Molecular dynamics simulation approach for discovering potential inhibitors against SARS-CoV-2: A structural review

Ghahremanian, Shabnam; Rashidi, Mohammad Mehdi; Raeisi, Kimai; Toghraie, Davood

doi:10.1016/j.molliq.2022.118901

Cited by 98 publications

(31 citation statements)

References 52 publications

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“…The Desmond MD simulation package was used to perform the simulation study of the best ligand-receptor complex [ 46 ] (human DPP-4 michelalbine and human amylin gentisic acid complex) to evaluate their safety. General workflows such as solvating the complex using a system builder and adding counter ions to neutralize the system were used.…”

Section: Methodsmentioning

confidence: 99%

MD Simulation Studies for Selective Phytochemicals as Potential Inhibitors against Major Biological Targets of Diabetic Nephropathy

et al. 2022

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Diabetes is emerging as an epidemic and is becoming a public health concern worldwide. Diabetic nephropathy is one of the serious complications of diabetes, and about 40% of individuals with diabetes develop diabetic nephropathy. The consistent feature of diabetes and its associated nephropathy is hyperglycemia, and in some cases, hyperamylinemia. Currently, the treatment includes the use of medication for blood pressure control, sugar control, and cholesterol control, and in the later stage requires dialysis and kidney transplantation, making the management of this complication very difficult. Bioactive compounds, herbal medicines, and extracts are extensively used in the treatment and prevention of several diseases, and some are reported to be efficacious in diabetes too. Therefore, in this study, we tried to identify the therapeutic potential of phytochemicals used in in silico docking and molecular dynamic simulation studies using a library of 5284 phytochemicals against the two potential targets of type 2 diabetes-associated nephropathy. We identified two phytochemicals (i.e., gentisic acid and michelalbine) that target human amylin peptide and dipeptidyl peptidase-4, respectively, with good binding affinity. These phytochemicals can be further evaluated using in vitro and in vivo studies for their anti-hyperglycemia and anti-hyperamylinemia effects.

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Section: Methodsmentioning

confidence: 99%

MD Simulation Studies for Selective Phytochemicals as Potential Inhibitors against Major Biological Targets of Diabetic Nephropathy

et al. 2022

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“…Although its RMSD values appear to have an ascending tendency, the simulation was run for 30 ns to confirm that equilibrium indeed occurred after 10 ns (results not shown). In any case, the RMSD values of the complex of raffinose ferulate are still below 3 Å, which is considered low enough to characterize the complex as stable [ 119 ].…”

Section: Resultsmentioning

confidence: 99%

The Inhibitory Potential of Ferulic Acid Derivatives against the SARS-CoV-2 Main Protease: Molecular Docking, Molecular Dynamics, and ADMET Evaluation

2022

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The main protease (Mpro) of SARS-CoV-2 is an appealing target for the development of antiviral compounds, due to its critical role in the viral life cycle and its high conservation among different coronaviruses and the continuously emerging mutants of SARS-CoV-2. Ferulic acid (FA) is a phytochemical with several health benefits that is abundant in plant biomass and has been used as a basis for the enzymatic or chemical synthesis of derivatives with improved properties, including antiviral activity against a range of viruses. This study tested 54 reported FA derivatives for their inhibitory potential against Mpro by in silico simulations. Molecular docking was performed using Autodock Vina, resulting in comparable or better binding affinities for 14 compounds compared to the known inhibitors N3 and GC376. ADMET analysis showed limited bioavailability but significantly improved the solubility for the enzymatically synthesized hits while better bioavailability and druglikeness properties but higher toxicity were observed for the chemically synthesized ones. MD simulations confirmed the stability of the complexes of the most promising compounds with Mpro, highlighting FA rutinoside and compound e27 as the best candidates from each derivative category.

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“…[ 16 ]. Ghahremanian et al [ 17 ] prepared an overview of discovering and studying standard treatment strategies by considering RMSD, RMSF, the radius of gyration, binding free energy, and Solvent-Accessible Surface Area as effective parameters for evaluation. Wacker and Schlüter established an implicit time-discrete SIR model and applied it to available data regarding the spread of COVID-19 in Germany and Iran [ 18 ].…”

Section: Methods Detailsmentioning

confidence: 99%

A mathematical system of COVID-19 disease model: Existence, uniqueness, numerical and sensitivity analysis

Sadri¹,

Aminikhah

2023

MethodsX

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Molecular dynamics simulation approach for discovering potential inhibitors against SARS-CoV-2: A structural review

Cited by 98 publications

References 52 publications

MD Simulation Studies for Selective Phytochemicals as Potential Inhibitors against Major Biological Targets of Diabetic Nephropathy

MD Simulation Studies for Selective Phytochemicals as Potential Inhibitors against Major Biological Targets of Diabetic Nephropathy

The Inhibitory Potential of Ferulic Acid Derivatives against the SARS-CoV-2 Main Protease: Molecular Docking, Molecular Dynamics, and ADMET Evaluation

A mathematical system of COVID-19 disease model: Existence, uniqueness, numerical and sensitivity analysis

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