Kinetic Isotope Effect Analysis of RNA 2′- O -Transphosphorylation

Kinetic analysis of RNA cleavage by coronavirus Nsp15 endonuclease: Evidence for acid base catalysis and substrate dependent metal ion activation

Understanding the functional properties of SARS-CoV-2 nonstructural proteins is essential for defining their roles in the viral life cycle, developing improved therapeutics and diagnostics, and countering future variants. Coronavirus nonstructural protein Nsp15 is a hexameric U-specific endonuclease whose functions, substrate specificity, mechanism, and dynamics have not been fully defined. Previous studies report SARS-CoV-2 Nsp15 requires Mn²⁺ ions for optimal activity; however, the effects of divalent ions on Nsp15 reaction kinetics have not been investigated in detail. Here, we analyzed the single and multiple turnover kinetics for model single-stranded RNA substrates. Our data confirm that divalent ions are dispensable for catalysis and show that Mn²⁺ activates Nsp15 cleavage of two different ssRNA oligonucleotide substrates, but not a dinucleotide. Furthermore, biphasic kinetics of ssRNA substrates demonstrates that Mn²⁺ stabilizes alternative enzyme states that have faster substrate cleavage on the enzyme. However, we did not detect Mn²⁺-induced conformational changes using CD and fluorescence spectroscopy. The pH-rate profiles in the presence and absence of Mn²⁺ are consistent with active site ionizable groups with similar pK_as of ca. 4.8-5.2. We found the Rp stereoisomer phosphorothioate modification at the scissile phosphate had minimal effect on catalysis, which supports a mechanism involving an anionic transition state. In contrast, the Sp stereoisomer is inactive due to weak binding, consistent with models that position the non-bridging phosphoryl oxygen deep in the active site. Together, these kinetic data demonstrate that Nsp15 employs a conventional acid-base catalytic mechanism passing through an anionic transition state, and that divalent ion activation is substrate-dependent.

Application of 1D 15 N and band-selective 2D 1 H-15 N CLIP-HSQMBC to detect 35/37 Cl isotope effect on nitrogen for unequivocal structure elucidation of the N-Cl moiety in molecules

An impurity, designated MS204, was isolated from a scale-up production of an intermediate toward the synthesis of an active pharmaceutical ingredient. Structural elucidation of this chloro-containing impurity was performed based on the analysis of the MS and NMR data. Band-selective 2D ¹ H-¹⁵ N CLIP-HSQMBC experiment was developed to unequivocally identify the ionic N-Cl moiety in the molecule by discovering the two isotope-shifted nitrogen peaks as 3 to 1 ratio separated by about ¹ Δ¹⁵ N(^37/35 Cl) = 19.6 ppb (1.19 Hz) due to the Cl isotope effect. 1D ¹⁵ N and 2D ¹ H-¹⁵ N CLIP-HSQMBC experiments were applied to commercially available compounds to further confirm the techniques by detecting the isotope shift of nitrogen peaks for the N-Cl moiety in molecules.

Protein structure and computational drug discovery

The first protein structures revealed a complex web of weak interactions stabilising the three-dimensional shape of the molecule. Small molecule ligands were then found to exploit these same weak binding events to modulate protein function or act as substrates in enzymatic reactions. As the understanding of ligand–protein binding grew, it became possible to firstly predict how and where a particular small molecule might interact with a protein, and then to identify putative ligands for a specific protein site. Computer-aided drug discovery, based on the structure of target proteins, is now a well-established technique that has produced several marketed drugs. We present here an overview of the various methodologies being used for structure-based computer-aided drug discovery and comment on possible future developments in the field.