scholarly journals Cytotoxicity, anti‐microbial studies of M( II )‐dithiocarbamate complexes, and molecular docking study against SARS COV2 RNA ‐dependent RNA polymerase

2021 ◽  
Author(s):  
Ahmed S. M. Al‐Janabi ◽  
Abdulrahman M. Saleh ◽  
Mohammad R. Hatshan
Keyword(s):  
Molecular Docking ◽  
Rna Polymerase ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Rna Dependent Rna Polymerase

scholarly journals Investigation of Anti-Coronavirus, Anti-HCV, Nucleotide Inhibitors, and Bioactive Molecules efficacy Against RNA-directed RNA polymerase of Nipah Virus: Molecular Docking Study

2021 ◽  
Vol 10 (1) ◽  
pp. 78
Author(s):  
Peter T. Habib
Keyword(s):  
Molecular Docking ◽  
Rna Polymerase ◽  
Nipah Virus ◽  
Docking Study ◽  
The Philippines ◽  
Bioactive Molecules ◽  
World Health ◽  
Energy Estimates ◽  
Molecular Docking Study ◽  
Rna Dependent Rna Polymerase

Introduction: The infections with the Nipah virus (NiV) are highly infectious and may lead to severe febrile encephalitis. High mortality rates in southeastern Asia, including Bengal, Malaysia, Papua New Guinea, Vietnam, Cambodia, Indonesia, Madagascar, the Philippines, Thailand, and India, have been reported in NiV outbreaks. Considering the high risk of an epidemic, NiV was declared a priority pathogen by the World Health Organization. However, for the treatment of this infection, there is no effective therapy or approved FDA medicines. RNA-dependent polymerase RNA (RdRp) plays an important role in viral replication among the nine well-known proteins of NiV.Material and Methods: Fourteen antiviral molecules have been computerized for NiV RNA-dependent RNA polymerase and demonstrated a potential inhibition effect against coronavirus (NiV-RdRp). A multi-step molecular docking process, followed by extensive analyzes of molecular binding interactions, binding energy estimates, synthetic accessibility assessments, and toxicity tests.Results: Molecular docking analysis reveals that Uprifosbuvir is the most suitable inhibitor for RdRp of Nipah Virus regarding the binding affinity and binding in the target cavity. Although, such studies need clinical confirmation.Conclusion: The role of anti-viral molecules as a ligand against RNA-dependent RNA polymerase is critical important in the current era. Computational tools such as molecular docking has proven its power in the analysis of molecules interaction. Our analysis reveals the Uprifosbuvir might be a candidate RdRp inhibitor. This study should further investigate the properties of the already identified anti-viral molecules followed by a pharmacological investigation of these in-silico findings in suitable models.

scholarly journals Potential Phytochemical Inhibitors of the Coronavirus RNA Dependent RNA Polymerase: A Molecular Docking Study

2020 ◽  
Author(s):  
Ardra. P ◽  
Prachi Singh ◽  
Hariprasad VR ◽  
Babu UV ◽  
Mohamed Rafiq ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Rna Polymerase ◽  
Metal Ion ◽  
Docking Study ◽  
Nucleoside Triphosphate ◽  
Root Extract ◽  
Amino Acid Residues ◽  
Molecular Docking Study ◽  
Rna Dependent Rna Polymerase ◽  
Phytochemical Compounds

Abstract The COVID-19 disease that originated in China by the end of 2019 has now become a pandemic and has affected 216 countries as on 08 June 2020. RNA dependent RNA polymerase (RdRp), the core enzyme in the multiprotein replicase-transcriptase complex of coronaviruses, serves as a classical target for inhibiting the coronavirus infectivity. In this study we performed molecular docking of sixty-nine different phytochemical compounds from various herbs with RdRp of both SARS-CoV-2 and its predecessor SARS-CoV. Our results show that various phytochemical constituents from Withania somnifera root extract, Hyssopus officinalis and Camellia sinensis leaf extract have high binding affinity towards RdRps and are comparable to the small molecule drug remdesivir. Their binding interactions reveal that they bind to the amino acid residues involved in nucleoside triphosphate (NTP) entry and recognition site and metal ion cofactor chelating site of both SARS-CoV-2 and SARS-CoV. Hence they are different from the classical nucleotide analog inhibitors of RdRp. This study paves a quick platform for development of targeted therapy using phytochemicals for COVID-19 and other potential SARS coronavirus related outbreaks in future.

scholarly journals Computational selection of flavonoid compounds as inhibitors against SARS-CoV-2 main protease, RNA-dependent RNA polymerase and spike proteins: A molecular docking study

2021 ◽  
Vol 28 (1) ◽  
pp. 448-458
Author(s):  
Marimuthu Ragavan Rameshkumar ◽  
Purushothaman Indu ◽  
Narasingam Arunagirinathan ◽  
Babu Venkatadri ◽  
Hamed A. El-Serehy ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Rna Polymerase ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Rna Dependent Rna Polymerase ◽  
Flavonoid Compounds ◽  
Main Protease ◽  
Selection Of ◽  
Spike Proteins

scholarly journals In silico analysis of RNA-dependent RNA polymerase of the SARS-CoV-2 and potentiality of the pre-existing drugs

2020 ◽  
Author(s):  
Samyabrata Mukhoty ◽  
Madhab Kumar Sen ◽  
Subhajit Ghosh ◽  
Himangsu Kundu ◽  
Suvankar Das ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Rna Polymerase ◽  
Evolutionary Relationship ◽  
In Silico Analysis ◽  
Close Relation ◽  
Emerging Diseases ◽  
Clear Understanding ◽  
Molecular Docking Study ◽  
Rna Dependent Rna Polymerase ◽  
Multiple Sequence

Abstract Background: The alarming increase in the number of SARS-CoV-2 cases worldwide, urgently demands far-reaching effective strategies to win the battle against emerging as well as re-emerging diseases. Many research laboratories are conducting clinical trials with different drugs, among which some became quite interestingly effective against this pandemic. Our aim is to investigate the potentiality of the pre-existing drugs and get a clear understanding of their effects on RNA-dependent RNA polymerase (RdRp) of the SARS-CoV-2. Methods: Multiple sequence alignment (MSA) alogwith molecular phylogeny analysis were performed using homologous sequences to identify the mutations within RdRp and evolutionary relationship. Based on the published literatures, we have chosen eight drug molecules like Ribavirin, Tenofovir, Sofosbuvir, IDX-184, YAK, Setrobuvir, Remdesivir and Galidesivir. Series of molecular docking studies between template RNA and RdRp of SARS-CoV-2 has been performed in absence or presence of those drugs and cofactors nsp7 and nsp8.Results: From MSA 13 exclusive mutations identified within RdRp of SARS-CoV-2 and phylogeny reveals its close relation with Bat coronavirus RaTG13. The interaction affinities and interacting residues as obtained from systematic molecular docking study led to a conclusion that the chosen drugs can prove to be effective against this pandemic partially. Conclusion: Therefore, designing of inhibitors which will specifically act against nsp12 and lower the binding affinity of nsp12 towards RNA template is necessary. In this article we additionally focus on the nsp7-8 hexadecameric complex and had suggested a list of amino acid residues of nsp12 and nsp7-8 complex to develop far-reaching effective drugs.

scholarly journals Investigation of Anti-Coronavirus, Anti-HCV, Nucleotide Inhibitors, and Bioactive Molecules efficacy Against RNA-directed RNA polymerase of Nipah Virus: Molecular Docking Study

2021 ◽  
Author(s):  
Peter T. Habib
Keyword(s):  
Molecular Docking ◽  
Rna Polymerase ◽  
Nipah Virus ◽  
Docking Study ◽  
The Philippines ◽  
Bioactive Molecules ◽  
World Health ◽  
Energy Estimates ◽  
Toxicity Tests ◽  
Molecular Docking Study

Abstract The infections with the Nipah virus (NiV) are highly infectious and may lead to severe febrile encephalitis. High rates of mortality in southeastern Asia including Bengal, Malaysia, Papua New Guinea, Vietnam, Cambodia, Indonesia, Madagascar, the Philippines, Thailand, and India have been reported in NiV outbreaks. Considering the high risk of an epidemic, NiV was declared a priority pathogen by the World Health Organization (WHO). However, for the treatment of this infection, there is no effective therapy or approved FDA medicines. RNA-dependent polymerase RNA (RdRp) plays an important role in viral replication among the nine well-known proteins of NiV. Therefore, fourteen antiviral molecules have been computerized for NiV RNA-dependent RNA polymerase and demonstrated a potential inhibition effect against coronavirus (NiV-RdRp). A multi-step molecular docking process, followed by extensive analyzes of molecular binding interactions, binding energy estimates, synthetic accessibility assessments, and toxicity tests. Analysis reveals that Uprifosbuvir is the most suitable inhibitor for RdRp of Nipah Virus regarding the binding affinity and binding in the target cavity. Although, such studies need clinical confirmation.

scholarly journals Inverse Molecular Docking Study of NS3-Helicase and NS5-RNA Polymerase of Zika Virus as Possible Therapeutic Targets of Ligands Derived from Marcetia taxifolia and Its Implications to Dengue Virus

ACS Omega ◽  
2021 ◽  
Vol 6 (9) ◽  
pp. 6134-6143
Author(s):  
Cristian Buendia-Atencio ◽  
Gilles Paul Pieffet ◽  
Santiago Montoya-Vargas ◽  
Jessica A. Martínez Bernal ◽  
Héctor Rafael Rangel ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Dengue Virus ◽  
Rna Polymerase ◽  
Zika Virus ◽  
Therapeutic Targets ◽  
Docking Study ◽  
Molecular Docking Study

scholarly journals Azole-acridine hybrids as potential enzymatic inhibitors of coronavirus-2 main protease and RNA polymerase by molecular modeling strategy

2020 ◽  
Author(s):  
Charles K. Rono ◽  
Banothile C.E. Makhubela
Keyword(s):  
Molecular Docking ◽  
Rna Polymerase ◽  
Docking Study ◽  
Living Cells ◽  
Binding Energies ◽  
Binding Affinities ◽  
Molecular Docking Study ◽  
Main Protease ◽  
Current Outbreak ◽  
Modeling Strategy

Abstract SARS-CoV-2 has been identified as the cause of the current outbreak of coronavirus disease (COVID-19). As part of the efforts to develop potential drugs with promise for clinical use, a molecular docking study on azole (triazole and pyrazole) based molecules on the main protease Mpro and RNA polymerase as possible inhibitors that could be elected for further experimental bioassays. Autodock has been employed to identify azole derivatives 1-6 preferred conformations in the active site of the enzyme and to estimate their binding affinities to the protease and RNA polymerase targets. From the molecular docking strategy, these new azole compounds though nonpeptides in nature display possible inhibition of Mpro activity with comparable affinities (-4.7 kcal/mol to -6.5 kcal/mol) to the recently reported peptide-like inhibitors such as α-ketoamide inhibitor 13b (-5.0 k/cal/mol). They also exhibit improved binding affinities to RNA polymerase (-6.3 to -7.1 kcal/mol) comparable to remdesivir (-6.6 kcal/mol). Based on the observed binding energies, these compounds may possess anti-coronavirus bioactivity through inhibition of the virus main protease as well as RNA polymerase activities in living cells.

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