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Small molecule correctors of F508del-CFTR discovered by structure-based virtual screening

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Abstract

Folding correctors of F508del-CFTR were discovered by in silico structure-based screening utilizing homology models of CFTR. The intracellular segment of CFTR was modeled and three cavities were identified at inter-domain interfaces: (1) Interface between the two Nucleotide Binding Domains (NBDs); (2) Interface between NBD1 and Intracellular Loop (ICL) 4, in the region of the F508 deletion; (3) multi-domain interface between NBD1:2:ICL1:2:4. We hypothesized that compounds binding at these interfaces may improve the stability of the protein, potentially affecting the folding yield or surface stability. In silico structure-based screening was performed at the putative binding-sites and a total of 496 candidate compounds from all three sites were tested in functional assays. A total of 15 compounds, representing diverse chemotypes, were identified as F508del folding correctors. This corresponds to a 3% hit rate, ~tenfold higher than hit rates obtained in corresponding high-throughput screening campaigns. The same binding sites also yielded potentiators and, most notably, compounds with a dual corrector-potentiator activity (dual-acting). Compounds harboring both activity types may prove to be better leads for the development of CF therapeutics than either pure correctors or pure potentiators. To the best of our knowledge this is the first report of structure-based discovery of CFTR modulators.

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Acknowledgments

This work was funded by Cystic Fibrosis Foundation Therapeutics. The authors would like to thank Luis Galietta and ChanTest, Inc. for their contribution to the in vitro screening presented in this paper. Special thanks to Melissa Ashlock, Julie Forman-Kay, David Gadsby, and Kevin Foskett for insightful discussions and advice. Excellent technical assistance was provided by Jan Harrington, Linda Coulson, Katelyn Cassidy and Linda Millen.

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Author notes

  1. Martin Mense

    Present address: Cystic Fibrosis Foundation Therapeutics, 529 Main Street—Suite 208, Charlestown, MA, 02129, USA

  2. Sharon Fischman

    Present address: Biolojic Design LTD, Tel Aviv, Israel

  3. Hermann Bihler

    Present address: CFRx LLC, 529 Main Street—Suite 208, Charlestown, MA, 02129, USA

  4. Alina Shitrit, Efrat Ben-Zeev & Nili Schutz

    Present address: Dynamix Pharmaceuticals Ltd, 13 Gad Feinstein Rd, 3rd Level, Suite 30, 76385, Rehovot, Israel

  5. Diana R. Wetmore

    Present address: Emerald BioStructures, 7869 NE Day Rd W, Bainbridge Island, WA, 98110, USA

  6. Yael Marantz

    Present address: Teva Pharmaceuticals Industries LTD, Global Inovative R&D, P. O Box 8077, 42504, Netanya, Israel

  7. Hanoch Senderowitz

    Present address: Department of Chemistry, Bar-Ilan University, 52900, Ramat Gan, Israel

Authors and Affiliations

  1. EPIX Pharmaceuticals Ltd, 3 Hayetzira Street, 52521, Ramat Gan, Israel

    Ori Kalid, Sharon Fischman, Alina Shitrit, Efrat Ben-Zeev, Nili Schutz, Yael Marantz & Hanoch Senderowitz

  2. Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel-Aviv University, 69978, Ramat Aviv, Israel

    Ori Kalid

  3. EPIX Pharmaceuticals Inc, 4 Maguire Road, Lexington, MA, 02421, USA

    Martin Mense & Hermann Bihler

  4. Advanced Biotechnology Center, L.go R. Benzi 10, 16132, Genoa, Italy

    Nicoletta Pedemonte

  5. Departments of Physiology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA

    Philip J. Thomas

  6. Departments of Physiology and Biophysics, Rosalind Franklin University of Medicine and Science, Chicago Medical School, 3333 Green Bay Road, North Chicago, IL, 60064, USA

    Robert J. Bridges

  7. Cystic Fibrosis Foundation Therapeutics, 6931 Arlington Road, Suite 200, Bethesda, MD, 20814, USA

    Diana R. Wetmore

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  1. Ori Kalid
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Kalid, O., Mense, M., Fischman, S. et al. Small molecule correctors of F508del-CFTR discovered by structure-based virtual screening. J Comput Aided Mol Des 24, 971–991 (2010). https://doi.org/10.1007/s10822-010-9390-0

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