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.

Universal and quantitative method to evaluate inhibitor potency for cysteinome proteins using a nonspecific activity-based protein profiling probe

Tomoya Sameshima, Yukiya Tanaka, and Ikuo Miyahisa
Biochemistry, Just Accepted Manuscript
DOI: 10.1021/acs.biochem.7b00190
Publication Date (Web): May 18, 2017

Recently, there have been limited number of new, validated targets for small-molecule drug discovery in the pharmaceutical industry. Although there are approximately 30,000 genes in the human genome, only 2% are targeted by currently approved small-molecule drugs. One reason that many targets remain neglected by drug discovery programs is the absence of biochemical assays enabling evaluation of the potency of inhibitors in a quantitative and high-throughput manner. To overcome this issue, we developed a biochemical assay to evaluate the potency of both reversible and irreversible inhibitors using a nonspecific thiol-labeling fluorescent probe. The assay can be applied to any targets with a cysteine residue in a pocket that can accommodate small-molecule ligands. By constructing a mathematical model, we showed that the potency of compounds can be quantitatively evaluated by performing an activity-based protein profiling assay. In addition, the validity of the theory was confirmed experimentally using epidermal growth factor receptor kinase as a model target. This approach provides an assay system for targets for which biochemical assays cannot be developed. Our approach can potentially not only expand the number of exploitable targets but also accelerate the lead optimization process by providing quantitative structure–activity relationship information.

Statistical Analysis and Prediction of Covalent Ligand Targeted Cysteine Residues

Weilin Zhang, Jianfeng Pei, and Luhua Lai
J. Chem. Inf. Model., Just Accepted Manuscript
DOI: 10.1021/acs.jcim.7b00163
Publication Date (Web): May 16, 2017

Targeted covalent compounds or drugs have good potency as they can bind to a specific target for a long time with low doses. Most currently known covalent ligands were discovered by chance or by modifying existing non-covalent compounds to make them covalently attached to a nearby reactive residue. Computational methods for novel covalent ligand binding prediction are highly demanded. We performed statistical analysis on protein complexes with covalent ligands attached to cysteine residues. We found that covalent modified cysteine residues have unique features compared to those not attached to covalent ligands, including lower pKa, higher exposure and higher ligand binding affinity. SVM models were built to predict cysteine residues suitable for covalent ligand design with prediction accuracy of 0.73. Given a protein structure, our method can be used to automatically detect druggable Cys residues for covalent ligand design, which is especially useful for identifying novel binding sites for covalent allosteric regulating ligand design.

Direct 11CN-Labeling of Unprotected Peptides via Palladium-Mediated Sequential Cross-Coupling Reactions

Wenjun Zhao†‡∥, Hong Geun Lee§∥, Stephen L. Buchwald*§, and Jacob M. Hooker*†‡ 

† Division of Nuclear Medicine and Molecular Imaging, Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States

‡ Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts 02129, United States

§ Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States

A practical procedure for 11CN-labeling of unprotected peptides has been developed. The method was shown to be highly chemoselective for cysteine over other potentially nucleophilic residues, and the radiolabeled products were synthesized and purified in less than 15 min. Appropriate for biomedical applications, the method could be used on an extremely small scale (20 nmol) with a high radiochemical yield. The success of the protocol stems from the use of a Pd-reagent based on a dihaloarene, which enables direct “nucleophile–nucleophile” coupling of the peptide and [11C]cyanide by temporal separation of nucleophile addition.

J. Am. Chem. Soc., Article ASAP

DOI: 10.1021/jacs.7b02761

Publication Date (Web): May 15, 2017

Thiol Specific and Tracelessly Removable Bioconjugation via Michael Addition to 5-Methylene Pyrrolones

Yingqian Zhang†⊥, Xiaoping Zhou†⊥, Yonghui Xie†, Marc M. Greenberg§ , Zhen Xi†‡, and Chuanzheng Zhou

† State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
‡ Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, China
§ Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States

J. Am. Chem. Soc., 2017, 139 (17), 6146–6151
DOI: 10.1021/jacs.7b00670

Chemistry World: Drugs, the permanent way

Exceptions to a long-held rule against chemically bonding to biological targets are powering new cancer medicines, finds Andy Extance

https://www.chemistryworld.com/feature/covalent-inhibitor-drugs/2500494.article