Computing Applications and Innovation, Department HPC, CINECA, via Magnanelli 6/3, 40033 Casalecchio di Reno, Italy
| | - Balasubramanian Chandramouli
- Super Computing Applications and Innovation, Department HPC, CINECA, via Magnanelli 6/3, 40033 Casalecchio di Reno, Italy
| | | | - Andrew Emerson
- Super Computing Applications and Innovation, Department HPC, CINECA, via Magnanelli 6/3, 40033 Casalecchio di Reno, Italy
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy
- Correspondence:
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187
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Jade D, Alzahrani A, Critchley W, Ponnambalam S, Harrison MA. Identification of FDA-approved drugs against SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) through computational virtual screening. Struct Chem 2022; 34:1005-1019. [PMID: 36467260 PMCID: PMC9702953 DOI: 10.1007/s11224-022-02072-1] [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: 06/01/2022] [Accepted: 09/24/2022] [Indexed: 11/27/2022]
Abstract
The SARS-CoV-2 coronavirus is responsible for the COVID-19 outbreak, which overwhelmed millions of people worldwide; hence, there is an urgency to identify appropriate antiviral drugs. This study focuses on screening compounds that inhibit RNA-dependent RNA-polymerase (RdRp) essential for RNA synthesis required for replication of positive-strand RNA viruses. Computational screening against RdRp using Food and Drug Administration (FDA)-approved drugs identified ten prominent compounds with binding energies of more than - 10.00 kcal/mol, each a potential inhibitor of RdRp. These compounds' binding energy is comparable to known RdRp inhibitors remdesivir (IC50 = 10.09 μM, SI = 4.96) and molnupiravir (EC50 = 0.67 - 2.66 µM) and 0.32-2.03 µM). Remdesivir and molnupiravir have been tested in clinical trial and remain authorized for emergency use in the treatment of COVID-19. In docking simulations, selected compounds are bound to the substrate-binding pocket of RdRp and showed hydrophobic and hydrogen bond interaction. For molecular dynamics simulation, capmatinib, pralsetinib, ponatinib, and tedizolid phosphate were selected from the initial ten candidate compounds. MD simulation indicated that these compounds are stable at 50-ns MD simulation when bound to RdRp protein. The screen hit compounds, remdesivir, molnupiravir, and GS-441524, are bound in the substrate binding pocket with good binding-free energy. As a consequence, capmatinib, pralsetinib, ponatinib, and tedizolid phosphate are potential new inhibitors of RdRp protein with potential of limiting COVID-19 infection by blocking RNA synthesis. Supplementary Information The online version contains supplementary material available at 10.1007/s11224-022-02072-1.
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Affiliation(s)
- Dhananjay Jade
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | - Areej Alzahrani
- School of Molecular & Cellular Biology, University of Leeds, Leeds, UK
| | - William Critchley
- School of Molecular & Cellular Biology, University of Leeds, Leeds, UK
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188
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Henri J, Minder L, Mohanasundaram K, Dilly S, Goupil-Lamy A, Di Primo C, Slama Schwok A. Neuropeptides, New Ligands of SARS-CoV-2 Nucleoprotein, a Potential Link between Replication, Inflammation and Neurotransmission. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27228094. [PMID: 36432196 PMCID: PMC9698730 DOI: 10.3390/molecules27228094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022]
Abstract
This work identifies new ligands of the nucleoprotein N of SARS-CoV-2 by in silico screening, which used a new model of N, built from an Alphafold model refined by molecular dynamic simulations. The ligands were neuropeptides, such as substance P (1-7) and enkephalin, bound at a large site of the C-terminal or associated with the N-terminal β-sheet. The BA4 and BA5 Omicron variants of N also exhibited a large site as in wt N, and an increased flexibility of the BA5 variant, enabling substance P binding. The binding sites of some ligands deduced from modeling in wt N were assessed by mutation studies in surface plasmon resonance experiments. Dynamic light scattering showed that the ligands impeded RNA binding to N, which likely inhibited replication. We suggest that the physiological role of these neuropeptides in neurotransmission, pain and vasodilation for cholecystokinin and substance P could be altered by binding to N. We speculate that N may link between viral replication and multiple pathways leading to long COVID-19 symptoms. Therefore, N may constitute a "danger hub" that needs to be inhibited, even at high cost for the host. Antivirals targeted to N may therefore reduce the risk of brain fog and stroke, and improve patients' health.
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Affiliation(s)
- Julien Henri
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, UMR-CNRS 7238, Sorbonne Université, F-75005 Paris, France
| | - Laetitia Minder
- Institut Européen de Chimie et Biologie (IECB), CNRS, INSERM UAR 3033, US001, Univ. Bordeaux, F-33000 Bordeaux, France
| | - Kevin Mohanasundaram
- Saint Antoine Hospital, Centre de Recherche Saint Antoine, Sorbonne Université, Biology and Cancer Therapeutics, INSERM U938, F-75231 Paris, France
| | - Sébastien Dilly
- Saint Antoine Hospital, Centre de Recherche Saint Antoine, Sorbonne Université, Biology and Cancer Therapeutics, INSERM U938, F-75231 Paris, France
| | - Anne Goupil-Lamy
- Biovia, Dassault Systèmes, 10 Rue Marcel Dassault, CS40501, CEDEX, F-78946 Vélizy-Villacoublay, France
| | - Carmelo Di Primo
- CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, Univ. Bordeaux, F-33000 Bordeaux, France
| | - Anny Slama Schwok
- Saint Antoine Hospital, Centre de Recherche Saint Antoine, Sorbonne Université, Biology and Cancer Therapeutics, INSERM U938, F-75231 Paris, France
- Correspondence: or
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189
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Structural Homology-Based Drug Repurposing Approach for Targeting NSP12 SARS-CoV-2. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227732. [PMID: 36431833 PMCID: PMC9694939 DOI: 10.3390/molecules27227732] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/03/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2, also known as SARS-CoV-2, is the causative agent of the COVID-19 global pandemic. SARS-CoV-2 has a highly conserved non-structural protein 12 (NSP-12) involved in RNA-dependent RNA polymerase (RdRp) activity. For the identification of potential inhibitors for NSP-12, computational approaches such as the identification of homologous proteins that have been previously targeted by FDA-approved antivirals can be employed. Herein, homologous proteins of NSP-12 were retrieved from Protein DataBank (PDB) and the evolutionary conserved sequence and structure similarity of the active site of the RdRp domain of NSP-12 was characterized. The identified homologous structures of NSP-12 belonged to four viral families: Coronaviridae, Flaviviridae, Picornaviridae, and Caliciviridae, and shared evolutionary conserved relationships. The multiple sequences and structural alignment of homologous structures showed highly conserved amino acid residues that were located at the active site of the RdRp domain of NSP-12. The conserved active site of the RdRp domain of NSP-12 was evaluated for binding affinity with the FDA-approved antivirals, i.e., Sofosbuvir and Dasabuvir in a molecular docking study. The molecular docking of Sofosbuvir and Dasabuvir with the active site that contains conserved motifs (motif A-G) of the RdRp domain of NSP-12 revealed significant binding affinity. Furthermore, MD simulation also inferred the potency of Sofosbuvir and Dasabuvir. In conclusion, targeting the active site of the RdRp domain of NSP-12 with Dasabuvir and Sofosbuvir might reduce viral replication and pathogenicity and could be further studied for the treatment of SARS-CoV-2.
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190
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Linoleic acid binds to SARS-CoV-2 RdRp and represses replication of seasonal human coronavirus OC43. Sci Rep 2022; 12:19114. [PMID: 36352079 PMCID: PMC9645759 DOI: 10.1038/s41598-022-23880-9] [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] [Received: 03/24/2022] [Accepted: 11/07/2022] [Indexed: 11/10/2022] Open
Abstract
Fatty acids belong to a group of compounds already acknowledged for their broad antiviral efficacy. However, little is yet known about their effect on replication of human coronaviruses. To shed light on this subject, we first screened 15 fatty acids, three lipid-soluble vitamins, and cholesterol, on SARS-CoV-2 RdRp, and identified the four fatty acids with the highest RdRp inhibitory potential. Among them, linoleic acid was found to have the greatest interaction with SARS-CoV-2 RdRp, with its direct binding to the cavity formed by the RNA double helix and protein. Linoleic acid forms hydrophobic interactions with multiple residues, and at the same time forms electrostatic interactions including the hydrogen bond with Lys593 and Asp865. In line with these results, a dose-dependent inhibition of HCoV-OC43 replication in vitro was observed, additionally strengthened by data from in vivo study, which also confirmed anti-inflammatory potential of linoleic acid. Based on these results, we concluded that our study provides a new understanding of the antiviral properties of fatty acids against human coronaviruses including the SARS-CoV-2 strain. Particularly, they lays down a new prospect for linoleic acid's RdRp-inhibitory activity, as a candidate for further studies, which are warranted to corroborate the results presented here.
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191
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Xu X, Chen Y, Lu X, Zhang W, Fang W, Yuan L, Wang X. An update on inhibitors targeting RNA-dependent RNA polymerase for COVID-19 treatment: Promises and challenges. Biochem Pharmacol 2022; 205:115279. [PMID: 36209840 PMCID: PMC9535928 DOI: 10.1016/j.bcp.2022.115279] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/27/2022] [Accepted: 09/27/2022] [Indexed: 01/18/2023]
Abstract
The highly transmissible variants of SARS-CoV-2, the causative pathogen of the COVID-19 pandemic, bring new waves of infection worldwide. Identification of effective therapeutic drugs to combat the COVID-19 pandemic is an urgent global need. RNA-dependent RNA polymerase (RdRp), an essential enzyme for viral RNA replication, is the most promising target for antiviral drug research since it has no counterpart in human cells and shows the highest conservation across coronaviruses. This review summarizes recent progress in studies of RdRp inhibitors, focusing on interactions between these inhibitors and the enzyme complex, based on structural analysis, and their effectiveness. In addition, we propose new possible strategies to address the shortcomings of current inhibitors, which may guide the development of novel efficient inhibitors to combat COVID-19.
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Affiliation(s)
- Xiaoying Xu
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China.
| | - Yuheng Chen
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Xinyu Lu
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311402, China
| | - Wanlin Zhang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311402, China
| | - Wenxiu Fang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311402, China
| | - Luping Yuan
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311402, China
| | - Xiaoyan Wang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311402, China.
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192
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Gangadharan S, Ambrose JM, Rajajagadeesan A, Kullappan M, Patil S, Gandhamaneni SH, Veeraraghavan VP, Nakkella AK, Agarwal A, Jayaraman S, Surapaneni KM. Repurposing of potential antiviral drugs against RNA-dependent RNA polymerase of SARS-CoV-2 by computational approach. J Infect Public Health 2022; 15:1180-1191. [PMID: 36240528 PMCID: PMC9514006 DOI: 10.1016/j.jiph.2022.09.007] [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: 08/10/2022] [Revised: 09/16/2022] [Accepted: 09/20/2022] [Indexed: 01/18/2023] Open
Abstract
The high incidences of COVID-19 cases are believed to be associated with high transmissibility rates, which emphasizes the need for the discovery of evidence-based antiviral therapies for curing the disease. The rationale of repurposing existing classes of antiviral small molecule therapeutics against SARS-CoV-2 infection has been expected to accelerate the tedious and expensive drug development process. While Remdesivir has been recently approved to be the first treatment option for specific groups of COVID-19 patients, combinatory therapy with potential antiviral drugs may be necessary to enhance the efficacy in different populations. Hence, a comprehensive list of investigational antimicrobial drug compounds such as Favipiravir, Fidaxomicin, Galidesivir, GC376, Ribavirin, Rifabutin, and Umifenovir were computationally evaluated in this study. We performed in silico docking and molecular dynamics simulation on the selected small molecules against RNA-dependent RNA polymerase, which is one of the key target proteins of SARS-CoV-2, using AutoDock and GROMACS. Interestingly, our results revealed that the macrocyclic antibiotic, Fidaxomicin, possesses the highest binding affinity with the lowest energy value of -8.97 kcal/mol binding to the same active sites of RdRp. GC376, Rifabutin, Umifenovir and Remdesivir were identified as the next best compounds. Therefore, the above-mentioned compounds could be considered good leads for further preclinical and clinical experimentations as potentially efficient antiviral inhibitors for combination therapies against SARS-CoV-2.
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Affiliation(s)
- Sivakumar Gangadharan
- Department of Chemistry, Panimalar Engineering College, Varadharajapuram, Poonamallee, Chennai 600123, Tamil Nadu, India.
| | - Jenifer Mallavarpu Ambrose
- Department of Research, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Chennai 600123, Tamil Nadu, India.
| | - Anusha Rajajagadeesan
- Department of Biochemistry, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Chennai 600123, Tamil Nadu, India.
| | - Malathi Kullappan
- Department of Research, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Chennai 600123, Tamil Nadu, India.
| | - Shankargouda Patil
- College of Dental Medicine, Roseman University of Health Sciences, South Jordan, UTAH-84095, USA; Centre of Molecular Medicine and Diagnostics ( COMManD), Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, India.
| | - Sri Harshini Gandhamaneni
- Department of General Medicine, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Chennai 600123, Tamil Nadu, India.
| | - Vishnu Priya Veeraraghavan
- Centre of Molecular Medicine and Diagnostics ( COMManD), Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, India.
| | - Aruna Kumari Nakkella
- Department of Engineering Chemistry, Dr B R Ambedkar University, Etcherla, Srikakulam 532410, Andhra Pradesh, India.
| | - Alok Agarwal
- Department of Chemistry, Chinmaya Degree College, BHEL, Haridwar 249403, Uttarakhand, India.
| | - Selvaraj Jayaraman
- Centre of Molecular Medicine and Diagnostics ( COMManD), Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, India.
| | - Krishna Mohan Surapaneni
- Departments of Biochemistry, Molecular Virology, Research, Clinical Skills & Simulation, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai 600123, Tamil Nadu, India.
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193
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Trifan A, Gorgun D, Salim M, Li Z, Brace A, Zvyagin M, Ma H, Clyde A, Clark D, Hardy DJ, Burnley T, Huang L, McCalpin J, Emani M, Yoo H, Yin J, Tsaris A, Subbiah V, Raza T, Liu J, Trebesch N, Wells G, Mysore V, Gibbs T, Phillips J, Chennubhotla SC, Foster I, Stevens R, Anandkumar A, Vishwanath V, Stone JE, Tajkhorshid E, A. Harris S, Ramanathan A. Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action. THE INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS 2022; 36:603-623. [PMID: 38464362 PMCID: PMC10923581 DOI: 10.1177/10943420221113513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) replication transcription complex (RTC) is a multi-domain protein responsible for replicating and transcribing the viral mRNA inside a human cell. Attacking RTC function with pharmaceutical compounds is a pathway to treating COVID-19. Conventional tools, e.g., cryo-electron microscopy and all-atom molecular dynamics (AAMD), do not provide sufficiently high resolution or timescale to capture important dynamics of this molecular machine. Consequently, we develop an innovative workflow that bridges the gap between these resolutions, using mesoscale fluctuating finite element analysis (FFEA) continuum simulations and a hierarchy of AI-methods that continually learn and infer features for maintaining consistency between AAMD and FFEA simulations. We leverage a multi-site distributed workflow manager to orchestrate AI, FFEA, and AAMD jobs, providing optimal resource utilization across HPC centers. Our study provides unprecedented access to study the SARS-CoV-2 RTC machinery, while providing general capability for AI-enabled multi-resolution simulations at scale.
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Affiliation(s)
- Anda Trifan
- Argonne National Laboratory
- University of Illinois Urbana-Champaign
| | - Defne Gorgun
- Argonne National Laboratory
- University of Illinois Urbana-Champaign
| | | | | | | | | | | | - Austin Clyde
- Argonne National Laboratory
- University of Chicago
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Ian Foster
- Argonne National Laboratory
- University of Chicago
| | - Rick Stevens
- Argonne National Laboratory
- University of Chicago
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194
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Banerjee S, Baidya SK, Adhikari N, Ghosh B, Jha T. Glycyrrhizin as a promising kryptonite against SARS-CoV-2: Clinical, experimental, and theoretical evidences. J Mol Struct 2022; 1275:134642. [DOI: 10.1016/j.molstruc.2022.134642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 10/24/2022] [Accepted: 11/24/2022] [Indexed: 11/27/2022]
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195
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Nabati F, kamyabiamineh A, Kosari R, Ghasemi F, Seyedebrahimi S, Mohammadi S, Moradi M. Virtual screening based on the structure of more than 105 compounds against four key proteins of SARS-CoV-2: MPro, SRBD, RdRp, and PLpro. INFORMATICS IN MEDICINE UNLOCKED 2022; 35:101134. [PMID: 36406927 PMCID: PMC9652154 DOI: 10.1016/j.imu.2022.101134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/11/2022] [Accepted: 11/11/2022] [Indexed: 11/15/2022] Open
Abstract
Background SARS-CoV-2 initially originated in Wuhan (China) around December 2019, and spread all over the world. Currently, WHO (Word Health Organization) has licensed several vaccines for this viral infection. However, not everyone can be vaccinated. People with underlying health conditions that weaken their immune systems or those with severe allergies to some vaccine components, may not be able to be vaccinated. Moreover, no vaccination is 100% safe, and the emergence of new SARS-CoV-2 mutations may reduce the efficacy of immunizations. Therefore, it is urgent to develop effective drugs to protect people against this virus. Material and method We performed structure-based virtual screening (SBVS) of a library that was built from ChemDiv and PubChem databases against four SARS-CoV-2 target proteins: S-protein (spike), main protease (MPro), RNA-dependent RNA polymerase, and PLpro. A virtual screening study was performed using PyRx and AutoDock tools. Results Our results suggest that twenty-five top-ranked drugs with the highest energy binding as the potential inhibitors against four SARS-CoV-2 targets, relative to the reference molecules. Based on the energy binding, we suggest that these compounds could be used to produce effective anti-viral drugs against SARS-CoV-2. Conclusion The discovery of novel compounds for COVID-19 using computer-aided drug discovery tools requires knowledge of the structure of coronavirus and various target proteins of the virus. These compounds should be further assessed in experimental assays and clinical trials to validate their actual activity against the disease. These findings may contribute to the drug design studies against COVID-19.
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196
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Joshi C, Chaudhari A, Joshi C, Joshi M, Bagatharia S. Repurposing of the herbal formulations: molecular docking and molecular dynamics simulation studies to validate the efficacy of phytocompounds against SARS-CoV-2 proteins. J Biomol Struct Dyn 2022; 40:8405-8419. [PMID: 33988079 PMCID: PMC8127611 DOI: 10.1080/07391102.2021.1922095] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/26/2021] [Indexed: 12/15/2022]
Abstract
Herbal formulations mentioned in traditional medicinal texts were investigated for in silico effect against SARS-COV-2 proteins involved in various functions of a virus such as attachment, entry, replication, transcription, etc. To repurpose and validate polyherbal formulations, molecular docking was performed to study the interactions of more than 150 compounds from various formulations against the SARS-CoV-2 proteins. Molecular dynamics (MD) simulation was performed to evaluate the interaction of top scored ligands with the various receptor proteins. The docking results showed that Liquiritic acid, Liquorice acid, Terchebulin, Glabrolide, Casuarinin, Corilagin, Chebulagic acid, Neochebulinic acid, Daturataturin A, and Taraxerol were effective against SARS-COV-2 proteins with higher binding affinities with different proteins. Results of MD simulations validated the stability of ligands from potent formulations with various receptors of SARS-CoV-2. Binding free energy analysis suggested the favourable interactions of phytocompounds with the recpetors. Besides, in silico comparison of the various formulations determined that Pathyadi kwath, Sanjeevani vati, Yashtimadhu, Tribhuvan Keeratiras, and Septillin were more effective than Samshamni vati, AYUSH-64, and Trikatu. Polyherbal formulations having anti-COVID-19 potential can be used for the treatment with adequate monitoring. New formulations may also be developed for systematic trials based on ranking from these studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Chinmayi Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Armi Chaudhari
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
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197
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Indari O, Kumar Singh A, Tiwari D, Chandra Jha H, Nath Jha A. Deciphering antiviral efficacy of malaria box compounds against malaria exacerbating viral pathogens- Epstein Barr Virus and SARS-CoV-2, an in silico study. MEDICINE IN DRUG DISCOVERY 2022; 16:100146. [DOI: 10.1016/j.medidd.2022.100146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 08/18/2022] [Accepted: 09/04/2022] [Indexed: 11/10/2022] Open
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198
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Dey R, Samadder A, Nandi S. Exploring the Targets of Novel Corona Virus and Docking-based Screening of Potential Natural Inhibitors to Combat COVID-19. Curr Top Med Chem 2022; 22:2410-2434. [PMID: 36281864 DOI: 10.2174/1568026623666221020163831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 09/07/2022] [Accepted: 09/21/2022] [Indexed: 01/20/2023]
Abstract
There is a need to explore natural compounds against COVID-19 due to their multitargeted actions against various targets of nCoV. They act on multiple sites rather than single targets against several diseases. Thus, there is a possibility that natural resources can be repurposed to combat COVID-19. However, the biochemical mechanisms of these inhibitors were not known. To reveal the mode of anti-nCoV action, structure-based docking plays a major role. The present study is an attempt to explore various potential targets of SARS-CoV-2 and the structure-based screening of various potential natural inhibitors to combat the novel coronavirus.
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Affiliation(s)
- Rishita Dey
- Department of Zoology, Cytogenetics and Molecular Biology Lab., University of Kalyani, Kalyani, Nadia, 741235, India.,Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur, 244713, India
| | - Asmita Samadder
- Department of Zoology, Cytogenetics and Molecular Biology Lab., University of Kalyani, Kalyani, Nadia, 741235, India
| | - Sisir Nandi
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur, 244713, India
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199
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Peng S, Wang H, Wang Z, Wang Q. Progression of Antiviral Agents Targeting Viral Polymerases. Molecules 2022; 27:7370. [PMID: 36364196 PMCID: PMC9654062 DOI: 10.3390/molecules27217370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/19/2022] [Accepted: 10/20/2022] [Indexed: 08/08/2023] Open
Abstract
Viral DNA and RNA polymerases are two kinds of very important enzymes that synthesize the genetic materials of the virus itself, and they have become extremely favorable targets for the development of antiviral drugs because of their relatively conserved characteristics. There are many similarities in the structure and function of different viral polymerases, so inhibitors designed for a certain viral polymerase have acted as effective universal inhibitors on other types of viruses. The present review describes the development of classical antiviral drugs targeting polymerases, summarizes a variety of viral polymerase inhibitors from the perspective of chemically synthesized drugs and natural product drugs, describes novel approaches, and proposes promising development strategies for antiviral drugs.
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200
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Dagotto G, Ventura JD, Martinez DR, Anioke T, Chung BS, Siamatu M, Barrett J, Miller J, Schäfer A, Yu J, Tostanoski LH, Wagh K, Baric RS, Korber B, Barouch DH. Immunogenicity and protective efficacy of a rhesus adenoviral vaccine targeting conserved COVID-19 replication transcription complex. NPJ Vaccines 2022; 7:125. [PMID: 36302778 PMCID: PMC9610341 DOI: 10.1038/s41541-022-00553-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 10/11/2022] [Indexed: 11/08/2022] Open
Abstract
The COVID-19 pandemic marks the third coronavirus pandemic this century (SARS-CoV-1, MERS, SARS-CoV-2), emphasizing the need to identify and evaluate conserved immunogens for a pan-sarbecovirus vaccine. Here we investigate the potential utility of a T-cell vaccine strategy targeting conserved regions of the sarbecovirus proteome. We identified the most conserved regions of the sarbecovirus proteome as portions of the RNA-dependent RNA polymerase (RdRp) and Helicase proteins, both of which are part of the coronavirus replication transcription complex (RTC). Fitness constraints suggest that as SARS-CoV-2 continues to evolve these regions may better preserve cross-reactive potential of T-cell responses than Spike, Nucleocapsid, or Membrane proteins. We sought to determine if vaccine-elicited T-cell responses to the highly conserved regions of the RTC would reduce viral loads following challenge with SARS-CoV-2 in mice using a rhesus adenovirus serotype 52 (RhAd52) vector. The RhAd52.CoV.Consv vaccine generated robust cellular immunity in mice and led to significant reductions in viral loads in the nasal turbinates following challenge with a mouse-adapted SARS-CoV-2. These data suggest the potential utility of T-cell targeting of conserved regions for a pan-sarbecovirus vaccine.
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Affiliation(s)
- Gabriel Dagotto
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - John D Ventura
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - David R Martinez
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tochi Anioke
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Benjamin S Chung
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Mazuba Siamatu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Julia Barrett
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jessica Miller
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Lisa H Tostanoski
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Kshitij Wagh
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
- The New Mexico Consortium, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
- The New Mexico Consortium, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
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