Comparative Docking Analysis of Rational Drugs Against COVID-19 Main Protease

Samant, Lalit R.; Javle, Vyomesh

doi:10.26434/chemrxiv.12136002

Cited by 3 publications

(2 citation statements)

References 7 publications

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“…The global search was doing Lamarckian genetic algorithm (Morris et al, 1998). Molecular Docking calculations with small molecules and chloroquine showed a standard of interaction with the Met49 residue, which makes it an important amino acid (Samant & Javle, 2020). This information was considered for the choice of the Grid Box which was centered on the Met49 with coordinates x ¼ 26.972 y¼ À15.931 and z ¼ 15.125, cubic box size was 80 Â 80 Â 80 points, spacing 0.375 Å and number step equal 100.…”

Section: Molecular Docking (Md)mentioning

confidence: 99%

Constituents of buriti oil (Mauritia flexuosa L.) like inhibitors of the SARS-Coronavirus main peptidase: an investigation by docking and molecular dynamics

Costa¹,

Sá

Bezerra

et al. 2020

Journal of Biomolecular Structure and Dynamics

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Statistics show alarming numbers of infected and killed in the world, caused by the Covid-19 pandemic, which still doesn't have a specific treatment and effective in combating all efforts to seek treatments and medications against this disease. Natural products are of relevant interest in the search for new drugs. Thus, Buriti oil (Mauritia flexuosa L.) is a natural product extracted from the fruit of the palm and is quite common in the legal Amazon region, Brazil. In the present work, the anti-Covid-19 biological activity of some constituents of Buriti oil was investigated using in silico methods of Molecular Docking and Molecular Dynamics Simulations. The main results of Molecular Docking revealed favorable interaction energies in the formation of the 2GTB peptidase complex (main peptidase of SARS-CoV) with the 13-cis-b-carotene ligands (DG bind ¼ À10.23Kcal mol À1 ), 9-cis -b-carotene (DG bind ¼ À9.82Kcal mol À1 ), and a-carotene (DG bind ¼ À8.34Kcal mol À1 ). Molecular Dynamics simulations demonstrated considerable interaction for these ligands with emphasis on a-carotene. Such theoretical results encourage and enable a direction for experimental studies in vitro and in vivo, essential in the development of new drugs with enzymatic inhibitory action for Covid-19.

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Section: Molecular Docking (Md)mentioning

confidence: 99%

Constituents of buriti oil (Mauritia flexuosa L.) like inhibitors of the SARS-Coronavirus main peptidase: an investigation by docking and molecular dynamics

Costa¹,

Sá

Bezerra

et al. 2020

Journal of Biomolecular Structure and Dynamics

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show abstract

“…Finally, the pdbqt files of the proteins were saved. 26 Chemical structures of the ligands were obtained from the Drug Bank (https://www.drugbank.ca/). The ligands unavailable in the Drug Bank were drawn in ChemDraw (Professional, version 19.0.1.28), passed to ChemDraw 3D (professional, version 19.0.1.28) and minimized.…”

Section: Experimental In Silico Partmentioning

confidence: 99%

Molecular Docking Study of Several Seconder Metabolites from Medicinal Plants as Potential Inhibitors of COVID-19 Main Protease

Bilginer¹,

Gözcü²,

Güvenalp³

2022

tjps

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and the disease is officially named as Coronavirus Disease-2019 (COVID-19) by World Health Organization (WHO). 2 According to WHO's COVID-19 Weekly Epidemiological Update Report released on May 11, 2021, the number of confirmed cases reached 157,362,408 including 3,277,834 deaths in the world as of May 9, 2021. 3Currently, there are several vaccines for COVID-19, but no antiviral drugs are available for specific treatment of COVID-19. However, some antiviral drugs such as lopinavir, ritonavir, remdesivir, and nelfinavir have been using to prevent further complications and organ damage caused by COVID-19. 4 Among all these drugs, nelfinavir, which has been used in clinics, was found as the most potential inhibitor drug against COVID-19 main protease (M pro ) based on its docking score according to the docking studies conducted by Xu et al. 5 In docking studies, M pro is used as a potential drug target to combat 2019-CoV. [6][7][8] Secondary metabolites obtained from medicinal plants and their semi-synthetic derivatives have been widely used in new

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Exploring the inhibitory potential of novel bioactive compounds from mangrove actinomycetes against nsp10 the major activator of SARS-CoV-2 replication

et al. 2022

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The current study reveals the inhibitory potential of novel bioactive compounds of mangrove actinomycetes against nsp10 of SARS-CoV-2. A total of fifty (50) novel bioactive (antibacterial, antitumor, antiviral, antioxidant, and anti-inflammatory) compounds of mangrove actinomycetes from different chemical classes such as alkaloids, dilactones, sesquiterpenes, macrolides, and benzene derivatives are used for interaction analysis against nsp10 of SARS-CoV-2. The six antiviral agents sespenine, xiamycin c, xiamycin d, xiamycin e, xiamycin methyl ester, and xiamycin A (obeyed RO5 rule) are selected based on higher binding energy, low inhibition constant values, and better-docked positions. The effective hydrogen and hydrophobic (alkyl, –sigma, – T shaped and -alkyl) interaction analysis reveals the four antivirals sespenine, xiamycin C, xiamycin methyl ester, and xiamycin A are supposed to be the most auspicious inhibitors against nsp10 of SARS-CoV-2. Quantum chemistry methods such as frontier molecular orbitals and molecular electrostatic potential are used to explain the thermal stability and chemical reactivity of ligands. The toxicity profile shows that selected ligands are safe by absorption, distribution, metabolism, excretion, and toxicity profiling and also effective for inhibition of nsp10 protein of SARS-CoV-2. The molecular dynamic simulation investigation of apo and halo forms of nsp10 done by RMSD of C atoms of nsp10, all amino acid residues RMSF, count total number of hydrogen bonds and radius of gyration ( R g ). MD simulations reveal the complexes are stable and increase the structural compactness of nsp10 in the binding pocket. The lead antiviral compounds sespenine, xiamycin C, xiamycin methyl ester, and xiamycin A are recommended as the most promising inhibitors against nsp10 of SARS-CoV-2 pathogenicity. Graphical abstract Supplementary Information The online version contains supplementary material available at 10.1007/s11696-021-01997-x.

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Comparative Docking Analysis of Rational Drugs Against COVID-19 Main Protease

Cited by 3 publications

References 7 publications

Constituents of buriti oil (Mauritia flexuosa L.) like inhibitors of the SARS-Coronavirus main peptidase: an investigation by docking and molecular dynamics

Constituents of buriti oil (Mauritia flexuosa L.) like inhibitors of the SARS-Coronavirus main peptidase: an investigation by docking and molecular dynamics

Molecular Docking Study of Several Seconder Metabolites from Medicinal Plants as Potential Inhibitors of COVID-19 Main Protease

Exploring the inhibitory potential of novel bioactive compounds from mangrove actinomycetes against nsp10 the major activator of SARS-CoV-2 replication

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