Structure–kinetic relationship study of CDK8/CycC specific compounds

Abstract

In contrast with the very well explored concept of structure-activity relationship, similar studies are missing for the dependency between binding kinetics and compound structure of a protein ligand complex, the structure-kinetic relationship. Here, we present a structure-kinetic relationship study of the cyclin-dependent kinase 8 (CDK8)/cyclin C (CycC) complex. The scaffold moiety of the compounds is anchored in the kinase deep pocket and extended with diverse functional groups toward the hinge region and the front pocket. These variations can cause the compounds to change from fast to slow binding kinetics, resulting in an improved residence time. The flip of the DFG motif ("DMG" in CDK8) to the inactive DFG-out conformation appears to have relatively little influence on the velocity of binding. Hydrogen bonding with the kinase hinge region contributes to the residence time but has less impact than hydrophobic complementarities within the kinase front pocket.kinetic profiling | structure-based drug design T he cyclin-dependent kinase 8/cyclin C (CDK8/CycC) complex is a potent oncogene (1-4), involved in transcription and regulation of transcriptional activity (5-10), linked to epigenetic processes (11), and regarded as an attractive drug target. The recent clinical success of the small molecule inhibitors sorafenib (BAY-43006, Bayer Pharma) and imatinib (STI-571, Novartis Pharma AG) has been attributed to their deep pocket binding mode (12). The "deep pocket" (13) is adjacent to the kinase ATP binding site and accessible in protein kinases by the rearrangement of the DFG motif (a short motif composed of the residues AspPhe-Gly near the N-terminal region of the activation loop) from the active (DFG-in) to the inactive state (DFG-out) (13,14). Binding of a type II compound to such a DFG-out conformation often includes slow binding kinetics (15) with a prolonged "residence time," which is defined as the period for which a target is occupied by a compound (16). Residence time is currently considered to be a key success factor for compound optimization during drug discovery and perhaps as important as the apparent affinity such as half-inhibitory concentration (IC 50 ) or dissociation constant (K d ) (16,17). Accordingly, residence time could be a key to providing enhanced potency in vivo (18) and a means to improve the correlation of in vitro and in vivo efficacy of drugs (19). Despite the increased acceptance of the need to understand binding kinetics, the interplay between compound-target interactions and binding kinetics is in general too complex and poorly understood to enable prediction of the essential dynamic properties. The impact of the combination of kinetic data of proteininhibitor interactions with crystallographic studies has been recognized with pioneer studies such as bovine trypsin in complex with the bovine pancreatic trypsin inhibitor (20). The concept of structure-activity relationships describing the interdependency between binding affinity and compound structure has been well explored in the l...

All-atomic molecular dynamic studies of human CDK8: Insight into the A-loop, point mutations and binding with its partner CycC

“…The published structure of the ternary complex of CDK8-CycC with CDK8 inhibitor sorafenib was the first to show a DFG-out conformation (DMG-out in CDK8) for a CDK in complex with a small-molecule inhibitor [25, 42]. The recent kinetic study indicated that the structure of CDK8-CycC implicates specificity in the CDK-cyclin family and reveals interaction with a deep pocket binder.…”

Drug–Target Kinetics in Drug Discovery

“…Examples where changes in structure within a compound series lead to a decrease in both IC 50 and k off include inhibitors of Pseudomonas LpxC, 21 human protein methyltransferase DOT1L, 32 and CDK8/CycC. 33 In addition, if stabilization of E-I also results in stabilization of the transition state, then once the theoretical limit for k on is reached, which is the second order rate constant for encounter of drug and target (10 9 M –1 s –1 ), any further increase in affinity must lead to a reduction in the off-rate. A simple calculation reveals that the residence time of a 1 pM drug on the target must be at least 12 min whereas a 1 fM drug will have a residence time of at least 11.5 days.…”

“…In addition, kinase enzymology has been heavily studied, and thus in many cases there is a detailed understanding of mechanisms that lead to long residence time inhibition, such as binding to the DFG-out conformation or the development of covalent inhibitors. 33,64,65 Finally, recognition of the potential importance of kinetic selectivity has stimulated the interrogation of structure kinetic relationships for both purified kinases and for kinase inhibitors in cell-based assays. 66−68 For example, as noted above, although lapatinib binds ∼10-fold less potently to EGFR than gefitinib ( K i app values of 3 and 0.4 nM, respectively), the residence time of lapatinib on EGFR is >30-fold longer (430 and <14 min).…”

Binding Thermodynamics and Kinetics Calculations Using Chemical Host and Guest: A Comprehensive Picture of Molecular Recognition

“…Efforts have been devoted to studies of kinetic–structure relations. 11–14 Computational methods, which have the advantage of an atomistic resolution, are useful tools to investigate the fundamentals of thermodynamics and kinetics. With the recent breakthrough in computational powers, molecular dynamics (MD) is able to simulate up to microsecond or millisecond time scale molecular motions.…”