Journal
JOURNAL OF CHEMICAL INFORMATION AND MODELING
Volume 57, Issue 12, Pages 3104-3123Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jcim.7b00528
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- National Institutes of Health (Intramural Research Program of the NIDDK) [ZIADK031117, ZIADK031126]
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We performed a molecular modeling analysis of 100 nucleotide-like bisphosphates and 46 non-nucleotide arylurea derivatives previously reported as P2Y(1)R binders using the recently solved hP2Y(1)R structures. We initially docked the compounds at the X-ray structures and identified the binding modes of representative compounds highlighting key patterns in the structure-activity relationship (SAR). We subsequently subjected receptor complexes with selected key agonists (2MeSADP and MRS2268) and antagonists (MRS2500 and BPTU) to membrane molecular dynamics (MD) simulations (at least 200 ns run in triplicate, simulation time 0.6-1.6 mu s per ligand system) while considering alternative protonation states of nucleotides. Comparing the temporal evolution of the ligand-protein interaction patterns with available site-directed mutagenesis (SDM) data and P2Y(1)R apo state simulation provided further SAR insights and suggested reasonable explanations for loss/gain of binding affinity as well as the most relevant charged species for nucleotide ligands. The MD analysis also predicted local conformational changes required for the receptor inactive state to accommodate nucleotide agonists.
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