Molecular simulations of SSTR2 dynamics and interaction with ligands

Abstract

The cyclic peptide hormone somatostatin regulates physiological processes involved in growth and metabolism, through its binding to G-protein coupled somatostatin receptors. The isoform 2 (SSTR2) is of particular relevance for the therapy of neuroendocrine tumours for which different analogues to somatostatin are currently in clinical use. We present an extensive and systematic computational study on the dynamics of SSTR2 in three different states: active agonist-bound, inactive antagonist-bound and apo inactive. We exploited the recent burst of SSTR2 experimental structures to perform μs-long multi-copy molecular dynamics simulations to sample conformational changes of the receptor and rationalize its binding to different ligands (the agonists somatostatin and octreotide, and the antagonist CYN154806). Our findings suggest that the apo form is more flexible compared to the holo ones, and confirm that the extracellular loop 2 closes upon the agonist octreotide but not upon the antagonist CYN154806. Based on interaction fingerprint analyses and free energy calculations, we found that all peptides similarly interact with residues buried into the binding pocket. Conversely, specific patterns of interactions are found with residues located in the external portion of the pocket, at the basis of the extracellular loops, particularly distinguishing the agonists from the antagonist. This study will help in the design of new somatostatin-based compounds for theranostics of neuroendocrine tumours.

Interaction of Radiopharmaceuticals with Somatostatin Receptor 2 Revealed by Molecular Dynamics Simulations

“…Overall, for all compounds, we found the known conserved interactions involving residues located in the bottom part of the binding pocket of SSTR2 ( i.e. , Asp122 3.32 , Gln126 3.36 ) and the D W4 and K5 motif of the ligands (Figure S4), as well as other residues already reported in previous works. ,, …”

“…The small differences in the peptide structure reflect not only on single-protein residue interaction but also on the overall dynamics of the receptor, especially of the very mobile ECL2. This loop is known to play a key role in the interaction with ligands , and it is characterized by opening and closing movements. , For this reason, we computed the percentage of MD frames in which the loop was found closed, according to the threshold values established in our previous work . These thresholds refer to geometric parameters, namely, distances and angles, characterizing the movements of this loop.…”

“…(1) The force field ff19SB was assigned to the peptide, and nonstandard residues ( i.e. , d -phenylalanine, naphthalene, d -tryptophan, threoninol) were parametrized as described previously . (2) Given the peculiarity of the metal coordination bond involving 68 Ga 3+ and 64 Cu 2+ and their challenging parametrization, we used the Metal Center Parameter Builder (MCPB.py) procedure implemented in Amber20.…”

“…In the last year, different structures of SSTR2 in multiple conformational states have been published. ,,,,, Noteworthy, most of these structures are in complex with agonist ligands, which is often somatostatin or its analogous, like the octa-peptide octreotide. Both experimental and computational studies explored the conformational features of SSTR2 that are common to those of other class A GPCRs, and the key elements characterizing the binding with different types of ligands (see Figure S1 for an overview of the three-dimensional structure of SSTR2 and its main domains) . The availability of such structural data can burst the development of new SSTR2 ligands able to bind the receptor with high affinity .…”

“…The choice of the radiopharmaceuticals was driven by the aim of exploring the influence of the different portions of the ligands in the interaction with the receptor by (1) considering the same radionuclide-chelator ( 68 Ga-DOTA) and changing the peptide (TOC, TATE, and NOC), (2) considering the same chelator-peptide (DOTA-TATE) and changing the radionuclide ( 68 Ga and 64 Cu), and (3) considering the same radionuclide-peptide ( 64 Cu-TATE) and changing the chelator (DOTA, TETA, SAR). Through multicopy μs-long molecular dynamics (MD) simulations based on a previous investigation on SSTR2 in different states, here we found analogies and differences in the interaction patterns characterizing the binding of the six compounds with SSTR2, and we discovered how each moiety can influence the dynamical behavior of the complexes. The detailed molecular-level analysis presented in this study, thoroughly mapping the SSTR2/ligand interactions, revealed previously unknown structural and mechanistic insights into molecular recognition processes of radiopharmaceuticals at SSTR2.…”