Protein conformational flexibility modulates kinetics and thermodynamics of drug binding

Abstract

Structure-based drug design has often been restricted by the rather static picture of protein–ligand complexes presented by crystal structures, despite the widely accepted importance of protein flexibility in biomolecular recognition. Here we report a detailed experimental and computational study of the drug target, human heat shock protein 90, to explore the contribution of protein dynamics to the binding thermodynamics and kinetics of drug-like compounds. We observe that their binding properties depend on whether the protein has a loop or a helical conformation in the binding site of the ligand-bound state. Compounds bound to the helical conformation display slow association and dissociation rates, high-affinity and high cellular efficacy, and predominantly entropically driven binding. An important entropic contribution comes from the greater flexibility of the helical relative to the loop conformation in the ligand-bound state. This unusual mechanism suggests increasing target flexibility in the bound state by ligand design as a new strategy for drug discovery.

Ligand‐Induced Conformational Changes in HSP90 Monitored Time Resolved and Label Free—Towards a Conformational Activity Screening for Drug Discovery

“…23 and this work). The compound interaction spectra of all eight compounds are shown in Figure S6 (black spectra).…”

“…SPR experiments on cmpds 4, 5, 7, and 8 were conducted as described previously23 for the other compounds (cmpds 1–3, 6, and 9–19). For details and further experimental information see the Supporting Information.…”

Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape

“…2,18,19 Several classes of pharmaceutically relevant proteins such as kinases, 20 transferases, 21 synthases, 22 and dehydrogenases 23 undergo structural rearrangements leading to compaction upon ligand binding. 24,25 In order to improve in silico structure-based drug design, it is crucial to account for these structural rearrangements (particularly those occurring at the binding site) when predicting drug binding and related thermodynamic and kinetic properties. 3,8,9,26 Several algorithms have been developed over the last decades to deal with protein flexibility in docking.…”

Exhaustive search of the configurational space of heat‐shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking

“…Analysis of the multicanonical ensemble also showed that more than 50% of the near‐native configurations was in a helical state, compared to only 6% percent in an unbound state. Amaral et al found that larger ligands tend to be bound to the helical conformation, while smaller ligand tend to be bound to the loop‐in conformation [ 32 ] This would suggest that steric clashes induced by the ligand upon binding flips the conformation from a loop‐in state to a helical one. Although CPD3 would be classified as a small ligand, also in part because the crystal structure of BSM is in a loop‐in conformation, the ligand still induces some steric effects upon the FHL.…”

“…Most inhibitors to Hsp90 such as geldanamycin [ 29 ] that bind to the nucleotide binding pocket of the N‐terminal domain inhibit ATP binding, leading to a reduction of the protein's function. Hsp90 consists of a highly flexible region called the lid that ranges from 107 to 141, [ 30 ] where residues 104 to 111, with the sequence INNLGTIA, are known to adopt either a loop (loop‐in or loop‐out) or helical conformation, depending on the ligand bound inside the pocket, [ 31,32 ] which we will refer to as the flexible helix loop (FHL) region from hereon.…”