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Hayes AJ, Satiaputra J, Sternicki LM, Paparella AS, Feng Z, Lee KJ, Blanco-Rodriguez B, Tieu W, Eijkelkamp BA, Shearwin KE, Pukala TL, Abell AD, Booker GW, Polyak SW. Advanced Resistance Studies Identify Two Discrete Mechanisms in Staphylococcus aureus to Overcome Antibacterial Compounds that Target Biotin Protein Ligase. Antibiotics (Basel) 2020; 9:antibiotics9040165. [PMID: 32268615 PMCID: PMC7235819 DOI: 10.3390/antibiotics9040165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/03/2020] [Accepted: 04/04/2020] [Indexed: 11/16/2022] Open
Abstract
Biotin protein ligase (BPL) inhibitors are a novel class of antibacterial that target clinically important methicillin-resistant Staphylococcus aureus (S. aureus). In S. aureus, BPL is a bifunctional protein responsible for enzymatic biotinylation of two biotin-dependent enzymes, as well as serving as a transcriptional repressor that controls biotin synthesis and import. In this report, we investigate the mechanisms of action and resistance for a potent anti-BPL, an antibacterial compound, biotinyl-acylsulfamide adenosine (BASA). We show that BASA acts by both inhibiting the enzymatic activity of BPL in vitro, as well as functioning as a transcription co-repressor. A low spontaneous resistance rate was measured for the compound (<10−9) and whole-genome sequencing of strains evolved during serial passaging in the presence of BASA identified two discrete resistance mechanisms. In the first, deletion of the biotin-dependent enzyme pyruvate carboxylase is proposed to prioritize the utilization of bioavailable biotin for the essential enzyme acetyl-CoA carboxylase. In the second, a D200E missense mutation in BPL reduced DNA binding in vitro and transcriptional repression in vivo. We propose that this second resistance mechanism promotes bioavailability of biotin by derepressing its synthesis and import, such that free biotin may outcompete the inhibitor for binding BPL. This study provides new insights into the molecular mechanisms governing antibacterial activity and resistance of BPL inhibitors in S. aureus.
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Affiliation(s)
- Andrew J. Hayes
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Jiulia Satiaputra
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Louise M. Sternicki
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Ashleigh S. Paparella
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Zikai Feng
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Kwang J. Lee
- School of Physical Sciences, University of Adelaide, South Australia 5005, Australia; (K.J.L.); (B.B.-R.); (W.T.); (T.L.P.); (A.D.A.)
| | - Beatriz Blanco-Rodriguez
- School of Physical Sciences, University of Adelaide, South Australia 5005, Australia; (K.J.L.); (B.B.-R.); (W.T.); (T.L.P.); (A.D.A.)
| | - William Tieu
- School of Physical Sciences, University of Adelaide, South Australia 5005, Australia; (K.J.L.); (B.B.-R.); (W.T.); (T.L.P.); (A.D.A.)
| | - Bart A. Eijkelkamp
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Keith E. Shearwin
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Tara L. Pukala
- School of Physical Sciences, University of Adelaide, South Australia 5005, Australia; (K.J.L.); (B.B.-R.); (W.T.); (T.L.P.); (A.D.A.)
| | - Andrew D. Abell
- School of Physical Sciences, University of Adelaide, South Australia 5005, Australia; (K.J.L.); (B.B.-R.); (W.T.); (T.L.P.); (A.D.A.)
- Centre for Nanoscale BioPhotonics (CNBP), University of Adelaide, Adelaide, SA 5005, Australia
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Grant W. Booker
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Steven W. Polyak
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
- Correspondence: ; Tel.: +61883021603
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Satiaputra J, Sternicki LM, Hayes AJ, Pukala TL, Booker GW, Shearwin KE, Polyak SW. Native mass spectrometry identifies an alternative DNA-binding pathway for BirA from Staphylococcus aureus. Sci Rep 2019; 9:2767. [PMID: 30808984 PMCID: PMC6391492 DOI: 10.1038/s41598-019-39398-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/15/2019] [Indexed: 11/09/2022] Open
Abstract
An adequate supply of biotin is vital for the survival and pathogenesis of Staphylococcus aureus. The key protein responsible for maintaining biotin homeostasis in bacteria is the biotin retention protein A (BirA, also known as biotin protein ligase). BirA is a bi-functional protein that serves both as a ligase to catalyse the biotinylation of important metabolic enzymes, as well as a transcriptional repressor that regulates biotin biosynthesis, biotin transport and fatty acid elongation. The mechanism of BirA regulated transcription has been extensively characterized in Escherichia coli, but less so in other bacteria. Biotin-induced homodimerization of E. coli BirA (EcBirA) is a necessary prerequisite for stable DNA binding and transcriptional repression. Here, we employ a combination of native mass spectrometry, in vivo gene expression assays, site-directed mutagenesis and electrophoretic mobility shift assays to elucidate the DNA binding pathway for S. aureus BirA (SaBirA). We identify a mechanism that differs from that of EcBirA, wherein SaBirA is competent to bind DNA as a monomer both in the presence and absence of biotin and/or MgATP, allowing homodimerization on the DNA. Bioinformatic analysis demonstrated the SaBirA sequence used here is highly conserved amongst other S. aureus strains, implying this DNA-binding mechanism is widely employed.
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Affiliation(s)
- Jiulia Satiaputra
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
- Harry Perkins Institute of Medical Research, Shenton Park, Western Australia, 6008, Australia
| | - Louise M Sternicki
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Andrew J Hayes
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
- Faculty of Health and Medical Sciences, Adelaide, South Australia, 5005, Australia
| | - Tara L Pukala
- School of Physical Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Grant W Booker
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Keith E Shearwin
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Steven W Polyak
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia.
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, 5001, Australia.
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Paparella AS, Feng J, Blanco-Rodriguez B, Feng Z, Phetsang W, Blaskovich MA, Cooper MA, Booker GW, Polyak SW, Abell AD. A template guided approach to generating cell permeable inhibitors of Staphylococcus aureus biotin protein ligase. Tetrahedron 2018. [DOI: 10.1016/j.tet.2017.10.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Paparella AS, Lee KJ, Hayes AJ, Feng J, Feng Z, Cini D, Deshmukh S, Booker GW, Wilce MCJ, Polyak SW, Abell AD. Halogenation of Biotin Protein Ligase Inhibitors Improves Whole Cell Activity against Staphylococcus aureus. ACS Infect Dis 2018; 4:175-184. [PMID: 29131575 DOI: 10.1021/acsinfecdis.7b00134] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We report the synthesis and evaluation of 5-halogenated-1,2,3-triazoles as inhibitors of biotin protein ligase from Staphylococcus aureus. The halogenated compounds exhibit significantly improved antibacterial activity over their nonhalogenated counterparts. Importantly, the 5-fluoro-1,2,3-triazole compound 4c displays antibacterial activity against S. aureus ATCC49775 with a minimum inhibitory concentration (MIC) of 8 μg/mL.
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Affiliation(s)
- Ashleigh S. Paparella
- Department of Molecular
and Cellular Biology, University of Adelaide, North Tce, Adelaide, South Australia 5005, Australia
| | - Kwang Jun Lee
- Department of Chemistry, University of Adelaide, North Tce, Adelaide, South Australia 5005, Australia
| | - Andrew J. Hayes
- Department of Molecular
and Cellular Biology, University of Adelaide, North Tce, Adelaide, South Australia 5005, Australia
| | - Jiage Feng
- Department of Chemistry, University of Adelaide, North Tce, Adelaide, South Australia 5005, Australia
- Centre
for Nanoscale BioPhotonics (CNBP), University of Adelaide, North Tce, Adelaide, South Australia 5005, Australia
| | - Zikai Feng
- Department of Molecular
and Cellular Biology, University of Adelaide, North Tce, Adelaide, South Australia 5005, Australia
| | - Danielle Cini
- School of Biomedical Science, Monash University, Wellington Road, Clayton, Victoria 3800, Australia
| | - Sonali Deshmukh
- Department of Molecular
and Cellular Biology, University of Adelaide, North Tce, Adelaide, South Australia 5005, Australia
| | - Grant W. Booker
- Department of Molecular
and Cellular Biology, University of Adelaide, North Tce, Adelaide, South Australia 5005, Australia
| | - Matthew C. J. Wilce
- School of Biomedical Science, Monash University, Wellington Road, Clayton, Victoria 3800, Australia
| | - Steven W. Polyak
- Department of Molecular
and Cellular Biology, University of Adelaide, North Tce, Adelaide, South Australia 5005, Australia
| | - Andrew D. Abell
- Department of Chemistry, University of Adelaide, North Tce, Adelaide, South Australia 5005, Australia
- Centre
for Nanoscale BioPhotonics (CNBP), University of Adelaide, North Tce, Adelaide, South Australia 5005, Australia
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Pendini NR, Yap MY, Traore DAK, Polyak SW, Cowieson NP, Abell A, Booker GW, Wallace JC, Wilce JA, Wilce MCJ. Structural characterization of Staphylococcus aureus biotin protein ligase and interaction partners: an antibiotic target. Protein Sci 2013; 22:762-73. [PMID: 23559560 DOI: 10.1002/pro.2262] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 03/26/2013] [Accepted: 03/26/2013] [Indexed: 11/06/2022]
Abstract
The essential metabolic enzyme biotin protein ligase (BPL) is a potential target for the development of new antibiotics required to combat drug-resistant pathogens. Staphylococcus aureus BPL (SaBPL) is a bifunctional protein, possessing both biotin ligase and transcription repressor activities. This positions BPL as a key regulator of several important metabolic pathways. Here, we report the structural analysis of both holo- and apo-forms of SaBPL using X-ray crystallography. We also present small-angle X-ray scattering data of SaBPL in complex with its biotin-carboxyl carrier protein substrate as well as the SaBPL:DNA complex that underlies repression. This has revealed the molecular basis of ligand (biotinyl-5'-AMP) binding and conformational changes associated with catalysis and repressor function. These data provide new information to better understand the bifunctional activities of SaBPL and to inform future strategies for antibiotic discovery.
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Affiliation(s)
- Nicole R Pendini
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Victoria, Australia
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Soares da Costa TP, Yap MY, Perugini MA, Wallace JC, Abell AD, Wilce MCJ, Polyak SW, Booker GW. Dual roles of F123 in protein homodimerization and inhibitor binding to biotin protein ligase fromStaphylococcus aureus. Mol Microbiol 2013; 91:110-20. [DOI: 10.1111/mmi.12446] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2013] [Indexed: 12/17/2022]
Affiliation(s)
| | - Min Y. Yap
- School of Biomedical Science; Monash University; Victoria 3800 Australia
| | - Matthew A. Perugini
- Department of Biochemistry; La Trobe Institute for Molecular Science; La Trobe University; Victoria 3086 Australia
| | - John C. Wallace
- School of Molecular and Biomedical Science; University of Adelaide; South Australia 5005 Australia
| | - Andrew D. Abell
- School of Chemistry and Physics; University of Adelaide; South Australia 5005 Australia
- Centre for Molecular Pathology; University of Adelaide; South Australia 5005 Australia
| | | | - Steven W. Polyak
- School of Molecular and Biomedical Science; University of Adelaide; South Australia 5005 Australia
- Centre for Molecular Pathology; University of Adelaide; South Australia 5005 Australia
| | - Grant W. Booker
- School of Molecular and Biomedical Science; University of Adelaide; South Australia 5005 Australia
- Centre for Molecular Pathology; University of Adelaide; South Australia 5005 Australia
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Soares da Costa TP, Tieu W, Yap MY, Zvarec O, Bell JM, Turnidge JD, Wallace JC, Booker GW, Wilce MCJ, Abell AD, Polyak SW. Biotin analogues with antibacterial activity are potent inhibitors of biotin protein ligase. ACS Med Chem Lett 2012; 3:509-14. [PMID: 24900501 DOI: 10.1021/ml300106p] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 05/23/2012] [Indexed: 01/06/2023] Open
Abstract
There is a desperate need to develop new antibiotic agents to combat the rise of drug-resistant bacteria, such as clinically important Staphylococcus aureus. The essential multifunctional enzyme, biotin protein ligase (BPL), is one potential drug target for new antibiotics. We report the synthesis and characterization of a series of biotin analogues with activity against BPLs from S. aureus, Escherichia coli, and Homo sapiens. Two potent inhibitors with K i < 100 nM were identified with antibacterial activity against a panel of clinical isolates of S. aureus (MIC 2-16 μg/mL). Compounds with high ligand efficiency and >20-fold selectivity between the isozymes were identified and characterized. The antibacterial mode of action was shown to be via inhibition of BPL. The bimolecular interactions between the BPL and the inhibitors were defined by surface plasmon resonance studies and X-ray crystallography. These findings pave the way for second-generation inhibitors and antibiotics with greater potency and selectivity.
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Affiliation(s)
| | | | - Min Y. Yap
- School of
Biomedical Science, Monash University,
Victoria, 3800, Australia
| | | | - Jan M. Bell
- Microbiology and Infectious
Diseases Directorate, SA Pathology, Women's and Children's Hospital, South Australia 5006, Australia
| | - John D. Turnidge
- Microbiology and Infectious
Diseases Directorate, SA Pathology, Women's and Children's Hospital, South Australia 5006, Australia
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Soares da Costa TP, Tieu W, Yap MY, Pendini NR, Polyak SW, Sejer Pedersen D, Morona R, Turnidge JD, Wallace JC, Wilce MCJ, Booker GW, Abell AD. Selective inhibition of biotin protein ligase from Staphylococcus aureus. J Biol Chem 2012; 287:17823-17832. [PMID: 22437830 DOI: 10.1074/jbc.m112.356576] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
There is a well documented need to replenish the antibiotic pipeline with new agents to combat the rise of drug resistant bacteria. One strategy to combat resistance is to discover new chemical classes immune to current resistance mechanisms that inhibit essential metabolic enzymes. Many of the obvious drug targets that have no homologous isozyme in the human host have now been investigated. Bacterial drug targets that have a closely related human homologue represent a new frontier in antibiotic discovery. However, to avoid potential toxicity to the host, these inhibitors must have very high selectivity for the bacterial enzyme over the human homolog. We have demonstrated that the essential enzyme biotin protein ligase (BPL) from the clinically important pathogen Staphylococcus aureus could be selectively inhibited. Linking biotin to adenosine via a 1,2,3 triazole yielded the first BPL inhibitor selective for S. aureus BPL over the human equivalent. The synthesis of new biotin 1,2,3-triazole analogues using click chemistry yielded our most potent structure (K(i) 90 nM) with a >1100-fold selectivity for the S. aureus BPL over the human homologue. X-ray crystallography confirmed the mechanism of inhibitor binding. Importantly, the inhibitor showed cytotoxicity against S. aureus but not cultured mammalian cells. The biotin 1,2,3-triazole provides a novel pharmacophore for future medicinal chemistry programs to develop this new antibiotic class.
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Affiliation(s)
- Tatiana P Soares da Costa
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - William Tieu
- School of Chemistry and Physics, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Min Y Yap
- School of Biomedical Science, Monash University, Victoria 3800, Australia
| | - Nicole R Pendini
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia; School of Biomedical Science, Monash University, Victoria 3800, Australia
| | - Steven W Polyak
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia.
| | - Daniel Sejer Pedersen
- School of Chemistry and Physics, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Renato Morona
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - John D Turnidge
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia; SA Pathology at Women's and Children's Hospital, South Australia 5006, Australia
| | - John C Wallace
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Matthew C J Wilce
- School of Biomedical Science, Monash University, Victoria 3800, Australia
| | - Grant W Booker
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Andrew D Abell
- School of Chemistry and Physics, University of Adelaide, Adelaide, South Australia 5005, Australia
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