Design and synthesis of reaction intermediate derivatives as biotin protein ligase inhibitors.

Abstract

This thesis reports the development of selective and potent small molecule inhibitors of Staphylococcus aureus biotin protein ligase (SaBPL) using 1,2,3-triazole and phosphodiester linkers as bioisosteric analogues of the phosphoroanhydride linker found in the reaction intermediate biotinyl-5’-AMP 1.03. Chapter one describes the structure and catalytic mechanism of the essential enzyme SaBPL. An overview of reaction intermediate mimics as ligase inhibitors is discussed and the utility of 1,2,3-triazole ring as a bioisosteric analogue is outlined. Chapter two investigates the phosphodiester reaction intermediate mimic biotinol-5’-AMP 1.05 as a potential inhibitor of SaBPL. Two different synthetic approaches towards biotinol-5’-AMP 1.05 were developed with the aim of scaling up the synthesis to enable biological characterisation and animal trials. Assay results indicated biotinol-5’-AMP 1.05 is a potent but a non-selective inhibitor of SaBPL (IC₅₀ = 0.12 ± 0.01 μM). Chapter three investigates the use of 1,2,3-triazole as a bioisostere of the phosphoroanhydride linker of the reaction intermediate biotinyl-5’-AMP 1.03. Both 1,4- triazole 3.25 and 1,5-triazole 3.33 were synthesized from biotin alkyne 3.12 and adenosine azide 3.16 using CuAAC and RuAAC. Optimisation of both CuAAC and RuAAC in the synthesis of 3.25 and 3.33 were also investigated. 1,4-Triazole 3.25 is the first reported selective inhibitor of BPL, inhibiting SaBPL (Ki = 1.83 ± 0.33 μM). Chapter four extends the work described in chapter three with an investigation of 1,2,3- triazole analogues based on triazole 3.25. Structure-activity relationships were developed and a general structure for this novel class of inhibitors was obtained. Triazole 4.01, the lead compound from this class of inhibitors, is a potent and selective inhibitor of SaBPL (Ki = 0.66 ± 0.15 μM). X-ray crystal structure of 4.01 bound to SaBPL illustrated the effective molecular recognition between the 1,2,3-triazole ring and SaBPL and emphasized the 1,2,3-triazole ring as an effective bioisostere of phosphoroanhydride linker. Additionally, a successful in situ click experiment was performed using a library of alkynes/azides fragments and R122G SaBPL mutant enzyme. The mutant enzyme was able to select the appropriate fragments and selectively synthesize the potent 1,4-triazole inhibitor 4.01. Chapter five examines analogues of biotin alkyne 3.12, a precursor to 1,2,3-triazole inhibitors and was found to be a potent inhibitor (SaBPL Ki = 0.30 ± 0.05 μM). Norbiotin alkyne 4.16 was found as highly effective inhibitor against SaBPL (Ki = 0.08 ± 0.01 μM) and an antibacterial agent against methicillin resistant staphylococcus aureus (MIC = 4 - 16 μg/ml). Chapter six extends the work described in chapter four. Using the general structure developed in chapter four, a series of analogues with modifications to the ATP binding component were synthesized and assayed against a SaBPL. Triazole 6.10 containing the privileged scaffold, 2-benzoxazolone, was found as a potent and selective inhibitor against SaBPL (Ki = 0.09 ± 0.02 μM). Chapter seven details the experimental procedures used to synthesize compounds described in chapter 2 – 6.