Computational and NMR spectroscopy insights into the conformation of cyclic di-nucleotides

Baifan Wang,Janez Plavec,Zhenghua Wang,Zhen Xi,Uroš Javornik

doi:10.1038/s41598-017-16794-4

Abstract

Cyclic di-nucleotides (CDNs) are second messengers in bacteria and metazoan that are as such controlling important biological processes. Here the conformational space of CDNs was explored systematically by a combination of extensive conformational search and DFT calculations as well as NMR methods. We found that CDNs adopt pre-organized conformations in solution in which the ribose conformations are North type and glycosidic bond conformations are anti type. The overall flexibility of CDNs as well as the backbone torsion angles depend on the cyclization of the phosphodiester bond. Compared to di-nucleotides, CDNs display high rigidity in the macrocyclic moieties. Structural comparison studies demonstrate that the pre-organized conformations of CDNs highly resemble the biologically active conformations. These findings provide information for the design of small molecules to modulate CDNs signalling pathways in bacteria or as vaccine adjuvants. The rigidity of the backbone of CDNs enables the design of high order structures such as molecular cages based on CDNs analogues.

Highlights

Cyclic di-nucleotides (CDNs) are composed of two nucleosides joined by two phosphate groups in a macrocycle (Fig. 1)
Replica exchange molecular dynamics (REMD)[27] simulations were performed on CDNs with 24 temperature states ranging from 273.0 to 583.5 K with simulation time up to 60 ns in implicit solvent
At 300 K the phase angles of pseudorotation[28,29] for all five CDNs are in the range from −60° to 60° corresponding to the N-type conformation (Fig. 2a)

Summary

Introduction

Cyclic di-nucleotides (CDNs) are composed of two nucleosides joined by two phosphate groups in a macrocycle (Fig. 1). Cyclic GMP-AMP whose phosphate groups connect the two nucleosides from the 2′- and 5′- positions of guanosine and the 3′- and 5′- positions of adenosine (denoted as 2′3′-cGAMP), serves as a second messenger in the cell signalling pathway. Bis-(3′–5′)-cyclic dimeric adenosine monophosphate (c-di-AMP) was identified as a crucial second messenger in the regulation of cell size, envelope stress control, fatty acid synthesis, ion transport and metabolite balance[7,8,9,10]. It has been shown that the conformation of CDNs in solution is crucial for the evaluation of the binding constants to their receptors[26] Such data are helpful for the understanding of the structure-activity relationship of either CDNs or their analogues and the design of potent therapeutic agents based on CDNs scaffold. The computational and NMR analysis provide parameters such as ribose puckering, conformational preference across glycosidic bond and backbone torsion angles

Methods

Results

Conclusion