Focus Your Screening Library: Rapid Identification of Novel PDE2 Inhibitors with in silico Driven Library Prioritization and MicroScale Thermophoresis

作者: Florian Kaiser , Maximilian G. Plach , Thomas Schubert , V. Joachim Haupt

DOI: 10.1101/2020.04.22.021360

关键词:

摘要: Accelerated development of lead structures is high interest to the pharmaceutical industry in order decrease times and costs. We showcase how an intelligent combination AI-based drug screening with state-of-the-art biophysics drives rapid identification novel inhibitor chemical diversity for cGMP-dependent 39,59-cyclic phosphodiesterase (PDE2). The starting point was off-the-shelve library two million drug-like compounds. In a single silico reduction step, we short-listed 125 compounds - focused as potential binders PDE2 tested their binding behavior vitro using MicroScale Thermophoresis (MST). Of this library, seven indicated PDE2, translating hit rate 6%. Three these have affinities lower micromolar range. compound highest affinity showed KD 10μM thus excellent further medicinal chemistry optimization. results show innovative structure-driven approaches can be used accelerate discovery obtain new molecular scaffolds at fraction costs time compared standard high-throughput screening.

参考文章(32)
David Rogers, Mathew Hahn, Extended-Connectivity Fingerprints Journal of Chemical Information and Modeling. ,vol. 50, pp. 742- 754 ,(2010) , 10.1021/CI100050T
Robert B. Russell, Peter D. Sasieni, Michael J.E. Sternberg, Supersites within superfolds. Binding site similarity in the absence of homology. Journal of Molecular Biology. ,vol. 282, pp. 903- 918 ,(1998) , 10.1006/JMBI.1998.2043
Mu Gao, Jeffrey Skolnick, A Comprehensive Survey of Small-Molecule Binding Pockets in Proteins PLoS Computational Biology. ,vol. 9, pp. e1003302- ,(2013) , 10.1371/JOURNAL.PCBI.1003302
Sebastian Salentin, Sven Schreiber, V. Joachim Haupt, Melissa F. Adasme, Michael Schroeder, PLIP: fully automated protein–ligand interaction profiler Nucleic Acids Research. ,vol. 43, ,(2015) , 10.1093/NAR/GKV315
Peter Buijnsters, Meri De Angelis, Xavier Langlois, Frederik J. R. Rombouts, Wendy Sanderson, Gary Tresadern, Alison Ritchie, Andrés A. Trabanco, Greet VanHoof, Yves Van Roosbroeck, José-Ignacio Andrés, Structure-Based Design of a Potent, Selective, and Brain Penetrating Pde2 Inhibitor with Demonstrated Target Engagement. ACS Medicinal Chemistry Letters. ,vol. 5, pp. 1049- 1053 ,(2014) , 10.1021/ML500262U
David Ryan Koes, Matthew P Baumgartner, Carlos J Camacho, None, Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise Journal of Chemical Information and Modeling. ,vol. 53, pp. 1893- 1904 ,(2013) , 10.1021/CI300604Z
V. Joachim Haupt, Simone Daminelli, Michael Schroeder, Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key. PLOS ONE. ,vol. 8, ,(2013) , 10.1371/JOURNAL.PONE.0065894
Jeffrey Skolnick, Mu Gao, Interplay of physics and evolution in the likely origin of protein biochemical function Proceedings of the National Academy of Sciences of the United States of America. ,vol. 110, pp. 9344- 9349 ,(2013) , 10.1073/PNAS.1300011110
André Iffland, Darcy Kohls, Simon Low, Jing Luan, Yan Zhang, Michael Kothe, Qing Cao, Ajith V. Kamath, Yuan-Hua Ding, Tom Ellenberger, Structural determinants for inhibitor specificity and selectivity in PDE2A using the wheat germ in vitro translation system. Biochemistry. ,vol. 44, pp. 8312- 8325 ,(2005) , 10.1021/BI047313H