Drug-target kinetics has recently emerged as an especially important facet of the drug discovery process. In particular, prolonged drug-target residence times may confer enhanced efficacy and selectivity in the open in vivo system. However, the lack of accurate kinetic and structural data for series of congeneric compounds hinders the rational design of inhibitors with decreased off-rates. Therefore, we chose the Staphylococcus aureus enoyl-ACP reductase (saFabI) - an important target for the development of new anti-staphylococcal drugs - as a model system to rationalize and optimize the drug-target residence time on a structural basis. Using our new, efficient and widely applicable mechanistically informed kinetic approach, we obtained a full characterization of saFabI inhibition by a series of 20 diphenyl ethers complemented by a collection of 9 saFabI-inhibitor crystal structures. We identified a strong correlation between the affinities of the investigated saFabI diphenyl ether inhibitors and their corresponding residence times, which can be rationalized on a structural basis. Due to its favorable interactions with the enzyme, the residence time of our most potent compound exceeds 10 hours. In addition, we found that affinity and residence time in this system can be significantly enhanced by modifications predictable by a careful consideration of catalysis. Our study provides a blueprint for investigating and prolonging drug-target kinetics and may aid in the rational design of long-residence-time inhibitors targeting the essential saFabI enzyme.
T-cell receptor variability gives rise to a functional hierarchy of human invariant Natural Killer T-cells through a powerful effect on CD1d binding affinity, which is independent of CD1d ligands.
Slow-onset enzyme inhibitors are
of great interest for drug discovery
programs since the slow dissociation of the inhibitor from the drug–target
complex results in sustained target occupancy leading to improved
pharmacodynamics. However, the structural basis for slow-onset inhibition
is often not fully understood, hindering the development of structure-kinetic
relationships and the rational optimization of drug-target residence
time. Previously we demonstrated that slow-onset inhibition of the Mycobacterium tuberculosis enoyl-ACP reductase InhA correlated
with motions of a substrate-binding loop (SBL) near the active site.
In the present work, X-ray crystallography and molecular dynamics
simulations have been used to map the structural and energetic changes
of the SBL that occur upon enzyme inhibition. Helix-6 within the SBL
adopts an open conformation when the inhibitor structure or binding
kinetics is substrate-like. In contrast, slow-onset inhibition results
in large-scale local refolding in which helix-6 adopts a closed conformation
not normally populated during substrate turnover. The open and closed
conformations of helix-6 are hypothesized to represent the EI and
EI* states on the two-step induced-fit reaction coordinate for enzyme
inhibition. These two states were used as the end points for nudged
elastic band molecular dynamics simulations resulting in two-dimensional
potential energy profiles that reveal the barrier between EI and EI*,
thus rationalizing the binding kinetics observed with different inhibitors.
Our findings indicate that the structural basis for slow-onset kinetics
can be understood once the structures of both EI and EI* have been
identified, thus providing a starting point for the rational control
of enzyme–inhibitor binding kinetics.
Background:The FabI inhibitor CG400549 is a promising new anti-staphylococcal drug candidate with recently validated human efficacy. Results: We revealed the molecular determinants conferring S. aureus FabI selectivity to rationally design a compound with an improved antibacterial activity spectrum.
Conclusion:The 4-pyridone PT166 represents a critical step toward Gram-negative and mycobacterial coverage. Significance: We provide an approach to expand the spectrum of antimicrobial activity.
The diaryl ethers are a novel class of antituberculosis drug candidates that inhibit InhA, the enoyl-ACP reductase involved in the fatty acid biosynthesis (FASII) pathway, and have antibacterial activity against both drug-sensitive and drug-resistant strains of Mycobacterium tuberculosis. In the present work we demonstrate that two time-dependent B-ring modified diaryl ether InhA inhibitors have antibacterial activity in a mouse model of TB infection when delivered by intraperitoneal injection. We propose that the efficacy of these compounds is related to their residence time on the enzyme, and to identify structural features that modulate drug-target residence time in this system, we have explored the inhibition of InhA by a series of B-ring modified analogues. Seven ortho substituted compounds were found to be time dependent inhibitors of InhA where the slow step leading to the final EI* complex is thought to correlate with closure and ordering of the InhA substrate binding loop. A detailed mechanistic understanding of the molecular basis for residence time in this system will facilitate the development of InhA inhibitors with improved in vivo activity.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.