4EW3

The structure of human glycinamide ribonucleotide transformylase in complex with 10R-methylthio-DDATHF.

Summary for 4EW3

• Entry DOI: 10.2210/pdb4ew3/pdb
• Related: 1NJS 4EW1 4EW2
• Descriptor: Trifunctional purine biosynthetic protein adenosine-3, PHOSPHATE ION, SULFATE ION, ... (5 entities in total)
• Functional Keywords: transferase-transferase inhibitor complex, transferase/transferase inhibitor
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 1
• Total formula weight: 23443.57

Authors

Connelly, S.,DeMartino, K.,Boger, D.L.,Wilson, I.A. (deposition date: 2012-04-26, release date: 2013-07-31, Last modification date: 2023-09-13)

Primary citation

Connelly, S.,Demartino, J.K.,Boger, D.L.,Wilson, I.A.
Biological and Structural Evaluation of 10R- and 10S-Methylthio-DDACTHF Reveals a New Role for Sulfur in Inhibition of Glycinamide Ribonucleotide Transformylase.
Biochemistry, 52:5133-5144, 2013

PubMed Abstract: Glycinamide ribonucleotide transformylase (GAR Tfase) is a folate-dependent enzyme in the de novo purine biosynthesis pathway, which has long been considered a potential target for development of anti-neoplastic therapeutics. Here we report the biological and X-ray crystallographic evaluations of both independent C10 diastereomers, 10S- and 10R-methylthio-DDACTHF, bound to human GAR Tfase, including the highest-resolution apo GAR Tfase structure to date (1.52 Å). Both diastereomers are potent inhibitors (Ki = 210 nM for 10R, and Ki = 180 nM for 10S) of GAR Tfase and exhibit effective inhibition of human leukemia cell growth (IC₅₀ = 80 and 50 nM, respectively). Their inhibitory activity was surprisingly high, and these lipophilic C10-substituted analogues show distinct advantages over their hydrophilic counterparts, most strikingly in retaining potency in mutant human leukemia cell lines that lack reduced folate carrier protein activity (IC₅₀ = 70 and 60 nM, respectively). Structural characterization reveals a new binding mode for these diastereoisomers, in which the lipophilic thiomethyl groups penetrate deeper into a hydrophobic pocket within the folate-binding site. In silico docking simulations of three other sulfur-containing folate analogues also indicate that this hydrophobic cleft represents a favorable region for binding lipophilic substituents. Overall, these results suggest sulfur and its substitutions play an important role in not only the binding of anti-folates to GAR Tfase but also the selectivity and cellular activity (growth inhibition), thereby presenting new possibilities for the future design of potent and selective anti-folate drugs that target GAR Tfase.

PubMed: 23869564
DOI: 10.1021/bi4005182

Experimental method

X-RAY DIFFRACTION (1.702 Å)