Probing the binding ability of vitamin B1 with bovine serum albumin: Calorimetric, light scattering, spectroscopic and volumetric studies

Interaction of the new inhibitor paxlovid (PF-07321332) and ivermectin with the monomer of the main protease SARS-CoV-2: A volumetric study based on molecular dynamics, elastic networks, classical thermodynamics and SPT

“…Although these amounts may seem small, they are indeed significant. Volumetric changes involved in folding or unfolding induced in proteins by ligand binding are very modest ( Azam et al, 2021 , Azam et al, 2020 , Ball, 2017 , Brovchenko et al, 2010 , Kaur et al, 2018 , Pereira et al, 2006 , Persson and Halle, 2018 , Petřek et al, 2007 , Pfeiffer et al, 2008 ). According to Eq.…”

“…1 and 2 ( Filfil et al, 2004 ). This thermodynamic quantity is equivalent to the volume of a cavity dry or anhydrous (know as Voronoi volume) ( Voloshin et al, 2015 ) in solution where the protein molecule has been placed ( Fleming and Fleming, 2018 , Kamerzell and Middaugh, 2008 , Kaur et al, 2018 ). This anhydrous volume will be defined herein after as of protein, which strictly and by definition, is equal to where is the internal void volume of protein and is the part of boundary empty space assigned to the solute ( Voloshin et al, 2015 ).…”

“…In computational biophysics studies, the molecular volume in a fluid is determined using the Voronoi-Delaunay model and this amount is 15% larger than the molecular volume previously defined in Eq. 1 and 2 ( Filfil et al, 2004 ). This thermodynamic quantity is equivalent to the volume of a cavity dry or anhydrous (know as Voronoi volume) ( Voloshin et al, 2015 ) in solution where the protein molecule has been placed ( Fleming and Fleming, 2018 , Kamerzell and Middaugh, 2008 , Kaur et al, 2018 ).…”