Conformational Preferences of Pyridone Adenine Dinucleotides from Molecular Dynamics Simulations

• Published in: International journal of molecular sciences Vol. 23; no. 19; p. 11866
• Main Authors: Buckley, David P., Migaud, Marie E., Tanner, John J.
• Format: Journal Article
• Language: English
• Published: Basel MDPI AG 01.10.2022; MDPI
• Subjects: Adenine; Adenosine; Aqueous solutions; Carbonyl groups; Carbonyls; Crystal structure; Enzymes; Hydrogen bonding; Metabolism; Molecular dynamics; molecular dynamics simulations; Nicotinamide; nicotinamide adenine dinucleotide; Oxidation; Oxidative stress; Population; Preferences; Proteins; Ribose; Simulation
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms231911866

Pyridone adenine dinucleotides (ox-NADs) are redox inactive derivatives of the enzyme cofactor and substrate nicotinamide adenine dinucleotide (NAD) that have a carbonyl group at the C2, C4, or C6 positions of the nicotinamide ring. These aberrant cofactor analogs accumulate in cells under stress and are potential inhibitors of enzymes that use NAD(H). We studied the conformational landscape of ox-NADs in solution using molecular dynamics simulations. Compared to NAD+ and NADH, 2-ox-NAD and 4-ox-NAD have an enhanced propensity for adopting the anti conformation of the pyridone ribose group, whereas 6-ox-NAD exhibits greater syn potential. Consequently, 2-ox-NAD and 4-ox-NAD have increased preference for folding into compact conformations, whereas 6-ox-NAD is more extended. ox-NADs have distinctive preferences for the orientation of the pyridone amide group, which are driven by intramolecular hydrogen bonding and steric interactions. These conformational preferences are compared to those of protein-bound NAD(H). Our results may help in identifying enzymes targeted by ox-NADs.