Chemical Probes for Proteins and Networks

2019 ◽  
pp. 127-158
Author(s):  
Scott Lovell ◽  
Charlotte L. Sutherell ◽  
Edward W. Tate
Keyword(s):  
Chemical Probes

Rapid Elaboration of Fragments into Leads Applied to Bromodomain-3 Extra Terminal Domain

2020 ◽  
Author(s):  
Luke Adams ◽  
Lorna E. Wilkinson-White ◽  
Menachem J. Gunzburg ◽  
Stephen J. Headey ◽  
Martin J. Scanlon ◽  
...  
Keyword(s):  
Binding Site ◽  
Systematic Approach ◽  
Structural Information ◽  
Peptide Binding ◽  
Chemical Diversity ◽  
Chemical Probes ◽  
Protein Targets ◽  
Structure Activity ◽  
Peptide Binding Site ◽  
Selection Of

The development of low-affinity fragment hits into higher affinity leads is a major hurdle in fragment-based drug design. Here we demonstrate an approach for the Rapid Elaboration of Fragments into Leads (REFiL) applying an integrated workflow that provides a systematic approach to generate higher-affinity binders without the need for structural information. The workflow involves the selection of commercial analogues of fragment hits to generate preliminary structure-activity relationships. This is followed by parallel microscale chemistry using chemoinformatically designed reagent libraries to rapidly explore chemical diversity. Upon completion of a fragment screen against Bromodomain-3 extra terminal (BRD3-ET) domain we applied the REFiL workflow, which allowed us to develop a series of tetrahydrocarbazole ligands that bind to the peptide binding site of BRD3-ET. With REFiL we were able to rapidly improve binding affinity >30-fold. The REFiL workflow can be applied readily to a broad range of protein targets without the need of a structure, allowing the efficient evolution of low-affinity fragments into higher affinity leads and chemical probes.<br>

Covalent-Fragment Screening of Brd4 Identifies a Ligandable Site Orthogonal to the Acetyl-Lysine Binding Sites

2019 ◽  
Author(s):  
Michael Olp ◽  
Daniel Sprague ◽  
Stefan Kathman ◽  
Ziyang Xu ◽  
Alexandar Statsyuk ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Binding Site ◽  
Binding Sites ◽  
Computational Prediction ◽  
Chemical Probes ◽  
Computational Docking ◽  
Fragment Screening ◽  
Covalent Inhibitors ◽  
Bet Protein ◽  
Proof Of Principle

<p>Brd4, a member of the bromodomain and extraterminal domain (BET) family, has emerged as a promising epigenetic target in cancer and inflammatory disorders. All reported BET family ligands bind within the bromodomain acetyl-lysine binding sites and competitively inhibit BET protein interaction with acetylated chromatin. Alternative chemical probes that act orthogonally to the highly-conserved acetyl-lysine binding sites may exhibit selectivity within the BET family and avoid recently reported toxicity in clinical trials of BET bromodomain inhibitors. Here, we report the first identification of a ligandable site on a bromodomain outside the acetyl-lysine binding site. Inspired by our computational prediction of hotspots adjacent to non-homologous cysteine residues within the <i>C</i>-terminal Brd4 bromodomain (Brd4-BD2), we performed a mid-throughput mass spectrometry screen to identify cysteine-reactive fragments that covalently and selectively modify Brd4. Subsequent mass spectrometry, NMR and computational docking analyses of electrophilic fragment hits revealed a novel ligandable site near Cys356 that is unique to Brd4 among all human bromodomains. This site is orthogonal to the Brd4-BD2 acetyl-lysine binding site as Cys356 modification did not impact binding of the pan-BET bromodomain inhibitor JQ1 in fluorescence polarization assays. Finally, we tethered covalent fragments to JQ1 and performed NanoBRET assays to provide proof of principle that this orthogonal site can be covalently targeted in intact human cells. Overall, we demonstrate the potential of targeting sites orthogonal to bromodomain acetyl-lysine binding sites to develop bivalent and covalent inhibitors that displace Brd4 from chromatin.</p>

Chemical Probes for Drug-Resistance Assessment by Binding Competition (RABC): Oseltamivir Susceptibility Evaluation

2012 ◽  
Vol 52 (1) ◽  
pp. 366-370 ◽  
Author(s):  
Ting-Jen R. Cheng ◽  
Shi-Yun Wang ◽  
Wen-Hsien Wen ◽  
Ching-Yao Su ◽  
Mengi Lin ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Chemical Probes ◽  
Binding Competition ◽  
Resistance Assessment ◽  
Susceptibility Evaluation

Chromo-fluorogenic sensors for chemical warfare agents in real-time analysis: journey towards accurate detection and differentiation

2021 ◽  
Vol 57 (28) ◽  
pp. 3430-3444
Author(s):  
Vinod Kumar
Keyword(s):  
Real Time ◽  
Chemical Warfare Agents ◽  
Chemical Warfare ◽  
Chemical Probes ◽  
Time Analysis ◽  
Specific Detection ◽  
Success Stories ◽  
Real Time Analysis ◽  
Warfare Agents ◽  
Unique Chemical

This article describes our journey and success stories in the development of chemical warfare detection, detailing the range of unique chemical probes and methods explored to achieve the specific detection of individual agents in realistic environments.

scholarly journals Substrate Scope for Human Histone Lysine Acetyltransferase KAT8

2021 ◽  
Vol 22 (2) ◽  
pp. 846
Author(s):  
Giordano Proietti ◽  
Yali Wang ◽  
Chiara Punzo ◽  
Jasmin Mecinović
Keyword(s):  
Main Chain ◽  
Coenzyme A ◽  
Side Chain ◽  
Histone H4 ◽  
Chemical Probes ◽  
Acetyl Coenzyme A ◽  
Acetyl Coenzyme ◽  
Histone Lysine ◽  
Lysine Acetyltransferase

Biomedically important histone lysine acetyltransferase KAT8 catalyses the acetyl coenzyme A-dependent acetylation of lysine on histone and other proteins. Here, we explore the ability of human KAT8 to catalyse the acetylation of histone H4 peptides possessing lysine and its analogues at position 16 (H4K16). Our synthetic and enzymatic studies on chemically and structurally diverse lysine mimics demonstrate that KAT8 also has a capacity to acetylate selected lysine analogues that possess subtle changes on the side chain and main chain. Overall, this work highlights that KAT8 has a broader substrate scope beyond natural lysine, and contributes to the design of new chemical probes targeting KAT8 and other members of the histone lysine acetyltransferase (KAT) family.

scholarly journals Chemical probes in plant epigenetics studies

2013 ◽  
Vol 8 (9) ◽  
pp. e25364 ◽  
Author(s):  
Huiming Zhang ◽  
Bangshing Wang ◽  
Cheng-Guo Duan ◽  
Jian-Kang Zhu
Keyword(s):  
Chemical Probes
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