Crystallographic and Computational Characterization of Methyl Tetrel Bonding in S-Adenosylmethionine-Dependent Methyltransferases

Abstract

Tetrel bonds represent a category of non-bonding interaction wherein an electronegative atom donates a lone pair of electrons into the sigma antibonding orbital of an atom in the carbon group of the periodic table. Prior computational studies have implicated tetrel bonding in the stabilization of a preliminary state that precedes the transition state in S_N2 reactions, including methyl transfer. Notably, the angles between the tetrel bond donor and acceptor atoms coincide with the prerequisite geometry for the S_N2 reaction. Prompted by these findings, we surveyed crystal structures of methyltransferases in the Protein Data Bank and discovered multiple instances of carbon tetrel bonding between the methyl group of the substrate S-adenosylmethionine (AdoMet) and electronegative atoms of small molecule inhibitors, ions, and solvent molecules. The majority of these interactions involve oxygen atoms as the Lewis base, with the exception of one structure in which a chlorine atom of an inhibitor functions as the electron donor. Quantum mechanical analyses of a representative subset of the methyltransferase structures from the survey revealed that the calculated interaction energies and spectral properties are consistent with the values for bona fide carbon tetrel bonds. The discovery of methyl tetrel bonding offers new insights into the mechanism underlying the S_N2 reaction catalyzed by AdoMet-dependent methyltransferases. These findings highlight the potential of exploiting these interactions in developing new methyltransferase inhibitors.

Keywords: AdoMet; S-adenosylmethionine; SAM; SN2 reaction; charge transfer; methyl transfer; methylation; methyltransferase; molecular electrostatic potential; noncovalent bond; sigma-hole; tetrel bond.

Figure 1

Representative examples of methyl tetrel bonding in crystal structures of AdoMet-dependent methyltransferases. AdoMet and small molecule inhibitors are depicted with green and yellow carbon atoms, respectively. Methyl tetrel bonding distances R(C∙∙∙X) and angles θ(S–C∙∙∙X) are denoted in blue. (a) COMT bound to AdoMet, DNC, and an Mg²⁺ ion (PDB accession code 5LSA). Key active site residues are illustrated, including the Mg²⁺-coordinating residues and the catalytic Lys194. (b) The SET domain KMT SMYD3 bound to AdoMet and an oxindole-containing inhibitor (5CCL). (c) SMYD2/AdoMet/SGC Probe BAY-598 ternary complex (5ARG). (d) SET domain KMT G9A bound to AdoMet and Inhibitor 13 (not shown) (5VSC). A water molecule in the substrate lysine binding channel of the enzyme engages in a methyl C∙∙∙O tetrel bond with AdoMet.

Figure 2

Two views of the molecular electrostatic potential surrounding the MeS⁺(Et)₂ sulfonium cation. Right view looks directly down the H₃C–S axis. Blue and red colors correspond respectively to +0.40 and +0.30 au.

Figure 3

Molecular structures of the models used to computationally analyze AdoMet methyl tetrel bonding in SET domain KMTs. (a) Model of MeS⁺(Et)₂ and dichlorobenzene in the SMYD2 structure; (b) MeS⁺(Et)₂ and oxindole in the SMYD3 structure; (c) MeS⁺(Et)₂ and a water molecule bound in the active site of G9A. Values for the tetrel bond distances and angles are reported in Angstrom and degrees, respectively.

Figure 4

Molecular structures of COMT models used to probe C∙∙∙O tetrel bonding between AdoMet and DNC. (a) MeS⁺(Et)₂ and the phenoxide anion of DNC; (b) Model in which the 3-nitro moiety of DNC is replaced with a methyl group; (c) Complex wherein the methyl group of MeS⁺(Et)₂ is replaced with a hydrogen atom, yielding HS⁺(Et)₂; (d) Model of DNC and the thioether S(Et)₂ representing the product AdoHcy; (e) Complex in which the phenoxide oxygen atom of DNC is substituted by a hydrogen atom.

Figure 5

Molecular structures of COMT active site models. (a) MeS⁺(Et)₂, the phenoxide anion of DNC, and the active site Mg²⁺ ion; (b) The model depicted in (a) that also includes the residues and water molecule that coordinate the Mg²⁺ ion and the catalytic residue Lys194.