High throughput virtual screening and molecular dynamics simulation analysis of phytomolecules against BfmR of <i>Acinetobacter baumannii</i>: anti-virulent drug development campaign

Lokhande, Kiran Bharat; Pawar, Sarika; Madkaiker, Smriti; Nawani, Neelu; Venkateswara, Swamy K; Ghosh, Payel

doi:10.1080/07391102.2022.2038271

Cited by 21 publications

(7 citation statements)

References 72 publications

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“…During the 20 ns MD simulation, the time step was 2 fs, and the structural coordinates were saved every 10 ps. We evaluated various parameters of MD, such as RMSD, Root Mean Square Fluctuation (RMSF), and hydrogen bonding (H-bond) monitoring reports 49 . In addition, the non-bond interaction energies between proteins and ligands, including short-range electrostatic interactions and van der Waals (Vdw), were also calculated 50 .…”

Section: Methodsmentioning

confidence: 99%

Bioinformatics and computational chemistry approaches to explore the mechanism of the anti-depressive effect of ligustilide

Zhang

Teng

et al. 2023

Sci Rep

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Depression affects people with multiple adverse outcomes, and the side effects of antidepressants are troubling for depression sufferers. Aromatic drugs have been widely used to relieve symptoms of depression with fewer side effects. Ligustilide (LIG) is the main component of volatile oil in angelica sinensis, exhibiting an excellent anti-depressive effect. However, the mechanisms of the anti-depressive effect of LIG remain unclear. Therefore, this study aimed to explore the mechanisms of LIG exerting an anti-depressive effect. We obtained 12,969 depression-related genes and 204 LIG targets by a network pharmacology approach, which were intersected to get 150 LIG anti-depressive targets. Then, we identified core targets by MCODE, including MAPK3, EGF, MAPK14, CCND1, IL6, CASP3, IL2, MYC, TLR4, AKT1, ESR1, TP53, HIF1A, SRC, STAT3, AR, IL1B, and CREBBP. Functional enrichment analysis of core targets showed a significant association with PI3K/AKT and MAPK signaling pathways. Molecular docking showed strong affinities of LIG with AKT1, MAPK14, and ESR1. Finally, we validated the interactions between these proteins and LIG by molecular dynamics (MD) simulations. In conclusion, this study successfully predicted that LIG exerted an anti-depressive effect through multiple targets, including AKT1, MAPK14, and ESR1, and the pathways of PI3K/AKT and MAPK. The study provides a new strategy to explore the molecular mechanisms of LIG in treating depression.

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Section: Methodsmentioning

confidence: 99%

Bioinformatics and computational chemistry approaches to explore the mechanism of the anti-depressive effect of ligustilide

Zhang

Teng

et al. 2023

Sci Rep

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“…In this study, chain A has been selected which was prepared using Schrodinger's Protein Preparation Wizard and utilized for next-level investigation. Input data of the receptor must be compiled by determining the receptor atoms, calculating the essential hydrogen atom's position, and defining and specifying the atoms of the binding site [ 51 , 52 ].…”

Section: Methodsmentioning

confidence: 99%

GC-MS profiling of Bauhinia variegata major phytoconstituents with computational identification of potential lead inhibitors of SARS-CoV-2 Mpro

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Lokhande

Swamy

et al. 2022

Computers in Biology and Medicine

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“…Furthermore, 50,000 steps of minimization and 100 ns of unrestrained MD were performed. Then, short-range electrostatic and van der Waals interactions were computed with a distance cut-off of 1.0 nm 18 , 44 , 45 . After equilibration, coordinates were saved every 2 ps during the sampling process.…”

Section: Methodsmentioning

confidence: 99%

The novel anti-cancer feature of Brazzein through activating of hTLR5 by integration of biological evaluation: molecular docking and molecular dynamics simulation

Poursalim

Shasaltaneh

Jafarian

et al. 2022

Sci Rep

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Many of plant proteins exhibit the properties similar to the antitumor proteins although the anticancer activity of Brazzein on modulating the autophagy signaling pathway has not been determined so far. The present study aimed to develop a simplified system to enable the rational design of the activating extracellular domain of human Toll-like receptor 5 (hTLR5). To identify the anticancer effect of Brazzein, HADDOCK program and molecular dynamics (MD) simulation were applied to examine the binding of the wild type (WT) and p.A19K mutant of Brazzein to the TLR5. The expression of MAP1S and TNF-α genes was estimated based on real-time PCR. The results clearly confirmed that the WT of Brazzein activated hTLR5 in the MCF-7 cell line since the genes were more and significantly less expressed in the cells treated with the WT and p.A19K mutant than the control, respectively. The snapshots of MD simulation exhibit the consistent close interactions of hTLR5 with the two helices of Brazzein on its lateral side. The results of per residue-free energy decomposition analysis substantiate those of intermolecular contact analysis perfectly one. We propose that the WT of Brazzein can act as an antitumor drug candidate.

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High throughput virtual screening and molecular dynamics simulation analysis of phytomolecules against BfmR of Acinetobacter baumannii: anti-virulent drug development campaign

Cited by 21 publications

References 72 publications

Bioinformatics and computational chemistry approaches to explore the mechanism of the anti-depressive effect of ligustilide

Bioinformatics and computational chemistry approaches to explore the mechanism of the anti-depressive effect of ligustilide

GC-MS profiling of Bauhinia variegata major phytoconstituents with computational identification of potential lead inhibitors of SARS-CoV-2 Mpro

The novel anti-cancer feature of Brazzein through activating of hTLR5 by integration of biological evaluation: molecular docking and molecular dynamics simulation

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