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bioRxiv · 10.1101/2023.01.03.522558

Investigating the Unbinding of Muscarinic Antagonists from the Muscarinic 3 Receptor.

Buigues Jorro, P. J.·Gehrke, S.·Badaoui, M.·Mandana, G.·Qi, T.·Bottegoni, G.·Rosta, E.
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Abstract

Patient symptom relief is often heavily influenced by the residence time of the inhibitor-target complex. For the human muscarinic receptor 3 (hMR3), tiotropium is a long-acting bronchodylator used in conditions such as asthma or chronic obstructive pulmonary disease (COPD). The mechanistic insights of this inhibitor remain unclear, specifically, elucidation of the main factors determining the unbinding rates could help develop the next generation of antimuscarinic agents. Using our novel unbinding algorithm, we were able to investigate ligand dissociation from hMR3. The unbinding paths of tiotropium and two of its analogues, N-methylscopolamin and homatropine methylbromide show a consistent qualitative mechanism and allowed us to identify the structural bottleneck of the process. Furthermore, our machine learning-based analysis identified key roles of the ECL2/TM5 junction involved at the transition state. Additionally, our results point at relevant changes at the intracellular end of the TM6 helix leading to the ICL3 kinase domain, highlighting the closest residue L482. This residue is located right between two main protein binding sites involved in signal transduction for hMR3s activation and regulation. We also highlight key pharmacophores of tiotropium that play determining roles in the unbinding kinetics and could aid towards drug design and lead optimization. Description O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/522558v2_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@2598b2org.highwire.dtl.DTLVardef@4bf425org.highwire.dtl.DTLVardef@89dfa8org.highwire.dtl.DTLVardef@1ba9f48_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical abstract of the work, showing the unbinding for ligands 1 (tiotropium, TTP), 2 (N-methylscopolamin, NMS) and 3 (homatropine methylbromide, CPD2). Using TTPs downhill simulations from its unbinding transition state, different protein-ligand and proteinprotein interactions were analyzed with MLTSA to find relevant CVs driving the different outcomes.

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Buigues Jorro, P. J., Gehrke, S., Badaoui, M., Mandana, G., Qi, T., Bottegoni, G., Rosta, E.. 2023-01-03. Investigating the Unbinding of Muscarinic Antagonists from the Muscarinic 3 Receptor.. https://doi.org/10.1101/2023.01.03.522558

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