Faculty Publications
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Item Computational insights into factor affecting the potency of diaryl sulfone analogs as Escherichia coli dihydropteroate synthase inhibitors(Elsevier Ltd, 2019) Das, B.K.; PV, P.; Chakraborty, D.Dihydropteroate synthase (DHPS) is an alluring target for designing novel drug candidates to prevent infections caused by pathogenic Escherichia coli strains. Diaryl Sulfone (SO) compounds are found to inhibit DHPS competitively with respect to the substrate pABA (p-aminobenzoate). The extra aromatic ring of diaryl sulfone compounds found to stabilize them in highly flexible pABA binding loops. In this present study, a statistically significant 3D-QSAR model was developed using a data set of diaryl sulfone compounds. The favourable and unfavourable contributions of substitutions in sulfone compounds were illustrated by contour plot obtained from the developed 3D-QSAR model. Molecular docking calculations were performed to investigate the putative binding mode of diaryl sulfone compounds at the catalytic pocket. DFT calculations were carried out using SCF approach, B3LYP- 6-31 G (d) basis set to compute the HOMO, LUMO energies and their respective location at pABA binding pocket. Further, the developed model was validated by FEP (Free Energy Perturbation) calculations. The calculated relative free energy of binding between the highly potent and less potent sulfone compound was found to be ?3.78 kcal/ mol which is comparable to the experimental value of ?5.85 kcal/mol. A 10 ns molecular dynamics simulation of inhibitor and DHPS confirmed its stability at pABA catalytic site. Outcomes of the present work provide deeper insight in designing novel drug candidates for pathogenic Escherichia coli strains. © 2018 Elsevier LtdItem Hydrophilicity of the hydrophobic group: Effect of cosolvents and ions(Elsevier B.V., 2019) Dilip, H.N.; Chakraborty, D.Classical molecular dynamics simulations were performed to study the effect of cosolvents and ions on the solvation structure of zwitterionic glycine in liquid water. Simulations were carried out for 2 M and 1 M concentration of TMAO, Urea, KCl and LiCl solutions to observe the changes in liquid structure of water near the glycine molecule. Radial distribution functions and spatial distribution functions showed the presence of protective hydration layer near the C ? in presence of TMAO which gets reduced in case of urea, KCl and minimum in case of LiCl. LiCl is found to disrupt severely the solvation structure near the glycine molecule. For LiCl system, a small hydration layer is found near C ? unit at higher distances which is mainly due to the first hydration shell of lithium ion bonded to the carboxylate group. Presence of these hydration layers gives extra stabilization energy to the glycine water system. Stabilizing and destabilizing effect of water near the glycine molecule is calculated in terms of Potential Mean Force. The anomalous behaviour of lithium salts with respect to Group I cation salts in protein stabilization can be explained on the basis of this behaviour. We found maximum hydrogen bond lifetime for water molecules in presence of TMAO followed by LiCl, KCl and least in case of urea. The higher lifetimes in presence of ions are found mainly due to their electrostatic force. The stabilization of the hydrophobic part of the glycine molecule can be correlated with the stabilization of proteins in presence of these cosolvents. © 2019 Elsevier B.V.Item Effect of cosolvents in the preferential binding affinity of water in aqueous solutions of amino acids and amides(Elsevier B.V., 2020) Dilip, H.N.; Chakraborty, D.Effects of two naturally occurring osmolytes, urea and trimethylamine-N-oxide (TMAO) on the solvation structure of hydrophobic moiety of alanine, glycine, N-methylacetamide and acetamide are investigated by classical molecular dynamics simulations. Our results are analysed in terms of site-site radial distribution functions (RDF), spatial distribution functions (SDF), number of hydrogen bonds, orientation profile, KB integrals, preferential binding coefficient and hydrogen bond dynamics. RDF and SDF showed presence of an extra hydration shell near the hydrophobic unit when TMAO is present in the solution. This hydration shell mainly consists of broken hydrogen bonds. In urea-water solution, intramolecular association is favoured compared to intermolecular association: which is in contrast to the TMAO-water solution. Alanine, glycine, NMA and acetamide showed preferred interactions with the water molecules in presence of TMAO compared to urea. Urea and TMAO both are found to be excluded from the alanine, glycine, NMA and acetamide surface but presence of urea was slightly favoured at higher distances in case of NMA and acetamide. The strong hydrogen bond between TMAO-water increases the hydrogen bond lifetime of other hydrogen bonds in the system. The preferential binding affinity of water with the protein molecules and strong hydrogen bonds are found to be the key reasons for stability in presence of TMAO. © 2019 Elsevier B.V.Item Structural and Thermophysical Anomalies of Liquid Water: A Tale of Molecules in the Instantaneous Low- And High-Density Regions(American Chemical Society service@acs.org, 2020) Priyadarsini, A.; Biswas, A.; Chakraborty, D.; Mallik, B.S.Water is believed to be a heterogeneous liquid comprising multiple density regions that arise because of the presence of interstitial molecules and can be differentiated by their structure as well as the existence of hydrogen-bonded pairs with varying strengths. First-principles molecular dynamics studies were performed at six different temperatures to investigate the effect of temperature on the thermophysical, structure, dynamics, and vibrational spectral properties of the water molecules using dispersion-corrected density functional theory. The variation of properties like density, cohesive energy, and compressibility with a change in temperature produces a trend that matches with the experiments and resembles the experimentally observed anomalous behavior. We explore the possibility of explaining the trends in calculated properties by analyzing the structure and dynamics of the water molecules in terms of instantaneous low- and instantaneous high-density regions that are found during the simulation time. The dynamics of these two types of water molecules were studied by calculating the lifetime from the proposed autocorrelation functions. The lifetime of formation of instantaneous low-density water is found to decrease with an increase in temperature, whereas the lifetime of instantaneous high-density water is found to be maximum at 298 K among all the considered temperatures. The presence of more interstitial water molecules is observed at this temperature. The signature of these water molecules is found in the radial distribution function, spatial distribution function, void distribution, configurational space, orientational dynamics, and spectral diffusion calculations. It is also found that around 298 K, these water molecules are present distinctively that mix up with the first and second solvation shells with the rise of the temperature. The outlook of the reported results can be extended to other thermodynamic conditions to explain some of the anomalous properties, which can be related to the presence of the interstitial molecules in water. © © 2020 American Chemical Society.Item In-silico epitope identification and design of Uricase mutein with reduced immunogenicity(Elsevier Ltd, 2020) Nelapati, A.K.; Das, B.K.; JagadeeshBabu, J.B.; Chakraborty, D.The clinical utilization of Uricase against gout is limited due to the immunogenicity. In the present article, we identified the antigenic determinants of Uricase and reduced their immunogenicity via in-silico mutagenesis. Multiple sequence alignment and motif analysis were carried out to identify the conserved residues in evolutionary process. Emini surface accessibility, Parker hydrophilicity, and Karplus & Schulz flexibility methods were employed to predict the linear B-cell epitopes of both Ag-Uricase and Bf-Uricase. Deimmunization approach identified T-cell epitopes and the hot spot residues. Reduced antigenic probability was obtained in case of T159W, D169C, N264W and Y203D mutations for Ag-Uricase, while S139 V, K215W, G216 F and I172 P mutations for Bf-Uricase. The binding affinity values of uric acid towards the catalytic pocket of Ag-Uricase and Bf-Uricase models were found to be -48.71 kcal/mol and -40.93 kcal/mol, respectively. This energy is further stabilized in the mutant model by -6.36 kcal/mol and -1.45 kcal/mol for Ag-Uricase and Bf-Uricase, respectively. About 100 ns molecular dynamics simulation was performed to evaluate the conformational stability of both native and mutated Uricase. Insights obtained from this study provide guidelines for experimental design of Uricase muteins with reduced antigenicity. © 2020 Elsevier LtdItem Structural and dynamical properties of water in surfactant-like peptide-based nanotubes: Effect of pore size, tube length and charge(Elsevier B.V., 2021) Dilip, H.N.; Chakraborty, D.Atomistic molecular dynamics simulations were carried out to study the structural and dynamical properties of water molecules around pre-assembled surfactant-like peptide (SLP) nanotubes in aqueous media. These SLPs can be thought as a class of biocompatible and biodegradable surfactants for biomedical applications. Nanotube-like structures were considered where glycine and lysine (G6K) are taken as the constituents for the composition of the SLPs. The nanotubes considered were of different dimensions; such as 18 × 15 (number of peptides on the circumference x number of peptides layers), 18 × 12 and 16 × 12 for both charged and neutral analogues. The charged composition consists of protonated nitrogen in the lysine subunit and chlorine/bromine as counter ions. It is found that the neutral SLPs have less hydrated inner core consisting of more tetrahedral water compared to their charged analogues. The hydrogen bond lifetime of water-water and water-peptide molecules increases in the inner pore and found to be maximum for charged 16 × 12 system. Outside the pore, charged analogue of 18 × 15 have more water-water hydrogen bond lifetime compared to all other systems. However, protein-water hydrogen bond lifetime was found to be more for neutral analogues outside the pore due to more probable interactions of SLPs with water molecules. © 2020 Elsevier B.V.Item Preferential binding affinity of ions and their effect on structure and dynamics of water near antimicrobial peptide(Elsevier B.V., 2021) Singh, O.; Chakraborty, D.Water containing dissolved salts is often found to play important roles in many chemical and biological processes. They affect the stability of the amino acids and proteins by altering the liquid water structure. The formation of a mixture of non-uniform density regions in liquid water; commonly known as Low-density water and High-density water is a well-known fact experimentally; which lends uniqueness to the ubiquitous water. The behavior of these different types of water at the interface and the bulk region of the biomolecules around the hydrophobic and hydrophilic residues under the influence of different alkali metal ions, such as LiCl, NaCl, and KCl is an important unexplored question in understanding of many biomolecular processes. To address this, we carried out MD simulation of antimicrobial peptide (PDB ID: 5Z32) for two different model potentials (CHARMM-SPC/E and AMBER-TIP4P) and performed the structural analysis of water in terms of the radial distribution function, number of hydrogen bonds, orientation, tetrahedral order parameter, voids analysis to analyze the related dynamical properties like preferential binding affinity, diffusion, hydrogen bond dynamics, entropy. The water molecules around the hydrophilic environment are found to be more disruptive containing more broken hydrogen bonds in comparison to the hydrophobic environment. It is also found that the water molecules present near the protein surface are of low density and that near the bulk is of high density. This leads to the higher self-diffusion coefficient of the water molecules and less hydrogen bond lifetime at the bulk. The maximum difference is found for the solutions containing high charge density, Lithium ions. Lithium ions have a strong preferential binding affinity towards protein surface resulting in strong solvation shells containing more tetrahedral-like water structure which has low diffusion, low entropy, and higher hydrogen bond lifetime. The diffusion of the water molecules, however, increases towards the higher solvation shells. Potassium on the other hand has less preference to live on protein surfaces resulting in similar diffusion values in the bulk and interface water molecules. © 2021 Elsevier B.V.Item Influence of Ion Specificity and Concentration on the Conformational Transition of Intrinsically Disordered Sheep Prion Peptide(John Wiley and Sons Inc, 2022) Singh, O.; Kumar das, B.; Chakraborty, D.The structural sensitivity of the intrinsically disordered proteins with the ions has been observed experimentally; however, it is still unclear how the presence of different metal ions affects structural stability. We performed an atomistic molecular dynamics simulation of sheep prion peptide (142–167) in presence of different monovalent, divalent ions at various concentrations to find out the effect of the size, charge, and ionic concentration on the structure of the peptide. It is found that Li+ ions have a higher survival probability compared to Na+, K+, and Mg2+ affecting the solvation structure of the protein leading to the alpha-helix structure. At high concentration, due to the increase in the ion-solvent and counter-ion interactions, the effect of the ions is screened on the surface of the protein and hence no ion specificity is observed. This study demonstrates how ions can be used to regulate the protein structure and function that can help in designing drugs. © 2022 Wiley-VCH GmbH.Item Understanding the role of water on temperature-dependent structural modifications of SARS CoV-2 main protease binding sites(Elsevier B.V., 2022) Venugopal, P.P.; Singh, O.; Chakraborty, D.Thermally stable and labile proteases are found in microorganisms. Protease mediates the cleavage of polyproteins in the virus replication and transcription process. 6 µs MD simulations were performed for monomer/dimer SARS CoV-2 main protease system in both SPC/E and mTIP3P water model to analyse the temperature-dependent behaviour of the protein. It is found that maximum conformational changes are observed at 348 K which is near the melting temperature. Network distribution of evolved conformations shows an increase in the number of communities with the rise in the temperature. The global conformation of the protein was found to be intact whereas a local conformational space evolved due to thermal fluctuations. The global conformational change in the free energy ΔΔG value for the monomer and the dimer between 278 K and 383 K is found to be 2.51 and 2.10 kJ/mol respectively. A detailed analysis was carried out on the effect of water on the temperature-dependent structural modifications of four binding pockets of SARS CoV-2 main protease namely, catalytic dyad, substrate-binding site, dimerization site and allosteric site. It is found that the water structure around the binding sites is altered with temperature. The water around the dimer sites is more ordered than the monomer sites regardless of the rise in temperature due to structural rigidity. The energy expense of binding the small molecules at substrate binding is less compared to the allosteric site. The water-water hydrogen bond lifetime is found to be more near the cavity of His41. Also, it is observed that mTIP3P water molecules have a similar effect to that of SPC/E water molecules on the main protease. © 2022 Elsevier B.V.Item Exploring the multiple conformational states of RNA genome through interhelical dynamics and network analysis(Elsevier Inc., 2022) Singh, O.; Venugopal, P.P.; Mathur, A.; Chakraborty, D.The structural variation of RNA is often very transient and can be easily missed in experiments. Molecular dynamics simulation studies along with network analysis can be an effective tool to identify prominent conformations of such dynamic biomolecular systems. Here we describe a method to effectively sample different RNA conformations at six different temperatures based on the changes in the interhelical orientations. This method gives the information about prominent states of the RNA as well as the probability of the existence of different conformations and their interconnections during the process of evolution. In the case of the SARS-CoV-2 genome, the change of prominent structures was found to be faster at 333 K as compared to higher temperatures due to the formation of the non-native base pairs. ΔΔG calculated between 288 K and 363 K are found to be 10.31 kcal/mol (88 nt) considering the contribution from the multiple states of the RNA which agrees well with the experimentally reported denaturation energy for E. coli α mRNA pseudoknot (∼16 kcal/mol, 112 nt) determined by calorimetry/UV hyperchromicity and human telomerase RNA telomerase (4.5–6.6 kcal/mol, 54 nt) determined by FRET analysis. © 2022 Elsevier Inc.