Vinyl sulfonamide synthesis for irreversible tethering via a novel α-selenoether protection strategy

Med. Chem. Commun., 2018 
DOI: 10.1039/C8MD00566D

Vinyl sulfonamides are valuable electrophiles for targeted protein modification and inhibition. We describe a novel approach to the synthesis of terminal vinyl sulfonamides which uses mild oxidative conditions to induce elimination of an α-selenoether masking group. The method complements traditional synthetic approaches and typically yields vinyl sulfonamides in high purity after aqueous work-up without requiring column chromatography of the final electrophilic product. The methodology is applied to the synthesis of covalent fragments for use in irreversible protein tethering and crucially enables the attachment of diverse fragments to the vinyl sulfonamide warhead via a chemical linker. Using thymidylate synthase as a model system, ethylene glycol is identified as a effective linker for irreversible protein tethering.

Emerging and Re-Emerging Warheads for Targeted Covalent Inhibitors: Applications in Medicinal Chemistry and Chemical Biology

Matthias Gehringer and Stefan A. Laufer
Journal of Medicinal Chemistry 
DOI: 10.1021/acs.jmedchem.8b01153

Targeted covalent inhibitors (TCIs) are designed to bind poorly conserved amino acids by means of reactive groups, the so-called warheads. Currently, targeting non-catalytic cysteine residues with acrylamides and other α,β-unsaturated carbonyl compounds is the predominant chemical strategy in TCI development. The recent ascent of covalent drugs has stimulated considerable efforts to characterize alternative warheads for the covalent-reversible and irreversible engagement of non-catalytic cysteine residues as well as other amino acids. This Perspective article provides an overview of warheads beyond α,β-unsaturated amides that were recently used in the design of targeted covalent ligands. Promising reactive groups that have not yet demonstrated their utility in TCI development are also highlighted. Special emphasis is placed on the discussion of reactivity and case studies illustrating applications in medicinal chemistry and chemical biology.

A Chemoproteomic Strategy for Direct and Proteome-wide Covalent Inhibitor Target-site Identification

Christopher Michael Browne, Baishan Jiang, Scott B Ficarro, Zainab M Doctor, Jared Lee Johnson, Joseph D Card, Sindhu Carmen Sivakumaren, William M Alexander, Tomer Yaron, Charles Joseph Murphy, Nicholas P Kwiatkowski, Tinghu Zhang, Lewis C. Cantley, Nathanael S Gray, and Jarrod A. Marto

Journal of the American Chemical Society 2018

DOI: 10.1021/jacs.8b07911

Despite recent clinical successes for irreversible drugs, potential toxicities mediated by unpredictable modification of off-target cysteines represents a major hurdle for expansion of covalent drug programs. Understanding the proteome-wide binding profile of covalent inhibitors can significantly accelerate their development; however, current mass spectrometry strategies typically do not provide a direct, amino acid level readout of covalent activity for complex, selective inhibitors. Here we report the development of CITe-Id, a novel chemoproteomic approach that employs covalent pharmacologic inhibitors as enrichment reagents in combination with an optimized proteomic platform to directly quantify dose-dependent binding at cysteine-thiols across the proteome. CITe-Id analysis of our irreversible CDK inhibitor THZ1 identified dose-dependent covalent modification of several unexpected kinases, including a previously unannotated cysteine (C840) on the understudied kinase PKN3. These data streamlined our development of JZ128 as a new selective covalent inhibitor of PKN3. Using JZ128 as a probe compound, we identified novel potential PKN3 substrates, thus offering an initial molecular view of PKN3 cellular activity. CITe-Id provides a powerful complement to current chemoproteomic platforms to characterize the selectivity of covalent inhibitors, identify new, pharmacologically-addressable cysteine-thiols, and inform structure-based drug design programs.

Overview of Current Type I/II Kinase Inhibitors

Zheng Zhao, Philip E. Bourne

https://arxiv.org/abs/1811.09718

Research on kinase-targeting drugs has made great strides over the last 30 years and is attracting greater attention for the treatment of yet more kinase-related diseases. Currently, 42 kinase drugs have been approved by the FDA, most of which (39) are Type I/II inhibitors. Notwithstanding these advances, it is desirable to target additional kinases for drug development as more than 200 diseases, particularly cancers, are directly associated with aberrant kinase regulation and signaling. Here, we review the extant Type I/II drugs systematically to obtain insights into the binding pocket characteristics, the associated features of Type I/II drugs, and the mechanism of action to facilitate future kinase drug design and discovery. We conclude by summarizing the main successes and limitations of targeting kinase for the development of drugs.

Covalent Docking Identifies a Potent and Selective MKK7 Inhibitor [@london_lab]

Amit Shraga, Evgenia Olshvang, Natalia Davidzohn, Payam Khoshkenar, Nicolas Germain, Khriesto Shurrush, Silvia Carvalho, Liat Avram, Shira Albeck, Tamar Unger, Bruce Lefker, Chakrapani Subramanyam, Robert L. Hudkins, Amir Mitchell, Ziv Shulman, Takayoshi Kinoshita, Nir London,
Covalent Docking Identifies a Potent and Selective MKK7 Inhibitor,
Cell Chemical Biology, 2018

DOI: 10.1016/j.chembiol.2018.10.011

The c-Jun NH2-terminal kinase (JNK) signaling pathway is central to the cell response to stress, inflammatory signals, and toxins. While selective inhibitors are known for JNKs and for various upstream MAP3Ks, no selective inhibitor is reported for MKK7––one of two direct MAP2Ks that activate JNK. Here, using covalent virtual screening, we identify selective MKK7 covalent inhibitors. We optimized these compounds to low-micromolar inhibitors of JNK phosphorylation in cells. The crystal structure of a lead compound bound to MKK7 demonstrated that the binding mode was correctly predicted by docking. We asserted the selectivity of our inhibitors on a proteomic level and against a panel of 76 kinases, and validated an on-target effect using knockout cell lines. Lastly, we show that the inhibitors block activation of primary mouse B cells by lipopolysaccharide. These MKK7 tool compounds will enable better investigation of JNK signaling and may serve as starting points for therapeutics.

Balancing reactivity and antitumor activity: Heteroarylthio acetamide derivatives as potent and time-dependent inhibitors of EGFR

Riccardo Castelli, Nicole Bozza, Andrea Cavazzoni, Mara Bonelli, Federica Vacondio, Francesca Ferlenghi, Donatella Callegari, Claudia Silva, Silvia Rivara, Alessio Lodola, Graziana Digiacomo, Claudia Fumarola, Roberta Alfieri, Pier Giorgio Petronini, Marco Mor

European Journal of Medicinal Chemistry, 2018
DOI: 10.1016/j.ejmech.2018.11.029

Second- and third-generation inhibitors of EGFR possess an acrylamide group which alkylates Cys797, allowing to overcome resistance due to insurgence of T790M mutation. Less reactive warheads, yet capable to bind the target cysteine, may be useful to design newer and safer inhibitors. In the present work, we synthesized a 2-chloro-N-(4-(phenylamino)quinazolin-6-yl)acetamide (8) derivative as a prototype of EGFR inhibitor potentially able to react with Cys797 by nucleophilic substitution. We then tuned the reactivity of the acetamide fragment by replacing the chlorine leaving group with (hetero)-aromatic thiols or carboxylate esters. Among the synthesized derivatives, the 2-((1H-imidazol-2-yl)thio)acetamide 16, while showing negligible reactivity with cysteine in solution, caused long-lasting inhibition of wild-type EGFR autophosphorylation in A549 cells, resulted able to bind recombinant EGFR L858R/T790M in a time-dependent manner, and inhibited both EGFR autophosphorylation and proliferation in gefitinib-resistant H1975 (EGFR L858R/T790M) lung cancer cells at low micromolar concentration.

Neolymphostin A is a Covalent Phosphoinositide-3-kinase (PI3-K)/Mammalian Target of Rapamycin (mTOR) Dual Inhibitor that Employs an Unusual Electrophilic Vinylogous Ester

Gabriel Castro-Falcón, Grant Seiler, Ozlem Demir, Manoj Rathinaswamy, David Hamelin, Reece M. Hoffmann, Stefanie Makowski, Anne-Catrin Letzel, Seth Field, John Burke, Rommie E. Amaro, and Chambers C. Hughes

Journal of Medicinal Chemistry 2018
DOI: 10.1021/acs.jmedchem.8b00975

Using a novel chemistry-based assay for identifying electrophilic natural products from unprocessed extracts, we identified the PI3-kinase/mTOR dual inhibitor neolymphostin A from Salinispora arenicola CNY-486. The method further showed that the vinylogous ester substituent on the neolymphostin core was the exact site for enzyme conjugation. Tandem MS/MS experiments on PI3Kα treated with the inhibitor revealed that neolymphostin covalently modified Lys802 with a shift in mass of +306 amu, corresponding to addition of the inhibitor and elimination of methanol. The binding pose of the inhibitor bound to PI3Kα was modelled, and hydrogen-deuterium exchange mass spectrometry experiments supported this model. Against a panel of kinases, neolymphostin showed good selectivity for PI3-kinase and mTOR. In addition, the natural product blocked AKT phosphorylation in live cells with an IC50 of ~3 nM. Taken together, neolymphostin is the first reported example of a covalent kinase inhibitor from the bacterial domain of life.