pone.0248034.s005.tif (3.22 MB)

Structural modeling of Compounds 1–3.

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posted on 2021-11-09, 18:32 authored by Steven A. Saenz, Andrea Local, Tiffany Carr, Arvind Shakya, Shivsmriti Koul, Haiqing Hu, Lisa Chourb, Justin Stedman, Jenna Malley, Laura Akullian D’Agostino, Veerabahu Shanmugasundaram, John Malona, C. Eric Schwartz, Lisa Beebe, Meghan Clements, Ganesh Rajaraman, John Cho, Lan Jiang, Alex Dubrovskiy, Matt Kreilein, Roman Shimanovich, Lawrence G. Hamann, Laure Escoubet, J. Michael Ellis

Structural models of compounds 1–3 were built in RORγt structures (5C4T, 6UCG). The crystal structures were imported into Maestro (Schrödinger Release 2020–2: Maestro, Glide, LigPrep, Epik, Schrödinger, LLC, New York, NY, 2020.). The structures were prepared using the Protein Preparation workflow as implemented in the Schrödinger Suite. Glide docking grids were generated by focusing the grid box on the center of the Cpd25 and MRL-673. The size of the box enclosing the grid was set to 10 Å. No other constraints, rotatable groups or excluded volumes were imposed. The three compounds 1–3 were then prepared for docking using LigPrep and the OPLS3e force field was used for minimizations; possible ionization states at pH 7.0 ± 2.0 were generated using Epik and tautomers were generated; specified chirality was retained.

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Structural modeling of Compounds 1–3.

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