From Steroid and Drug Metabolism to Glycobiology, Using Sulfotransferase Structures to Understand and Tailor Function

Sulfotransferases are ubiquitous enzymes that transfer a sulfo group from the universal cofactor donor 3'-phosphoadenosine 5'-phosphosulfate to a broad range of acceptor substrates. In humans, the cytosolic sulfotransferases are involved in the sulfation of endogenous compounds such as steroids, neurotransmitters, hormones, and bile acids as well as xenobiotics including drugs, toxins, and environmental chemicals. The Golgi associated membrane-bound sulfotransferases are involved in post-translational modification of macromolecules from glycosaminoglycans to proteins. The sulfation of small molecules can have profound biologic effects on the functionality of the acceptor, including activation, deactivation, or enhanced metabolism and elimination. Sulfation of macromolecules has been shown to regulate a number of physiologic and pathophysiological pathways by enhancing binding affinity to regulatory proteins or binding partners. Over the last 25 years, crystal structures of these enzymes have provided a wealth of information on the mechanisms of this process and the specificity of these enzymes. This review will focus on the general commonalities of the sulfotransferases, from enzyme structure to catalytic mechanism as well as providing examples into how structural information is being used to either design drugs that inhibit sulfotransferases or to modify the enzymes to improve drug synthesis. SIGNIFICANCE STATEMENT: This manuscript honors Dr. Masahiko Negishi's contribution to the understanding of sulfotransferase mechanism, specificity, and roles in biology by analyzing the crystal structures that have been solved over the last 25 years.

In silico drug discovery for a complex immunotherapeutic target - human c-Rel protein

Target evaluation and rational drug design rely on identifying and characterising small-molecule binding sites on therapeutically relevant target proteins. Immunotherapeutics development is especially challenging because of complex disease etiology and heterogenous nature of targets. c-Rel protein, a promising target in many human inflammatory and cancer pathologies, was selected as a case study for an effective in silico screening platform development since this transcription factor currently has no successful therapeutic inhibitors or modulators. This study introduces a novel in silico screening approach to probe binding sites using structural validation sets, molecular modelling and describes a method of a computer-aided drug design when a crystal structure is not available for the target of interest. In addition, we showed that binding sites can be analysed with the machine learning as well as molecular simulation approaches to help assess and systematically analyse how drug candidates can exert their mode of action. Finally, this cutting-edge approach was subjected to a high through-put virtual screen of selected 34 M drug-like compounds filtered from a library of 659 M compounds by identifying the most promising structures and proposing potential action mechanisms for the future development of highly selective human c-Rel inhibitors and/or modulators.

How a multimeric macromolecule is affected by divalent salts? Experimental and simulation study

Salts exist in any cell and living organism in contact with biological macromolecules. How these salts affect biomolecules such as enzyme is important from both basic sciences and practical technologies. It was observed that divalent salts can change structure and function of protein at higher concentrations. Here, we investigated the effect of divalent salt on the behavior of a multimeric enzyme. We treated glucose oxidase as dimer-active enzyme in different CaCl₂ concentration and seen that the enzyme become inactive at high concentration of salt. These experimental results are in agreement with recently published researches. To find a possible mechanism, a series of molecular dynamics simulation of the enzyme were performed at different salt concentration. According to the MD simulation, the conformational changes at the active site and FAD-binding site support the hypothesis of enzyme inactivation at high CaCl₂ concentration. MD simulations also showed that enzyme has an unstable conformation at higher salt concentration which is in agreement with our experimental data. Detailed structural properties of the enzyme have been analyzed under different conditions. To the best of our knowledge, this is the first study that bears detailed structural mechanism about the salt effects on multimeric macromolecules.

Effects of Mutations on Structure-Function Relationships of Matrix Metalloproteinase-1

Matrix metalloproteinase-1 (MMP-1) is one of the most widely studied enzymes involved in collagen degradation. Mutations of specific residues in the MMP-1 hemopexin-like (HPX) domain have been shown to modulate activity of the MMP-1 catalytic (CAT) domain. In order to reveal the structural and conformational effects of such mutations, a molecular dynamics (MD) study was performed of in silico mutated residues in the X-ray crystallographic structure of MMP-1 complexed with a collagen-model triple-helical peptide (THP). The results indicate an important role of the mutated residues in MMP-1 interactions with the THP and communication between the CAT and the HPX domains. Each mutation has a distinct impact on the correlated motions in the MMP-1•THP. An increased collagenase activity corresponded to the appearance of a unique anti-correlated motion and decreased correlated motions, while decreased collagenase activity corresponded both to increased and decreased anti-correlated motions.

Dimerization and ligand binding in tyrosylprotein sulfotransferase-2 are influenced by molecular motions

Tyrosylprotein sulfotransferase-2 catalyses important, but a less explored posttranslational modification of proteins.