Identification of (2<i>R</i>,3<i>R</i>)-2-(3,4-dihydroxyphenyl)chroman-3-yl-3,4,5-trihydroxy benzoate as multiple inhibitors of SARS-CoV-2 targets; a systematic molecular modelling approach

Selvaraj, Jubie; P, Shyam Sundar; Logesh, Rajan; Selvaraj, Divakar; Palanisamy, Dhanabal; Pk, Krishnan Namboori; Mohankumar, Suresh Kumar

doi:10.1039/d1ra01603b

Cited by 4 publications

(4 citation statements)

References 37 publications

(42 reference statements)

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“…Finally, the hydrogen receptors were merged into the target receptor molecule using the Discovery Studio 4.1 client. 20 Prepared protein was validated through a Ramachandran plot ( Fig. 2 ).…”

Section: Methodsmentioning

confidence: 99%

“…Before and aer protein reduction, the potential energy, van der Waals energy, electrostatic energy, and RMS gradient of the complex were measured, and the pH used was 7.4. Finally, the hydrogen receptors were merged into the target receptor molecule using the Discovery 20 Prepared protein was validated through a Ramachandran plot (Fig. 2).…”

Section: Molecular Docking Studiesmentioning

confidence: 99%

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Synthesis and screening of cyclic diketone indanedione derivatives as future scaffolds for neutrophil elastase inhibition

et al. 2023

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Section: Methodsmentioning

confidence: 99%

Section: Molecular Docking Studiesmentioning

confidence: 99%

Synthesis and screening of cyclic diketone indanedione derivatives as future scaffolds for neutrophil elastase inhibition

et al. 2023

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“…The obtained data suggested that tannic acid was a potential inhibitor of the targeted enzyme, as it was found to form a thermodynamically stable complex with Mpro. Cinnamtannin-B is another naturally occurring tannin that has been reported as a top hit against SARS-CoV-2 Mpro [ 137 ]. Cinnamtannin-B is derived from the cinnamon plant ( Cinnamomum zeylanicum ) and can only be isolated from a limited number of plants such as Linderae umbellatae and bay laurel ( Laurus nobilis ) [ 138 ].…”

Section: Phytochemicals As a Reservoir To Search For Sars-cov-2 Mpro ...mentioning

confidence: 99%

The Main Protease of SARS-CoV-2 as a Target for Phytochemicals against Coronavirus

Issa

Сокорнова

Zhidkin

et al. 2022

Plants

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In late December 2019, the first cases of COVID-19 emerged as an outbreak in Wuhan, China that later spread vastly around the world, evolving into a pandemic and one of the worst global health crises in modern history. The causative agent was identified as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although several vaccines were authorized for emergency use, constantly emerging new viral mutants and limited treatment options for COVID-19 drastically highlighted the need for developing an efficient treatment for this disease. One of the most important viral components to target for this purpose is the main protease of the coronavirus (Mpro). This enzyme is an excellent target for a potential drug, as it is essential for viral replication and has no closely related homologues in humans, making its inhibitors unlikely to be toxic. Our review describes a variety of approaches that could be applied in search of potential inhibitors among plant-derived compounds, including virtual in silico screening (a data-driven approach), which could be structure-based or fragment-guided, the classical approach of high-throughput screening, and antiviral activity cell-based assays. We will focus on several classes of compounds reported to be potential inhibitors of Mpro, including phenols and polyphenols, alkaloids, and terpenoids.

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“…Molecular dynamics (MD) simulations − are widely used to investigate spatial and temporal fluctuations of biomolecules. MD simulations of processes such as protein–drug interactions − and folding/unfolding of proteins in the explicit solvent − require micro- to millisecond length simulations to provide the chemical and biological inferences that researchers commonly probe. The number of iterations or time steps can range from tens to hundreds of millions.…”

Section: Introductionmentioning

confidence: 99%

Review of Electrostatic Force Calculation Methods and Their Acceleration in Molecular Dynamics Packages Using Graphics Processors

George

Mondal²,

Purnaprajna

et al. 2022

ACS Omega

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Molecular dynamics (MD) simulations probe the conformational repertoire of macromolecular systems using Newtonian dynamic equations. The time scales of MD simulations allow the exploration of biologically relevant phenomena and can elucidate spatial and temporal properties of the building blocks of life, such as deoxyribonucleic acid (DNA) and protein, across microsecond (μs) time scales using femtosecond (fs) time steps. A principal bottleneck toward extending MD calculations to larger time scales is the long-range electrostatic force measuring component of the naive nonbonded force computation algorithm, which scales with a complexity of ( N , number of atoms). In this review, we present various methods to determine electrostatic interactions in often-used open-source MD packages as well as the implementation details that facilitate acceleration of the electrostatic interaction calculation.

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Identification of (2R,3R)-2-(3,4-dihydroxyphenyl)chroman-3-yl-3,4,5-trihydroxy benzoate as multiple inhibitors of SARS-CoV-2 targets; a systematic molecular modelling approach

Abstract: Structure-based insilico-guided screening of potential polytargeting anti-COVID phytochemical: gallocatechin gallate analogue.

Cited by 4 publications

References 37 publications

Synthesis and screening of cyclic diketone indanedione derivatives as future scaffolds for neutrophil elastase inhibition

Synthesis and screening of cyclic diketone indanedione derivatives as future scaffolds for neutrophil elastase inhibition

The Main Protease of SARS-CoV-2 as a Target for Phytochemicals against Coronavirus

Review of Electrostatic Force Calculation Methods and Their Acceleration in Molecular Dynamics Packages Using Graphics Processors

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