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Zhao J, Huang Y, Liukang C, Yang R, Tang L, Sun L, Zhao Y, Zhang G. Dissecting infectious bronchitis virus-induced host shutoff at the translation level. J Virol 2024; 98:e0083024. [PMID: 38940559 DOI: 10.1128/jvi.00830-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 06/01/2024] [Indexed: 06/29/2024] Open
Abstract
Viruses have evolved a range of strategies to utilize or manipulate the host's cellular translational machinery for efficient infection, although the mechanisms by which infectious bronchitis virus (IBV) manipulates the host translation machinery remain unclear. In this study, we firstly demonstrate that IBV infection causes host shutoff, although viral protein synthesis is not affected. We then screened 23 viral proteins, and identified that more than one viral protein is responsible for IBV-induced host shutoff, the inhibitory effects of proteins Nsp15 were particularly pronounced. Ribosome profiling was used to draw the landscape of viral mRNA and cellular genes expression model, and the results showed that IBV mRNAs gradually dominated the cellular mRNA pool, the translation efficiency of the viral mRNAs was lower than the median efficiency (about 1) of cellular mRNAs. In the analysis of viral transcription and translation, higher densities of RNA sequencing (RNA-seq) and ribosome profiling (Ribo-seq) reads were observed for structural proteins and 5' untranslated regions, which conformed to the typical transcriptional characteristics of nested viruses. Translational halt events and the number of host genes increased significantly after viral infection. The translationally paused genes were enriched in translation, unfolded-protein-related response, and activation of immune response pathways. Immune- and inflammation-related mRNAs were inefficiently translated in infected cells, and IBV infection delayed the production of IFN-β and IFN-λ. Our results describe the translational landscape of IBV-infected cells and demonstrate new strategies by which IBV induces host gene shutoff to promote its replication. IMPORTANCE Infectious bronchitis virus (IBV) is a γ-coronavirus that causes huge economic losses to the poultry industry. Understanding how the virus manipulates cellular biological processes to facilitate its replication is critical for controlling viral infections. Here, we used Ribo-seq to determine how IBV infection remodels the host's biological processes and identified multiple viral proteins involved in host gene shutoff. Immune- and inflammation-related mRNAs were inefficiently translated, the translation halt of unfolded proteins and immune activation-related genes increased significantly, benefitting IBV replication. These data provide new insights into how IBV modulates its host's antiviral responses.
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Affiliation(s)
- Jing Zhao
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yahui Huang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Chengyin Liukang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ruihua Yang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Lihua Tang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Lu Sun
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ye Zhao
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Guozhong Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
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Ramachandran B, Nadeem A, Mohanprasanth A, Saravanan M. Prediction of deleterious non-synonymous SNPs of TMPRSS2 protein combined with Molecular Dynamics Simulations and free energy analysis to identify the potential peptide substrates against SARS-CoV-2. J Biomol Struct Dyn 2024:1-15. [PMID: 38592189 DOI: 10.1080/07391102.2024.2330710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 03/08/2024] [Indexed: 04/10/2024]
Abstract
Globally the SARS-CoV-2 viral infection demands for the new drugs, the TMPRSS2 target plays a vital role in facilitating the virus entry. The aim of the present study is to identify the potential peptide substrate from the Anti-viral database against TMPRSS2 of SARS-CoV-2. The compound screening and variation analysis were performed using molecular docking analysis and online tools such as PROVEAN and SNAP2 server, respectively. The re-docked crystal structure peptide substrate exhibits -128.151 kcal/mol whereas the RRKK peptide substrate shows -134.158 kcal/mol. Further, the selected compounds were proceeded with Molecular Dynamics Simulation, it explores the stability of the complex by revealing the hotspot residues (His296 and Ser441) were active for nucleophilic attack against TMPRSS2. The average Binding Free Energy values computed through MM/GBSA for RRKK, Camostat, and Crystal Structure were shown -69.9278 kcal/mol, -64.5983 kcal/mol, and -63.9755 kcal/mol, respectively against TMPRSS2. The 'rate of acylation' emerges as an indicator for RRKK's efficacy, it maintains the distance of 3.2 Å with Ser441 resembles, whilst its -NH backbone stabilizes at 2.5 Å 'Michaelis Complex' which leads to prevent the entry of SARS-CoV-2 to human cells. The sequence variation analysis explores that the V160 and G6 substitutions are essential to emphasize the uncover possibilities for the ongoing drug discovery research. Therefore, the identified peptide substrate found to be potent against SARS-CoV-2 and these results will be valuable for ongoing drug discovery research.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Balajee Ramachandran
- Structural and Computational Biology Lab, Department of Bioinformatics, Alagappa University, Science Block, Karaikudi, Tamil Nadu, India
- Department of Pharmacology, Physiology and Biophysics, Boston University School of Medicine, Boston, MA, USA
| | - Ahmed Nadeem
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Aruchamy Mohanprasanth
- AMR & Nanotherapeutics Lab, Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical, Sciences (SIMATS), Chennai, Tamil Nadu, India
| | - Muthupandian Saravanan
- AMR & Nanotherapeutics Lab, Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical, Sciences (SIMATS), Chennai, Tamil Nadu, India
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Eltayeb A, Al-Sarraj F, Alharbi M, Albiheyri R, Mattar E, Abu Zeid IM, Bouback TA, Bamagoos A, Aljohny BO, Uversky VN, Redwan EM. Overview of the SARS-CoV-2 nucleocapsid protein. Int J Biol Macromol 2024; 260:129523. [PMID: 38232879 DOI: 10.1016/j.ijbiomac.2024.129523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 01/12/2024] [Accepted: 01/13/2024] [Indexed: 01/19/2024]
Abstract
Since the emergence of SARS-CoV in 2003, researchers worldwide have been toiling away at deciphering this virus's biological intricacies. In line with other known coronaviruses, the nucleocapsid (N) protein is an important structural component of SARS-CoV. As a result, much emphasis has been placed on characterizing this protein. Independent research conducted by a variety of laboratories has clearly demonstrated the primary function of this protein, which is to encapsidate the viral genome. Furthermore, various accounts indicate that this particular protein disrupts diverse intracellular pathways. Such observations imply its vital role in regulating the virus as well. The opening segment of this review will expound upon these distinct characteristics succinctly exhibited by the N protein. Additionally, it has been suggested that the N protein possesses diagnostic and vaccine capabilities when dealing with SARS-CoV. In light of this fact, we will be reviewing some recent headway in the use cases for N protein toward clinical purposes within this article's concluding segments. This forward movement pertains to both developments of COVID-19-oriented therapeutic targets as well as diagnostic measures. The strides made by medical researchers offer encouragement, knowing they are heading toward a brighter future combating global pandemic situations such as these.
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Affiliation(s)
- Ahmed Eltayeb
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Faisal Al-Sarraj
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Mona Alharbi
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Raed Albiheyri
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ehab Mattar
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Isam M Abu Zeid
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, P.O. Box 80200, Jeddah, Saudi Arabia
| | - Thamer A Bouback
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, P.O. Box 80200, Jeddah, Saudi Arabia
| | - Atif Bamagoos
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Bassam O Aljohny
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
| | - Elrashdy M Redwan
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technology Applications, New Borg EL-Arab, 21934 Alexandria, Egypt.
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Yazdani B, Sirous H, Brogi S, Calderone V. Structure-Based High-Throughput Virtual Screening and Molecular Dynamics Simulation for the Discovery of Novel SARS-CoV-2 NSP3 Mac1 Domain Inhibitors. Viruses 2023; 15:2291. [PMID: 38140532 PMCID: PMC10747130 DOI: 10.3390/v15122291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/16/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
Since the emergence of SARS-CoV-2, many genetic variations within its genome have been identified, but only a few mutations have been found in nonstructural proteins (NSPs). Among this class of viral proteins, NSP3 is a multidomain protein with 16 different domains, and its largest domain is known as the macrodomain or Mac1 domain. In this study, we present a virtual screening campaign in which we computationally evaluated the NCI anticancer library against the NSP3 Mac1 domain, using Molegro Virtual Docker. The top hits with the best MolDock and Re-Rank scores were selected. The physicochemical analysis and drug-like potential of the top hits were analyzed using the SwissADME data server. The binding stability and affinity of the top NSC compounds against the NSP3 Mac1 domain were analyzed using molecular dynamics (MD) simulation, using Desmond software, and their interaction energies were analyzed using the MM/GBSA method. In particular, by applying subsequent computational filters, we identified 10 compounds as possible NSP3 Mac1 domain inhibitors. Among them, after the assessment of binding energies (ΔGbind) on the whole MD trajectories, we identified the four most interesting compounds that acted as strong binders of the NSP3 Mac1 domain (NSC-358078, NSC-287067, NSC-123472, and NSC-142843), and, remarkably, it could be further characterized for developing innovative antivirals against SARS-CoV-2.
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Affiliation(s)
- Behnaz Yazdani
- Bioscience Department, Faculty of Science and Technology (FCT), Universitat de Vic—Universitat Central de Catalunya (Uvic-UCC), 08500 Vic, Spain;
| | - Hajar Sirous
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan 81746-73461, Iran
| | - Simone Brogi
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan 81746-73461, Iran
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy;
| | - Vincenzo Calderone
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy;
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Mbatha LS, Akinyelu J, Chukwuma CI, Mokoena MP, Kudanga T. Current Trends and Prospects for Application of Green Synthesized Metal Nanoparticles in Cancer and COVID-19 Therapies. Viruses 2023; 15:741. [PMID: 36992450 PMCID: PMC10054370 DOI: 10.3390/v15030741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/02/2023] [Accepted: 03/07/2023] [Indexed: 03/16/2023] Open
Abstract
Cancer and COVID-19 have been deemed as world health concerns due to the millions of lives that they have claimed over the years. Extensive efforts have been made to develop sophisticated, site-specific, and safe strategies that can effectively diagnose, prevent, manage, and treat these diseases. These strategies involve the implementation of metal nanoparticles and metal oxides such as gold, silver, iron oxide, titanium oxide, zinc oxide, and copper oxide, formulated through nanotechnology as alternative anticancer or antiviral therapeutics or drug delivery systems. This review provides a perspective on metal nanoparticles and their potential application in cancer and COVID-19 treatments. The data of published studies were critically analysed to expose the potential therapeutic relevance of green synthesized metal nanoparticles in cancer and COVID-19. Although various research reports highlight the great potential of metal and metal oxide nanoparticles as alternative nanotherapeutics, issues of nanotoxicity, complex methods of preparation, biodegradability, and clearance are lingering challenges for the successful clinical application of the NPs. Thus, future innovations include fabricating metal nanoparticles with eco-friendly materials, tailor making them with optimal therapeutics for specific disease targeting, and in vitro and in vivo evaluation of safety, therapeutic efficiency, pharmacokinetics, and biodistribution.
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Affiliation(s)
- Londiwe Simphiwe Mbatha
- Department of Biotechnology and Food Science, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - Jude Akinyelu
- Department of Biochemistry, Federal University Oye-Ekiti, Private Mail Bag 373, Ekiti State 370111, Nigeria
| | - Chika Ifeanyi Chukwuma
- Centre for Quality of Health and Living, Faculty of Health and Environmental Sciences, Central University of Technology, Private Bag X20539, Bloemfontein 9301, South Africa
| | - Mduduzi Paul Mokoena
- Department of Pathology, Pre-Clinical Sciences Division, University of Limpopo, Private Bag X1106, Sovenga 0727, South Africa
| | - Tukayi Kudanga
- Department of Biotechnology and Food Science, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
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Chauhan A, Avti PK, Shekhar N, Prajapat M, Sarma P, Sangwan N, Singh J, Bhattacharyya A, Kumar S, Kaur H, Sharma S, Prakash A, Medhi B. An insight into the simulation directed understanding of the mechanism in SARS CoV-2 N-CTD, dimer integrity, and RNA-binding: Identifying potential antiviral inhibitors. J Biomol Struct Dyn 2022; 40:13912-13924. [PMID: 34751101 DOI: 10.1080/07391102.2021.1996463] [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
Coronavirus 2019 is a transmissible disease and has caused havoc throughout the world. The present study identifies the novel potential antiviral inhibitors against the nucleocapsid C-terminal domain that aids in RNA-binding and replication. A total of 485,629 compounds were screened, and MD was performed. The trajectory analysis (DCCM & PCA), structural integrity, and degree of compaction depicted the protein-ligand complex stability (PDB-PISA and Rgyr). Results obtained from screening shortlists 13 compounds possessing high Docking score. Further, seven compounds had a permissible RMSD limit (3 Å), with robust RMSF. Post-MD analysis of the top two compounds (204 and 502), DCCM & PCA analysis show a positive atomic displacements correlation among residues of active sites-dimer (Chain A and Chain B) & residual clustering. The ΔGint of RNA-bound (-83.5 kcal/mol) and drug-bound N-CTD-204 (-40.8 kcal/mol) and 502(-39.7 kcal/mol) as compared to Apo (-35.95 kcal/mol) suggests stabilization of protein, with less RNA-binding possibility. The Rgyr values depict the loss of compactness on RNA-binding when compared to the drug-bound N-CTD complex. Further, overlapping the protein complexes (0 ns and 100 ns) display significant changes in RMSD of the protein (204-2.07 Å and 502-1.89 Å) as compared to the Apo (1.72 Å) and RNA-bound form (1.76 Å), suggesting strong interaction for compound 204 as compared to 502. ADMET profiling indicates that these compounds can be used for further experiments (in vitro and pre-clinical). Compound 204 could be a promising candidate for targeting the N-protein-RNA assembly and viral replication.
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Affiliation(s)
- Arushi Chauhan
- Department of Biophysics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Pramod K Avti
- Department of Biophysics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Nishant Shekhar
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Manisha Prajapat
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Phulen Sarma
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Namrata Sangwan
- Department of Biophysics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Jitender Singh
- Department of Biophysics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Anusuya Bhattacharyya
- Department of Ophthalmology, Government Medical College and Hospital, Chandigarh, India
| | - Subodh Kumar
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Hardeep Kaur
- Department of Pediatrics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Saurabh Sharma
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Ajay Prakash
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Bikash Medhi
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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Lu J, Lu W, Jiang H, Yang C, Dong X. Molecular Docking and Dynamics of Phytochemicals From Chinese Herbs With SARS-CoV-2 RdRp. Nat Prod Commun 2022. [DOI: 10.1177/1934578x221105693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is causing coronavirus disease 2019 (COVID-19) pandemic. Ancient Chinese herbal formulas are effective for diseases caused by viral infection, and their effects on COVID-19 are currently being examined. To directly evaluate the role of Chinese herbs in inhibiting replication of SARS-CoV-2, we investigated how the phytochemicals from Chinese herbs interact with the viral RNA-dependent RNA polymerase (RdRP). Total 1025 compounds were screened, and then 181compounds were selected for molecular docking analysis. Four phytochemicals licorice glycoside E, diisooctyl phthalate, (-)-medicocarpin, and glycyroside showed good binding affinity with RdRp. The best complex licorice glycoside E/RdRp forms 3 hydrogen bonds, 4 hydrophobic interactions, 1 pair of Pi-cation/stacking, and 4 salt bridges. Furthermore, docking complexes licorice glycoside E/RdRp and diisooctyl phthalate/RdRp were optimized by molecular dynamics simulation to obtain the stable conformation. These studies indicate that they are promising as antivirals against SARS-CoV-2.
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Affiliation(s)
- Jingyao Lu
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, China
- The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine, Yangzhou, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Wenpeng Lu
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
| | - Houli Jiang
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
| | - Changshui Yang
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
| | - Xiaoyun Dong
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, China
- The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine, Yangzhou, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
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Role of Stress Granules in Suppressing Viral Replication by the Infectious Bronchitis Virus Endoribonuclease. J Virol 2022; 96:e0068622. [PMID: 35638780 DOI: 10.1128/jvi.00686-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Infectious bronchitis virus (IBV), a γ-coronavirus, causes the economically important poultry disease infectious bronchitis. Cellular stress response is an effective antiviral strategy that leads to stress granule (SG) formation. Previous studies suggested that SGs were involved in the antiviral activity of host cells to limit viral propagation. Here, we aimed to delineate the molecular mechanisms regulating the SG response to pathogenic IBV strain infection. We found that most chicken embryo kidney (CEK) cells formed no SGs during IBV infection and IBV replication inhibited arsenite-induced SG formation. This inhibition was not caused by changes in the integrity or abundance of SG proteins during infection. IBV nonstructural protein 15 (Nsp15) endoribonuclease activity suppressed SG formation. Regardless of whether Nsp15 was expressed alone, with recombinant viral infection with Newcastle disease virus as a vector, or with EndoU-deficient IBV, the Nsp15 endoribonuclease activity was the main factor inhibiting SG formation. Importantly, uridine-specific endoribonuclease (EndoU)-deficient IBV infection induced colocalization of IBV N protein/dsRNA and SG-associated protein TIA1 in infected cells. Additionally, overexpressing TIA1 in CEK cells suppressed IBV replication and may be a potential antiviral factor for impairing viral replication. These data provide a novel foundation for future investigations of the mechanisms by which coronavirus endoribonuclease activity affects viral replication. IMPORTANCE Endoribonuclease is conserved in coronaviruses and affects viral replication and pathogenicity. Infectious bronchitis virus (IBV), a γ-coronavirus, infects respiratory, renal, and reproductive systems, causing millions of dollars in lost revenue to the poultry industry worldwide annually. Mutating the viral endoribonuclease poly(U) resulted in SG formation, and TIA1 protein colocalized with the viral N protein and dsRNA, thus damaging IBV replication. These results suggest a new antiviral target design strategy for coronaviruses.
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Pramanik D, Pawar AB, Roy S, Singh JK. Mechanistic insights of key host proteins and potential repurposed inhibitors regulating SARS-CoV-2 pathway. J Comput Chem 2022; 43:1237-1250. [PMID: 35535951 PMCID: PMC9348233 DOI: 10.1002/jcc.26888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/03/2022] [Accepted: 04/22/2022] [Indexed: 12/16/2022]
Abstract
The emergence of pandemic situations originated from severe acute respiratory syndrome (SARS)‐CoV‐2 and its new variants created worldwide medical emergencies. Due to the non‐availability of efficient drugs and vaccines at these emergency hours, repurposing existing drugs can effectively treat patients critically infected by SARS‐CoV‐2. Finding a suitable repurposing drug with inhibitory efficacy to a host‐protein is challenging. A detailed mechanistic understanding of the kinetics, (dis)association pathways, key protein residues facilitating the entry–exit of the drugs with targets are fundamental in selecting these repurposed drugs. Keeping this target as the goal of the paper, the potential repurposing drugs, Nafamostat, Camostat, Silmitasertib, Valproic acid, and Zotatifin with host‐proteins HDAC2, CSK22, eIF4E2 are studied to elucidate energetics, kinetics, and dissociation pathways. From an ensemble of independent simulations, we observed the presence of single or multiple dissociation pathways with varying host‐proteins‐drug systems and quantitatively estimated the probability of unbinding through these specific pathways. We also explored the crucial gateway residues facilitating these dissociation mechanisms. Interestingly, the residues we obtained for HDAC2 and CSK22 are also involved in the catalytic activity. Our results demonstrate how these potential drugs interact with the host machinery and the specific target residues, showing involvement in the mechanism. Most of these drugs are in the preclinical phase, and some are already being used to treat severe COVID‐19 patients. Hence, the mechanistic insight presented in this study is envisaged to support further findings of clinical studies and eventually develop efficient inhibitors to treat SARS‐CoV‐2.
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Affiliation(s)
- Debabrata Pramanik
- Department of Chemical Engineering, Indian Institute of Technology Kanpur, Kanpur, India
| | | | - Sudip Roy
- Prescience Insilico Private Limited, Bangalore, India
| | - Jayant Kumar Singh
- Department of Chemical Engineering, Indian Institute of Technology Kanpur, Kanpur, India.,Prescience Insilico Private Limited, Bangalore, India
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Rudrapal M, Gogoi N, Chetia D, Khan J, Banwas S, Alshehri B, Alaidarous MA, Laddha UD, Khairnar SJ, Walode SG. Repurposing of Phytomedicine-Derived Bioactive Compounds with Promising Anti-SARS-CoV-2 Potential: Molecular Docking, MD Simulation and Drug-Likeness/ ADMET Studies. Saudi J Biol Sci 2021; 29:2432-2446. [PMID: 34924801 PMCID: PMC8667520 DOI: 10.1016/j.sjbs.2021.12.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 11/28/2021] [Accepted: 12/08/2021] [Indexed: 12/14/2022] Open
Abstract
In view of the potential of traditional plant-based remedies (or phytomedicines) in the management of COVID-19, the present investigation was aimed at finding novel anti-SARS-CoV-2 molecules by in silico screening of bioactive phytochemicals (database) using computational methods and drug repurposing approach. A total of 160 compounds belonging to various phytochemical classes (flavonoids, limonoids, saponins, triterpenoids, steroids etc.) were selected (as initial hits) and screened against three specific therapeutic targets (Mpro/3CLpro, PLpro and RdRp) of SARS-CoV-2 by docking, molecular dynamics simulation and drug-likeness/ADMET studies. From our studies, six phytochemicals were identified as notable ant-SARS-CoV-2 agents (best hit molecules) with promising inhibitory effects effective against protease (Mpro and PLpro) and polymerase (RdRp) enzymes. These compounds are namely, ginsenoside Rg2, saikosaponin A, somniferine, betulinic acid, soyasapogenol C and azadirachtin A. On the basis of binding modes and dynamics studies of protein–ligand intercations, ginsenoside Rg2, saikosaponin A, somniferine were found to be the most potent (in silico) inhibitors potentially active against Mpro, PLpro and RdRp, respectively. The present investigation can be directed towards further experimental studies in order to confirm the anti-SARS-CoV-2 efficacy along with toxicities of identified phytomolecules.
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Affiliation(s)
- Mithun Rudrapal
- Department of Pharmaceutical Chemistry, Rasiklal M. Dhariwal Institute of Pharmaceutical Education and Research, Chinchwad, Pune 411019, Maharashtra, India
| | - Neelutpal Gogoi
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh 786004, Assam, India
| | - Dipak Chetia
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh 786004, Assam, India
| | - Johra Khan
- Department of Pharmaceutical Chemistry, Rasiklal M. Dhariwal Institute of Pharmaceutical Education and Research, Chinchwad, Pune 411019, Maharashtra, India.,Health and Basic Sciences Research Center, Majmaah University, Majmaah 11952, Saudi Arabia
| | - Saeed Banwas
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia.,Health and Basic Sciences Research Center, Majmaah University, Majmaah 11952, Saudi Arabia.,Department of Biomedical Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Bader Alshehri
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia.,Health and Basic Sciences Research Center, Majmaah University, Majmaah 11952, Saudi Arabia
| | - Mohammed A Alaidarous
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia.,Health and Basic Sciences Research Center, Majmaah University, Majmaah 11952, Saudi Arabia
| | - Umesh D Laddha
- MET Institute of Pharmacy, Bhujbal Knowledge City, Adgaon, Nasik 422003, Maharashtra, India
| | - Shubham J Khairnar
- MET Institute of Pharmacy, Bhujbal Knowledge City, Adgaon, Nasik 422003, Maharashtra, India
| | - Sanjay G Walode
- Department of Pharmaceutical Chemistry, Rasiklal M. Dhariwal Institute of Pharmaceutical Education and Research, Chinchwad, Pune 411019, Maharashtra, India
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11
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Sharma DJ, Deb A, Sarma P, Mallick B, Bhattacharjee P. Comparative Safety and Efficacy of Remdesivir Versus Remdesivir Plus Convalescent Plasma Therapy (CPT) and the Effect of Timing of Initiation of Remdesivir in COVID-19 Patients: An Observational Study From North East India. Cureus 2021; 13:e19976. [PMID: 34984135 PMCID: PMC8715228 DOI: 10.7759/cureus.19976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2021] [Indexed: 12/24/2022] Open
Abstract
Introduction As per the COVID-19 treatment guidelines of India, remdesivir and convalescent plasma therapy (CPT) are indicated in moderate and severe patients. In this study, we have evaluated the comparative safety and efficacy of remdesivir versus remdesivir CPT combination and effect of early versus late initiation of remdesivir. Materials and methods A hospital-based observational study was conducted among hospitalized moderate and severe COVID-19 patients treated with either remdesivir and/or CPT as per national guidelines. Response to therapy was evaluated in terms of mortality, mechanical ventilation requirement, ICU requirement, and safety. Results and observations A total of 95 moderate and severe COVID-19 patients on remdesivir (n=35) or remdesivir + CPT combination (n=60) were included. Both the remdesivir and remdesivir + CPT groups were comparable in terms of baseline characteristics, however, proportion of patients with baseline serum creatinine >1.5 was higher in the remdesivir group. No difference was seen between both the groups in terms of mortality, mechanical ventilation requirement, ICU requirement, and safety parameters in the overall moderate and severe COVID-19 populations and when each of these severity categories (moderate and severe) were analyzed separately. Early initiation (<9 days from symptom onset) of remdesivir was associated with better treatment outcome in terms of mortality and requirement of ICU. Post-therapy shortness of breath and LFTs (liver function tests) elevation was more in the late initiation of remdesivir group, which may be due to the lack of efficacy and subsequent disease progression or a direct effect of the drug. The beneficial effect of remdesivir was maintained even after adjustment for important prognostic factors and baseline imbalances (age, sex, disease severity, CPT use, and serum creatinine level). Conclusions Early initiation of remdesivir was associated with clinical benefit in terms of mortality and mechanical ventilation requirement. However, addition of convalescent plasma therapy as an additional therapeutic modality to remdesivir was not found to be beneficial.
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12
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Khuntia BK, Sharma V, Qazi S, Das S, Sharma S, Raza K, Sharma G. Ayurvedic Medicinal Plants Against COVID-19: An In Silico Analysis. Nat Prod Commun 2021. [DOI: 10.1177/1934578x211056753] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Even after one and a half years since the outbreak of COVID-19, its complete and effective control is still far from being achieved despite vaccination drives, symptomatic management with available drugs, and wider lockdowns. This has inspired researchers to screen potential phytochemicals from medicinal plants against SARS-CoV-2, adopting a bio-informatics approach. The current study aimed to assess anti-viral activity of the phytochemicals derived from Ayurvedic medicinal plants against SARS-CoV-2 drug targets [3-chymotrypsin-like protease (3CLpro) and RNA dependent RNA polymerase (RdRp)] using validated in silico methods.3D Structures of 196 phytochemicals from three Ayurvedic plants were retrieved from PubChem and KNApSAcK databases and screened for Absorption Distribution Metabolism Excretion and Toxicity(ADMET) to predict drug-likeness. The phytochemicals were subjected to molecular docking and only three showed promise: Acetovanillonewith a binding affinity of −4.7Kcal/mol with RdRp and −4.1 Kcal/mol with 3CL pro; myrtenol with equivalent values of −4.3 Kcal/mol with RdRP and −3.2 Kcal/mol with 3CLpro; and nimbochalcin with equivalent values of −5.0Kcal/mol with RdRp and −4.9 Kcal/mol with 3CLpro. Molecular dynamics simulation (50ns) analysis was made of 3CLpro and RdRp using Autodock Vina 1.1.2 software and VMD software. After ADMET analysis, 78 phytochemicals were found suitable for molecular docking. Three, namely acetovanillone, myrtenol and nimbochalcin from Picrorhiza kurroa, Azadirachta indica and Cyperus rotundus,respectively,exhibited good binding affinity with 3CLproand RdRp of SARS-CoV-2. Interaction analysis, molecular dynamics simulations and MM-PBSA calculations were executed for two complexes, acetovanillone_RdRp and myrtenol_3CL pro.Acetovanillone_RdRpcomplex did not display any structural change after MD simulation as compared to myrtenol_3CL pro. The overall stability of acetovanillone_6NUR was 154.7 kJ/mol, and for myrtenol_1UJ1 90.5 kJ/mol. In silico analysis revealed that acetovanillone ( Picrorhiza kurroa) and myrtenol ( Cyperus rotundus) possess anti SARS-CoV-2 activity. Further studies are needed to validate their efficacy in biological models.
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Affiliation(s)
- Bharat Krushna Khuntia
- Center for Integrative Medicine & Research (CIMR), All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Vandna Sharma
- Center for Integrative Medicine & Research (CIMR), All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Sahar Qazi
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Soumi Das
- ICMR-National Institute of Pathology, New Delhi, India
| | - Shruti Sharma
- ICMR-National Institute of Pathology, New Delhi, India
| | - Khalid Raza
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Gautam Sharma
- Center for Integrative Medicine & Research (CIMR), All India Institute of Medical Sciences (AIIMS), New Delhi, India
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13
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Chittum JE, Sankaranarayanan NV, O’Hara CP, Desai UR. On the Selectivity of Heparan Sulfate Recognition by SARS-CoV-2 Spike Glycoprotein. ACS Med Chem Lett 2021; 12:1710-1717. [PMID: 34786180 PMCID: PMC8525342 DOI: 10.1021/acsmedchemlett.1c00343] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 10/05/2021] [Indexed: 12/22/2022] Open
Abstract
SARS-CoV-2 infects human cells through its surface spike glycoprotein (SgP), which relies on host cell surface heparan sulfate (HS) proteoglycans that facilitate interaction with the ACE2 receptor. Targeting this process could lead to inhibitors of early steps in viral entry. Screening a microarray of 24 HS oligosaccharides against recombinant S1 and receptor-binding domain (RBD) proteins led to identification of only eight sequences as potent antagonists; results that were supported by detailed dual-filter computational studies. Competitive studies using the HS microarray suggested almost equivalent importance of IdoA2S-GlcNS6S and GlcNS3S structures, which were supported by affinity studies. Exhaustive virtual screening on a library of >93 000 sequences led to a novel pharmacophore with at least two 3-O-sulfated GlcN residues that can engineer unique selectivity in recognizing the RBD. This work puts forward the key structural motif in HS that should lead to potent and selective HS or HS-like agents against SARS-CoV-2.
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Affiliation(s)
- John E. Chittum
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Nehru Viji Sankaranarayanan
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Connor P. O’Hara
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Umesh R. Desai
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
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14
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Sarma P, Bhattacharyya A, Prakash A, Kaur H, Prajapat M, Borah M, Kumar S, Bansal S, Sharma S, Kaur G, Kumar H, Sharma DJ, Das KK, Avti P, Medhi B. Yogic Neti-Kriya Using Povidone Iodine: Can it have a Preventive Role Against SARS-CoV-2 Infection Gateway? Indian J Otolaryngol Head Neck Surg 2021; 74:3186-3192. [PMID: 34692450 PMCID: PMC8520578 DOI: 10.1007/s12070-021-02885-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 09/18/2021] [Indexed: 12/29/2022] Open
Abstract
During this COVID-19 pandemic, except steroid, none of the therapeutic measures have showed any evidence of efficacy. Traditionally jala-neti using lukewarm salted water remains a yogic way of maintaining upper airway hygiene. Saline irrigation decreases the concentration of inflammatory mediators (e.g. histamine, leukotriene etc.) in nasal secretions, reduces the severity and frequency of sinusitis, reduce need of antibiotic therapy and restores competency of nasal mucosa. Jala-neti is an integral part of six cleansing techniques of yogic kriyas practised in India since thousands of years. Jala-neti can clean the upper airways, prevents colonization of infectious agents, removes foreign bodies, prevents stasis of mucous and subsequently enhances the drainage of paranasal sinuses and maintain health. Regular practice of Jala neti improves nasal symptoms and overall health status of patients with sinusitis. Jala-neti sample can even be used for COVID-19 diagnosis. Povidone iodine (PVP-I) has been utilized as a time tested antimicrobial agent with broad spectrum coverage against wide range of bacteria and viruses. Anti-SARS-CoV-2 action of PVP-I was seen at a concentration as low as 0.45%. PVP-I is generally well tolerated upto 5%, however nasal ciliotoxicity is reported at this concentration, however, this toxicity is not reported with lower concentrations(1.25% and 0.5%). So, theoretically, by using neti-kriya with povidone iodine (0.5–1%) as irrigation solution can combine and enhance the protection against COVID-19 and this can be an important armor in the fight against COVID-19. However, this hypothesis needs to be validated in real life clinical trial scenario before implementing.
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Affiliation(s)
- Phulen Sarma
- Department of Pharmacology, PGIMER, Chandigarh, Pin 160012 India
| | - Anusuya Bhattacharyya
- Department of Ophthalmology, Government Medical College and Hospital, Sector 32, Chandigarh, India
| | - Ajay Prakash
- Department of Pharmacology, PGIMER, Chandigarh, Pin 160012 India
| | - Hardeep Kaur
- Department of Pharmacology, PGIMER, Chandigarh, Pin 160012 India
| | - Manisha Prajapat
- Department of Pharmacology, PGIMER, Chandigarh, Pin 160012 India
| | - Mukundam Borah
- Department of Pharmacology, Gauhati Medical College and Hospital, Guwahati, Assam India
| | - Subodh Kumar
- Department of Pharmacology, PGIMER, Chandigarh, Pin 160012 India
| | - Seema Bansal
- Department of Pharmacology, PGIMER, Chandigarh, Pin 160012 India
| | - Saurabh Sharma
- Department of Pharmacology, PGIMER, Chandigarh, Pin 160012 India
| | - Gurjeet Kaur
- Department of Pharmacology, PGIMER, Chandigarh, Pin 160012 India
| | - Harish Kumar
- Department of Pharmacology, PGIMER, Chandigarh, Pin 160012 India
| | - Dibya Jyoti Sharma
- Department of Internal Medicine, Silchar Medical College and Hospital, Silchar, Assam India
| | - Karuna Kumar Das
- Department of Anaesthesiology, Assam Medical College and Hospital, Dibrugarh, Assam India
| | - Pramod Avti
- Department of Biophysics, PGIMER, Chandigarh, India
| | - Bikash Medhi
- Department of Pharmacology, PGIMER, Chandigarh, Pin 160012 India
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15
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Qazi S, Das S, Khuntia BK, Sharma V, Sharma S, Sharma G, Raza K. In Silico Molecular Docking and Molecular Dynamic Simulation Analysis of Phytochemicals From Indian Foods as Potential Inhibitors of SARS-CoV-2 RdRp and 3CLpro. Nat Prod Commun 2021. [DOI: 10.1177/1934578x211031707] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
With the current pandemic of the novel coronavirus disease 2019 (COVID-19) in hand, researchers around the globe are dexterously working to find the best suitable drug candidates and overcome vaccination-related challenges, to achieve efficient control over the second surge of COVID-19. The medical consultants time and again have been reiterating the need to abide by the precautionary steps to prevent the spread of the coronavirus by maintaining social distancing when outside, sanitizing hands regularly, and wearing masks and gloves. They also suggest taking a good and hygienic meal so as to boost immunity. Indians have an inborn nature of using natural spices, food, and medicines in their daily lives. Indian researchers have paid heed to deploy compounds from natural sources to explore potential antiviral agents against COVID-19 as the chances of acquiring side effects are perceived as less, and the efficacy of phytochemicals from medicinal plants is sometimes greater when compared to their synthetic counterparts. In the present study, we performed an in silico molecular docking and molecular dynamic simulation analysis of screened phytochemicals from a comprehensive list of Ayurvedic herbs/functional foods that are present in natural food products against key receptor proteins of severe acute respiratory syndrome coronavirus 2. We found that Aegle marmelos, Vetiveria zizanoides, Moringaolifera, and Punica granatum have antiviral potential to prevent coronavirus infection in the populace.
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Affiliation(s)
- Sahar Qazi
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Soumi Das
- ICMR-National Institute of Pathology, New Delhi, India
| | - Bharat Krushna Khuntia
- Center for Integrative Medicine and Research (CIMR), All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Vandna Sharma
- Center for Integrative Medicine and Research (CIMR), All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Shruti Sharma
- ICMR-National Institute of Pathology, New Delhi, India
| | - Gautam Sharma
- Center for Integrative Medicine and Research (CIMR), All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Khalid Raza
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
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16
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Kaur H, Sarma P, Bhattacharyya A, Sharma S, Chhimpa N, Prajapat M, Prakash A, Kumar S, Singh A, Singh R, Avti P, Thota P, Medhi B. Efficacy and safety of dihydroorotate dehydrogenase (DHODH) inhibitors "leflunomide" and "teriflunomide" in Covid-19: A narrative review. Eur J Pharmacol 2021; 906:174233. [PMID: 34111397 PMCID: PMC8180448 DOI: 10.1016/j.ejphar.2021.174233] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 05/30/2021] [Accepted: 06/02/2021] [Indexed: 01/12/2023]
Abstract
Dihydroorotate dehydrogenase (DHODH) is rate-limiting enzyme in biosynthesis of pyrimidone which catalyzes the oxidation of dihydro-orotate to orotate. Orotate is utilized in the biosynthesis of uridine-monophosphate. DHODH inhibitors have shown promise as antiviral agent against Cytomegalovirus, Ebola, Influenza, Epstein Barr and Picornavirus. Anti-SARS-CoV-2 action of DHODH inhibitors are also coming up. In this review, we have reviewed the safety and efficacy of approved DHODH inhibitors (leflunomide and teriflunomide) against COVID-19. In target-centered in silico studies, leflunomide showed favorable binding to active site of MPro and spike: ACE2 interface. In artificial-intelligence/machine-learning based studies, leflunomide was among the top 50 ligands targeting spike: ACE2 interaction. Leflunomide is also found to interact with differentially regulated pathways [identified by KEGG (Kyoto Encyclopedia of Genes and Genomes) and reactome pathway analysis of host transcriptome data] in cogena based drug-repurposing studies. Based on GSEA (gene set enrichment analysis), leflunomide was found to target pathways enriched in COVID-19. In vitro, both leflunomide (EC50 41.49 ± 8.8 μmol/L) and teriflunomide (EC50 26 μmol/L) showed SARS-CoV-2 inhibition. In clinical studies, leflunomide showed significant benefit in terms of decreasing the duration of viral shredding, duration of hospital stay and severity of infection. However, no advantage was seen while combining leflunomide and IFN alpha-2a among patients with prolonged post symptomatic viral shredding. Common adverse effects of leflunomide were hyperlipidemia, leucopenia, neutropenia and liver-function alteration. Leflunomide/teriflunomide may serve as an agent of importance to achieve faster virological clearance in COVID-19, however, findings needs to be validated in bigger sized placebo controlled studies.
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Affiliation(s)
- Hardeep Kaur
- Department of Pharmacology, PGIMER, Chandigarh, India
| | - Phulen Sarma
- Department of Pharmacology, PGIMER, Chandigarh, India
| | | | | | | | | | - Ajay Prakash
- Department of Pharmacology, PGIMER, Chandigarh, India
| | - Subodh Kumar
- Department of Pharmacology, PGIMER, Chandigarh, India
| | | | - Rahul Singh
- Department of Pharmacology, PGIMER, Chandigarh, India
| | - Pramod Avti
- Department of Biophysics, PGIMER, Chandigarh, India
| | - Prasad Thota
- Department of Pharmacology, PGIMER, Chandigarh, India
| | - Bikash Medhi
- Department of Pharmacology, PGIMER, Chandigarh, India.
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17
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Prajapat M, Handa V, Sarma P, Prakash A, Kaur H, Sharma S, Bhattacharyya A, Kumar S, Sharma AR, Avti P, Medhi B. Update on geographical variation and distribution of SARS-nCoV-2: A systematic review. Indian J Pharmacol 2021; 53:310-316. [PMID: 34414910 PMCID: PMC8411960 DOI: 10.4103/ijp.ijp_483_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Knowledge of a new mutant strain of SARS-coronavirus (CoV-2) is enormously essential to identify a targeted drug and for the development of the vaccine. In this article, we systematically reviewed the different mutation strains (variant of concern [VOC] and variant of interest [VOI]) which were found in different countries such as the UK, Singapore, China, Germany, Vietnam, Western Africa, Dublin, Ireland, Brazil, Iran, Italy, France, America, and Philippines. We searched four literature databases (PubMed, EMBASE, NATURE, and Willey online library) with suitable keywords and the time filter was November 2019 to June 16, 2021. To understand the worldwide spread of variants of SARS-CoV-2, we included a total of 27 articles of case reports, clinical and observational studies in the systematic review. However, these variants mostly spread because of their ability to increase transmission, virulence, and escape immunity. So, in this paper is we found mutated strains of SARS-CoV-2 like VOCs that are found in different regions across the globe are ALPHA strain in the U.K, BETA strain in South Africa, GAMMA strain in Brazil, Gamma and Beta strains in European Countries, and some VOIs like Theta variant in the Philippines.
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Affiliation(s)
- Manisha Prajapat
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Vrishbhanu Handa
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Phulen Sarma
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Ajay Prakash
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Hardeep Kaur
- Department of Paediatrics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Saurabh Sharma
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Anusuya Bhattacharyya
- Department of Ophthalmology, Government Medical College and Hospital, Chandigarh, India
| | - Subodh Kumar
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Amit Raj Sharma
- Department of Neurology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Pramod Avti
- Department of Biophysics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Bikash Medhi
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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18
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Wu M, Ma L, Xue L, Zhu Q, Zhou S, Dai J, Yan W, Zhang J, Wang S. Co-expression of the SARS-CoV-2 entry molecules ACE2 and TMPRSS2 in human ovaries: Identification of cell types and trends with age. Genomics 2021; 113:3449-3460. [PMID: 34418496 PMCID: PMC8372464 DOI: 10.1016/j.ygeno.2021.08.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 08/02/2021] [Accepted: 08/14/2021] [Indexed: 01/29/2023]
Abstract
The high rate of SARS-CoV-2 infection poses a serious threat to public health. Previous studies have suggested that SARS-CoV-2 can infect human ovary, the core organ of the female reproductive system. However, it remains unclear which type of ovarian cells are easily infected by SARS-CoV-2 and whether ovarian infectivity differs from puberty to menopause. In this study, public datasets containing bulk and single-cell RNA-Seq data derived from ovarian tissues were analyzed to demonstrate the mRNA expression and protein distribution of the two key entry receptors for SARS-CoV-2—angiotensin-converting enzyme 2 (ACE2) and type II transmembrane serine protease (TMPRSS2). Furthermore, an immunohistochemical study of ACE2 and TMPRSS2 in human ovaries of different ages was conducted. Differentially expressed gene (DEG) analysis of ovaries of different ages and with varying ovarian reserves was conducted to explore the potential functions of ACE2 and TMPRSS2 in the ovary. The analysis of the public datasets indicated that the co-expression of ACE2 and TMPRSS2 was observed mostly in oocytes and partially in granulosa cells. However, no marked difference was observed in ACE2 or TMPRSS2 expression between young and old ovaries and ovaries with low and high reserves. Correspondingly, ACE2 and TMPRSS2 were detected in the human ovarian cortex and medulla, especially in oocytes of different stages, with no observed variations in their expression level in ovaries of different ages, which was consistent with the results of bioinformatic analyses. Remarkably, DEG analysis showed that a series of viral infection-related pathways were more enriched in ACE2-positive ovarian cells than in ACE2-negative ovarian cells, suggesting that SARS-CoV-2 may potentially target specific ovarian cells and affect ovarian function. However, further fundamental and clinical research is still needed to monitor the process of SARS-CoV-2 entry into ovarian cells and the long-term effects of SARS-CoV-2 infection on the ovarian function in recovered females.
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Affiliation(s)
- Meng Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lingwei Ma
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Liru Xue
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qingqing Zhu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Su Zhou
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jun Dai
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wei Yan
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jinjin Zhang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Shixuan Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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19
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Hanan N, Doud RL, Park IW, Jones HP, Mathew SO. The Many Faces of Innate Immunity in SARS-CoV-2 Infection. Vaccines (Basel) 2021; 9:vaccines9060596. [PMID: 34199761 PMCID: PMC8228170 DOI: 10.3390/vaccines9060596] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/19/2021] [Accepted: 06/01/2021] [Indexed: 12/15/2022] Open
Abstract
The innate immune system is important for initial antiviral response. SARS-CoV-2 can result in overactivity or suppression of the innate immune system. A dysregulated immune response is associated with poor outcomes; with patients having significant Neutrophil-to-Lymphocyte ratios (NLR) due to neutrophilia alongside lymphopenia. Elevated interleukin (IL)-6 and IL-8 leads to overactivity and is a prominent feature of severe COVID-19 patients. IL-6 can result in lymphopenia; where COVID-19 patients typically have significantly altered lymphocyte subsets. IL-8 attracts neutrophils; which may play a significant role in lung tissue damage with the formation of neutrophil extracellular traps leading to cytokine storm or acute respiratory distress syndrome. Several factors like pre-existing co-morbidities, genetic risks, viral pathogenicity, and therapeutic efficacy act as important modifiers of SARS-CoV-2 risks for disease through an interplay with innate host inflammatory responses. In this review, we discuss the role of the innate immune system at play with other important modifiers in SARS-CoV-2 infection.
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Affiliation(s)
- Nicholas Hanan
- Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; (N.H.); (R.L.D.J.); (I.-W.P.); (H.P.J.)
| | - Ronnie L. Doud
- Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; (N.H.); (R.L.D.J.); (I.-W.P.); (H.P.J.)
| | - In-Woo Park
- Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; (N.H.); (R.L.D.J.); (I.-W.P.); (H.P.J.)
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Harlan P. Jones
- Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; (N.H.); (R.L.D.J.); (I.-W.P.); (H.P.J.)
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Stephen O. Mathew
- Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; (N.H.); (R.L.D.J.); (I.-W.P.); (H.P.J.)
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
- Correspondence: ; Tel.: +1-817-735-5407
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20
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Peele KA, Kumar V, Parate S, Srirama K, Lee KW, Venkateswarulu TC. Insilico drug repurposing using FDA approved drugs against Membrane protein of SARS-CoV-2. J Pharm Sci 2021; 110:2346-2354. [PMID: 33684397 PMCID: PMC7934671 DOI: 10.1016/j.xphs.2021.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The novel coronavirus (SARS-CoV-2) outbreak has started taking away the millions of lives worldwide. Identification of known and approved drugs against novel coronavirus disease (COVID-19) seems to be an urgent need for the repurposing of the existing drugs. So, here we examined a safe strategy of using approved drugs of SuperDRUG2 database against modeled membrane protein (M-protein) of SARS-CoV-2 which is essential for virus assembly by using molecular docking-based virtual screening. A total of 3639 drugs from SuperDRUG2 database and additionally 14 potential drugs reported against COVID-19 proteins were selected. Molecular docking analyses revealed that nine drugs can bind the active site of M-protein with desirable molecular interactions. We therefore applied molecular dynamics simulations and binding free energy calculation using MM-PBSA to analyze the stability of the compounds. The complexes of M-protein with the selected drugs were simulated for 50 ns and ranked according to their binding free energies. The binding mode of the drugs with M-protein was analyzed and it was observed that Colchicine, Remdesivir, Bafilomycin A1 from COVID-19 suggested drugs and Temozolomide from SuperDRUG2 database displayed desirable molecular interactions and higher binding affinity towards M-protein. Interestingly, Colchicine was found as the top most binder among tested drugs against M-protein. We therefore additionally identified four Colchicine derivatives which can bind efficiently with M-protein and have better pharmacokinetic properties. We recommend that these drugs can be tested further through in vitro studies against SARS-CoV-2 M-protein.
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Affiliation(s)
- K Abraham Peele
- Department of Bio-Technology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, 522213, Andhra Pradesh, India
| | - Vikas Kumar
- Division of Life Science, Department of Bio & Medical Big Data (BK4 Program), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea
| | - Shraddha Parate
- Division of Applied Life Sciences, Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Krupanidhi Srirama
- Department of Bio-Technology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, 522213, Andhra Pradesh, India
| | - Keun Woo Lee
- Division of Life Science, Department of Bio & Medical Big Data (BK4 Program), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea.
| | - T C Venkateswarulu
- Department of Bio-Technology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, 522213, Andhra Pradesh, India.
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21
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Chauhan A, Avti P, Shekhar N, Prajapat M, Sarma P, Bhattacharyya A, Kumar S, Kaur H, Prakash A, Medhi B. Structural and conformational analysis of SARS CoV 2 N-CTD revealing monomeric and dimeric active sites during the RNA-binding and stabilization: Insights towards potential inhibitors for N-CTD. Comput Biol Med 2021; 134:104495. [PMID: 34022485 PMCID: PMC8123409 DOI: 10.1016/j.compbiomed.2021.104495] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/11/2021] [Accepted: 05/11/2021] [Indexed: 11/29/2022]
Abstract
The advent of SARS-CoV-2 has become a universal health issue with no appropriate cure available to date. The coronavirus nucleocapsid (N) protein combines viral genomic RNA into a ribonucleoprotein and protects the viral genome from the host's nucleases. Structurally, the N protein comprises two independent domains: the N-terminal domain (NTD) for RNA-binding and C-terminal domain (CTD) involved in RNA-binding, protein dimerization, and nucleocapsid stabilization. The present study explains the structural aspects associated with the involvement of nucleocapsid C-terminal domain in the subunit assembly that helps the RNA binding and further stabilizing the virus assembly by protecting RNA from the hosts exonucleases degradation. The molecular dynamics (MD) simulations of the N-CTD and RNA complex suggests two active sites (site I: a monomer) and (site II: a dimer) with structural stability (RMSD: ~2 Å), Cα fluctuations (RMSF: ~3 Å) and strong protein-ligand interactions were estimated through the SiteMap module of Schrodinger. Virtual screening of 2456 FDA-approved drugs using structure-based docking identified top two leads distinctively against Site-I (monomer): Ceftaroline fosamil (MM-GBSA = -47.12 kcal/mol) and Cefoperazone (-45.84 kcal/mol); and against Site-II (dimer): Boceprevir, (an antiviral protease inhibitor, -106.78 kcal/mol) and Ceftaroline fosamil (-99.55 kcal/mol). The DCCM and PCA of drugs Ceftaroline fosamil (PC1+PC2 = 71.9%) and Boceprevir (PC1 +PC2 = 61.6%) show significant correlated residue motions which suggests highly induced conformational changes in the N-CTD dimer. Therefore, we propose N-CTD as a druggable target with two active binding sites (monomer and dimer) involved in specific RNA binding and stability. The RNA binding site with Ceftaroline fosamil binding can prevent viral assembly and can act as an antiviral for coronavirus.
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Affiliation(s)
- Arushi Chauhan
- Department of Biophysics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Pramod Avti
- Department of Biophysics, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
| | - Nishant Shekhar
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Manisha Prajapat
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Phulen Sarma
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | | | - Subodh Kumar
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Hardeep Kaur
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Ajay Prakash
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Bikash Medhi
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
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22
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Avti P, Chauhan A, Shekhar N, Prajapat M, Sarma P, Kaur H, Bhattacharyya A, Kumar S, Prakash A, Sharma S, Medhi B. Computational basis of SARS-CoV 2 main protease inhibition: an insight from molecular dynamics simulation based findings. J Biomol Struct Dyn 2021; 40:8894-8904. [PMID: 33998950 PMCID: PMC8127165 DOI: 10.1080/07391102.2021.1922310] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is caused by newly discovered severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2). One of the striking targets amongst all the proteins in coronavirus is the main protease (Mpro), as it plays vital biological roles in replication and maturation of the virus, and hence the potential target. The aim of this study is to repurpose the Food and Drug Administration (FDA) approved molecules via computer-aided drug designing against Mpro (PDB ID: 6Y2F) of SARS CoV-2 due to its high x-ray resolution of 1.95 Å as compared to other published Mprostructures. High Through Virtual Screening (HTVS) of 2456 FDA approved drugs using structure-based docking were analyzed. Molecular Dynamics simulations were performed to check the overall structural stability (RMSD), Cα fluctuations (RMSF) and protein-ligand interactions. Further, trajectory analysis was performed to assess the binding quality by exploiting the protein-residue motion cross correlation (DCCM) and binding free energy (MM/GBSA). Tenofovir, an antiretroviral for HIV-proteases and Terlipressin, a vasoconstrictor show stable RMSD, RMSF, better MM/GBSA with good cross correlation as compared to the Apo and O6K. Moreover, the results show concurrence with Nelfinavir, Lopinavir and Ritonavir which have shown significant inhibition in in vitro studies. Therefore, we conclude that Tenofovir and Terlipresssin might also show protease inhibition but are still open to clinical validation in case of SARS-CoV 2 treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pramod Avti
- Department of Biophysics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Arushi Chauhan
- Department of Biophysics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Nishant Shekhar
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Manisha Prajapat
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Phulen Sarma
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Hardeep Kaur
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | | | - Subodh Kumar
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Ajay Prakash
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Saurabh Sharma
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Bikash Medhi
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India,CONTACT Bikash Medhi Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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23
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Koulgi S, Jani V, Uppuladinne V. N. M, Sonavane U, Joshi R. Natural plant products as potential inhibitors of RNA dependent RNA polymerase of Severe Acute Respiratory Syndrome Coronavirus-2. PLoS One 2021; 16:e0251801. [PMID: 33984041 PMCID: PMC8118514 DOI: 10.1371/journal.pone.0251801] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 05/03/2021] [Indexed: 01/18/2023] Open
Abstract
Drug repurposing studies targeting inhibition of RNA dependent RNA polymerase (RdRP) of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) have exhibited the potential effect of small molecules. In the present work a detailed interaction study between the phytochemicals from Indian medicinal plants and the RdRP of SARS-CoV-2 has been performed. The top four phytochemicals obtained through molecular docking were, swertiapuniside, cordifolide A, sitoindoside IX, and amarogentin belonging to Swertia chirayita, Tinospora cordifolia and Withania somnifera. These ligands bound to the RdRP were further studied using molecular dynamics simulations. The principal component analysis of these systems showed significant conformational changes in the finger and thumb subdomain of the RdRP. Hydrogen bonding, salt-bridge and water mediated interactions supported by MM-GBSA free energy of binding revealed strong binding of cordifolide A and sitoindoside IX to RdRP. The ligand-interacting residues belonged to either of the seven conserved motifs of the RdRP. These residues were polar and charged amino acids, namely, ARG 553, ARG 555, ASP 618, ASP 760, ASP 761, GLU 811, and SER 814. The glycosidic moieties of the phytochemicals were observed to form favourable interactions with these residues. Hence, these phytochemicals may hold the potential to act as RdRP inhibitors owing to their stability in binding to the druggable site.
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Affiliation(s)
- Shruti Koulgi
- High Performance Computing—Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Pune, India
| | - Vinod Jani
- High Performance Computing—Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Pune, India
| | | | - Uddhavesh Sonavane
- High Performance Computing—Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Pune, India
| | - Rajendra Joshi
- High Performance Computing—Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Pune, India
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24
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Kumar SU, Priya NM, Nithya SR, Kannan P, Jain N, Kumar DT, Magesh R, Younes S, Zayed H, Doss CGP. A review of novel coronavirus disease (COVID-19): based on genomic structure, phylogeny, current shreds of evidence, candidate vaccines, and drug repurposing. 3 Biotech 2021; 11:198. [PMID: 33816047 PMCID: PMC8003899 DOI: 10.1007/s13205-021-02749-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 03/16/2021] [Indexed: 12/15/2022] Open
Abstract
Coronavirus disease (COVID-19) pandemic is instigated by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of March 13, 2021, more than 118.9 million cases were infected with COVID-19 worldwide. SARS-CoV-2 is a positive-sense single-stranded RNA beta-CoV. Most COVID-19 infected individuals recover within 1-3 weeks. Nevertheless, approximately 5% of patients develop acute respiratory distress syndrome and other systemic complications, leading to death. Structural genetic analyses of SARS-CoV-2 have shown genomic resemblances but a low evolutionary correlation to SARS-CoV-1 responsible for the 2002-2004 outbreak. The S glycoprotein is critical for cell adhesion and the entrance of the virus into the host. The process of cell entry uses the cellular receptor named angiotensin-converting enzyme 2. Recent evidence proposed that the CD147 as a SARS-CoV-2's potential receptor. The viral genome is mainly held by two non-structural proteins (NSPs), ORF1a and ORF1ab, along with structural proteins. Although NSPs are conserved among the βCoVs, mutations in NSP2 and NSP3 may play critical roles in transmitting the virus and cell tropism. To date, no specific/targeted anti-viral treatments exist. Notably, more than 50 COVID-19 candidate vaccines in clinical trials, and a few being administered. Preventive precautions are the primary strategy to limit the viral load transmission and spread, emphasizing the urgent need for developing significant drug targets and vaccines against COVID-19. This review provides a cumulative overview of the genomic structure, transmission, phylogeny of SARS-CoV-2 from Indian clusters, treatment options, updated discoveries, and future standpoints for COVID-19. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02749-0.
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Affiliation(s)
- S. Udhaya Kumar
- Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology, Tamil Nadu, Vellore, 632 014 India
| | - N. Madhana Priya
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Tamil Nadu, Porur, Chennai, 600116 India
| | - S. R. Nithya
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Tamil Nadu, Porur, Chennai, 600116 India
| | - Priyanka Kannan
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Tamil Nadu, Porur, Chennai, 600116 India
| | - Nikita Jain
- Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology, Tamil Nadu, Vellore, 632 014 India
| | - D. Thirumal Kumar
- Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology, Tamil Nadu, Vellore, 632 014 India
- Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, 602105 India
| | - R. Magesh
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Tamil Nadu, Porur, Chennai, 600116 India
| | - Salma Younes
- Department of Biomedical Sciences, College of Health and Sciences, QU Health, Qatar University, Doha, Qatar
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, QU Health, Qatar University, Doha, Qatar
| | - C. George Priya Doss
- Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology, Tamil Nadu, Vellore, 632 014 India
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25
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Ballesteros N, Muñoz M, Patiño LH, Hernández C, González-Casabianca F, Carroll I, Santos-Vega M, Cascante J, Angel A, Feged-Rivadeneira A, Palma-Cuero M, Flórez C, Gomez S, van de Guchte A, Khan Z, Dutta J, Obla A, Alshammary HA, Gonzalez-Reiche AS, Hernandez MM, Sordillo EM, Simon V, van Bakel H, Paniz-Mondolfi AE, Ramírez JD. Deciphering the introduction and transmission of SARS-CoV-2 in the Colombian Amazon Basin. PLoS Negl Trop Dis 2021; 15:e0009327. [PMID: 33857136 PMCID: PMC8078805 DOI: 10.1371/journal.pntd.0009327] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/27/2021] [Accepted: 03/24/2021] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND The SARS-CoV-2 pandemic has forced health authorities across the world to take important decisions to curtail its spread. Genomic epidemiology has emerged as a valuable tool to understand introductions and spread of the virus in a specific geographic location. METHODOLOGY/PRINCIPAL FINDINGS Here, we report the sequences of 59 SARS-CoV-2 samples from inhabitants of the Colombian Amazonas department. The viral genomes were distributed in two robust clusters within the distinct GISAID clades GH and G. Spatial-temporal analyses revealed two independent introductions of SARS-CoV-2 in the region, one around April 1, 2020 associated with a local transmission, and one around April 2, 2020 associated with other South American genomes (Uruguay and Brazil). We also identified ten lineages circulating in the Amazonas department including the P.1 variant of concern (VOC). CONCLUSIONS/SIGNIFICANCE This study represents the first genomic epidemiology investigation of SARS-CoV-2 in one of the territories with the highest report of indigenous communities of the country. Such findings are essential to decipher viral transmission, inform on global spread and to direct implementation of infection prevention and control measures for these vulnerable populations, especially, due to the recent circulation of one of the variants of concern (P.1) associated with major transmissibility and possible reinfections.
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Affiliation(s)
- Nathalia Ballesteros
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Luz Helena Patiño
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Carolina Hernández
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Felipe González-Casabianca
- Gestión y desarrollo urbanos, Facultad de Estudios Internacionales, Políticos y Urbanos, Universidad del Rosario, Bogotá, Colombia
| | - Iván Carroll
- Facultad de Ingeniería, Universidad de Los Andes, Bogotá, Colombia
| | - Mauricio Santos-Vega
- Grupo de biología matemática y computacional, Departamento de Ingeniería Biomédica, Universidad de los Andes, Bogotá, Colombia
| | - Jaime Cascante
- Grupo de biología matemática y computacional, Departamento de Ingeniería Biomédica, Universidad de los Andes, Bogotá, Colombia
| | - Andrés Angel
- Departamento de Matemáticas, Universidad de Los Andes, Bogotá, Colombia
| | - Alejandro Feged-Rivadeneira
- Gestión y desarrollo urbanos, Facultad de Estudios Internacionales, Políticos y Urbanos, Universidad del Rosario, Bogotá, Colombia
| | - Mónica Palma-Cuero
- Laboratorio de Salud Púbica Departamental de Amazonas, Leticia, Colombia
| | | | | | - Adriana van de Guchte
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Zenab Khan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Jayeeta Dutta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Ajay Obla
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Hala Alejel Alshammary
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Ana S. Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Matthew M. Hernandez
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Emilia Mia Sordillo
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Alberto E. Paniz-Mondolfi
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
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Synowiec A, Szczepański A, Barreto-Duran E, Lie LK, Pyrc K. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): a Systemic Infection. Clin Microbiol Rev 2021; 34:e00133-20. [PMID: 33441314 PMCID: PMC7849242 DOI: 10.1128/cmr.00133-20] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
To date, seven identified coronaviruses (CoVs) have been found to infect humans; of these, three highly pathogenic variants have emerged in the 21st century. The newest member of this group, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first detected at the end of 2019 in Hubei province, China. Since then, this novel coronavirus has spread worldwide, causing a pandemic; the respiratory disease caused by the virus is called coronavirus disease 2019 (COVID-19). The clinical presentation ranges from asymptomatic to mild respiratory tract infections and influenza-like illness to severe disease with accompanying lung injury, multiorgan failure, and death. Although the lungs are believed to be the site at which SARS-CoV-2 replicates, infected patients often report other symptoms, suggesting the involvement of the gastrointestinal tract, heart, cardiovascular system, kidneys, and other organs; therefore, the following question arises: is COVID-19 a respiratory or systemic disease? This review aims to summarize existing data on the replication of SARS-CoV-2 in different tissues in both patients and ex vivo models.
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Affiliation(s)
- Aleksandra Synowiec
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Artur Szczepański
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Emilia Barreto-Duran
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Laurensius Kevin Lie
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Krzysztof Pyrc
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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27
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Coronavirus Endoribonuclease Ensures Efficient Viral Replication and Prevents Protein Kinase R Activation. J Virol 2021; 95:JVI.02103-20. [PMID: 33361429 PMCID: PMC8092692 DOI: 10.1128/jvi.02103-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Coronavirus (CoV) nsp15 is an endoribonuclease conserved throughout the CoV family. The enzymatic activity and crystal structure of infectious bronchitis virus (IBV) nsp15 are undefined, and the protein's role in replication remains unclear. We verified the uridylate-specific endoribonuclease (EndoU) activity of IBV and found that the EndoU active sites were located in the C-terminus of nsp15 and included His223, His238, Lys278 and Tyr334. We further constructed an infectious clone of the IBV-rSD strain (rSD-wild-type [WT]) and EndoU-deficient IBVs by changing the codon for the EndoU catalytic residues to alanine. Both the rSD-WT and EndoU-deficient viruses propagated efficiently in embryonated chicken eggs. Conversely, EndoU-deficient viral propagation was severely impaired in chicken embryonic kidney cells, which was reflected in the lower viral mRNA accumulation and protein synthesis. After infecting chickens with the parental rSD-WT strain and EndoU-deficient viruses, the EndoU-deficient-virus-infected chickens presented reduced mortality, tissue injury and viral shedding.IMPORTANCE Coronaviruses can emerge from animal reservoirs into naive host species to cause pandemic respiratory and gastrointestinal diseases with significant mortality in humans and domestic animals. Infectious bronchitis virus (IBV), a γ-coronavirus, infects respiratory, renal and reproductive systems, causing millions of dollars in lost revenue worldwide annually. Mutating the viral endoribonuclease resulted in an attenuated virus and prevented protein kinase R activation. Therefore, EndoU activity is a virulence factor in IBV infections, thus providing an approach for generating live-attenuated vaccine candidates for emerging coronaviruses.
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Koulgi S, Jani V, V N MU, Sonavane U, Joshi R. Structural insight into the binding interactions of NTPs and nucleotide analogues to RNA dependent RNA polymerase of SARS-CoV-2. J Biomol Struct Dyn 2021; 40:7230-7244. [PMID: 33682633 DOI: 10.1080/07391102.2021.1894985] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
RNA dependent RNA polymerase (RdRP) from positive-stranded RNA viruses has always been a hot target for designing of new drugs. Major class of drugs that are targeted against RdRP are nucleotide analogues. Extensive docking and molecular dynamics study describing the binding of natural nucleotides (NTPs) and its analogues leading to significant structural variation in the RdRP has been presented here. RdRP simulations in its apo, NTP-bound, and analogue-bound form have been performed. Nucleotide analogues included in this study were, favipiravir, galidesivir, lamivudine, ribavirin, remdesivir and sofosbuvir. The conformational flexibility of the RdRP molecule has been explored using principal component (PCA) and Markov state modeling (MSM) analysis. PCA inferred the presence of correlated motions among the conserved motifs of RdRP. Inter-domain distances between the finger and thumb subdomain flanking the nascent RNA template entry site sampled open and closed conformations. The ligand and template binding motifs F and G showed negatively correlated motions. K551, R553, and R555, a part of motif F appear to form strong interactions with the ligand molecules. R836, a primer binding residue was observed to strongly bind to the analogues. MSM analysis helped to extract statistically distinct conformations explored by the RdRP. Ensemble docking of the ligands on the Markov states also suggested the involvement of the above residues in ligand interactions. Markov states obtained clearly demarcated the open/closed conformations of the template entry site. These observations on residues from the conserved motifs involved in binding to the ligands may provide an insight into designing new inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shruti Koulgi
- High Performance Computing-Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchawati, Pashan, Pune, India
| | - Vinod Jani
- High Performance Computing-Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchawati, Pashan, Pune, India
| | - Mallikarjunachari Uppuladinne V N
- High Performance Computing-Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchawati, Pashan, Pune, India
| | - Uddhavesh Sonavane
- High Performance Computing-Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchawati, Pashan, Pune, India
| | - Rajendra Joshi
- High Performance Computing-Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchawati, Pashan, Pune, India
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Mapping major SARS-CoV-2 drug targets and assessment of druggability using computational fragment screening: Identification of an allosteric small-molecule binding site on the Nsp13 helicase. PLoS One 2021; 16:e0246181. [PMID: 33596235 PMCID: PMC7888625 DOI: 10.1371/journal.pone.0246181] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/14/2021] [Indexed: 01/18/2023] Open
Abstract
The 2019 emergence of, SARS-CoV-2 has tragically taken an immense toll on human life and far reaching impacts on society. There is a need to identify effective antivirals with diverse mechanisms of action in order to accelerate preclinical development. This study focused on five of the most established drug target proteins for direct acting small molecule antivirals: Nsp5 Main Protease, Nsp12 RNA-dependent RNA polymerase, Nsp13 Helicase, Nsp16 2'-O methyltransferase and the S2 subunit of the Spike protein. A workflow of solvent mapping and free energy calculations was used to identify and characterize favorable small-molecule binding sites for an aromatic pharmacophore (benzene). After identifying the most favorable sites, calculated ligand efficiencies were compared utilizing computational fragment screening. The most favorable sites overall were located on Nsp12 and Nsp16, whereas the most favorable sites for Nsp13 and S2 Spike had comparatively lower ligand efficiencies relative to Nsp12 and Nsp16. Utilizing fragment screening on numerous possible sites on Nsp13 helicase, we identified a favorable allosteric site on the N-terminal zinc binding domain (ZBD) that may be amenable to virtual or biophysical fragment screening efforts. Recent structural studies of the Nsp12:Nsp13 replication-transcription complex experimentally corroborates ligand binding at this site, which is revealed to be a functional Nsp8:Nsp13 protein-protein interaction site in the complex. Detailed structural analysis of Nsp13 ZBD conformations show the role of induced-fit flexibility in this ligand binding site and identify which conformational states are associated with efficient ligand binding. We hope that this map of over 200 possible small-molecule binding sites for these drug targets may be of use for ongoing discovery, design, and drug repurposing efforts. This information may be used to prioritize screening efforts or aid in the process of deciphering how a screening hit may bind to a specific target protein.
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Sarkar PK, Das Mukhopadhyay C. Ayurvedic metal nanoparticles could be novel antiviral agents against SARS-CoV-2. INTERNATIONAL NANO LETTERS 2021; 11:197-203. [PMID: 33425283 PMCID: PMC7786161 DOI: 10.1007/s40089-020-00323-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/21/2020] [Indexed: 12/20/2022]
Abstract
PURPOSE OF REVIEW The pandemic COVID-19 has affected more than seventy million people globally. The whole world is eagerly waiting for an effective antiviral therapy to combat COVID-19, but it is yet to get. The emergence of COVID-19 makes imperative the need for safe and potent antiviral drugs. Many metal nanoparticles exhibit significant antiviral potential against many viral diseases. The Ayurvedic system of medicine is the treasure of many metal nanoparticulate drugs termed as Bhasma. RECENT FINDINGS Gold, silver, copper, zinc and iron oxide nanoparticles are effective against coronavirus. A possible mechanism of action of the metal nanoparticles against coronavirus is a disruption of outer layers of coronavirus. Swarna Bhasma, Rajata Bhasma, Tamra Bhasma and Yashada Bhasma are recommended for COVID-19 treatment due to the ability to reduce the plasma interleukins, interferons and TNFα levels. SUMMARY The Ayurvedic Bhasma preparations are unique metal nanoparticles. These metal nanoparticles are safe, stable in solid state and are having excellent biological activities. Ayurvedic metal nanoparticles, Swarna Bhasma, Rajata Bhasma, Tamra Bhasma and Yashada Bhasma could be proved as novel antiviral agents against SARS-CoV-2 for their anti-inflammatory, immunomodulatory, antiviral and adjuvant activities.
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Affiliation(s)
- Prasanta Kumar Sarkar
- Department of Rasashastra, J. B. Roy State Ayurvedic Medical College and Hospital West Bengal University of Health Sciences, Kolkata, 700004 West Bengal India
| | - Chitrangada Das Mukhopadhyay
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science Technology, Shibpur, Howrah, 711103 West Bengal India
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Kaur H, Kaur M, Bhattacharyya A, Prajapat M, Thota P, Sarma P, Kumar S, Kaur G, Sharma S, Prakash A, Saifuddin PK, Medhi B. Indian contribution toward biomedical research and development in COVID-19: A systematic review. Indian J Pharmacol 2021; 53:63-72. [PMID: 33976001 PMCID: PMC8216129 DOI: 10.4103/ijp.ijp_168_21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/12/2021] [Accepted: 04/17/2021] [Indexed: 12/13/2022] Open
Abstract
COVID-19 pandemic led to an unprecedented collaborative effort among industry, academia, regulatory bodies, and governments with huge financial investments. Scientists and researchers from India also left no stone unturned to find therapeutic and preventive measures against COVID-19. Indian pharmaceutical companies are one of the leading manufacturers of vaccine in the world, are utilizing its capacity to its maximum, and are one among the forerunners in vaccine research against COVID-19 across the globe. In this systematic review, the information regarding contribution of Indian scientists toward COVID-19 research has been gathered from various news articles across Google platform apart from searching PubMed, WHO site, COVID-19 vaccine tracker, CTRI, clinicaltrials.gov, and websites of pharmaceutical companies. The article summarizes and highlights the various therapeutic and vaccine candidates, diagnostic kits, treatment agents, and technology being developed and tested by Indian researcher community against COVID-19.
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Affiliation(s)
- Hardeep Kaur
- Department of Pediatric, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Manpreet Kaur
- Department of Nursing, AIIMS, Rishikesh, Uttarakhand, India
| | | | - Manisha Prajapat
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Prasad Thota
- Indian Pharmacopoeia Commission, Ghaziabad, Uttar Pradesh, India
| | - Phulen Sarma
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | | | - Gurjeet Kaur
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Saurabh Sharma
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Ajay Prakash
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - P. K. Saifuddin
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Bikash Medhi
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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Xiao Y, Xu H, Guo W, Zhao Y, Luo Y, Wang M, He Z, Ding Z, Liu J, Deng L, Sha F, Ma X. Update on treatment and preventive interventions against COVID-19: an overview of potential pharmacological agents and vaccines. MOLECULAR BIOMEDICINE 2020; 1:16. [PMID: 34765999 PMCID: PMC7711057 DOI: 10.1186/s43556-020-00017-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 11/11/2020] [Indexed: 02/06/2023] Open
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) triggered by the new member of the coronaviridae family, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has created an unprecedented challenge for global health. In addition to mild to moderate clinical manifestations such as fever, cough, and fatigue, severe cases often developed lethal complications including acute respiratory distress syndrome (ARDS) and acute lung injury. Given the alarming rate of infection and increasing trend of mortality, the development of underlying therapeutic and preventive treatment, as well as the verification of its effectiveness, are the top priorities. Current research mainly referred to and evaluated the application of the empirical treatment based on two precedents, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), including antiviral drugs targeting different stages of virus replication, immunotherapy modulating the overactivated inflammation response, and other therapies such as herbal medicine and mesenchymal stem cells. Besides, the ongoing development of inventing prophylactic interventions such as various vaccines by companies and institutions worldwide is crucial to decline morbidity and mortality. This review mainly focused on promising candidates for the treatment of COVID-19 and collected recently updated evidence relevant to its feasibility in clinical practice in the near future.
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Affiliation(s)
- Yinan Xiao
- Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 China
- West China School of Medicine, West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Hanyue Xu
- West China School of Medicine, West China Hospital, Sichuan University, Chengdu, 610041 China
- West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Wen Guo
- West China School of Medicine, West China Hospital, Sichuan University, Chengdu, 610041 China
- West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Yunuo Zhao
- Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 China
- West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Yuling Luo
- Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 China
- West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Ming Wang
- Infectious Diseases Center, West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Zhiyao He
- Department of Pharmacy, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Zhenyu Ding
- Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 China
- West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Jiyan Liu
- Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 China
- West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Lei Deng
- Jacobi Medical Center, Albert Einstein College of Medicine, Bronx, New York, 10465 USA
| | - Fushen Sha
- Department of Internal Medicine, State University of New York, Downstate Medical Center, Brooklyn, New York, 11203 USA
| | - Xuelei Ma
- Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 China
- West China Hospital, Sichuan University, Chengdu, 610041 China
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Prajapat M, Shekhar N, Sarma P, Avti P, Singh S, Kaur H, Bhattacharyya A, Kumar S, Sharma S, Prakash A, Medhi B. Virtual screening and molecular dynamics study of approved drugs as inhibitors of spike protein S1 domain and ACE2 interaction in SARS-CoV-2. J Mol Graph Model 2020; 101:107716. [PMID: 32866780 PMCID: PMC7442136 DOI: 10.1016/j.jmgm.2020.107716] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/15/2020] [Accepted: 08/09/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND The receptor binding domain (RBD) of spike protein S1 domain SARS-CoV-2 plays a key role in the interaction with ACE2, which leads to subsequent S2 domain mediated membrane fusion and incorporation of viral RNA into host cells. In this study we tend to repurpose already approved drugs as inhibitors of the interaction between S1-RBD and the ACE2 receptor. METHODS 2456 approved drugs were screened against the RBD of S1 protein of SARS-CoV-2 (target PDB ID: 6M17). As the interacting surface between S1-RBD and ACE2 comprises of bigger region, the interacting surface was divided into 3 sites on the basis of interactions (site 1, 2 and 3) and a total of 5 grids were generated (site 1, site 2, site 3, site 1+site 2 and site 2+site 3). A virtual screening was performed using GLIDE implementing HTVS, SP and XP screening. The top hits (on the basis of docking score) were further screened for MM-GBSA. All the top hits were further evaluated in molecular dynamics studies. Performance of the virtual screening protocol was evaluated using enrichment studies. RESULT and discussion: We performed 5 virtual screening against 5 grids generated. A total of 42 compounds were identified after virtual screening. These drugs were further assessed for their interaction dynamics in molecular dynamics simulation. On the basis of molecular dynamics studies, we come up with 10 molecules with favourable interaction profile, which also interacted with physiologically important residues (residues taking part in the interaction between S1-RBD and ACE2. These are antidiabetic (acarbose), vitamins (riboflavin and levomefolic acid), anti-platelet agents (cangrelor), aminoglycoside antibiotics (Kanamycin, amikacin) bronchodilator (fenoterol), immunomodulator (lamivudine), and anti-neoplastic agents (mitoxantrone and vidarabine). However, while considering the relative side chain fluctuations when compared to the S1-RBD: ACE2 complex riboflavin, fenoterol, cangrelor and vidarabine emerged out as molecules with prolonged relative stability. CONCLUSION We identified 4 already approved drugs (riboflavin, fenoterol, cangrelor and vidarabine) as possible agents for repurposing as inhibitors of S1:ACE2 interaction. In-vitro validation of these findings are necessary for identification of a safe and effective inhibitor of S1: ACE2 mediated entry of SARS-CoV-2 into the host cell.
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Affiliation(s)
| | | | - Phulen Sarma
- Dept. of Pharmacology, PGIMER, Chandigarh, India.
| | - Pramod Avti
- Dept. of Biophysics, PGIMER, Chandigarh, India.
| | - Sanjay Singh
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, India.
| | - Hardeep Kaur
- Dept. of Pharmacology, PGIMER, Chandigarh, India.
| | | | - Subodh Kumar
- Dept. of Pharmacology, PGIMER, Chandigarh, India.
| | | | - Ajay Prakash
- Dept. of Pharmacology, PGIMER, Chandigarh, India.
| | - Bikash Medhi
- Dept. of Pharmacology, PGIMER, Chandigarh, India.
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Sarma P, Bhattacharyya A, Kaur H, Prajapat M, Prakash A, Kumar S, Bansal S, Kirubakaran R, Reddy DH, Muktesh G, Kaushal K, Sharma S, Shekhar N, Avti P, Thota P, Medhi B. Efficacy and safety of steroid therapy in COVID-19: A rapid systematic review and Meta-analysis. Indian J Pharmacol 2020; 52:535-550. [PMID: 33666200 PMCID: PMC8092185 DOI: 10.4103/ijp.ijp_1146_20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 12/15/2022] Open
Abstract
PURPOSE Although the use of steroids in the management of COVID-19 has been addressed by a few systematic review and meta-analysis, however, they also used data from "SARS-CoV" and "MERS-CoV." Again, most of these studies addressed only one severity category of patients or addressed only one efficacy endpoint (mortality). In this context, we conducted this meta-analysis to evaluate the efficacy and safety of steroid therapy among all severity categories of patients with COVID-19 (mild to moderate and severe to critical category) in terms of "mortality," "requirement of mechanical ventilation," "requirement of ICU" and clinical cure parameters. METHODS 11 databases were screened. Only randomized controlled trials (RCTs) or high quality (on the basis of risk of bias analysis) comparative-observational studies were included in the analysis. RevMan5.3 was used for the meta-analysis. RESULTS A total of 15 studies (3 RCT and 12 comparative-observational studies) were included. In the mechanically-ventilated COVID-19 population, treatment with dexamethasone showed significant protection against mortality (single study). Among severe and critically ill combined population, steroid administration was significantly associated with lowered mortality (risk ratio [RR] 0.83 [0.76-0.910]), lowered requirement of mechanical ventilation (RR 0.59 [0.51-0.69]), decreased requirement of intensive care unit (ICU) (RR 0.62 [0.45-0.86]), lowered length of ICU stay (single-study) and decreased duration of mechanical ventilation (two-studies). In mild to moderate population, steroid treatment was associated with a higher "duration of hospital stay," while no difference was seen in other domains. In patients at risk of progression to "acute respiratory distress syndrome," steroid administration was associated with "reduced requirement of mechanical ventilation" (single-study). CONCLUSION This study guides the use of steroid across patients with different severity categories of COVID-19. Among mechanically ventilated patients, steroid therapy may be beneficial in terms of reduced mortality. Among "severe and critical" patients; steroid therapy was associated with lowered mortality, decreased requirement of mechanical ventilation, and ICU. However, no benefit was observed in "mild to moderate" population. To conclude, among properly selected patient populations (based-upon clinical severity and biomarker status), steroid administration may prove beneficial in patients with COVID-19.
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Affiliation(s)
- Phulen Sarma
- Department of of Pharmacology, PGIMER Chandigarh, India
| | | | - Hardeep Kaur
- Department of of Pharmacology, PGIMER Chandigarh, India
| | | | - Ajay Prakash
- Department of of Pharmacology, PGIMER Chandigarh, India
| | - Subodh Kumar
- Department of of Pharmacology, PGIMER Chandigarh, India
| | - Seema Bansal
- Department of of Pharmacology, PGIMER Chandigarh, India
| | | | | | | | - Karanvir Kaushal
- Department of Clinical Biochemistry, AIIMS, Rishikesh, Uttarakhand, India
| | | | | | - Pramod Avti
- Department of Biophysics, PGIMER, Chandigarh, India
| | - Prasad Thota
- Department of pharmacology, Indian Pharmacopoeia Commission, Ghaziabad, UP, India
| | - Bikash Medhi
- Department of of Pharmacology, PGIMER Chandigarh, India
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Sarma P, Kaur H, Medhi B, Bhattacharyya A. Letter to the editor: Possible role of topical povidone iodine in case of accidental ocular exposure to SARS-CoV-2. Graefes Arch Clin Exp Ophthalmol 2020; 258:2575-2578. [PMID: 32725405 PMCID: PMC7387256 DOI: 10.1007/s00417-020-04864-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 07/17/2020] [Accepted: 07/23/2020] [Indexed: 12/16/2022] Open
Affiliation(s)
- Phulen Sarma
- Department of Pharmacology, PGIMER, Chandigarh, India
| | - Hardeep Kaur
- Department of Pharmacology, PGIMER, Chandigarh, India
| | - Bikash Medhi
- Department of Pharmacology, PGIMER, Chandigarh, India
| | - Anusuya Bhattacharyya
- Department of Ophthalmology, Government Medical College and Hospital, Sector 32, Chandigarh, India
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Bhattacharyya A, Kumar S, Sarma P, Kaur H, Prajapat M, Shekhar N, Bansal S, Avti P, Hazarika M, Sharma S, Mahendru D, Prakash A, Medhi B. Safety and efficacy of lopinavir/ritonavir combination in COVID-19: A systematic review, meta-analysis, and meta-regression analysis. Indian J Pharmacol 2020; 52:313-323. [PMID: 33078733 PMCID: PMC7722914 DOI: 10.4103/ijp.ijp_627_20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/07/2020] [Accepted: 10/02/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Being protease inhibitors and owing to their efficacy in SARS-CoV, lopinavir + ritonavir (L/R) combination is being used in the management of COVID-19. In this systematic review and meta-analysis, we have evaluated the comparative safety and efficacy of L/R combination. MATERIALS AND METHODS Comparative, observational studies and controlled clinical trials comparing L/R combination to standard of care (SOC)/control or any other antiviral agent/combinations were included. A total of 10 databases were searched to identify 13 studies that fulfilled the predefined inclusion/exclusion criteria. RESULTS No discernible beneficial effect was seen in the L/R group in comparison to SOC/control in terms of "progression to more severe state" (4 studies, odds ratio [OR]: 1.446 [0.722-2.895]), "mortality" (3 studies, OR: 1.208 [0.563-2.592]), and "virological cure on days 7-10" (3 studies, OR: 0.777 [0.371-1.630]), while the L/R combination arm performed better than the SOC/control arm in terms of "duration of hospital stay" (3 studies, mean difference (MD): -1.466 [-2.403 to - 0.529]) and "time to virological cure" (3 studies, MD: -3.272 [-6.090 to - 0.454]). No difference in efficacy was found between L/R versus hydroxychloroquine (HCQ) and L/R versus arbidol. However, in a single randomized controlled trail (open label), chloroquine (CQ) performed better than L/R. The combination L/R with arbidol may be beneficial (in terms of virological clearance and radiological improvement); however, we need more dedicated studies. Single studies report efficacy of L/R + interferon (IFN, either alpha or 1-beta) combination. We need more studies to delineate the proper effect size. Regarding adverse effects, except occurrence of diarrhea (higher in the L/R group), safety was comparable to SOC. CONCLUSION In our study, no difference was seen between the L/R combination and the SOC arm in terms of "progression to more severe state," "mortality," and virological cure on days 7-10;" however, some benefits in terms of "duration of hospital stay" and "time to virological cure" were seen. No significant difference in efficacy was seen when L/R was compared to arbidol and HCQ monotherapy. Except for the occurrence of diarrhea, which was higher in the L/R group, safety profile of L/R is comparable to SOC. Compared to L/R combination, CQ, L/R + arbidol, L/R + IFN-α, and L/R + IFN-1β showed better efficacy, but the external validity of these findings is limited by limited number of studies (1 study each).
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Affiliation(s)
- Anusuya Bhattacharyya
- Department of Ophthalmology, Government Medical College and Hospital, Sector 32, Chandigarh, India
| | - Subodh Kumar
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research, Chandigarh, Chandigarh, India
| | - Phulen Sarma
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research, Chandigarh, Chandigarh, India
| | - Hardeep Kaur
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research, Chandigarh, Chandigarh, India
| | - Manisha Prajapat
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research, Chandigarh, Chandigarh, India
| | - Nishant Shekhar
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research, Chandigarh, Chandigarh, India
| | - Seema Bansal
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research, Chandigarh, Chandigarh, India
| | - Pramod Avti
- Department of Biophysics, Post Graduate Institute of Medical Education and Research, Chandigarh, Chandigarh, India
| | - Mythili Hazarika
- Department of Psychiatry, Gauhati Medical College and Hospital, Guwahati, Assam, India
| | - Saurabh Sharma
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research, Chandigarh, Chandigarh, India
| | - Dhruv Mahendru
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research, Chandigarh, Chandigarh, India
| | - Ajay Prakash
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research, Chandigarh, Chandigarh, India
| | - Bikash Medhi
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research, Chandigarh, Chandigarh, India
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