Computational investigation of phytochemicals identified from medicinal plant extracts against tuberculosis

Elucidating the therapeutic potential of indazole derivative bindarit against K-ras receptor: An in-silico analysis using molecular dynamics exploration

Ras gene is frequently mutated in cancer. Among different subtypes of Ras gene, K-Ras mutation occurs in nearly 30 % of human cancers. K-Ras mutation, specifically K-Ras (G12D) mutation is prevalent in cancers like lung, colon and pancreatic cancer. During cancer occurrence, mutant Ras remain in activated form (GTP bound state) for cancer cell proliferation. In the quest for a potential K-Ras inhibitor, nitrogen-containing indazole derivatives can show promise as inhibitors, as they have numerous therapeutic properties like anti-inflammatory, anti-viral and anti-tumor. Furthermore, among various indazole derivatives, "Bindarit" is an important therapeutic compound which could have potential inhibitory action against K-Ras due to its structural resemblance with reference compound "Benzimidazole". So, the current study is an attempt to find out the inhibitory effect of Bindarit against K-Ras activation by binding to a pocket which is adjacent to the switch I/II regions of the K-Ras receptor. AutoDock tool was used to investigate the binding affinity of protein ligand interaction and GROMACS package was utilised to assess their interactions in a dynamic setting. Bindarit shows better binding affinity than reference with binding energy of -7.3 kcal/mol. Upon ligand binding conformational changes take place, which could lead to the loss of GTPase activity. Consequently, further downstream signalling of the K-Ras pathway would be blocked and this could lead to the inhibition of K-Ras dependent cancer cell proliferation. However, further validation of present study can be done through experimental assay such as cytotoxic and protein expression analysis.

Anti-diabetic drug discovery using the bioactive compounds of Momordica charantia by molecular docking and molecular dynamics analysis

Diabetes mellitus (DM) is a multifactorial life-threatening endocrine disease characterized by abnormalities in glucose metabolism. It is a chronic metabolic disease that involves multiple enzymes such as α-amylase and α-glucosidases. Inhibition of these enzymes has been identified as a promising method for managing diabetes, and researchers are currently focusing on discovering novel α-amylase and α-glucosidase inhibitors for diabetes therapy. Hence, we have selected 12 bioactive compounds from the Momordica charantia (MC) plant and performed a virtual screening and molecular dynamics investigation to identify natural inhibitors of α-amylase and α-glucosidases. Our in silico result revealed that phytocompound Rutin showed the highest binding affinity against α-amylase (1HNY) enzymes at (-11.68 kcal/mol), followed by Karaviloside II (-9.39), Momordicoside F (-9.19), Campesterol (-9.11. While docking against α-glucosidases (4J5T), Rutin again showed the greatest binding affinity (-11.93 kcal/mol), followed by Momordicine (-9.89), and Campesterol (-8.99). Molecular dynamics (MD) simulation research is currently the gold standard for drug design and discovery. Consequently, we conducted simulations of 100 nanoseconds (ns) to assess the stability of protein-ligand complexes based on parameters like RMSD, RMSF, RG, PCA, and FEL. The significance of our findings indicates that rutin from MC might serve as an effective natural therapeutic agent for diabetes management due to its strongest binding affinities with α-amylase and α-glucosidase enzymes. Further research in animals and humans is essential to validate the efficacy of these drug molecules.

Rosmarinic acid and its derivative's duel as antitubercular agents: insights from computational prediction to functional response in vitro

Tuberculosis is one of the most dreadful infectious diseases, afflicting global populations with anguish. With the emergence of multi-drug resistant strains of mycobacteria, the imperative for new anti-tuberculosis drugs has grown exponentially. Thus, the current study delves into evaluating the impact of Perovskia abrotanoides and its active metabolites-namely, rosmarinic acid and its derivatives-against strains of Mycobacterium tuberculosis (Mtb). Through the use of the CRI assay, the antimycobacterial potential of the high-altitude medicinal plant P. abrotanoides was gauged, while docking and molecular dynamics simulations unveiled plausible targets. Of these, the peak antimycobacterial effectiveness was observed in the P. abrotanoides ethyl acetate extract with 125 µg/mL as minimum inhibitory concentration against various strains of M. tuberculosis, encompassing H37Rv and strains resistant to multiple drugs. Following bioassay-guided fractionation and isolation, rosmarinic acid and rosmarinic acid methyl ester emerged as potent molecules against H37Rv and multidrug-resistant M. tuberculosis strains; minimum inhibitory concentration ranging from 15 to 32 µg/mL. Additionally, out of 22 targets explored, Mtb lipoamide dehydrogenase (PDB: 3II4) and Rv2623 (PDB: 3CIS) were forecasted as potential Mtb targets for rosmarinic acid and rosmarinic acid methyl ester, respectively, a supposition further affirmed by molecular simulations (100 ns). The stability of both complexes throughout the simulation was measured by protein backbone root-mean-square deviation, substantiating their roles as respective targets for antimycobacterial activities.Communicated by Ramaswamy H. Sarma.