4 research outputs found
Shielded Hydrogen Bonds as Structural Determinants of Binding Kinetics: Application in Drug Design
Time scale control of molecular interactions is an essential part of biochemical systems, but very little is known about the structural factors governing the kinetics of molecular recognition. In drug design, the lifetime of drug–target complexes is a major determinant of pharmacological effects but the absence of structure–kinetic relationships precludes rational optimization of this property. Here we show that almost buried polar atomsa common feature on protein binding sitestend to form hydrogen bonds that are shielded from water. Formation and rupture of this type of hydrogen bonds involves an energetically penalized transition state because it occurs asynchronously with dehydration/rehydration. In consequence, water-shielded hydrogen bonds are exchanged at slower rates. Occurrence of this phenomenon can be anticipated from simple structural analysis, affording a novel tool to interpret and predict structure–kinetics relationships. The validity of this principle has been investigated on two pairs of Hsp90 inhibitors for which detailed thermodynamic and kinetic data has been experimentally determined. The agreement between macroscopic observables and molecular simulations confirms the role of water-shielded hydrogen bonds as kinetic traps and illustrates how our finding could be used as an aid in structure-based drug discovery
Off-Rate Screening (ORS) By Surface Plasmon Resonance. An Efficient Method to Kinetically Sample Hit to Lead Chemical Space from Unpurified Reaction Products
The dissociation rate constant <i>k</i><sub>d</sub> (off-rate) is the component of ligand–protein
binding with the most significant potential to enhance compound potency.
Here we provide theoretical and empirical data to show that this parameter
can be determined accurately from unpurified reaction products containing
designed test compounds. This screening protocol is amenable to parallel
chemistry, provides efficiencies of time and materials, and complements
existing methodologies for the hit-to-lead phase in fragment-based
drug discovery
Application of Off-Rate Screening in the Identification of Novel Pan-Isoform Inhibitors of Pyruvate Dehydrogenase Kinase
Libraries of nonpurified
resorcinol amide derivatives were screened
by surface plasmon resonance (SPR) to determine the binding dissociation
constant (off-rate, <i>k</i><sub>d</sub>) for compounds
binding to the pyruvate dehydrogenase kinase (PDHK) enzyme. Parallel
off-rate measurements against HSP90 and application of structure-based
drug design enabled rapid hit to lead progression in a program to
identify pan-isoform ATP-competitive inhibitors of PDHK. Lead optimization
identified selective sub-100-nM inhibitors of the enzyme which significantly
reduced phosphorylation of the E1α subunit in the PC3 cancer
cell line <i>in vitro</i>
Application of Off-Rate Screening in the Identification of Novel Pan-Isoform Inhibitors of Pyruvate Dehydrogenase Kinase
Libraries of nonpurified
resorcinol amide derivatives were screened
by surface plasmon resonance (SPR) to determine the binding dissociation
constant (off-rate, <i>k</i><sub>d</sub>) for compounds
binding to the pyruvate dehydrogenase kinase (PDHK) enzyme. Parallel
off-rate measurements against HSP90 and application of structure-based
drug design enabled rapid hit to lead progression in a program to
identify pan-isoform ATP-competitive inhibitors of PDHK. Lead optimization
identified selective sub-100-nM inhibitors of the enzyme which significantly
reduced phosphorylation of the E1α subunit in the PC3 cancer
cell line <i>in vitro</i>