Elucidating structural and molecular requirements of somatostatin subtype-4 agonist bound complexes using quantum mechanics approaches

Somatotropin-release Inhibiting Factor (SRIF) binds somatostatin subtype-4 receptor (sst4) within the neocortex to increase amyloid beta catabolism, and possibly effects neuronal plaque formation and disease progression of Alzheimer's disease. Recently, sst4 in complex with SRIF or a small molecule agonist were resolved using cryo-EM, and mutagenesis identified amino acid residues that contributed to activity. In the present study, we used mixed Quantum Mechanics/Molecular Mechanics (QM/MM) to refine the experimental sst4 complexes and decipher agonist-sst4 interactions. SRIF rendered the complex more stable, while interactions with asparagines 199 and 293 seen in the experimental complexes were lost and replaced with Gln279. We also addressed long-standing questions related to sst4 agonist binding. Toward that end, we used quantum mechanics, molecular docking, and QM/MM refinement methods and employed pair-wise comparisons or matched molecular pairs to explore the effects of chemical substitutions on ligand properties and energetics. We identified amino acid interactions that were consistent among all refined complexes, and those that differentiated high affinity binders. Finally, we considered several parameters to discern which correlated best with affinity, and highlighted aspects often overlooked or yet to be explored in order to enhance lead optimization outcomes.