Biology subjects

Khedkar, A.

Publications and source records attributed to Khedkar, A..

3 recordsLinked to original sources

bioRxiv2023

Mapping Structural Drivers of Insulin and its Analogs at the IGF-1 Receptor Using Molecular Dynamics and Free Energy Calculations

Insulin and insulin-like growth factor-1 receptors (IR, IGF-1R) belong to the family of receptor tyrosine kinases (RTKs), and share close structural resemblance. However, these receptors exhibit distinct activity profiles and functions in vivo. Binding of insulin to IGF-1R results in additional growth-factor-like behavior and cell proliferation, but its [~]100-fold reduced affinity to IGF-1R limits off-target activity. However, insulin analogs with increased potency at IGF-1R have oncogenicity as a key safety concern. Hence, the ability to accurately predict potency of novel analogs at IGF-1R could represent a key breakthrough towards rational insulin design. To date, a comprehensive molecular level understanding of insulin interactions at IGF-1R has remained elusive. This study capitalized on recent advancements in structural biology that provided high resolution structures of IGF-1R bound to IGF-1 and insulin. Initially, molecular dynamics (MD) simulations were employed to unravel the intricate interactions that characterize the receptor-ligand pairs. Next, free energy perturbation (FEP) calculations were performed to understand the increased affinity observed in insulin analogs, X10 and glargine. Subsequently, multiple mutations at the B10 position of insulin spanning different activities at IGF-1R and different metabolites of insulin glargine, encompassing various mitogenic potencies were studied using FEP. The calculations successfully captured directional shifts in potency for all studied mutants, with approximately 50% of the predicted values falling within 1 kcal/mol of experiment. Beyond its impressive accuracy, FEPs ability to provide a detailed understanding of protein- and solvent-mediated contributions to the observed functional profiles underscores its utility in designing safe IGF-1R selective novel insulin analogs.

biophysics↗

bioRxiv2022

Mapping the Structural Drivers of Insulin Recognition and Specificity Using Molecular Dynamics and Free Energy Calculations

A century on from the discovery of insulin, a complete understanding of insulin interactions with the insulin receptor (IR) at atomic level remains elusive. In this work, we have leveraged recent advancements in structural biology that have resulted in multiple high-resolution structures of the insulin-IR complex. As a first step, we employed molecular dynamics (MD) simulations to unravel atomic insights into the interactions between insulin-IR complexes in order to better understand ligand recognition at the receptor. The MD simulations were followed up with free energy perturbation (FEP) calculations to discriminate between and elucidate the drivers for ligand association for various natural and man-made insulin analogs. As an example, these calculations were utilized to understand the molecular mechanisms that characterized the loss-of-function seen in disease-associated insulin mutations seen in different populations. Further, multiple man-made insulin analogs spanning a range of potencies, mutations, and sequence lengths were studied using FEP and a comprehensive molecular level map of potency determinants were established. [~]85% of FEP calculations captured the direction of shift of potency, and in [~]53% of cases the predictions were within 1 kcal/mol of experiment. The impressive accuracy of FEP in recapitulating functional profiles across such a span of insulin analogs and potency profiles provided clear evidence of its utility in computational mutagenesis. In addition to the impressive accuracy, the ability of FEP to provide a dissected understanding of protein residue, solvent and solvent-mediated contributions to binding energy clearly establishes its utility in the design of novel insulins and peptides in general.

biophysics↗

bioRxiv2020

Isolation, identification and functional characterization of cultivable bacteria from Arabian Sea and Bay of Bengal water samples reveals high diversity

The oxygen minimum zone of the Arabian Sea (AS) and Bay of Bengal (BOB) is rich in organic matter and is an unusual niche. Bacteria present in the oceanic water play an important role in ecology since they are responsible for decomposing, mineralizing of organic matter and in elemental cycling like nitrogen, sulfur, phosphate. This study focuses on culturing bacteria from oxygen minimum zones (OMZ) and non-OMZ regions and their phylogenetic as well as the functional characterization. Genotypic characterization of the isolates using amplified rDNA based 16SrRNA sequencing grouped them into various phylogenetic groups such as alpha-proteobacteria, gamma-proteobacteria and unaffiliated bacteria. The cultivable bacterial assemblages encountered belonged to the genus Halomonas, Marinobacter, Idiomarina, Pshyctobacter and Pseudoalteromonas. Among the enzymatic activities, carbohydrate utilization activity was most predominant (100%) and microorganisms possessed amylase, cellulase, xylanase and chitinase. A large proportion of these bacteria (60%) were observed to be hydrocarbon consuming and many were resistant to ampicillin, chloramphenicol, kanamycin and streptomycin. The high diversity and high percentage of extracellular hydrolytic enzyme activities along with hydrocarbon degradation activity of the culturable bacteria reflects their important ecological role in oceanic biogeochemical cycling. Further assessment confirmed the presence of nitrogen reduction capability in these cultivable bacteria which highlights their importance in oceanic geochemical cycling.

microbiology↗