Studies on 8-tertbutyl Caffeine: An in silico approach to mechanistic studies

Amminecobalt (III) promoted aerial oxidation of alkyl hydrazines undergoing homolytic alkylation of xanthines selectively at C-8 position. No modeling studies have been done previously on these compounds. An attempt was made to predict the mechanism involved in this spontaneous reaction using molecular modeling. The predictions revealed that homolytic aromatic substitution of alkyl radical exhibits primary isotopic effect. We try to correlate the importance of in silico approaches towards mechanistic studies in such compounds

A Molecular Docking and Pharmacokinetic Prediction of Thiazolidine-2, 4-dione Derivatives: Toward Novel Therapeutic Targets for Type-2 Diabetes Mellitus

Type 2 diabetes mellitus (T2DM) is a leading endocrine disorder that affects millions of people worldwide. It is characterized by hyperglycemia and high insulin resistance. The commonly prescribed oral therapeutic for insulin resistance in T2DM is Thiazolidine-2, 4-diones (TZDs). TZDs are a class of oral hypoglycemic agents that act on Peroxisome proliferator activating receptor-γ (PPAR-γ) receptors and are mainly expressed in the adipose tissues. In this work, we derive novel classes of TZDs and predict the nature of structural affinity using docking studies against the PPAR-γ.

The CAPCI Network: A CAncer Prostate Consortium of India for Conducting Next-Generation Genomic Sequencing Studies

The CAncer Prostate Consortium of India (CAPCI) was established in September 2020 by a group of researchers and clinicians interested in identifying inherited and somatic risk factors that are related to theonset of prostate cancer (PCa). The consortium aims to improve the patient care and treatment in India byexploring and expanding the utility of genomic repositories associated with PCa. These aims are reached by advancing discovery in genome science particular to Indian phenotypes, translating scientific discoveries to improved standard of care. One of the impending goals of the consortium is to combine the data from the west and other sub-population ancestries, and identify common and exclusive risk profiles associated with PCa in Indian scenarios. These findings would additionally allow us to validate in experimental settings to explore the molecular mechanisms underlying pathogenesis of PCa besides understanding new personalized therapeutic regimens

Temperature-Dependent Structure–Function Properties of Bacterial Xylose Isomerase Enzyme for Food Applications: An In Silico Study

Xylose Isomerase (XI) is an intramolecular oxidoreductase enzyme and catalyzes the reversible conversion of ketoses and aldoses in addition to the bioconversion of ethanol from xylose in the production of bioethanol from hemicellulose. It has a broad range of industrial applications in the food and pharmaceutical sectors, particularly in the production of the sweetener high fructose corn syrup (HFCS). It is one of the most widely used industrial enzymes after protease. Taking this into consideration, four bacterial XI sources were selected based on growth temperature, i.e., psychrophile, mesophile, thermophile, and hyperthermophile, for analyzing Xylose Isomerase’s structure-function characteristics. It was found that thermophilic XI was structurally less stable than mesophilic and hyperthermophilic XI, whereas structural plasticity ran opposite towards mesophiles. The interaction of xylose isomerase (XI) with two ligands, namely Amino-2-Hydroxymethyl-Propane-1,3-Diol and (4R)-2-Methylpentane-2,4- Diol, was also studied. Mesophilic XI demonstrated better binding affinity with structurally stabilizing amino acids (Ala, Asp, Gly, Leu, and Arg). In comparison, Thermophilic XI showed nearly similar binding affinity with both Amino-2-Hydroxymethyl-Propane-1,3-Diol and (4R)-2-Methylpentane-2,4-Diol. The results of this investigation suggest that thermophilic XI, followed by mesophilic XI, would be the most appropriate for establishing process stability and sustainability in the food industry

Temperature-Dependent Structure–Function Properties of Bacterial Xylose Isomerase Enzyme for Food Applications: An In Silico Study

Xylose Isomerase (XI) is an intramolecular oxidoreductase enzyme and catalyzes the reversible conversion of ketoses and aldoses in addition to the bioconversion of ethanol from xylose in the production of bioethanol from hemicellulose. It has a broad range of industrial applications in the food and pharmaceutical sectors, particularly in the production of the sweetener high fructose corn syrup (HFCS). It is one of the most widely used industrial enzymes after protease. Taking this into consideration, four bacterial XI sources were selected based on growth temperature, i.e., psychrophile, mesophile, thermophile, and hyperthermophile, for analyzing Xylose Isomerase’s structure-function characteristics. It was found that thermophilic XI was structurally less stable than mesophilic and hyperthermophilic XI, whereas structural plasticity ran opposite towards mesophiles. The interaction of xylose isomerase (XI) with two ligands, namely Amino-2-Hydroxymethyl-Propane-1,3-Diol and (4R)-2-Methylpentane-2,4- Diol, was also studied. Mesophilic XI demonstrated better binding affinity with structurally stabilizing amino acids (Ala, Asp, Gly, Leu, and Arg). In comparison, Thermophilic XI showed nearly similar binding affinity with both Amino-2-Hydroxymethyl-Propane-1,3-Diol and (4R)-2-Methylpentane-2,4-Diol. The results of this investigation suggest that thermophilic XI, followed by mesophilic XI, would be the most appropriate for establishing process stability and sustainability in the food industry

The making of the Women in Biology forum (WiB) at Bioclues.

The Women in Biology forum (WiB) of Bioclues (India) began in 2009 to promote and support women pursuing careers in bioinformatics and computational biology. WiB was formed in order to help women scientists deprived of basic research, boost the prominence of women scientists particularly from developing countries, and bridge the gender gap to innovation. WiB has also served as a platform to highlight the work of established female scientists in these fields. Several award-winning women researchers have shared their experiences and provided valuable suggestions to WiB. Headed by Mohanalatha Chandrasekharan and supported by Dr. Reeta Rani Singhania and Renuka Suravajhala, WiB has seen major progress in the last couple of years particularly in the two avenues Mentoring and Research, off the four avenues in Bioclues: Mentoring, Outreach, Research and Entrepreneurship (MORE). In line with the Bioclues vision for bioinformatics in India, the WiB Journal Club (JoC) recognizes women scientists working on functional genomics and bioinformatics, and provides scientific mentorship and support for project design and hypothesis formulation. As a part of Bioclues, WiB members practice the group's open-desk policy and its belief that all members are free to express their own thoughts and opinions. The WiB forum appreciates suggestions and welcomes scientists from around the world to be a part of their mission to encourage women to pursue computational biology and bioinformatics

Computational exploration of novel antimicrobial modalities targeting fucose-binding lectins and ribosomes in <i>Mycobacterium smegmatis</i> using tRNA-encoded peptides

tRNA-Encoded Peptides (tREPs), encoded by small open reading frames (smORFs) within tRNA genes, have recently emerged as a new class of functional peptides exhibiting antiparasitic activity. The discovery of tREPs has led to a re-evaluation of the role of tRNAs in biology and has expanded our understanding of the genetic code. This presents an immense, unexplored potential in the realm of tRNA-peptide interactions, paving the way for groundbreaking discoveries and innovative applications in various biological functions. This study explores the antimicrobial potential of tREPs against protein targets by employing a computational method that uses verified data sources and highly recognized predictive algorithms to provide a sorted list of likely antimicrobial peptides, which were then filtered for toxicity, cell permeability, allergenicity and half-life. These peptides were then docked with screened protein targets and computationally validated using molecular dynamics (MD) simulations for 150 ns and the binding free energy was estimated. The peptides Pep2 (VVLWRKPRVRKTG) and Pep6 (HRLRLRRRKPWW) exhibited good binding affinities of −110.5 +/− 2.5 and −129.0 +/− 3.9, respectively, with RMSD values of 0.4 and 0.25 nm against the fucose-binding lectin (7NEF) and the 30S ribosome of Mycobacterium smegmatis (5O5J) protein targets. The 7NEF-Pep2 and 5O5J-Pep6 complexes indicated higher negative binding free energies of −52.55 kcal/mol and −55.52 kcal/mol respectively, as calculated by Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA). Thus, the tREPs derived peptides designed as a part of this study, provide novel approaches for potential anti-bacterial therapeutic modalities. Communicated by Ramaswamy H. Sarma</p