Advances of small molecule targeting of kinases

Norbert Berndt, Rezaul M Karim, Ernst Schönbrunn

Current Opinion in Chemical Biology
Volume 39, August 2017, Pages 126–132

doi: 10.1016/j.cbpa.2017.06.015

Reversible protein phosphorylation regulates virtually all aspects of life in the cell. As a result, dysregulation of protein kinases, the enzymes responsible for transferring phosphate groups from ATP to proteins, are often the cause or consequence of many human diseases including cancer. Almost three dozen protein kinase inhibitors (PKIs) have been approved for clinical applications since 1995, the vast majority of them for the treatment of cancer. According to the NCI, there are more than 100 types of cancer. However, FDA-approved PKIs only target 14 of them. Importantly, of the more than 500 protein kinases encoded by the human genome, only 22 are targets for currently approved PKIs, suggesting that the reservoir of PKIs still has room to grow significantly. In this short review we will discuss the most recent advances, challenges, and alternatives to currently adopted strategies in this burgeoning field.

Covalent Enzyme Inhibition through Fluorosulfate Modification of a Noncatalytic Serine Residue

Olugbeminiyi O. Fadeyi, Lise R. Hoth, Chulho Choi, Xidong Feng, Ariamala Gopalsamy, Erik C. Hett, Robert E. Kyne Jr., Ralph P. Robinson, and Lyn H. Jones

Medicine Design, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
Medicine Design, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States

ACS Chem. Biol., Article ASAP
DOI: 10.1021/acschembio.7b00403

Irreversible enzyme inhibitors and covalent chemical biology probes often utilize the reaction of a protein cysteine residue with an appropriately positioned electrophile (e.g., acrylamide) on the ligand template. However, cysteine residues are not always available for site-specific protein labeling, and therefore new approaches are needed to expand the toolkit of appropriate electrophiles (“warheads”) that target alternative amino acids. We previously described the rational targeting of tyrosine residues in the active site of a protein (the mRNA decapping scavenger enzyme, DcpS) using inhibitors armed with a sulfonyl fluoride electrophile. These inhibitors subsequently enabled the development of clickable probe technology to measure drug-target occupancy in live cells. Here we describe a fluorosulfate-containing inhibitor (aryl fluorosulfate probe (FS-p1)) with excellent chemical and metabolic stability that reacts selectively with a noncatalytic serine residue in the same active site of DcpS as confirmed by peptide mapping experiments. Our results suggest that noncatalytic serine targeting using fluorosulfate electrophilic warheads could be a suitable strategy for the development of covalent inhibitor drugs and chemical probes.

Discovery of a covalent kinase inhibitor from a DNA encoded small-molecule library X protein library selection

Discovery of a Covalent Kinase Inhibitor from a DNA-Encoded Small-Molecule Library × Protein Library Selection

Alix I. Chan, Lynn M. McGregor, Tara Jain, and David R. Liu
The Broad Institute of Harvard and MIT, Howard Hughes Medical Institute, and the Department of Chemistry and Chemical Biology, Harvard University, 75 Ames Street, Cambridge, Massachusetts 02142, United States
J. Am. Chem. Soc., Article ASAP
DOI: 10.1021/jacs.7b04880

We previously reported interaction determination using unpurified proteins (IDUP), a method to selectively amplify DNA sequences encoding ligand:target pairs from a mixture of DNA-linked small molecules and unpurified protein targets in cell lysates. In this study, we applied IDUP to libraries of DNA-encoded bioactive compounds and DNA-tagged human kinases to identify ligand:protein binding partners out of 32 096 possible combinations in a single solution-phase library × library experiment. The results recapitulated known small molecule:protein interactions and also revealed that ethacrynic acid is a novel ligand and inhibitor of MAP2K6 kinase. Ethacrynic acid inhibits MAP2K6 in part through alkylation of a nonconserved cysteine residue. This work validates the ability of IDUP to discover ligands for proteins of biomedical relevance.

1,6-Cyclophellitol Cyclosulfates: A New Class of Irreversible Glycosidase Inhibitor

Marta Artola , Liang Wu, Maria J. Ferraz, Chi-Lin Kuo§, Lluís Raich∥, Imogen Z. Bree‡, Wendy A. Offen, Jeroen D. C. Codée , Gijsbert A. van der Marel, Carme Rovira, Johannes M. F. G. Aerts, Gideon J. Davies , and Herman S. Overkleeft

ACS Cent. Sci., Article ASAP
DOI: 10.1021/acscentsci.7b00214

The essential biological roles played by glycosidases, coupled to the diverse therapeutic benefits of pharmacologically targeting these enzymes, provide considerable motivation for the development of new inhibitor classes. Cyclophellitol epoxides and aziridines are recently established covalent glycosidase inactivators. Inspired by the application of cyclic sulfates as electrophilic equivalents of epoxides in organic synthesis, we sought to test whether cyclophellitol cyclosulfates would similarly act as irreversible glycosidase inhibitors. Here we present the synthesis, conformational analysis, and application of novel 1,6-cyclophellitol cyclosulfates. We show that 1,6-epi-cyclophellitol cyclosulfate (α-cyclosulfate) is a rapidly reacting α-glucosidase inhibitor whose 4C1 chair conformation matches that adopted by α-glucosidase Michaelis complexes. The 1,6-cyclophellitol cyclosulfate (β-cyclosulfate) reacts more slowly, likely reflecting its conformational restrictions. Selective glycosidase inhibitors are invaluable as mechanistic probes and therapeutic agents, and we propose cyclophellitol cyclosulfates as a valuable new class of carbohydrate mimetics for application in these directions.

Discovery of Heteroaromatic Sulfones As A New Class of Biologically Compatible Thiol-Selective Reagents

Xiaofei Chen, Hanzhi Wu, Chung-Min Park, Thomas H. Poole, Gizem Keceli, Nelmi O. Devarie Baez, Allen W. Tsang, W. Todd Lowther, Leslie B. Poole, S. Bruce King, Ming Xian, and Cristina M. Furdui

ACS Chem. Biol., 2017
DOI: 10.1021/acschembio.7b00444

The selective reaction of chemical reagents with reduced protein thiols is critical to biological research. This reaction is utilized to prevent crosslinking of cysteine-containing peptides in common proteomics workflows and is applied widely in discovery and targeted redox investigations of the mechanisms underlying physiological and pathological processes. However, known and commonly used thiol blocking reagents like iodoacetamide, N-ethylmaleimide and others were found to cross-react with oxidized protein sulfenic acids (-SOH) introducing significant errors in studies employing these reagents. We have investigated and are reporting here a new heteroaromatic alkylsulfone, 4-(5-Methanesulfonyl-[1,2,3,4]tetrazol-1-yl)-phenol (MSTP), as selective and highly reactive -SH blocking reagent compatible with biological applications.

Drug-Target Kinetics in Drug Discovery

Peter J Tonge
ACS Chem. Neurosci., Just Accepted Manuscript
DOI: 10.1021/acschemneuro.7b00185

The development of therapies for the treatment of neurological cancer faces a number of major challenges including the synthesis of small molecule agents that can penetrate the blood brain barrier (BBB). Given the likelihood that in many cases drug exposure will be lower in the CNS than in systemic circulation, it follows that strategies should be employed that can sustain target engagement at low drug concentration. Time dependent target occupancy is a function of both the drug and target concentration as well as the thermodynamic and kinetic parameters that describe the binding reaction coordinate, and sustained target occupancy can be achieved through structural modifications that increase target (re)binding and/or that decrease the rate of drug dissociation. The discovery and deployment of compounds with optimized kinetic effects requires information on the structure-kinetic relationships that modulate the kinetics of binding, and the molecular factors that control the translation of drug-target kinetics to time-dependent drug activity in the disease state. This review first introduces the potential benefits of drug-target kinetics, such as the ability to delineate both thermodynamic and kinetic selectivity, and then describes factors, such as target vulnerability, that impact the utility of kinetic selectivity. The review concludes with a description of a mechanistic PK/PD model that integrates drug-target kinetics into predictions of drug activity.