Assessment of blinded virtual screenings and pose predictions of a challenging protein-fragment crystallographic dataset
Creators: name: Harold, Grosjean
Publisher: name: Zenodo
Year: 2020
Subjects: SAMPL7 Fragments Crystallography Bromodomain Dockings Screenings

description: The pleckstrin homology domain interacting protein (PHIP) is a multidomain protein that is involved in cell morphology and cytoskeletal organization. It is suggested that PHIP regulates insulin-like growth factor signalling pathways. Suppression of its expression inhibits melanoma, breast, and lung tumour cell proliferation and invasion making it a drug target of choice [1]. The protein is composed of 8 WD repeats, which are known to fold into a ß-propeller domain, and two bromodomains. The second bromodomain of PHIP (PHIP2) is the only domain that has been structurally characterized. Bromodomains participate in gene expression modulation through the binding of acetylated lysine containing peptides located on histone tails. Multiple probes and drug-candidates have been designed to inhibit these proteins [2]. A highly reproducible and well-diffracting PHIP2 crystal was obtained in a C2 space group, thereby providing necessary material for an XChem [3] high-throughput crystallographic fragment screening experiment. Crystals were are soaked with 799 fragments, fished and shot in a semi-supervised and high-throughput fashion resulting in hundreds of data sets. Of these, 47 hits were identified at the pharmacologically relevant acetylated lysine binding site. This was done using the PanDDa4 method that takes advantage of the abundance of datasets to perform statistical extraction of weak binding events. The resulting structures were used as a challenging data set for the 7th edition of the SAMPL challenge for protein-ligands. The challenge was divided into 3 stages: First, participants were tasked to predict binders from non-binders. In the second stage, participants were asked to predict the poses of all 47 known fragments. Lastly, participants were asked to mine a database and propose follow-up compounds that would bind. Only a small number of groups participated, and their predictions were rather inaccurate, highlighting the sense that predictions on fragment-protein complexes appear to be harder than for larger, more drug-like compounds. We discuss the implications of these results and consider where the community should focus its efforts in the future. [1] de Semir, D., Bezrookove, V., Nosrati, M., Dar, A., Wu, C., Shen, J., Rieken, C., Venkatasubramanian, M., Miller, J., Desprez, P., McAllister, S., Soroceanu, L., Debs, R., Salomonis, N., Schadendorf, D., Cleaver, J. and Kashani-Sabet, M., 2018. PHIP as a therapeutic target for driver-negative subtypes of melanoma, breast, and lung cancer. Proceedings of the National Academy of Sciences, 115(25), pp.E5766-E5775. [2] Cochran, A., Conery, A. and Sims, R., 2019. Bromodomains: a new target class for drug development. Nature Reviews Drug Discovery, 18(8), pp.609-628. [3] Douangamath, A., Fearon, D., Gehrtz, P., Krojer, T., Lukacik, P., Owen, C., Resnick, E., Strain-Damerell, C., Aimon, A., Ábrányi-Balogh, P., Brandão-Neto, J., Carbery, A., Davison, G., Dias, A., Downes, T., Dunnett, L., Fairhead, M., Firth, J., Jones, S., Keeley, A., Keserü, G., Klein, H., Martin, M., Noble, M., O’Brien, P., Powell, A., Reddi, R., Skyner, R., Snee, M., Waring, M., Wild, C., London, N., von Delft, F. and Walsh, M., 2020. Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease. Nature Communications, 11(1). [4] Pearce, N., Krojer, T., Bradley, A., Collins, P., Nowak, R., Talon, R., Marsden, B., Kelm, S., Shi, J., Deane, C. and von Delft, F., 2017. A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density. Nature Communications, 8(1).