Peptide Tethering: Pocket-Directed Fragment Screening for Peptidomimetic Inhibitor Discovery

2022 ◽  
Author(s):  
Ashley E. Modell ◽  
Frank Marrone ◽  
Nihar R. Panigrahi ◽  
Yingkai Zhang ◽  
Paramjit S. Arora
Keyword(s):  
Fragment Screening ◽  
Inhibitor Discovery

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>

Identification of new building blocks by fragment screening for discovering GyrB inhibitors

2021 ◽  
pp. 105040
Author(s):  
Ying Yu ◽  
Junsong Guo ◽  
Zhengjun Cai ◽  
Yingchen Ju ◽  
Jun Xu ◽  
...  
Keyword(s):  
Building Blocks ◽  
Fragment Screening

Fragment-based drug design facilitates selective kinase inhibitor discovery

2021 ◽  
Author(s):  
Zhi-Zheng Wang ◽  
Xing-Xing Shi ◽  
Guang-Yi Huang ◽  
Ge-Fei Hao ◽  
Guang-Fu Yang
Keyword(s):  
Drug Design ◽  
Kinase Inhibitor ◽  
Inhibitor Discovery ◽  
Selective Kinase Inhibitor

waveRAPID—A Robust Assay for High-Throughput Kinetic Screens with the Creoptix WAVEsystem

2021 ◽  
pp. 247255522110138
Author(s):  
Önder Kartal ◽  
Fabio Andres ◽  
May Poh Lai ◽  
Rony Nehme ◽  
Kaspar Cottier
Keyword(s):  
Drug Discovery ◽  
Fold Increase ◽  
Microtiter Plate ◽  
Experimental Conditions ◽  
Short Pulses ◽  
Cycle Times ◽  
Fragment Screening ◽  
New Instrument ◽  
Single Well ◽  
Compound Screening

Surface-based biophysical methods for measuring binding kinetics of molecular interactions, such as surface plasmon resonance (SPR) or grating-coupled interferometry (GCI), are now well established and widely used in drug discovery. Increasing throughput is an often-cited need in the drug discovery process and this has been achieved with new instrument generations where multiple interactions are measured in parallel, shortening the total measurement times and enabling new application areas within the field. Here, we present the development of a novel technology called waveRAPID for a further—up to 10-fold—increase in throughput, consisting of an injection method using a single sample. Instead of sequentially injecting increasing analyte concentrations for constant durations, the analyte is injected at a single concentration in short pulses of increasing durations. A major advantage of the new method is its ability to determine kinetics from a single well of a microtiter plate, making it uniquely suitable for kinetic screening. We present the fundamentals of this approach using a small-molecule model system for experimental validation and comparing kinetic parameters to traditional methods. By varying experimental conditions, we furthermore assess the robustness of this new technique. Finally, we discuss its potential for improving hit quality and shortening cycle times in the areas of fragment screening, low-molecular-weight compound screening, and hit-to-lead optimization.

NMR Fragment Screening Hit Induces Plasticity of BRD7/9 Bromodomains

ChemBioChem ◽  
2016 ◽  
Vol 17 (15) ◽  
pp. 1456-1463 ◽  
Author(s):  
Na Wang ◽  
Fudong Li ◽  
Hongyu Bao ◽  
Jie Li ◽  
Jihui Wu ◽  
...  
Keyword(s):  
Fragment Screening
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