Crystallography-based exploration of non-covalent interactions for the design and synthesis of coumarin for stronger protein binding

Abstract

Most of the biological processes are the results of some protein-small molecules interactions. Thus the protein molecules have appeared as a good target for inhibition or promotion of biological processes....

In vitro retardation and modulation of human insulin amyloid fibrillation by Fe3+ and Cu2+ ions

“…ANS is an extrinsic fluorescent probe that interacts nonspecifically with the surface hydrophobic patches of protein molecules 47 with a significant increase of quantum yield. Opening of the hydrophobic clusters in proteins and change of its microenvironment during aggregation is monitored through ANS-fluorescence measurements.…”

“…ThT is a cationic dye having a benzothiazole nucleus that binds strongly with the crossed b-sheet structure of the amyloid fibrils and causes a remarkable enhancement of the emission maxima. 46,47 ThT stock solution of 3.136 mM (1 mg mL À1 ) was prepared by dissolving ThT in HPLC water. From each set of heat incubated and control solutions, aliquots were withdrawn and mixed with ThT solution.…”

“…ANS is an extrinsic fluorescent probe that interacts nonspecifically with the surface hydrophobic patches of protein molecules 47 with a significant increase of quantum yield.…”

Identification of 4-acrylamido-N-(pyridazin-3-yl)benzamide as anti-COVID-19 compound: a DFTB, molecular docking, and molecular dynamics study

“…The binding free energy for the interaction of SARS-CoV-2 M pro protein with Z144 was calculated by the MM-GB/SA method through the surface area-based generalized Born model with a hydrophobic solvent. 54 All the steric clashes of amino acid residues present within 5.0 Å of Z144 was minimized using Prime MM-GB/SA. Here, these residues was allowed to be flexible during the minimization of the system under exploration.…”

Unveiling the catecholase activities and DNA binding interaction of mono-, di-, and polymeric Cu(ii) complexes derived from heterogeneous Schiff base ligands

“…The results of docking studies provide information on the affinity, position, and mode of binding. [46][47][48] In this study, molecular docking was performed to find all the aforementioned parameters for the binding of complexes 1, 2, and 3 with CT-DNA (Fig. 8a-c).…”