Exploring the potential of phytoconstituents from Phaseolus vulgaris L against C-X-C motif chemokine receptor 4 : a bioinformatic and molecular dynamic simulations approach

• Published in: Egyptian Journal of Medical Human Genetics 2024-12, Vol.25 (1), p.52-19
• Main Authors: Wahono, Cesarius Singgih, Syaban, Mokhamad Fahmi Rizki, Pratama, Mirza Zaka, Rahman, Perdana Aditya, Erwan, Nabila Erina
• Format: Article
• Language: English
• Subjects: Antagonists; Antioxidants; Arthritis; Beans; Bioavailability; Cancer; Care and treatment; Catechin; Chemokine receptors; Chemokines; CXCR4 protein; Drug development; Flavonoids; G proteins; Health aspects; HIV; HIV infection; Human immunodeficiency virus; Hydrogen bonds; Immune response; Indonesia; Inflammation; Kaempferol; Legumes; Ligands; Lipids; Literature reviews; Macromolecules; Membrane permeability; Membrane proteins; Metastases; Metastasis; Mimosaceae; Molecular dynamics; Mutagenesis; Natural resources; Permeability; Pharmacokinetics; Phaseolus vulgaris; Physiological aspects; Phytochemicals; Proteins; Quercetin; Resveratrol; Simulation; Simulation methods; Software; Stem cells; Toxicity; Tumorigenesis
• ISSN: 1110-8630; 2090-2441
• DOI: 10.1186/s43042-024-00510-9

Introduction The CXCR4 chemokine receptor is a G protein-coupled receptor that plays a role in many physiological processes and diseases, such as cancer metastasis, HIV infection, and immune response. Because of this, it may be possible to target it therapeutically. In addition, the active ingredient of Phaseolus vulgaris L (PVL) has been reported to have anti-inflammatory, antioxidant, and anticancer properties. Novel CXCR4 antagonists from natural resources can be a promising drug development product using a computational approach. This study aims to explore the active compound in PVL that has the responsibility to inhibit CXCR4 using molecular docking and dynamics simulation. Materials and methods Pharmacokinetic analysis were performed using the pkCSM, OSIRIS for toxicity risk analysis, and the PerMM for membrane permeability assessment. Molecular docking was performed using PyRx software to determine the interaction between the CXCR4 target protein from the PDB database and the active component of PVL from the PubChem database. A molecular dynamics (MD) simulation was performed to determine the stability of the interaction using the WEBGRO Macromolecular Simulations online server. The analysis were performed by comparing the results with plerixafor as a control ligand. Results and discussion The pharmacokinetic analysis of quercetin, kaempferol, myricetin, catechin, 3,4-dihydroxybenzoic acid, and daidzin in PVL showed that they met the drug-like criteria. These chemicals were expected to have medium-risk effects on mutagenesis and tumorigenesis, with the exception of catechin, which has no risk of toxicity, and daidzin, which has high-risk effects on mutagenesis and reproduction. Molecular docking identified that quercetin (- 6.6 kcal/mol), myricetin (- 6.6 kcal/mol), catechin (- 6.5 kcal/mol), and 3,4-dihydroxybenzoic acid (- 5.4 kcal/mol) bind to CXCR4 with the highest affinity compared to plerixafor (- 5.0 kcal/mol) and can bind to the same binding pocket with key residues Asp187, Asp97, and Glu288. The MD simulation analysis showed that quercetin has a similar stability interaction compared to the control. Conclusions Considering the pharmacokinetic analysis, molecular docking, and MD simulations, quercetin, myricetin, and 3,4-dihydroxybenzoic acid have the potential to become CXCR4 agonists with their good oral bioavailability and safety properties for the novel drug candidates. Future studies are needed to consider the molecular docking result.