3D-QSAR study, docking molecular and simulation dynamic on series of benzimidazole derivatives as anti-cancer agents

Mchichi, L. El; Tabti, Kamal; Kasmi, Rania; El-Mernissi, Reda; Aisouq, A. El; En-nahli, Fatima; Belhassan, Assia; Lakhlifi, Tahar; Bouachrine, Mohammed

doi:10.1016/j.jics.2022.100582

Cited by 19 publications

(6 citation statements)

References 34 publications

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“…The Discovery Studio, version 17.2.0. is a suite of software to simulate systems of small molecules and macromolecules [ 8 ]. The product includes features to view and edit data and tools to perform database estimation [ 9 , 10 ].…”

Section: Methodsmentioning

confidence: 99%

Discover the Medication Potential of Algerian Medicinal Plants Against Sars-Cov-2 Main Protease (Mpro): Molecular Docking, Molecular Dynamic Simulation, and ADMET Analysis

Soudani

Zaki²,

Alaqarbeh³

et al. 2023

Chemistry Africa

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At the end of 2019, the world faced a big challenge and crisis caused by the SARS-CoV-2 virus. It spreads rapidly and is contagious; no treatment has officially been found. Algeria has used medicinal plants native to the country to defend against this pandemic. The objective of this paper is based on a molecular docking study of the active compounds of five Algerian medicinal plants with their target Sars-2Cov-2 virus protease to assess their potential antiviral activity against COVID-19. Innovative software and computerized databases were introduced into the in-silico domain, mainly the Auto-Dock software version 1.5.6. Similar results were obtained for all ligands, with a better chemical affinity of − 5.600 kcal/mol for the protease target 6LU7 and − 5.700 kcal/mol for the protease target 6WTT, with an average of − 4.227 kcal/mol and − 4.221 kcal/mol, respectively. The protease targets 6LU7 and 6WTT. In the ADME-Tox study, the active compounds of Algerian medicinal plants also demonstrated an excellent pharmacokinetic and toxic profile. Best scores were noted for cedrol, camphor, and eucalyptol. A molecular dynamics simulation showed the stability of camphor-6LU7 and cedrol-6LU7 complexes, favoring the biological potential of white artemisia and cypress plants. Graphical Abstract

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Section: Methodsmentioning

confidence: 99%

Discover the Medication Potential of Algerian Medicinal Plants Against Sars-Cov-2 Main Protease (Mpro): Molecular Docking, Molecular Dynamic Simulation, and ADMET Analysis

Soudani

Zaki²,

Alaqarbeh³

et al. 2023

Chemistry Africa

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show abstract

“…68 Studies have suggested that the RMSD value should be less than 2.0 Å for the procedure to be reliable. 69 The Autodock Vina programme and Autodock Tools 1.5.6 were used to conduct molecular docking calculations, starting by removing water molecules from the protein structure. 6 Polar hydrogen bonds were added, and Kollman and Gasteiger loadings were distributed over the entire protein structure.…”

Section: Molecular Dockingmentioning

confidence: 99%

Computational approach: 3D-QSAR, molecular docking, ADMET, molecular dynamics simulation investigations, and retrosynthesis of some curcumin analogues as PARP-1 inhibitors targeting colon cancer

Zrinej,

Elmchichi,

Alaqarbeh

et al. 2023

New J. Chem.

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“…The 3D QSAR models were generated using the partial least squares (PLS) method, an extension of multiple regression analysis (Vistoli and Pedretti, 2007). For cross-validation, the leave-one-out method (LOO) was first applied (el Mchichi et al, 2022). Here, a single inhibitor was removed from the data set and the derived model was used to make predictions about the activity of that inhibitor.…”

Section: Partial Least Square Analysismentioning

confidence: 99%

Potent VEGFR-2 inhibitors for resistant breast cancer: a comprehensive 3D-QSAR, ADMET, molecular docking and MMPBSA calculation on triazolopyrazine derivatives

Baammi,

El Allali,

Daoud

2023

Front. Mol. Biosci.

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More people are being diagnosed with resistant breast cancer, increasing the urgency of developing new effective treatments. Several lines of evidence suggest that blocking the kinase activity of VEGFR-2 reduces angiogenesis and slows tumor growth. In this study, we developed novel VEGFR-2 inhibitors based on the triazolopyrazine template by using comparative molecular field analysis (CoMFA) and molecular similarity indices (CoMSIA) models for 3D-QSAR analysis of 23 triazolopyrazine-based compounds against breast cancer cell lines (MCF -7). Both CoMFA (Q2 = 0.575; R2 = 0.936, Rpred2 = 0.956) and CoMSIA/SE (Q2 = 0.575; R2 = 0.936, Rpred2 = 0.847) results demonstrate the robustness and stability of the constructed model. Six novel compounds with potent inhibitory activity were carefully designed, and screening of ADMET properties revealed their good oral bioavailability and ability to diffuse through various biological barriers. When compared with the most active molecule in the data set and with Foretinib (breast cancer drug), molecular docking revealed that the six designed compounds had strengthened affinity (−8.9 to −10 kcal/mol) to VEGFR-2. Molecular Dynamics Simulations and MMPBSA calculations were applied to the selected compound T01 with the highest predicted inhibitory activity, confirming its stability in the active pocket of VEGFR-2 over 100 ns. The present results provided the basis for the chemical synthesis of new compounds with improved inhibitory properties against the breast cancer cell line (MCF -7).

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3D-QSAR study, docking molecular and simulation dynamic on series of benzimidazole derivatives as anti-cancer agents

Cited by 19 publications

References 34 publications

Discover the Medication Potential of Algerian Medicinal Plants Against Sars-Cov-2 Main Protease (Mpro): Molecular Docking, Molecular Dynamic Simulation, and ADMET Analysis

Discover the Medication Potential of Algerian Medicinal Plants Against Sars-Cov-2 Main Protease (Mpro): Molecular Docking, Molecular Dynamic Simulation, and ADMET Analysis

Computational approach: 3D-QSAR, molecular docking, ADMET, molecular dynamics simulation investigations, and retrosynthesis of some curcumin analogues as PARP-1 inhibitors targeting colon cancer

Potent VEGFR-2 inhibitors for resistant breast cancer: a comprehensive 3D-QSAR, ADMET, molecular docking and MMPBSA calculation on triazolopyrazine derivatives

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