Privileged Electrophile Sensors: A Resource for Covalent Drug Development

Marcus John Curtis Long, Yimon Aye

Cell Chemical Biology

10.1016/j.chembiol.2017.05.023

This Perspective delineates how redox signaling affects the activity of specific enzyme isoforms and how this property may be harnessed for rational drug design. Covalent drugs have resurged in recent years and several reports have extolled the general virtues of developing irreversible inhibitors. Indeed, many modern pharmaceuticals contain electrophilic appendages. Several invoke a warhead that hijacks active-site nucleophiles whereas others take advantage of spectator nucleophilic side chains that do not participate in enzymatic chemistry, but are poised to bind/react with electrophiles. The latest data suggest that innate electrophile sensing—which enables rapid reaction with an endogenous signaling electrophile—is a quintessential resource for the development of covalent drugs. For instance, based on recent work documenting isoform-specific electrophile sensing, isozyme non-specific drugs may be converted to isozyme-specific analogs by hijacking privileged first-responder electrophile-sensing cysteines. Because this approach targets functionally relevant cysteines, we can simultaneously harness previously untapped moonlighting roles of enzymes linked to redox sensing

Residue-Specific Peptide Modification: A Chemist’s Guide

Justine N. deGruyter, Lara R. Malins, and Phil S. Baran

Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037

DOI: 10.1021/acs.biochem.7b00536

Advances in bioconjugation and native protein modification are appearing at a blistering pace, making it increasingly time consuming for practitioners to identify the best chemical method to modify a specific amino acid residue in a complex setting. The purpose of this perspective is to provide an informative, graphically-rich manual highlighting significant advances in the field over the past decade. This guide will help triage candidate methods for peptide alteration, and will serve as a starting point for those seeking to solve longstanding challenges.

2-Chloropropionamide as a low-reactivity electrophile for irreversible small-molecule probe identification

Dharmaraja Allimuthu and Drew J. Adams

ACS Chem. Biol., 2017, Just Accepted Manuscript
DOI: 10.1021/acschembio.7b00424

Abstract

Resurgent interest in covalent target engagement in drug discovery has demonstrated that small molecules containing weakly reactive electrophiles can be safe and effective therapies. Several recently FDA-approved drugs feature an acrylamide functionality to selectively engage cysteine side chains of kinases (Ibrutinib, Afatinib, and Neratinib). Additional electrophilic functionalities whose reactivity is compatible with highly selective target engagement and in vivo application could open new avenues in covalent small molecule discovery. Here we report the synthesis and evaluation of a library of small molecules containing the 2-chloropropionamide functionality, which we demonstrate is less reactive than typical acrylamide electrophiles. Although many library members do not appear to label proteins in cells, we identified S-CW3554 as selectively labeling protein disulfide isomerase and inhibiting its enzymatic activity. Subsequent profiling of the library against five diverse cancer cell lines showed unique cytotoxicity for S-CW3554 in cells derived from multiple myeloma, a cancer recently reported to be sensitive to PDI inhibition. Our novel PDI inhibitor highlights the potential of 2-chloropropionamides as weak and stereochemically-tunable electrophiles for covalent drug discovery.

Farnesyltransferase-Mediated Delivery of a Covalent Inhibitor Overcomes Alternative Prenylation to Mislocalize K-Ras

Chris J. Novotny, Gregory L. Hamilton, Frank McCormick, and Kevan M. Shokat
 
† Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
‡ NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21701, United States
§ Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94158, United States

ACS Chem. Biol., Article ASAP

DOI: 10.1021/acschembio.7b00374

Mutationally activated Ras is one of the most common oncogenic drivers found across all malignancies, and its selective inhibition has long been a goal in both pharma and academia. One of the oldest and most validated methods to inhibit overactive Ras signaling is by interfering with its post-translational processing and subsequent cellular localization. Previous attempts to target Ras processing led to the development of farnesyltransferase inhibitors, which can inhibit H-Ras localization but not K-Ras due to its ability to bypass farnesyltransterase inhibition through alternative prenylation by geranylgeranyltransferase. Here, we present the creation of a neo-substrate for farnesyltransferase that prevents the alternative prenlation by geranylgeranyltransferase and mislocalizes oncogenic K-Ras in cells.

Expanding the Scope of Electrophiles Capable of Targeting K-Ras Oncogenes

Lynn M. McGregor, Meredith L. Jenkins, Caitlin Kerwin, John E. Burke, and Kevan M. Shokat
Biochemistry, Article ASAP
DOI: 10.1021/acs.biochem.7b00271

There is growing interest in reversible and irreversible covalent inhibitors that target noncatalytic amino acids in target proteins. With a goal of targeting oncogenic K-Ras variants (e.g., G12D) by expanding the types of amino acids that can be targeted by covalent inhibitors, we survey a set of electrophiles for their ability to label carboxylates. We functionalized an optimized ligand for the K-Ras switch II pocket with a set of electrophiles previously reported to react with carboxylates and characterized the ability of these compounds to react with model nucleophiles and oncogenic K-Ras proteins. Here, we report that aziridines and stabilized diazo groups preferentially react with free carboxylates over thiols. Although we did not identify a warhead that potently labels K-Ras G12D, we were able to study the interactions of many electrophiles with K-Ras, as most of the electrophiles rapidly label K-Ras G12C. We characterized the resulting complexes by crystallography, hydrogen/deuterium exchange, and differential scanning fluorimetry. Our results both demonstrate the ability of a noncatalytic cysteine to react with a diverse set of electrophiles and emphasize the importance of proper spatial arrangements between a covalent inhibitor and its intended nucleophile. We hope that these results can expand the range of electrophiles and nucleophiles of use in covalent protein modulation.

Structure-activity relationship investigation for benzonaphthyridinone derivatives as novel potent Bruton's tyrosine kinase (BTK) irreversible inhibitors

Beilei Wanga, Yuanxin Denga, Yongfei Chena, Kailin Yua, Aoli Wanga, Qianmao Lianga, Wei Wanga, Cheng Chena, Hong Wua, Chen Hua, Weili Miaod, Wooyoung Hure, Wenchao Wanga

doi: 10.1016/j.ejmech.2017.06.016

Abstract

Through a structure-based drug design approach, a tricyclic benzonaphthyridinone pharmacophore was used as a starting point for carrying out detailed medicinal structure-activity relationhip (SAR) studies geared toward characterization of a panel of proposed BTK inhibitors, including 6 (QL-X-138), 7 (BMX-IN-1) and 8 (QL-47). These studies led to the discovery of the novel potent irreversible BTK inhibitor, compound 18 (CHMFL-BTK-11). Kinetic analysis of compound 18 revealed an irreversible binding efficacy (k_inact/K_i) of 0.01 μM⁻¹s⁻¹. Compound 18 potently inhibited BTK kinase Y223 auto-phosphorylation (EC₅₀ < 100 nM), arrested cell cycle in G0/G1 phase, and induced apoptosis in Ramos, MOLM13 and Pfeiffer cells. We believe these features would make 18 a good pharmacological tool for studying BTK-related pathologies.

Covalent inhibitors design and discovery

Stephane De Cesco, Jerry Kurian, Caroline Dufresne, Anthony Mittermaier, Nicolas Moitessier

doi: 10.1016/j.ejmech.2017.06.019

Abstract 

In the history of therapeutics, covalent drugs occupy a very distinct category. While representing a significant fraction of the drugs on the market, very few have been deliberately designed to interact covalently with their biological target. In this review, the prevalence of covalent drugs will first be briefly covered, followed by an introduction to their mechanisms of action and more detailed discussions of their discovery and the development of safe and efficient covalent enzyme inhibitors. All stages of a drug discovery program will be covered, from target considerations to lead optimization, strategies to tune reactivity and computational methods. The goal of this article is to provide an overview of the field and to outline good practices that are needed for the proper assessment and development of covalent inhibition as well as good understanding of the potential and limitations of current computational methods for the design of covalent drugs.

Activity-based protein profiling reveals off-target proteins of the FAAH inhibitor BIA 10-2474

Science  09 Jun 2017: Vol. 356, Issue 6342  1084-1087

Annelot C. M. van Esbroeck1,*, 

Antonius P. A. Janssen1,*, 

Armand B. Cognetta III2,*, 

Daisuke Ogasawara2,*, 

Guy Shpak3, 

Mark van der Kroeg3, 

Vasudev Kantae4, 

Marc P. Baggelaar1, 

Femke M. S. de Vrij3, 

Hui Deng1, 

Marco Allarà5, 

Filomena Fezza6, 

Zhanmin Lin7, 

Tom van der Wel1, 

Marjolein Soethoudt1, 

Elliot D. Mock1, 

Hans den Dulk1, 

Ilse L. Baak1, 

Bogdan I. Florea8, 

Giel Hendriks9, 

Luciano De Petrocellis5, 

Herman S. Overkleeft8, 

Thomas Hankemeier4, 

Chris I. De Zeeuw7,10, 

Vincenzo Di Marzo5, 

Mauro Maccarrone11,12, 

Benjamin F. Cravatt2, 

Steven A. Kushner3,†, 

Mario van der Stelt

DOI: 10.1126/science.aaf7497

A recent phase 1 trial of the fatty acid amide hydrolase (FAAH) inhibitor BIA 10-2474 led to the death of one volunteer and produced mild-to-severe neurological symptoms in four others. Although the cause of the clinical neurotoxicity is unknown, it has been postulated, given the clinical safety profile of other tested FAAH inhibitors, that off-target activities of BIA 10-2474 may have played a role. Here we use activity-based proteomic methods to determine the protein interaction landscape of BIA 10-2474 in human cells and tissues. This analysis revealed that the drug inhibits several lipases that are not targeted by PF04457845, a highly selective and clinically tested FAAH inhibitor. BIA 10-2474, but not PF04457845, produced substantial alterations in lipid networks in human cortical neurons, suggesting that promiscuous lipase inhibitors have the potential to cause metabolic dysregulation in the nervous system.

Modeling Covalent-Modifier Drugs

Ernest Awoonor-Williams, Andrew G. Walsh, Christopher N. Rowley

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

doi: 10.1016/j.bbapap.2017.05.009

In this review, we present a summary of how computer modeling has been used in the development of covalent modifier drugs. Covalent modifier drugs bind by forming a chemical bond with their target. This covalent binding can improve the selectivity of the drug for a target with complementary reactivity and result in increased binding affinities due to the strength of the covalent bond formed. In some cases, this results in irreversible inhibition of the target, but some targeted covalent inhibitor (TCI) drugs bind covalently but reversibly. Computer modeling is widely used in drug discovery, but different computational methods must be used to model covalent modifiers because of the chemical bonds formed. Structural and bioinformatic analysis has identified sites of modification that could yield selectivity for a chosen target. Docking methods, which are used to rank binding poses of large sets of inhibitors, have been augmented to support the formation of protein–ligand bonds and are now capable of predicting the binding pose of covalent modifiers accurately. The pKa’s of amino acids can be calculated in order to assess their reactivity towards electrophiles. QM/MM methods have been used to model the reaction mechanisms of covalent modification. The continued development of these tools will allow computation to aid in the development of new covalent modifier drugs.