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Synthesis, Biological Evaluation, Molecular Docking, and Molecular Dynamic Simulation Studies of Some New 5-(3,4,5-Trimethoxybenzyl)pyrimidine-2,4-diamine (Trimethoprim) Derivatives via Modified Mannich-Type Reaction
AbstractObjective: This article is focused on synthesis and characterisation of...
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Comparative assessment of different anti-CD147/Basigin 2 antibodies as a potential therapeutic anticancer target by molecular modeling and dynamic simulation
Cluster of differentiation 147 (CD147) is an attractive target for anticancer therapy since it is pivotal in develo** and progressing several of...
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Pharmacophore study, molecular docking and molecular dynamic simulation of virgin coconut oil derivatives as anti-inflammatory agent against COX-2
BackgroundVirgin coconut oil is mostly made up of saturated fatty acids in which approximately 72% are medium chain triglycerides. Medium chain...
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Identification of phytocompounds from Paris polyphylla Smith as potential inhibitors for HER2 & VEGFR2 cancer genes using molecular docking and molecular dynamics simulation studies
In the present studies, molecular docking and molecular dynamic simulation analyses were done to identify phytocompounds from Paris polyphylla as...
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Peptide-Membrane Docking and Molecular Dynamic Simulation of In Silico Detected Antimicrobial Peptides from Portulaca oleracea’s Transcriptome
The main issue with clinical infections is multidrug resistance to traditional antibiotics. As they are essential to innate immunity, shielding hosts...
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Molecular Dynamics Simulation Methods to Study Structural Dynamics of Proteins
Molecular dynamics (MD) simulation is a computational technique for understanding the physical motions of atomic and molecular particles. In this...
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Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS
BackgroundThe molecular dynamics is an approach to obtain kinetic and thermodynamic characteristics of biomolecular structures. The molecular...
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Network pharmacology, molecular docking, and molecular dynamics simulation analysis reveal the molecular mechanism of halociline against gastric cancer
Halociline, a derivative of alkaloids, was isolated from the marine fungus Penicillium griseofulvum by our group. This remarkable compound exhibits...
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Validation of catalytic site residues of Ubiquitin Specific Protease 2 (USP2) by molecular dynamic simulation and novel kinetics assay for rational drug design
Post-translational modifications of proteins such as protein ubiquitination are crucial for regulating conformation, stability and localization of...
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Network pharmacology, molecular docking, and molecular dynamics simulation to elucidate the mechanism of anti-aging action of Tinospora cordifolia
Scientific research has demonstrated that Tinospora cordifolia acts as an anti-aging agent in several experimental models, generating global interest...
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Advancing the field of computational drug design using multicanonical molecular dynamics-based dynamic docking
Multicanonical molecular dynamics (McMD)-based dynamic docking is a powerful tool to not only predict the native binding configuration between two...
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Identification of potential JNK3 inhibitors through virtual screening, molecular docking and molecular dynamics simulation as therapeutics for Alzheimer’s disease
Alzheimer’s disease (AD) is a complex neurological disorder and no effective drug is available for its treatment. Numerous pathological conditions...
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Study of Glabranin as an Inhibitor Against Prostate Cancer: Molecular Docking, Molecular Dynamics Simulation, MM-PBSA Calculation and QSAR Prediction
Prostate cancer is the World's second most frequent malignancy, with the fifth-highest male mortality rate. In advanced prostate cancer patients,...
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Towards new bioactive fluorine-containing 1,3,4-oxadiazole-amide derivatives: synthesis, antibacterial activity, molecular docking and molecular dynamics simulation study
Through the approach of molecular hybridization, this study rationally designed and synthesized new trifluoromethyl-1,3,4-oxadiazole amide...
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Molecular Dynamics Simulation to Study Thermal Unfolding in Proteins
The proper folding of a protein is essential for its biological functions. Thermal denaturation of protein structure has been used as an essential...
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Protein-Protein Interaction Studies Using Molecular Dynamics Simulation
Protein-protein interactionProtein-protein interaction (PPI) is a crucial event for many biological functions. Studying the molecular details of PPI...
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Design, synthesis, molecular docking, and dynamic studies of novel thiazole derivatives incorporating benzimidazole moiety and assessment as antibacterial agents
A general and sustainable approach for the synthesis of benzimidazole-thiazole compounds via an efficient, one-pot, domino, pseudo-four-component...
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Design and Simulation of an Autonomous Molecular Mechanism Using Spatially Localized DNA Computation
As a well-established technique, DNA synthesis offers interesting possibilities for designing multifunctional nanodevices. The micro-processing...
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Molecular Simulation of Stapled Peptides
Constrained peptides represent a relatively new class of biologic therapeutics, which have the potential to overcome several limitations of...
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Optimizing the binding of OGT and a peptidic substrate towards pseudo-substrate inhibitors via molecular dynamic simulations
Elevated O -GlcNAcylation has been shown to be closely correlated with the occurrence and development of cancer, and inhibiting O -GlcNAc transferase...
