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      A comprehensive spectroscopic and computational investigation on the binding of the anti-asthmatic drug triamcinolone with serum albumin

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          Abstract

          Binding study of triamcinolone with BSA through in vitro and in silico approaches, helping in the development of drugs with better therapeutic efficacy.

          Abstract

          The biomolecular interaction of triamcinolone with bovine serum albumin (BSA) was studied using various multi-spectroscopic techniques in combination with in silico studies. UV-visible absorption, fluorescence spectroscopy and resonance Rayleigh scattering studies confirmed the formation of a BSA–triamcinolone complex. The binding constant was found to be in the order of 10 3 M −1. Conformational and microenvironmental changes in BSA after addition of triamcinolone were confirmed by circular dichroism and 3D fluorescence spectroscopy, respectively. The negative values of Δ G and Δ H confirmed spontaneous and exothermic binding. The average binding distance between BSA and triamcinolone was also calculated through FRET. Additionally, the effect of metal ions and β-cyclodextrin on the binding of triamcinolone with BSA was also investigated. Molecular docking and site marker displacement experiments unveiled the binding of triamcinolone to BSA at site III located in subdomain IB of BSA. Molecular dynamics simulation showed lower RMSD values and negative total energy, suggesting favourable binding between BSA and triamcinolone.

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          VMD: Visual molecular dynamics

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            Principles of Fluorescence Spectroscopy

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              g_mmpbsa--a GROMACS tool for high-throughput MM-PBSA calculations.

              Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA), a method to estimate interaction free energies, has been increasingly used in the study of biomolecular interactions. Recently, this method has also been applied as a scoring function in computational drug design. Here a new tool g_mmpbsa, which implements the MM-PBSA approach using subroutines written in-house or sourced from the GROMACS and APBS packages is described. g_mmpbsa was developed as part of the Open Source Drug Discovery (OSDD) consortium. Its aim is to integrate high-throughput molecular dynamics (MD) simulations with binding energy calculations. The tool provides options to select alternative atomic radii and different nonpolar solvation models including models based on the solvent accessible surface area (SASA), solvent accessible volume (SAV), and a model which contains both repulsive (SASA-SAV) and attractive components (described using a Weeks-Chandler-Andersen like integral method). We showcase the effectiveness of the tool by comparing the calculated interaction energy of 37 structurally diverse HIV-1 protease inhibitor complexes with their experimental binding free energies. The effect of varying several combinations of input parameters such as atomic radii, dielectric constant, grid resolution, solute-solvent dielectric boundary definition, and nonpolar models was investigated. g_mmpbsa can also be used to estimate the energy contribution per residue to the binding energy. It has been used to identify those residues in HIV-1 protease that are most critical for binding a range of inhibitors.
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                Author and article information

                Contributors
                (View ORCID Profile)
                Journal
                NJCHE5
                New Journal of Chemistry
                New J. Chem.
                Royal Society of Chemistry (RSC)
                1144-0546
                1369-9261
                March 4 2019
                2019
                : 43
                : 10
                : 4137-4151
                Affiliations
                [1 ]Department of Biochemistry, Faculty of Life Sciences
                [2 ]A.M. University
                [3 ]Aligarh
                [4 ]India
                [5 ]Department of Chemistry
                [6 ]Faculty of Science
                Article
                10.1039/C8NJ05486J
                a5427f2e-9021-41b0-a278-c013995e297c
                © 2019

                http://rsc.li/journals-terms-of-use

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