GTP Cyclohydrolase I as a Potential Drug Target: New Insights into Its Allosteric Modulation via Normal Mode Analysis

Abstract

Guanosine triphosphate (GTP) cyclohydrolase I (GCH1) catalyzes the conversion of GTP into dihydroneopterin triphosphate (DHNP). DHNP is the first intermediate of the folate de novo biosynthesis pathway in prokaryotic and lower eukaryotic microorganisms and the tetrahydrobiopterin (BH4) biosynthesis pathway in higher eukaryotes. The de novo folate biosynthesis provides essential cofactors for DNA replication, cell division, and synthesis of key amino acids in rapidly replicating pathogen cells, such as Plasmodium falciparum (P. falciparum), a causative agent of malaria. In eukaryotes, the product of the BH4 biosynthesis pathway is essential for the production of nitric oxide and several neurotransmitter precursors. An increased copy number of the malaria parasite P. falciparum GCH1 gene has been reported to influence antimalarial antifolate drug resistance evolution, whereas mutations in the human GCH1 are associated with neuropathic and inflammatory pain disorders. Thus, GCH1 stands as an important and attractive drug target for developing therapeutics. The GCH1 intrinsic dynamics that modulate its activity remains unclear, and key sites that exert allosteric effects across the structure are yet to be elucidated. This study employed the anisotropic network model to analyze the intrinsic motions of the GCH1 structure alone and in complex with its regulatory partner protein. We showed that the GCH1 tunnel-gating mechanism is regulated by a global shear motion and an outward expansion of the central five-helix bundle. We further identified hotspot residues within sites of structural significance for the GCH1 intrinsic allosteric modulation. The obtained results can provide a solid starting point to design novel antineuropathic treatments for humans and novel antimalarial drugs against the malaria parasite P. falciparum GCH1 enzyme.

Mechanism of Allosteric Modulation of Nicotinamide Phosphoribosyltransferase to Elevate Cellular NAD+

“…The question of N-PAM effects on k cat is more difficult to assess because the crystal structures of N-PAM-bound NAMPT do not show any perturbation of NAM nor active site residues. Enzymes have been shown by normal-mode analysis (NMA) to have open and closed conformations that correlate with activity; and, ligand binding of an allosteric modulator would be predicted to stabilize conformers that regulate activity . Using NMA, crystal structures obtained in this work were compared to key NAMPT structures from the literature.…”

“…Enzymes have been shown by normal-mode analysis (NMA) 27 to have open and closed conformations that correlate with activity; and, ligand binding of an allosteric modulator would be predicted to stabilize conformers that regulate activity. 28 Using NMA, crystal structures obtained in this work were compared to key NAMPT structures from the literature. The NAMPT structures with BeF 3 − coordinated to His-247 provide a mimic of the phospho-H247 phosphoenzyme (PDB: 3DKL; 3DHF; Figure 1B).…”

The mechanism of nicotinamide phosphoribosyltransferase whereby positive allosteric modulation elevates cellular NAD+

“…Enzymes have been shown by normal-mode analysis (NMA) (Bahar, Lezon, Bakan, & Shrivastava, 2010) to have open and closed con -formations that correlate with activity; and, ligand bindin g of an allosteric modulator would be predicted to stabilize conformers that regulate activity. (Khairallah, Ross, & Tastan Bishop, 2021) Using NMA, crystal structures obtained in this work were compared to key NAMPT structures from the literature. The NAMPT structures with BeF3¯ coordinated to His-247 provide a mimic of the phospho-H247 phosphoenzyme (PDB: 3DKL; 3DHF; Fig.…”

Allosteric modulation of SHP2: Quest from known to unknown

“…NMA (Normal Mode Analysis) is a computational method used to generate ensembles of protein conformations. In this method, both apo and holo can be subjected to NMA to analyze the resulting conformations (Khairallah et al, 2021). Initially, the apo is used as input to identify potential binding sites, and perturbations are induced by introducing pseudoligands to trigger conformational changes.…”