Inhibitors of riboflavin biosynthetic pathway enzymes as potential antibacterial drugs

Abstract

Multiple drug resistance is the main obstacle in the treatment of bacterial diseases. Resistance against antibiotics demands the exploration of new antimicrobial drug targets. A variety of in silico and genetic approaches show that the enzymes of the riboflavin biosynthetic pathway are crucial for the survival of bacteria. This pathway is absent in humans thus enzymes of the riboflavin biosynthetic pathway are emerging drug targets for resistant pathogenic bacterial strains. Exploring the structural details, their mechanism of action, intermediate elucidation, and interaction analysis would help in designing suitable inhibitors of these enzymes. The riboflavin biosynthetic pathway consists of seven distinct enzymes, namely, 3,4-dihydroxy-2-butanone 4-phosphate synthase, GTP cyclohydrolase II, pyrimidine deaminase/reductase, phosphatase, lumazine synthase, and riboflavin synthase. The present review summarizes the research work that has been carried out on these enzymes in terms of their structures, active site architectures, and molecular mechanism of catalysis. This review also walks through small molecule inhibitors that have been developed against several of these enzymes.

Keywords: 3,4-dihydroxy-2-butanone 4-phosphate synthase; inhibitors; lumazine synthase; riboflavin biosynthetic pathway; riboflavin synthase.

FIGURE 1

Enzymes involved in riboflavin biosynthetic pathway. GTP is converted to ArP through four reactions catalysed consecutively by GTP cyclohydrolase II, pyrimidine deaminase, pyrimidine reductas, and pyrimidine phosphatase. Similarly, DHBP is formed Ru5P catalyzed by 3,4-dihydroxy-2-butanone-4-phosphate synthase. The two products condensed to form DRL in a reaction catalyzed by lumazine synthase. Riboflavin synthase converts two molecules of DRL to riboflavin and ArP. DARPP, 2,5-diamino-6-ribosyl-amino-4(3H)pyrimidinedione 5′-phosphate; ARPP, 5-amino-6-ribosyl-amino-2.4(1H, 3H)pyrimidinedione 5′-phosphate; ArPP 5-amino-6-ribitylamino-2.4-(1H, 3H)-pyrimidinedione-5′-phosphate; ArP 5-amino-6-ribitylamino-2.4-(1H, 3H)-pyrimidinedione; DHBP 3,4-dihydroxy-2-butanone-4-phosphate; DRL 6,7-dimethyl-8-ribityl-lumazine; FMN, flavin mononucleotide; FAD, flavin adenine dinucleotide.

FIGURE 2

Structures of 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBPS) from V. cholera. Crystal structure of DHBPS in complexed with substrate (Ru5P) and metal ions (PDBID: 4P8E) showing the active site architecture (left). Similarly, crystal structure of DHBPS in complexed with inhibitor (4PEH) and zinc ions (PDBID: 4P6P) highlighting the binding of inhibitor and metal (right).

FIGURE 3

Structures of Escherichia coli GTP cyclohydrolase II (GCH II). Cartoon representation of Escherichia coli GCH II in apo form (PDBID: 2BZ1) revealing the intrinsic metal binding (left). Crystal Structure of Escherichia coli GCH II in complex with GMPCPP and Zinc (PDBID: 2BZ0) enlightening the inhibitor binding (right). Zinc is shown as grey ball.

FIGURE 4

Structures of Escherichia coli bifunctional deaminase/reductase. Cartoon representation of the crystal structure of Escherichia coli deaminase/reductase in apo form (PDBID: 2G6V) underlining the domain organization and their relative orientation (left). The crystal structure of Escherichia coli bifunctional deaminase/reductase in complex with cofactor, NADPH (PDBID: 2O7P) binding in the active site of the reductase domain (middle). Structure of E. coli deaminase/reductase in complex with a substrate analogue, ribose 5-phosphate (R5P), bound to the active site of the reductase domain (right).

FIGURE 5

Structures of lumazine synthase (LS) in several oligomeric states. Pentamer assembly of LS from M. tuberculosis bound to inhibitor TS50 (5-(1,3,7-trihydro-9-day-ribityl-2,4,8-purinetrione-7-yl)pentane 1-phosphate) at active sites (PDBID: 2C94). Each subunit is represented in different colour (upper). Crystal Structure of LS from B. abortus (PDBID: 1XN1) showing as dimer of pentamer (lower left). Surface representation of icosahedral assembly of S. typhimurium LS showing each pentamer in different colour (PDBID: 3MK3) (lower right).

FIGURE 6

Structures of trimeric riboflavin synthase (RS). Crystal structure of RS from Escherichia coli (PDBID: 1I8D). Each subunit is shown in different colour (left). Structure of trimeric RS from B. abortus in complex with one riboflavin (PDBID: 4E0F) (middle). Crystal structure of RS from B. abortus in complex with 5-Nitro-6-(D-Ribitylamino)-2.4(1H, 3H) Pyrimidinedione (PDBID: 4GQN) highlighting the inhibitor binding in active sites (right).