In silico molecular docking and ADME/T analysis of Quercetin compound with its evaluation of broad-spectrum therapeutic potential against particular diseases

Hasan, Md Mahmudul; Khan, Zidan; Chowdhury, Mohammed Salahuddin; Khan, Md. Arif; Moni, Mohammad Ali; Rahman, Habibur

doi:10.1016/j.imu.2022.100894

Cited by 28 publications

(12 citation statements)

References 46 publications

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“…The free energy for hydrogen bonding can range from −1.5 to −4.7 kcal/mol 73,74 . The stronger the H‐bond, the closer it gets to perfect geometry 75,76 . However, strong hydrogen bonding with less than 2.5 Å is subject to dramatically increase the binding affinity 77,78 .…”

Section: Resultsmentioning

confidence: 99%

“…73,74 The stronger the H-bond, the closer it gets to perfect geometry. 75,76 However, strong hydrogen bonding with less than 2.5 Å is subject to dramatically increase the binding affinity. 77,78 In protein-ligand complexes, hydrogen bond interactions increase the specificity and hence contribute to the strength of the interaction.…”

Section: Stabilizing Interactions For Ligands From Bindingdb and Drug...mentioning

confidence: 99%

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In silico identification and analysis of potential inhibitors for acid phosphatase, HppA from Helicobacter pylori

Sisodia

Mazumdar²,

Madhurantakam

2023

J of Molecular Recognition

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Helicobacter pylori is the most common cause of gastric ulcers and is associated with gastric cancer. The enzyme HppA of class C nonspecific acid phosphohydrolases (NSAPs) of H. pylori plays a crucial role in the electron transport chain. Herein, we report an in silico homology model of HppA consisting of a monomeric α + β model. A high throughput structure‐based virtual screening approach yielded potential inhibitors against HppA with higher binding energies. Further analyses of molecular interaction maps and protein–ligand fingerprints, followed by molecular mechanics‐generalized Born surface area (MM‐GBSA) end point binding energy calculations of docked complexes, resulted in the detection of top binders/ligands. Our investigations identified potential substrate‐competitive small molecule inhibitors of HppA, with admissible pharmacokinetic properties. These molecules may provide a starting point for developing novel therapeutic agents against H. pylori.

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Section: Resultsmentioning

confidence: 99%

Section: Stabilizing Interactions For Ligands From Bindingdb and Drug...mentioning

confidence: 99%

In silico identification and analysis of potential inhibitors for acid phosphatase, HppA from Helicobacter pylori

Sisodia

Mazumdar²,

Madhurantakam

2023

J of Molecular Recognition

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“…The Qikprop ADMET results showed quercetin (hit compound) has better pharmacological properties compared to acarbose. The reported ADME properties of quercetin, as well as its tolerable oral toxicity, decreased rat oral toxicology, in addition to the noncarcinogenic or mutagenic potential, 69 further supporting our result.…”

Section: Pharmacokinetic Analysismentioning

confidence: 99%

In Silico and In Vitro Analyses to Repurpose Quercetin as a Human Pancreatic α-Amylase Inhibitor

Raut,

Upadhyaya,

Bashyal

et al. 2023

ACS Omega

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Human pancreatic α-amylase (HPA), situated at the apex of the starch digestion hierarchy, is an attractive therapeutic approach to precisely regulate blood glucose levels, thereby efficiently managing diabetes. Polyphenols offer a natural and multifaceted approach to moderate postprandial sugar spikes, with their slight modulation in carbohydrate digestion and potential secondary benefits, such as antioxidant and antiinflammatory effects. Taking into consideration the unfavorable side effects of currently available commercial medications, we aimed to study a library of polyphenols attributed to their remarkable antidiabetic properties and screened the most potent HPA inhibitor via a comprehensive in silico study encompassing molecular docking, molecular mechanics with generalized Born and surface area solvation (MM/GBSA) calculation, molecular dynamics (MD) simulation, density functional theory (DFT) study, and pharmacokinetic properties followed by an in vitro assay. Significant hydrogen bonding with the catalytic triad residues of HPA, prominent MM/ GBSA binding energy of −27.03 kcal/mol, and the stable nature of the protein−ligand complex with regard to 100 ns MD simulation screened quercetin as the best HPA inhibitor. Additionally, quercetin showed strong reactivity in the substrate-binding pocket of HPA and exhibited favorable pharmacokinetic properties with a considerable inhibitory concentration (IC 50 ) of 57.37 ± 0.9 μg/mL against α-amylase. This study holds prospects for HPA inhibition and suggests quercetin as an approach to therapy for diabetes; however, it is imperative to conduct further research.

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“…In this study, prime MM-GBSA (molecular mechanics/ generalized Born model and solvent accessibility) with the OPLS_2005 force field, VSGB solvent model, 28 and rotamer search algorithms was employed to determine the binding energies and strain energies of thiazolidinediones. The relative binding affinity of ligands to the receptor was evaluated using MM/GBSA calculations, reported in kcal mol −1 .…”

Section: Mm-gbsa Calculationsmentioning

confidence: 99%

Development of novel thiazolidine-2,4-dione derivatives as PPAR-γ agonists through design, synthesis, computational docking, MD simulation, and comprehensive in vitro and in vivo evaluation

Gowdru Srinivasa,

B. C.,

Prabhu

et al. 2023

RSC Med. Chem.

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In silico molecular docking and ADME/T analysis of Quercetin compound with its evaluation of broad-spectrum therapeutic potential against particular diseases

Cited by 28 publications

References 46 publications

In silico identification and analysis of potential inhibitors for acid phosphatase, HppA from Helicobacter pylori

In silico identification and analysis of potential inhibitors for acid phosphatase, HppA from Helicobacter pylori

In Silico and In Vitro Analyses to Repurpose Quercetin as a Human Pancreatic α-Amylase Inhibitor

Development of novel thiazolidine-2,4-dione derivatives as PPAR-γ agonists through design, synthesis, computational docking, MD simulation, and comprehensive in vitro and in vivo evaluation

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