Computational approach investigation bioactive molecules from Saussurea Costus plant as SARS-CoV-2 main protease inhibitors using reverse docking, molecular dynamics simulation, and pharmacokinetic ADMET parameters

Hajji, Halima; Alaqarbeh, Marwa; Lakhlifi, Tahar; Ajana, Mohammed Aziz; Alsakhen, Nada; Bouachrine, Mohammed

doi:10.1016/j.compbiomed.2022.106209

Cited by 15 publications

(3 citation statements)

References 37 publications

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“…According to the visualization results, the interaction between the M pro and cyanropicrin 49 was the best one, as proved by the molecular docking (MD) simulation study. The drug-likeness of cyanropicrin 49 was confirmed using ADMET analysis and Lipinski’s rule [ 66 ]. The phytocompounds from Indian medicinal plants and some polyphenols were examined as potential inhibitors of SARS-CoV-2’s main protease.…”

Section: In Silico Studiesmentioning

confidence: 99%

“…Moreover, carotenoids, such as crocin 63 , showed potent anticoronavirus properties by inhibiting the coronavirus targets (the M pro , spike glycoproteins, RdRp, helicases, and ADP-phosphates) [ 73 ]. The other drug classes, i.e., alkaloids (tubocuraine 74 [ 83 ] and palmatine 126 [ 105 ]), terpenes (cyanopyrin 49 [ 66 ], ferolide 68 [ 80 ], and abietatriene 178 [ 128 ]), steroids (withanolide R 50 [ 67 ], withacoagulin H 60 [ 72 ], withacoagulin 62 [ 72 ], ajugin E 61 [ 72 ], sterenin M 65 [ 75 ], and stigmasterol 77 [ 85 ]), quinones (pycnanthuquinone C 47 [ 65 ] and pycnanthuquinone B 48 [ 65 ]), polyphenols (geraniin 177 [ 132 ], ellagitannin punicalin 202 [ 79 ], and ellagic acid 206 [ 121 ]), and glycosides (cyanidin 203 [ 77 ], arctiin 196 [ 135 ], forsythiaside A 46 [ 64 ], and hesperidin 51 [ 86 ]) have also been found to show promising anti-SARS-CoV-2 activities. It is anticipated that the phytoconstituents discussed in this report will aid the development of an effective and safe anti-SARS-CoV-2 treatment option from naturally procured compounds.…”

Section: In Silico Studiesmentioning

confidence: 99%

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A Comprehensive Update of Various Attempts by Medicinal Chemists to Combat COVID-19 through Natural Products

et al. 2023

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The ongoing COVID-19 pandemic has resulted in a global panic because of its continual evolution and recurring spikes. This serious malignancy is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since the outbreak, millions of people have been affected from December 2019 till now, which has led to a great surge in finding treatments. Despite trying to handle the pandemic with the repurposing of some drugs, such as chloroquine, hydroxychloroquine, remdesivir, lopinavir, ivermectin, etc., against COVID-19, the SARS-CoV-2 virus continues its out-of-control spread. There is a dire need to identify a new regimen of natural products to combat the deadly viral disease. This article deals with the literature reports to date of natural products showing inhibitory activity towards SARS-CoV-2 through different approaches, such as in vivo, in vitro, and in silico studies. Natural compounds targeting the proteins of SARS-CoV-2—the main protease (Mpro), papain-like protease (PLpro), spike proteins, RNA-dependent RNA polymerase (RdRp), endoribonuclease, exoribonuclease, helicase, nucleocapsid, methyltransferase, adeno diphosphate (ADP) phosphatase, other nonstructural proteins, and envelope proteins—were extracted mainly from plants, and some were isolated from bacteria, algae, fungi, and a few marine organisms.

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Section: In Silico Studiesmentioning

confidence: 99%

Section: In Silico Studiesmentioning

confidence: 99%

A Comprehensive Update of Various Attempts by Medicinal Chemists to Combat COVID-19 through Natural Products

et al. 2023

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“…ADMET was employed to study the pharmacokinetic properties of absorption, distribution, metabolism, and excretion. 14 Chemometric tools were used to collect and analyze complex data from the biologically active molecules to build computer models that link their chemical properties to biological activity. Also, the statistical agreement of the developed models was evaluated based on their relative ability in the training set and their predicted ability in the external test set.…”

Section: Introductionmentioning

confidence: 99%

A computational study of Di-substituted 1,2,3-triazole derivatives as potential drug candidates against Mycobacterium tuberculosis: 3D-QSAR, molecular docking, molecular dynamics, and ADMETox

et al. 2023

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Antitrypanosomal Potential of Chalcone‐Based Ursolic Acid Derivatives via Ligand‐Based Virtual Screening, DMPK Analyses, Molecular Dynamics Simulation, and MM/GBSA Binding Energy

Nunes,

da Rocha,

de de Oliveira

et al. 2024

ChemistrySelect

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Chagas disease, caused by the protozoan parasite Trypanosoma cruzi and transmitted mainly by triatomine insects, represents a significant challenge to public health, especially in impoverished regions. Current treatments, such as benznidazole and nifurtimox, have limitations, including serious side effects and reduced efficacy in the chronic phase. This work aims to evaluate the antitrypanosomal activity of ursolic acid‐derived chalcones (UACD) using a ligand‐based virtual screening approach. To this end, a series of independent molecular docking simulations were carried out (via AutoDock Vina code) with the parasite proliferation cycle enzymes TcGAPDH and cruzain. The most favorable candidates underwent drug metabolism and pharmacokinetics (DMPK) analyses and molecular dynamics (MD) simulations to estimate the pharmacokinetic and pharmacodynamic profile. Molecular docking simulations showed that the UACD derivatives showed better specificity for the TcGAPDH enzyme, emphasizing the ursolic acid and UACD3 derivatives (affinity energy = −9.4 kcal/mol for each). The DMPK prediction showed that the derivatives present viable apparent permeability (Papp) that promotes an excellent absorbed fraction (in 10⁻⁶ cm/s). MD simulations showed that the UACD3 derivative showed better free energy when binding to the TcGAPDH enzyme (−13.27 ± 1.87 kcal/mol) and interacting with the active site residues Cys166 and Thr167. However, both ligands appear to be alternative therapies in treating Chagas disease.

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Computational approach investigation bioactive molecules from Saussurea Costus plant as SARS-CoV-2 main protease inhibitors using reverse docking, molecular dynamics simulation, and pharmacokinetic ADMET parameters

Cited by 15 publications

References 37 publications

A Comprehensive Update of Various Attempts by Medicinal Chemists to Combat COVID-19 through Natural Products

A Comprehensive Update of Various Attempts by Medicinal Chemists to Combat COVID-19 through Natural Products

A computational study of Di-substituted 1,2,3-triazole derivatives as potential drug candidates against Mycobacterium tuberculosis: 3D-QSAR, molecular docking, molecular dynamics, and ADMETox

Antitrypanosomal Potential of Chalcone‐Based Ursolic Acid Derivatives via Ligand‐Based Virtual Screening, DMPK Analyses, Molecular Dynamics Simulation, and MM/GBSA Binding Energy

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