Binding Kinetics Survey of the Drugged Kinome

Abstract

Target residence time is emerging as an important optimization parameter in drug discovery, yet target and off-target engagement dynamics have not been clearly linked to the clinical performance of drugs. Here we developed high-throughput binding kinetics assays to characterize the interactions of 270 protein kinase inhibitors with 40 clinically relevant targets. Analysis of the results revealed that on-rates are better correlated with affinity than off-rates and that the fraction of slowly dissociating drug–target complexes increases from early/preclinical to late stage and FDA-approved compounds, suggesting distinct contributions by each parameter to clinical success. Combining binding parameters with PK/ADME properties, we illustrate in silico and in cells how kinetic selectivity could be exploited as an optimization strategy. Furthermore, using bio- and chemoinformatics we uncovered structural features influencing rate constants. Our results underscore the value of binding kinetics information in rational drug design and provide a resource for future studies on this subject.

A structure–kinetic relationship study using matched molecular pair analysis

“…The kinetic dataset KIND (KINetic Dataset) contains a total of 3812 structures and their kinetic data triplets (k on , k off , K D ). It has been compiled from 21 publications 16,19,[24][25][26][27][28][29][30][31][32][33][34][35][36][37][38][39][40][41][42] and the K4DD database (for details see the ESI, † the dataset is provided in KIND.xlsx). For the literature search, only papers containing numerical values for all three parameters investigated (K D , k on and k off ) were selected.…”

Drug Discovery Researches on Modulators of Lysine-Modifying Enzymes Based on Strategic Chemistry Approaches

“…Our drug discovery studies based on "strategic chemistry approaches" have been successful in the pharmaceutical science field. The achievements have further accelerated our researches and we are currently performing drug discovery studies on modulators for lysine-modifying enzymes based on enzyme inhibition kinetics [152][153][154][155] and in situ click chemistry. [156][157][158] The findings will be presented as articles in the near future.…”

Considerations for improved performance of competition association assays analysed with the Motulsky–Mahan's “kinetics of competitive binding” model

“…The Case 1 described in the introduction prompted us to ask if on‐rates are precisely fitted when the corresponding off‐rates and affinities cannot be determined; the underlying question being whether it is justified to calculate off‐rates as proposed in previous work (Georgi et al, ; Schiele et al, ). Likewise, to better understand if and to what extent Case 2 results can be trusted, we decided to explore the range of rate constants that can be quantified with acceptable precision and accuracy under our experimental conditions for competition association assays.…”

“…In recent years, our laboratory routinely performed high throughput homogenous TR‐FRET‐based competition association assays (also known as kPCA: kinetic probe competition assay, Schiele et al, ) to evaluate hundreds of compounds interacting with several dozens of targets (see Bosma et al, ; de Witte et al, ; Georgi et al, ; Heroven et al, ; Nederpelt et al, ; Schiele et al, ). Typically, k on , k off , and derived affinities ( K D,kin ) of test compounds showed excellent agreement among replicates, and with reference values.…”

“…The second problem ( Case 2 ) manifested itself by k on and k off parameters determined with poor precision (CV > 50%) despite acceptable data quality, and the fact that the corresponding K D,kin was consistent with K D,eq . While in Case 1 , the k off was obtained by multiplying the on‐rate by the K Deq from ePCAs (Schiele et al, ; Georgi et al, ) no meaningful BK values could be extracted from measurements described by Case 2 (Georgi et al, ).…”