Direct evidences for the groove binding of the Clomifene to double stranded DNA

Computational and theoretical exploration for clinical suitability of Remdesivir drug to SARS-CoV-2

“…As per Kamps and Moradi et al ( Kamps et al, 2015 ; Moradi et al, 2018 ), case (i) leads to the dominance of van der Waals interactions along with the hydrogen bonds and case (ii) leads to the dominance of electrostatic interactions in the system respectively. For the present study, Table 2 states that the magnitude of electrostatic interaction [ Linh et al, 2020 ] is highest and hence is dominating over other non-bonded type interactions.…”

“…Here, we are limited to concentrate on entropy term only since = -ve exists in both the cases. We know that entropy is a measure of disorder or randomness in atoms and molecules in a system and since = +ve, implies that the overall increase in degree of the freedom of the system suggest the destruction [ Moradi et al, 2018 ] (disorder) of SARS-CoV-2 (apo form of min protease) with the binding of Remdesivir (ligand).…”

Insights from a combination of theoretical and experimental methods for probing the biomolecular interactions between human serum albumin and clomiphene

“…41 When DH > 0 and DS > 0, the main interaction forces are hydrophobic; a combination of DH < 0 and DS < 0 implies the existence of hydrogen bonds and van der Waals interactions; and the combination DH < 0 and DS > 0 indicates electrostatic interactions. 42 In our work, the negative DG implies a spontaneous interaction process and the negative values for DH and DS indicate that hydrogen bonds and van der Waals interaction forces are involved in CLO and HSA interactions.…”

“…The 3D structure of crystalline HSA shows that this polypeptide contains three homologous domains (named I, II, and III): I (residues 1-195), II (196-383) and III (384-585); and each domain has two distinct subdomains (A and B) that resemble heart shaped molecules. 19,42 The important sites of ligand binding to HSA are located in hydrophobic cavities in the two subdomains IIA and IIIA, which correspond respectively to sites I and II. A tryptophan residue (Trp214) is located in subdomain IIA of HSA.…”

Target SARS-CoV-2: computation of binding energies with drugs of dexamethasone/umifenovir by molecular dynamics using OPLS-AA force field

“…The changes in magnitude and sign of the thermodynamic parameters can be predicted from the main interactions computed between a protein and a ligand (Moradi et al 2018). If changes in enthalpy and entropy are represented by ΔH and ΔS, respectively, then for ΔH > 0 and ΔS > 0, the main dominating interaction forces are hydrophobic; a combination of ΔH < 0 and ΔS < 0 implies the existence and dominance of van der Waals interactions (with hydrogen bonds); and the combination ΔH < 0 and ΔS > 0 indicates the dominance of electrostatic interactions.…”