Biotin Protein Ligase Is a Target for New Antibacterials

Abstract

There is a desperate need for novel antibiotic classes to combat the rise of drug resistant pathogenic bacteria, such as Staphylococcus aureus. Inhibitors of the essential metabolic enzyme biotin protein ligase (BPL) represent a promising drug target for new antibacterials. Structural and biochemical studies on the BPL from S. aureus have paved the way for the design and development of new antibacterial chemotherapeutics. BPL employs an ordered ligand binding mechanism for the synthesis of the reaction intermediate biotinyl-5'-AMP from substrates biotin and ATP. Here we review the structure and catalytic mechanism of the target enzyme, along with an overview of chemical analogues of biotin and biotinyl-5'-AMP as BPL inhibitors reported to date. Of particular promise are studies to replace the labile phosphoroanhydride linker present in biotinyl-5'-AMP with alternative bioisosteres. A novel in situ click approach using a mutant of S. aureus BPL as a template for the synthesis of triazole-based inhibitors is also presented. These approaches can be widely applied to BPLs from other bacteria, as well as other closely related metabolic enzymes and antibacterial drug targets.

Keywords: Staphylococcus aureus; X-ray crystallography; antibiotic; biotin; biotin protein ligase; in situ click chemistry; inhibitor design.

Scheme I

The catalytic mechanism of protein biotinylation catalyzed by biotin protein ligase (BPL).

Scheme II

Synthesis of 1,4-triazole 20 and 1,5-triazole 21 from biotin acetylene 12 and azide 19. Conditions and reagents. (a) (i) copper nano powder, 2:1 AcCN/H₂O, 4 h, sonication, 35 °C; (b) (i) Cp*RuCl(PPh₃)₂, 1:1 THF/DMF, 4 h, 70 °C.

Scheme III

(a) In situ click reactions of acetylene 12 with azides 19 in the presence of wild type SaBPL, 1,4-triazole 20 was confirmed by HPLC; (b) In situ click reactions of acetylene 12 with azides 25–28 in the presence of wild type SaBPL, no triazole products were observed by HPLC; (c) In situ click reactions of acetylene 12 with azides 25–28 in the presence of SaBPL Arg122-Gly, 1,4-triazole 23 was confirmed by HPLC.

Figure 1

3D depiction of SaBPL with biotinyl-5′-AMP 3 bound (PDB: 3V8L). The β sheets are shown in purple, α helices in orange, biotin-binding loop in green and ATP-binding loop in blue.

Figure 2

Schematic diagram of the three classes of BPL. The conserved catalytic (grey) and C-terminal domains (black) are highlighted. The relative sizes of the N-terminal extensions on class II and class III BPLs are represented.

Figure 3

3D depiction of reaction intermediate biotinyl-5′-AMP 3 (highlighted in magenta) bound to SaBPL (PDB: 3V8L) with a close examination of the biotin-binding pocket. Green ribbon highlights the biotin-binding loop and black dashes indicating hydrogen-bonding interactions between the ureido ring of biotin and SaBPL.

Figure 4

3D depiction of reaction intermediate biotinyl-5′-AMP 3 (highlighted in magenta) bound to SaBPL (PDB: 3V8L) with a close examination of the phosphate-binding pocket. The biotin-binding loop is shown in green.

Figure 5

3D depiction of reaction intermediate biotinyl-5′-AMP 3 (highlighted in magenta) bound to SaBPL (PDB: 3V8L) with a close examination of the ATP-binding pocket. Green ribbon highlighting the biotin-binding loop and blue ribbon highlighting the ATP-binding loop [31].

Figure 6

3D depiction of biotin 1 (highlighted in magenta) bound to SaBPL (PDB: 3V8K) with a side view of biotin binding pocket (left); Chemical structures of biotin 1 and its analogues 5 and 6 (right).

Figure 7

Reaction intermediate biotinyl-5′-AMP 3 and its mimics, biotinol-5′-AMP 14, β-ketophosphonate 15, β-hydroxyphosphonate 16, acylsulfamate 17, and acylsulfonamide 18.

Figure 8

The assignment of 1,2,3-triazole with the potential intermolecular interaction sites.

Figure 9

3D depiction of 1,4-triazole 22 bound to SaBPL (PDB: 3V7C) (left); Chemical structures of 1,2,3-triazole analogues: 1,4-triazole 22 and 1,4-triazole 23 (right).