Evaluating the Contribution of Transition-State Destabilization to Changes in the Residence Time of Triazole-Based InhA Inhibitors.
A critical goal of lead compound selection and optimization is to maximize target engagement while minimizing off-target binding. Since target engagement is a function of both the thermodynamics and kinetics of drug-target interactions, it follows that the structures of both the ground states and transition states on the binding reaction coordinate are needed to rationally modulate the lifetime of the drug-target complex. Previously, we predicted the structure of the rate-limiting transition state that controlled the time-dependent inhibition of the enoyl-ACP reductase InhA. This led to the discovery of a triazole-containing diphenyl ether with an increased residence time on InhA due to transition-state destabilization rather than ground-state stabilization. In the present work, we evaluate the inhibition of InhA by 14 triazole-based diphenyl ethers and use a combination of enzyme kinetics and X-ray crystallography to generate a structure-kinetic relationship for time-dependent binding. We show that the triazole motif slows the rate of formation for the final drug-target complex by up to 3 orders of magnitude. In addition, we identify a novel inhibitor with a residence time on InhA of 220 min, which is 3.5-fold longer than that of the INH-NAD adduct formed by the tuberculosis drug, isoniazid. This study provides a clear example in which the lifetime of the drug-target complex is controlled by interactions in the transition state for inhibitor binding rather than the ground state of the enzyme-inhibitor complex, and demonstrates the important role that on-rates can play in drug-target residence time.
Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States.
Lauren A
LA
Spagnuolo
Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg , 97080 Würzburg, Germany.
Sandra
S
Eltschkner
Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States.
Weixuan
W
Yu
Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States.
Fereidoon
F
Daryaee
Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States.
Shabnam
S
Davoodi
Department of Microbiology, Immunology and Pathology, Colorado State University , Fort Collins, Colorado 80523-2025, United States.
Susan E
SE
Knudson
Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States.
Eleanor K H
EK
Allen
Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States.
Jonathan
J
Merino
Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg , 97080 Würzburg, Germany.
Annica
A
Pschibul
Biodesy, Inc. , 384 Oyster Point Boulevard, South San Francisco, California 94080, United States.
Ben
B
Moree
Great Neck South High School , 341 Lakeville Road, Great Neck, New York 11020, United States.
Neil
N
Thivalapill
Great Neck South High School , 341 Lakeville Road, Great Neck, New York 11020, United States.
James J
JJ
Truglio
Biodesy, Inc. , 384 Oyster Point Boulevard, South San Francisco, California 94080, United States.
Joshua
J
Salafsky
Department of Microbiology, Immunology and Pathology, Colorado State University , Fort Collins, Colorado 80523-2025, United States.
Richard A
RA
Slayden
Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg , 97080 Würzburg, Germany.
Caroline
C
Kisker
Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States.
Peter J
0000-0003-1606-3471
PJ
Tonge
D018360:Crystallography, X-Ray; D006801:Humans; D007265:Inhibins / Q000037:antagonists & inhibitors* / Q000378:metabolism; D007700:Kinetics; D008958:Models, Molecular; D015394:Molecular Structure; D013816:Thermodynamics; D013997:Time Factors; D014230:Triazoles / Q000737:chemistry / Q000494:pharmacology*
D014230:Triazoles; C094377:inhibin-alpha subunit; D007265:Inhibins