Kinetic and Thermodynamic Analysis of Dimerization Inhibitors Binding to HIV Protease Monomers by Surface Plasmon Resonance

Abstract

Here, we describe the analysis of kinetic and thermodynamic parameters for binding of peptide and nonpeptide dimerization inhibitors to immobilized HIV protease (HIVp) monomers by using surface plasmon resonance. Molecular interactions were investigated at different inhibitors concentrations (0-80 μM) and temperatures (15-35°C). The kinetic, equilibrium and thermodynamic parameters have been determined. It was found that both inhibitors were characterized by similar interaction parameters. The complex formation is entropically driven process for both inhibitors. The entropic term(-ТΔS) had the value about -20 kcal/mol while the enthalpic term (ΔH) had the positive value about 14 kcal/mol and counteracted the complex formation.

Mechanism of the Affinity-Enhancing Effect of Isatin on Human Ferrochelatase and Adrenodoxin Reductase Complex Formation: Implication for Protein Interactome Regulation

“…The low level of ADR binding in the Fc4 channel with the FECH dimers could be explained by contaminations with FECH monomers in the channel. The presence of small amounts of monomers after the chemical stabilization of the dimeric form of other proteins was also noted earlier [ 15 , 16 ].…”

Kinetic and thermodynamic analysis of dimerization inhibitors binding to HIV protease monomers by surface plasmon resonance

“…The immobilized HIVp was subsequently monomerized by long term washing with the running buffer; this procedure was accompa nied by gradual dissociation of HIVp dimers [18].…”

“…In our previous study by using bioinformatic methods we predicted several small organic com pounds, which could bind at the interface of HIVp dimerization. Subsequent SPR based biosensoric screening in the monomer dimer test system showed that one potential nonpeptide inhibitor (NPI) of HIVp dimerization (compound NCS 134382, NCI data base) selectively interacted only with the HIVp mono mer and inhibited HIVp enzymatic activity in vitro with the IC 50 value of about 10 -6 M [17,18].…”

“…The main goal of the present study consisted in the comparative kinetic and thermodynamic analysis of interaction of HIVp monomers with known peptide dimerization inhibitor (PI) [19] and NPI found in our previous studies [17,18]. For this purpose we have used the optical biosensor Biacore 3000 based on the effect of surface plasmon resonance (SPR).…”

In Silico Prediction of the Dissociation Rate Constants of Small Chemical Ligands by 3D-Grid-Based VolSurf Method

“…Recently, it has become increasingly apparent that kinetic properties-especially dissociation rate constant (k off ) or drug-target residence time (τ)-are more important for drug potency and are gradually being used in real-world lead optimization and drug design [1][2][3][4][5]. At present, kinetic properties are mainly determined by laboratory techniques, such as capillary electrophoresis, [6] affinity chromatography [7] and surface plasmon resonance methods [8,9], etc. However, there are still many technical difficulties need to be addressed, e.g., more time consumed, high cost and large measurement errors, which limit drug R&D to a large degree.…”