Abstract 20: Targeting difficult targets with lysine-covalent ligands: Expanding the druggable space for covalent drugs

Author(s):  
Maurizio Pellecchia
Keyword(s):  
2019 ◽  
Author(s):  
Patrick R. A. Zanon ◽  
Lisa Lewald ◽  
Stephan M. Hacker

Rapid development of bacterial resistance has led to an urgent need to find new druggable targets for antibiotics. In this context, residue-specific chemoproteomic approaches enable proteome-wide identification of binding sites for covalent inhibitors. Here, we describe isotopically labeled desthiobiotin azide (isoDTB) tags that are easily synthesized, shorten the chemoproteomic workflow and allow an increased coverage of cysteines in bacterial systems. We quantify 59% of all cysteines in essential proteins in <i>Staphylococcus aureus</i> and discover 88 cysteines with high reactivity, which correlates with functional importance. Furthermore, we identify 268 cysteines that are engaged by covalent ligands. We verify inhibition of HMG-CoA synthase, which will allow addressing the bacterial mevalonate pathway through a new target. Overall, a comprehensive map of the bacterial cysteinome is obtained, which will facilitate the development of antibiotics with novel modes-of-action.


2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Haixia Su ◽  
Sheng Yao ◽  
Wenfeng Zhao ◽  
Yumin Zhang ◽  
Jia Liu ◽  
...  

AbstractThe ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) urgently needs an effective cure. 3CL protease (3CLpro) is a highly conserved cysteine proteinase that is indispensable for coronavirus replication, providing an attractive target for developing broad-spectrum antiviral drugs. Here we describe the discovery of myricetin, a flavonoid found in many food sources, as a non-peptidomimetic and covalent inhibitor of the SARS-CoV-2 3CLpro. Crystal structures of the protease bound with myricetin and its derivatives unexpectedly revealed that the pyrogallol group worked as an electrophile to covalently modify the catalytic cysteine. Kinetic and selectivity characterization together with theoretical calculations comprehensively illustrated the covalent binding mechanism of myricetin with the protease and demonstrated that the pyrogallol can serve as an electrophile warhead. Structure-based optimization of myricetin led to the discovery of derivatives with good antiviral activity and the potential of oral administration. These results provide detailed mechanistic insights into the covalent mode of action by pyrogallol-containing natural products and a template for design of non-peptidomimetic covalent inhibitors against 3CLpros, highlighting the potential of pyrogallol as an alternative warhead in design of targeted covalent ligands.


2018 ◽  
Vol 24 (2) ◽  
pp. 169-174 ◽  
Author(s):  
Zhengrong Zhu ◽  
LaShadric C. Grady ◽  
Yun Ding ◽  
Kenneth E. Lind ◽  
Christopher P. Davie ◽  
...  

DNA-encoded libraries (DELs) have been broadly applied to identify chemical probes for target validation and lead discovery. To date, the main application of the DEL platform has been the identification of reversible ligands using multiple rounds of affinity selection. Irreversible (covalent) inhibition offers a unique mechanism of action for drug discovery research. In this study, we report a developing method of identifying irreversible (covalent) ligands from DELs. The new method was validated by using 3C protease (3CP) and on-DNA irreversible tool compounds (rupintrivir derivatives) spiked into a library at the same concentration as individual members of that library. After affinity selections against 3CP, the irreversible tool compounds were specifically enriched compared with the library members. In addition, we compared two immobilization methods and concluded that microscale columns packed with the appropriate affinity resin gave higher tool compound recovery than magnetic beads.


2020 ◽  
Vol 56 (24) ◽  
pp. 3555-3558 ◽  
Author(s):  
Aline Umuhire Juru ◽  
Zhengguo Cai ◽  
Adina Jan ◽  
Amanda E. Hargrove

This study establishes the applicability of imine-based dynamic combinatorial chemistry to discover non-covalent ligands for RNA targets.


2017 ◽  
Vol 12 (4) ◽  
pp. 899-904 ◽  
Author(s):  
Allison M. Roberts ◽  
David K. Miyamoto ◽  
Tucker R. Huffman ◽  
Leslie A. Bateman ◽  
Ashley N. Ives ◽  
...  

2022 ◽  
Author(s):  
Mostafa Jamshidiha ◽  
Thomas Lanyon-Hogg ◽  
Charlotte L. Sutherell ◽  
Gregory B. Craven ◽  
Montse Tersa ◽  
...  

A novel Rab27A construct enables elucidation of covalent ligand binding, paving the way for structure-guided approaches against this challenging target.


2021 ◽  
Author(s):  
James D Vasta ◽  
D. Matthew Peacock ◽  
Qinheng Zheng ◽  
Joel A Walker ◽  
Ziyang Zhang ◽  
...  

Current small molecule inhibitors of KRAS (G12C) bind irreversibly in the switch-II pocket, exploiting the strong nucleophilicity of the acquired cysteine as well as the preponderance of the GDP-bound form of this mutant. Nevertheless, many oncogenic KRAS mutants lack these two features, and it remains unknown whether targeting the switch-II pocket is a practical therapeutic approach for KRAS mutants beyond G12C. Here we use NMR spectroscopy and a novel cellular KRAS engagement assay to address this question by examining a collection of SII-P ligands from the literature and from our own laboratory. We show that the switch-II pockets of many GTP hydrolysis-deficient KRAS hotspot (G12, G13, Q61) mutants are accessible using non-covalent ligands, and that this accessibility is not necessarily coupled to the GDP state of KRAS. The results we describe here emphasize the switch-II pocket as a privileged drug binding site on KRAS and unveil new therapeutic opportunities in RAS-driven cancer.


2020 ◽  
Vol 49 (5) ◽  
pp. 1487-1516 ◽  
Author(s):  
Tianxiao Jiang ◽  
Haocheng Zhang ◽  
Yongzheng Ding ◽  
Suchen Zou ◽  
Rui Chang ◽  
...  

This review summarizes transition-metal catalyzed reactions with reductive elimination between covalent ligands and dative ligands as the key elementary step.


2019 ◽  
Vol 12 (4) ◽  
pp. 168 ◽  
Author(s):  
Stephanie Federico ◽  
Lucia Lassiani ◽  
Giampiero Spalluto

Research on the adenosine receptors has been supported by the continuous discovery of new chemical probes characterized by more and more affinity and selectivity for the single adenosine receptor subtypes (A1, A2A, A2B and A3 adenosine receptors). Furthermore, the development of new techniques for the detection of G protein-coupled receptors (GPCR) requires new specific probes. In fact, if in the past radioligands were the most important GPCR probes for detection, compound screening and diagnostic purposes, nowadays, increasing importance is given to fluorescent and covalent ligands. In fact, advances in techniques such as fluorescence resonance energy transfer (FRET) and fluorescent polarization, as well as new applications in flow cytometry and different fluorescence-based microscopic techniques, are at the origin of the extensive research of new fluorescent ligands for these receptors. The resurgence of covalent ligands is due in part to a change in the common thinking in the medicinal chemistry community that a covalent drug is necessarily more toxic than a reversible one, and in part to the useful application of covalent ligands in GPCR structural biology. In this review, an updated collection of available chemical probes targeting adenosine receptors is reported.


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