Introduction of Intrinsic Kinetics of Protein–Ligand Interactions and Their Implications for Drug Design

Abstract

Structure-kinetic relationship analyses and identification of dominating interactions for optimization of lead compounds should ideally be based on intrinsic rate constants instead of the more easily accessible observed kinetic constants, which also account for binding-linked reactions. The intrinsic rate constants for sulfonamide inhibitors and pharmacologically relevant isoforms of carbonic anhydrase were determined by a novel surface plasmon resonance (SPR) biosensor-based approach, using chemodynamic analysis of binding-linked pH-dependent effects. The observed association rates ( k) were pH-dependent and correlated with the fraction of deprotonated inhibitor and protonated zinc-bound water molecule. The intrinsic association rate constants ( k) were pH independent and higher than k. By contrast, the observed and intrinsic dissociation rate constants were identical and pH-independent, demonstrating that the observed association and dissociation mechanisms are inherently different. A model accounting for the differences between intrinsic and observed rate constants was developed, useful also for other interactions with binding-linked protonation reactions.

Pyrophosphate release acts as a kinetic checkpoint during high-fidelity DNA replication by the Staphylococcus aureus replicative polymerase PolC

“…The biphasic reaction kinetics and the hyperbolic dependence of the fast phase amplitude on nucleotide concentration indicate that the chemical step of bond formation is reversible and is in equilibrium with nucleotide binding, assuming dNTP binding to the Pol•DNA n complex equilibrates rapidly (Figure 1B , steps 2–3), as would be expected for diffusion-limited binding of a small molecule ligand to a macromolecule ( 36 ). Moreover, for such an equilibrium to be established, bond formation must be followed by a slower step, which can be attributed to the post-chemistry steps leading to the release of pyrophosphate (PP i ) byproduct (Figure 1B , step 4).…”

Thermodynamic, kinetic, and structural parameterization of human carbonic anhydrase interactions toward enhanced inhibitor design

“…An example of raw SPR data. Interaction of 368 with CA II at pH 8.0 as described by Linkuvienė et al (2018). The data are shown in black while the globally fitted curvesin red.…”

“…It has been shown that sulfonamide inhibitors bind CAs with an unusually slow association kinetics, too slow to be explained by a diffusion-limited association (Linkuvienė et al ., 2016 b ). We have performed the kinetic measurements as a function of pH and showed that the apparent discrepancy may be explained by the application of the same model that was applied to determine the intrinsic thermodynamic parameters of binding (Linkuvienė et al ., 2018). After the correction of the association rates by the available fractions of the binding-ready deprotonated sulfonamides, the rates appeared to be much more consistent with the diffusion-limited single-step kinetics.…”

Insights into the Molecular Mechanisms of Protein-Ligand Interactions by Molecular Docking and Molecular Dynamics Simulation: A Case of Oligopeptide Binding Protein

“…Protein-ligand interactions play an important role in most biological processes, such as signal transduction, cell regulation, and immune response [16, 17]. Studying protein-ligand interactions continues to be very important in life science fields [18–21].…”