Intermolecular Interactions of Nucleoside Antibiotic Tunicamycin with On-Target MraYCB-TUN and Off-Target DPAGT1-TUN in the Active Sites Delineated by Quantum Mechanics/Molecular Mechanics Calculations

Elahe K Astani; Saeid Malek Zadeh; Ning-Shian Hsu; Kuan-Hung Lin; Soroush Sardari; Tsung-Lin Li

doi:10.1021/acsomega.2c02213

Intermolecular Interactions of Nucleoside Antibiotic Tunicamycin with On-Target MraY_CB-TUN and Off-Target DPAGT1-TUN in the Active Sites Delineated by Quantum Mechanics/Molecular Mechanics Calculations

ACS Omega. 2022 Sep 6;7(37):32970-32987. doi: 10.1021/acsomega.2c02213. eCollection 2022 Sep 20.

Authors

Elahe K Astani^{1

2}, Saeid Malek Zadeh^{3

4

5}, Ning-Shian Hsu³, Kuan-Hung Lin³, Soroush Sardari¹, Tsung-Lin Li^{3

4

6

7}

Affiliations

¹ Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 13169-43551, Iran.
² Department of Chemistry, Faculty of Science, Tarbiat Modares University, Tehran 14115-175, Iran.
³ Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.
⁴ Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.
⁵ Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan.
⁶ Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.
⁷ Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan.

Abstract

Tunicamycin (TUN) is a nucleoside antibiotic with a complex structure comprising uracil, tunicamine sugar, N-acetylglucosamine (GlcNAc), and fatty acyl tail moieties. TUN, known as a canonical inhibitor, blocks vital functions of certain transmembrane protein families, for example, the insect enzyme dolichyl phosphate α-N-acetylglucosaminylphosphotransferase (DPAGT1) of Spodoptera frugiperda and the bacterial enzyme phospho-N-acetylmuramoylpentapeptide translocase (MraY_CB) of Clostridium bolteae. Accurate description of protein-drug interactions has an immense impact on structure-based drug design, while the main challenge is to create proper topology and parameter entries for TUN in modeling protein-TUN interactions given the structural complexity. Starting from DPAGT1-TUN and MraY_CB-TUN crystal structures, we first sketched these structural complexes on the basis of the CHARMM36 force field and optimized each of them using quantum mechanics/molecular mechanics (QM/MM) calculations. By continuing calculations on the active site (QM region) of each optimized structure, we specified the characteristics of intermolecular interactions contributing to the binding of TUN to each active site by quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses at the M06-2X/6-31G** level. The results outlined that TUN insertion into each active site requires multiple weak, moderate, and strong hydrogen bonds accompanying charge-dipole, dipole-dipole, and hydrophobic interactions among different TUN moieties and adjacent residues. The water-mediated interactions also play central roles in situating the uracil and tunicamine moieties of TUN within the DPAGT1 active site as well as in preserving the uracil-binding pocket in the MraY_CB active site. The TUN binds more strongly to DPAGT1 than to MraY_CB. The information garnered here is valuable particularly for better understanding mode of action at the molecular level, as it is conducive to developing next generations of nucleoside antibiotics.