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NMR insights on the soluble Guanylyl Cyclase conformational dynamics to illuminate the SIGNaling pathway

Periodic Reporting for period 1 - NMRSIGN (NMR insights on the soluble Guanylyl Cyclase conformational dynamics to illuminate the SIGNaling pathway)

Reporting period: 2018-08-01 to 2020-07-31

Gas-sensing proteins play an important role in mediating biological events. Soluble guanylate cyclase (sGC) is activated when nitric oxide (NO) binds to heme Fe of sGC, resulting to the stimulation of the cyclization of guanosine 5- triphosphate (GTP) to the second messenger cyclic guanosine 3,5-monophosphate (cGMP), which in turn has a direct role in the control of a variety of physiological processes in several signal transduction pathways. Disruptions in the NO/sGC/cGMP signalling pathway have been linked to a variety of diseases including congestive heart failure, stroke, hypertension and neurodegeneration.
The H-NOX domain of sGC is a hot target for drug discovery because it appears to play a pivotal role in the control of a variety of physiological processes in several signal transduction pathways, with a significant impact on cardiovascular system. NMRSIGN investigates the changes in the structure and dynamics of H-NOX domain upon ligand binding using advanced state-of-the-art NMR techniques, molecular dynamics simulations and free energy calculations. This novel approach of combining NMR and computational MD data to identify receptor conformations that play a major role in biomolecular recognition before commencing the structure-based virtual screening is expected to have a major impact in the field of drug design.
With the aim to characterise the structural dynamics of ligand-bound H-NOX domain at time scales ranging from picosecond to microseconds we have carried out all-atom molecular dynamics simulations of the H-NOX domain from cyanobacterium Nostoc sp. (Ns H‐NOX), both in its native (heme-bound) state and in complex with the known sGC activator, cinaciguat. The computational data in conjunction with the experimental investigation of Ns H-NOX structure and its dynamics over a large range of timescales using state-of-the-art Nuclear Magnetic Resonance (NMR) methods provide the first full characterisation of both structure and dynamics of the Ns-HNOX system in solution. Our results reveal that the binding of the activator has distinct effects on the backbone order parameters of H-NOX, and changes in order parameters upon activator binding are observed for residues that are connected via hydrogen bonds or sidechain interactions. Accumulating evidence from our experiments and calculations suggest that these different responses to binding of activator appear to involve dynamical modes that transmit through such interactions, and therefore this long-range communication via dynamics changes may transferred through sGC domains and activate the distal C-terminal catalytic guanylyl cyclase domain.

The results obtained have been disseminated to the scientific community through:
1) Open-access publication, “Backbone and side chain NMR assignments of the H-NOX domain from Nostoc sp. in complex with BAY58-2667 (cinaciguat)” published in the Biomolecular NMR Assignments (BNMR).
2) An oral presentation at the University of Edinburgh, School of Chemistry, 22 January 2019, Edinburgh, UK.
3) An oral presentation with the title “Solution NMR spectroscopy and enhanced conformational sampling computational approaches to study the H-NOX domain of soluble guanylate cyclase” at the Edinburgh Parallel Computing Centre, 28 February 2019, Edinburgh, UK.
4) Poster presentation with the title “NMR insights into the structural and functional properties of soluble guanylate cyclase (sGC)”, at the 3rd Symposium “Chemistry at the Interface of Biology and Medicine”, September 23-26, 2019, Department of Pharmacy, University of Patras, Greece.
Over the last 20 years, several studies gave insights into sGC activation and binding of activators; however, no candidate of this drug class is available to date. NMRSIGN highlight significant changes in H-NOX domain conformational dynamics caused by activator binding and complement the static, classical picture of the complex as revealed by the X-ray structures. Our results are expected to provide valuable, atomic-level insights, in the design of new, original, and more effective pharmaceutical drugs for the activation of sGC.
Structural location of residues that show differences in the order parameters upon ligand binding