Terpenoid phytocompounds from mangrove plant Xylocarpus moluccensis as possible inhibitors against SARS-CoV-2: In silico strategy

Exploring the DPP IV inhibitory potential: molecular docking and dynamic simulations of pyridine-3-carboxylic acid and pyrrolidine-2-carboxylic acid analogs

Diabetes mellitus remains a global challenge, with Type 2 Diabetes Mellitus (T2DM) prevalence increasing from 4% to 6.4% in the past 30 years. Presently oral hypoglycaemic agents like GLP-1 agonists, biguanides, sulphonylureas, glinides, and thiazolidinediones are employed in clinical practice. Very recently, novel targets including Dipeptidyl peptidase IV (DPP IV), PPAR, GIP, FFA1, and melatonin have been in the limelight for the development of novel treatment strategies. The present study focuses on the development of DPP IV inhibitors through computational approaches. DPP IV, also referred to as CD26 (cluster of differentiation 26) or adenosine deaminase complexing protein 2, is a protein that is encoded by the DPP IV gene in humans. This enzyme is involved in the metabolism of incretin hormones such as glucagon-like peptides (GLP-1). DPP IV inhibitors prevent the degradation of GLP-1, glucose-dependent insulinotropic peptide (GIP), thereby controlling the concentration of glucose in the blood. Considering the safety and efficacy of DPP IV inhibitors newer molecules were designed with better binding affinity with the protein as compared to existing Sitagliptin, and Vildagliptin-like drugs. Derivatives of nicotinic acid and proline were designed and studied using molecular docking and dynamic simulations. Docking results demonstrated that the NA-13 molecule possesses potent binding affinity with target protein 6B1E (-38.1498 kcal/mol) as compared to standard Sitagliptin (-33.3187 kcal/mol). MD simulation studies showcased that there are fewer variations of RMSD and RMSF for 6B1E-NA-13, 6B1E-P1, and 6B1E-P7 complexes, suggesting the potential of the designed DPP IV inhibitors in the management of T2DM.

Cracking a cancer code DNA methylation in epigenetic modification: an in-silico approach on efficacy assessment of Sri Lanka-oriented nutraceuticals

DNA methyltransferase (DNMTs) are essential epigenetic modifiers that play a critical role in gene regulation. These enzymes add a methyl group to cytosine's 5'-carbon, specifically within CpG dinucleotides, using S-adenosyl-L-methionine. Abnormal overexpression of DNMTs can alter the gene expression patterns and contribute to cancer development in the human body. Therefore, the inhibition of DNMT is a promising therapeutic approach to cancer treatment. This study was aimed to identify potential nutraceutical inhibitors from the Sri Lanka Flora database using computational methods, which provided an atomic-level description of the drug binding site and examined the interactions between nutraceuticals and amino acids of the DNMT enzyme. A series of nutraceuticals from Sri Lanka-oriented plants were selected and evaluated to assess their inhibitory effects on DNMT using absorption, distribution, metabolism, excretion and toxicity analysis, virtual screening, molecular docking, molecular dynamics simulation and trajectory analysis. Azacitidine, a DNMT inhibitor approved by the US Food and Drug Administration, was selected as a reference inhibitor. The complexes with more negative binding energies were selected and further assessed for their potency. Seven molecules were identified from 200 nutraceuticals, demonstrating significantly negative binding energies against the DNMT enzyme. Various trajectory analyses were conducted to investigate the stability of the DNMT enzyme. The results indicated that petchicine (NP#0003), ouregidione (NP#0011) and azacitidine increased the stability of the DNMT enzyme. Consequently, these two nutraceuticals showed inhibitory efficacies similar to azacitidine, making them potential candidates for therapeutic interventions targeting DNMT enzyme-related cancers. Additional bioassay testing is recommended to confirm the efficacies of these nutraceuticals and explore their applicability in clinical treatments.