Structure-based analysis of Bacilli and plasmid dihydrofolate reductase evolution

Abstract

Dihydrofolate reductase (DHFR), a key enzyme in tetrahydrofolate-mediated biosynthetic pathways, has a structural motif known to be highly conserved over a wide range of organisms. Given its critical role in purine and amino acid synthesis, DHFR is a wellestablished therapeutic target for treating a wide range of prokaryotic and eukaryotic infections as well as certain types of cancer. Here we present a structural-based computer analysis of bacterial (Bacilli) and plasmid DHFR evolution. We generated a structure-based sequence alignment using 7 wild-type DHFR x-ray crystal structures obtained from the RCSB Protein Data Bank and 350 chromosomal and plasmid homology models we generated from sequences obtained from the NCBI Protein Database. We used these alignments to compare active site and non-active site conservation in terms of amino acid residues, secondary structure and amino acid residue class. With respect to amino acid sequences and residue classes, active-site positions in both plasmid and chromosomal DHFR are significantly more conserved than non-active site positions. Secondary structure conservation was similar for active site and non-active site positions. Plasmid-encoded DHFR proteins have greater degree of sequence and residue class conservation, particularly in sequence positions associated with a network of concerted protein motions, than chromosomalencoded DHFR proteins. These structure-based were used to build DHFR specific phylogenetic trees from which evidence for horizontal gene transfer was identified.

A Computational Chemistry-Driven Hypothesis on the Mode of Action of Hipposudoric Acid and Related Analogs

“…[5,6] DHFR is conserved among both prokaryotic and eukaryotic species, and therefore it is an attractive target to produce novel antimicrobial, anticancer, antifungal, and antiparasitic agents. [7,8] Among the most well-known antifolate medications include Methotrexate (MTX) which is a competitive inhibitor of the target with an affinity several orders of magnitude higher than endogenous dihydrofolic acid. [9][10][11] 1.1 Pharmacophore based approach for drug design…”