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Computational studies of drug-binding kinetics

Ganotra, Gaurav Kumar

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The drug-receptor binding kinetics are defined by the rate at which a given drug associates with and dissociates from its binding site on its macromolecular receptor. The lead optimization stage of drug discovery programs usually emphasizes optimizing the affinity (as described by the equilibrium dissociation constant, Kd) of a drug which depends on the strength of its binding to a specific target. Since affinity is optimized under equilibrium conditions, it does not always ensures higher potency in vivo. There has been a growing consensus that, in addition to Kd, kinetic parameters (kon and koff ) should be optimized to improve the chances of a good clinical outcome. However, current understanding of the physicochemical features that contribute to differences in binding kinetics is limited. Experimental methods that are used to determine kinetic parameters for drug binding and unbinding are often time consuming and labor-intensive. Therefore, robust, high-throughput in silico methods are needed to predict binding kinetic parameters and to explore the mechanistic determinants of drug-protein binding. As the experimental data on drug-binding kinetics is continuously growing and the number of crystallographic structures of ligand-receptor complexes is also increasing, methods to compute three dimensional (3D) Quantitative-Structure-Kinetics relationships (QSKRs) offer great potential for predicting kinetic rate constants for new compounds. COMparative BINding Energy(COMBINE) analysis is one example of such approach that was developed to derive target-specific scoring functions based on molecular mechanics calculations. It has been used extensively to predict properties such as binding affinity, target selectivity, and substrate specificity. In this thesis, I made the first application of COMBINE analysis to derive Quantitative Structure-Kinetics Relationships (QSKRs) for the dissociation rates. I obtained models for koff of inhibitors of HIV-1 protease and heat shock protein 90 (HSP90) with very good predictive power and identified the key ligand-receptor interactions that contribute to the variance in binding kinetics.

With technological and methodological advances, the use of all-atom unbiased Molecular Dynamics (MD) simulations can allow sampling upto the millisecond timescale and investigation of the kinetic profile of drug binding and unbinding to a receptor. However, the residence times of drug-receptor complexes are usually longer than the timescales that are feasible to simulate using conventional molecular dynamics techniques. Enhanced sampling methods can allow faster sampling of protein and ligand dynamics, thereby resulting in application of MD techniques to study longer timescale processes. I have evaluated the application of Tau-Random Acceleration Molecular Dynamics (Tau-RAMD), an enhanced sampling method based on MD, to compute the relative residence times of a series of compounds binding to Haspin kinase. A good correlation (R2 = 0.86) was observed between the computed residence times and the experimental residence times of these compounds. I also performed interaction energy calculations, both at the quantum chemical level and at the molecular mechanics level, to explain the experimental observation that the residence times of kinase inhibitors can be prolonged by introducing halogen-aromatic pi interactions between halogen atoms of inhibitors and aromatic residues at the binding site of kinases. I determined different energetic contributions to this highly polar and directional halogen-bonding interaction by partitioning the total interaction energy calculated at the quantum-chemical level into its constituent energy components. It was observed that the major contribution to this interaction energy comes from the correlation energy which describes second-order intermolecular dispersion interactions and the correlation corrections to the Hartree-Fock energy.

In addition, a protocol to determine diffusional kon rates of low molecular weight compounds from Brownian Dynamics (BD) simulations of protein-ligand association was established using SDA 7 software. The widely studied test case of benzamidine binding to trypsin was used to evaluate a set of parameters and a robust set of optimal parameters was determined that should be generally applicable for computing the diffusional association rate constants of a wide range of protein-ligand binding pairs. I validated this protocol on inhibitors of several targets with varying complexity such as Human Coagulation Factor Xa, Haspin kinase and N1 Neuraminidase, and the computed diffusional association rate constants were compared with the experiments. I contributed to the development of a toolbox of computational methods: KBbox (, which provides information about various computational methods to study molecular binding kinetics, and different computational tools that employ them. It was developed to guide researchers on the use of the different computational and simulation approaches available to compute the kinetic parameters of drug-protein binding.

Item Type: Dissertation
Supervisor: Wade, Prof. Dr. Rebecca
Place of Publication: Heidelberg
Date of thesis defense: 13 November 2019
Date Deposited: 19 Nov 2019 14:45
Date: 2020
Faculties / Institutes: The Faculty of Bio Sciences > Dean's Office of the Faculty of Bio Sciences
Subjects: 500 Natural sciences and mathematics
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