Arginase Structure and Inhibition: Catalytic Site Plasticity Reveals New Modulation Possibilities

Abstract

Metalloenzyme arginase is a therapeutically relevant target associated with tumor growth. To fight cancer immunosuppression, arginase activity can be modulated by small chemical inhibitors binding to its catalytic center. To better understand molecular mechanisms of arginase inhibition, a careful computer-aided mechanistic structural investigation of this enzyme was conducted. Using molecular dynamics (MD) simulations in the microsecond range, key regions of the protein active site were identified and their flexibility was evaluated and compared. A cavity opening phenomenon was observed, involving three loops directly interacting with all known ligands, while metal coordinating regions remained motionless. A novel dynamic 3D pharmacophore analysis method termed dynophores has been developed that allows for the construction of a single 3D-model comprising all ligand-enzyme interactions occurring throughout a complete MD trajectory. This new technique for the in silico study of intermolecular interactions allows for loop flexibility analysis coupled with movements and conformational changes of bound ligands. Presented MD studies highlight the plasticity of the size of the arginase active site, leading to the hypothesis that larger ligands can enter the cavity of arginase. Experimental testing of a targeted fragment library substituted by different aliphatic groups validates this hypothesis, paving the way for the design of arginase inhibitors with novel binding patterns.

Next generation 3D pharmacophore modeling

“…In a virtual screening campaign against the metalloenzyme arginase, dynophores were employed to explore the plasticity of the binding pocket in the presence of small molecule inhibitors and suggested the possibility for additional lipophilic contacts. This resulted in two novel fragment arginase inhibitors that could aid the development of anticancer drugs . The dynophore methodology enables researchers to escape the static nature of classical 3D pharmacophore approaches and provides new opportunities to describe and analyze ligand binding modes as dynamic events (Figure ) .…”

“…This resulted in two novel fragment arginase inhibitors that could aid the development of anticancer drugs . The dynophore methodology enables researchers to escape the static nature of classical 3D pharmacophore approaches and provides new opportunities to describe and analyze ligand binding modes as dynamic events (Figure ) . The probability density functions representing the feature distribution of the super‐features can be directly used for virtual screening, providing new possibilities for efficiently incorporating information from molecular dynamics simulations into fast and efficient virtual screening.…”

GC-MS Analysis of Major Compounds and Antihyperglycemic and Cytotoxicity Properties of Ficus racemosa L. fruit Extract: An in-vitro and in-silico Study

“…Pharmacophore modeling is a computationally effective and pragmatic technique for the discovery and optimisation of biologically active compounds (Wolber et al, 2008) and the study of intermolecular interactions in silico (Mortier et al, 2017). In current drug discovery eld, pharmacophore features is most commonly used drug designing tool that led to establishment of more stable and targeted drugs with no or limited side effect in the host, as they are supposed to more precisely targeted (Bredel and Jacoby, 2004).…”

Functional characterization and mechanistic modeling of the human cytochrome P450 enzyme CYP4A22

“…Grouping up points belonging to the same interaction results in three‐dimensional clouds yielding the spatial distribution and frequency of occurrence of the interaction. The dynophore algorithm, which is implemented within the LigandScout framework , has already been successfully applied to in‐depth investigations of ligand binding to muscarinic M2 receptors and revealed new arginase inhibition opportunities .…”