Effect of thiol compounds on human complement component C4

Understanding the Structure-Activity Relationship through Density Functional Theory: A Simple Method Predicts Relative Binding Free Energies of Metalloenzyme Fragment-like Inhibitors

Despite being involved in several human diseases, metalloenzymes are targeted by a small percentage of FDA-approved drugs. Development of novel and efficient inhibitors is required, as the chemical space of metal binding groups (MBGs) is currently limited to four main classes. The use of computational chemistry methods in drug discovery has gained momentum thanks to accurate estimates of binding modes and binding free energies of ligands to receptors. However, exact predictions of binding free energies in metalloenzymes are challenging due to the occurrence of nonclassical phenomena and interactions that common force field-based methods are unable to correctly describe. In this regard, we applied density functional theory (DFT) to predict the binding free energies and to understand the structure-activity relationship of metalloenzyme fragment-like inhibitors. We tested this method on a set of small-molecule inhibitors with different electronic properties and coordinating two Mn²⁺ ions in the binding site of the influenza RNA polymerase PA_N endonuclease. We modeled the binding site using only atoms from the first coordination shell, hence reducing the computational cost. Thanks to the explicit treatment of electrons by DFT, we highlighted the main contributions to the binding free energies and the electronic features differentiating strong and weak inhibitors, achieving good qualitative correlation with the experimentally determined affinities. By introducing automated docking, we explored alternative ways to coordinate the metal centers and we identified 70% of the highest affinity inhibitors. This methodology provides a fast and predictive tool for the identification of key features of metalloenzyme MBGs, which can be useful for the design of new and efficient drugs targeting these ubiquitous proteins.

Investigating the selectivity of metalloenzyme inhibitors

The inhibitory activity of a broad group of known metalloenzyme inhibitors against a panel of metalloenzymes was evaluated. Clinically approved inhibitors were selected as well as several other reported metalloprotein inhibitors in order to represent a broad range of metal binding groups (MBGs), including hydroxamic acid, carboxylate, hydroxypyridinonate, thiol, and N-hydroxyurea functional groups. A panel of metalloenzymes, including carbonic anhydrase (hCAII), several matrix metalloproteinases (MMPs), angiotensin converting enzyme (ACE), histone deacetylase (HDAC-2), and tyrosinase (TY), was selected based on their clinical importance for a range of pathologies. In addition, each inhibitor was evaluated for its ability to remove Fe(3+) from holo-transferrin to gauge the ability of the inhibitors to access Fe(3+) from a primary transport protein. The results show that the metalloenzyme inhibitors are quite selective for their intended targets, suggesting that despite their ability to bind metal ions, metalloprotein inhibitors are not prone to widespread off-target enzyme inhibition activity.