Computational study of molecular electrostatic potential, docking and dynamics simulations of gallic acid derivatives as ABL inhibitors

Raghi, K. R.; Sherin, D.R.; Saumya, M. J.; Arun, P; Sobha, V.N.; Manojkumar, T.K.

doi:10.1016/j.compbiolchem.2018.04.001

Cited by 52 publications

(5 citation statements)

References 30 publications

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“…The molecular electrostatic potential (MEP) can be used to understand hydrogen bonding and the process of biological gratitude [ 53 ]. The MEP also aids in predicting the physicochemical characteristics of a drug-like molecule, allowing it to function as both a hydrogen bond donor and acceptor within its receptor [ 54 ]. The intense red color, indicating electron-rich regions, signifies sites favorable for electrophilic attacks due to an abundance of electrons.…”

Section: Resultsmentioning

confidence: 99%

Modification of ibuprofen to improve the medicinal effect; structural, biological, and toxicological study

Rahman,

Afrin,

Zong

et al. 2024

Heliyon

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Section: Resultsmentioning

confidence: 99%

Modification of ibuprofen to improve the medicinal effect; structural, biological, and toxicological study

Rahman,

Afrin,

Zong

et al. 2024

Heliyon

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“…A multiscale strategy was followed to develop the GA-CG model based on AA-MD simulations. 41,53,54 This work paves the way to enhance our knowledge on the molecular interactions involved in the solvation of biomolecules in QAILS aqueous solutions. In turn, it may help in designing more and highly efficient solubility-enhancing systems for a wide array of substances.…”

Section: Marrink Et Al Developed the Transferable Martini Cg Model Fo...mentioning

confidence: 88%

Using coarse-grained molecular dynamics to rationalize biomolecule solubilization mechanisms in ionic liquid-based colloidal systems

Bastos

Bento

Schaeffer

et al. 2020

Phys. Chem. Chem. Phys.

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“…The most basic demand force of the system is minimized by adding counterions to the system and conjugate gradient algorithm. All operations of the system were carried out under isothermal isobaric ensemble at a pressure of 1.013 bar and a temperature of 300 K [52] . The RMSD diagram of the ligand‐binding protein and protein backbone atoms were generated to understand the relative stability of the ligand within its binding sac and to visualize the ligand‐receptor complex.…”

Section: Methodsmentioning

confidence: 99%

Active Components of Rosa laevigata Michx. Isolated Using Activity‐Guided Methods Based on LC‐MS/MS for Treating Alzheimer's Disease through Multitarget Mechanisms

Gao

Chen

et al. 2023

ChemistrySelect

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Rosa laevigata Michx., a member of the Rosaceae family, is a famous traditional Chinese medicine and edible food in Asian countries. The major active ingredient is triterpenoid, which has anti‐Alzheimer's Disease (AD), antioxidant and neuroprotection properties. However, the properties of “multi‐component structure” and “multi‐directional target” make it impossible to explain the molecular mechanism by conventional ways. The present study aimed to predict the multi‐target mechanisms of triterpenoids in R. laevigata against AD using high performance liquid chromatography equipped with quadrupole time‐of‐flight mass spectrometer (HPLC‐Q‐TOF MS) approach, network pharmacology analysis, dynamics simulation (MDs) and validation of the predicted results with straight‐target tests as well as neuroprotection model. Firstly, bioassay‐guided fractionation of R. laevigata integrated with LC‐MS/MS analysis of the most prospective enriched fractions in terms of anti‐AD efficacy was commenced. Subsequently, multi‐level network model of “multi components‐multi‐targets‐multiple pathways” was established based on the identification of 69 triterpenoids. Complementarily, 64 AD‐related targets were identified through various databases. Network structure analysis illuminated that the intricate pharmacological mechanisms improving cognitive dysfunction of AD was superiorly combined with the crucial targets of APP, APOE, VEGFA, IL1B, MAPT, PSEN1 and BACE and further regulation of principal pathways as HIF‐1 and Calcium signaling pathways. In addition, AChE, BChE and BACE inhibitory activities in vitro showed that nine compounds exhibited potential inhibitory activities. The neuroprotective effects also had a similar effect on H2O2‐induced SH‐SY5Y cell injury. The results show that R. laevigata and its bioactive triterpenoids can pave the way for potential application as inhibitors for treatment of AD.

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Computational study of molecular electrostatic potential, docking and dynamics simulations of gallic acid derivatives as ABL inhibitors

Cited by 52 publications

References 30 publications

Modification of ibuprofen to improve the medicinal effect; structural, biological, and toxicological study

Modification of ibuprofen to improve the medicinal effect; structural, biological, and toxicological study

Using coarse-grained molecular dynamics to rationalize biomolecule solubilization mechanisms in ionic liquid-based colloidal systems

Active Components of Rosa laevigata Michx. Isolated Using Activity‐Guided Methods Based on LC‐MS/MS for Treating Alzheimer's Disease through Multitarget Mechanisms

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