1
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Cronan JE. Biotin protein ligase as you like it: Either extraordinarily specific or promiscuous protein biotinylation. Proteins 2024; 92:435-448. [PMID: 37997490 PMCID: PMC10932917 DOI: 10.1002/prot.26642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023]
Abstract
Biotin (vitamin H or B7) is a coenzyme essential for all forms of life. Biotin has biological activity only when covalently attached to a few key metabolic enzyme proteins. Most organisms have only one attachment enzyme, biotin protein ligase (BPL), which attaches biotin to all target proteins. The sequences of these proteins and their substrate proteins are strongly conserved throughout biology. Structures of both the biotin ligase- and biotin-acceptor domains of mammals, plants, several bacterial species, and archaea have been determined. These, together with mutational analyses of ligases and their protein substrates, illustrate the exceptional specificity of this protein modification. For example, the Escherichia coli BPL biotinylates only one of the >4000 cellular proteins. Several bifunctional bacterial biotin ligases transcriptionally regulate biotin synthesis and/or transport in concert with biotinylation. The human BPL has been demonstrated to play an important role in that mutations in the BPL encoding gene cause one form of the disease, biotin-responsive multiple carboxylase deficiency. Promiscuous mutant versions of several BPL enzymes release biotinoyl-AMP, the active intermediate of the ligase reaction, to solvent. The released biotinoyl-AMP acts as a chemical biotinylation reagent that modifies lysine residues of neighboring proteins in vivo. This proximity-dependent biotinylation (called BioID) approach has been heavily utilized in cell biology.
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Affiliation(s)
- John E Cronan
- Department of Microbiology, University of Illinois, Urbana, Illinois, USA
- Department of Biochemistry, University of Illinois, Urbana, Illinois, USA
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2
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Stachura D, Nguyen S, Polyak SW, Jovcevski B, Bruning JB, Abell AD. Structural Study of Potent Triazole-Based Inhibitors of Staphylococcus aureus Biotin Protein Ligase. ACS Med Chem Lett 2023; 14:285-290. [PMID: 36923924 PMCID: PMC10009792 DOI: 10.1021/acsmedchemlett.2c00505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/17/2023] [Indexed: 02/23/2023] Open
Abstract
The rise of multidrug-resistant bacteria, such as Staphylococcus aureus, has highlighted global urgency for new classes of antibiotics. Biotin protein ligase (BPL), a critical metabolic regulatory enzyme, is an important target that shows significant promise in this context. Here we report the in silico docking, synthesis, and biological assay of a new series of N1-diphenylmethyl-1,2,3-triazole-based S. aureus BPL (SaBPL) inhibitors (8-19) designed to probe the adenine binding site and define whole-cell activity for this important class of inhibitor. Triazoles 13 and 14 with N1-propylamine and -butanamide substituents, respectively, were particularly potent with K i values of 10 ± 2 and 30 ± 6 nM, respectively, against SaBPL. A strong correlation was apparent between the K i values for 8-19 and the in silico docking, with hydrogen bonding to amino acid residues S128 and N212 of SaBPL likely contributing to potent inhibition.
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Affiliation(s)
- Damian
L. Stachura
- Department
of Chemistry and Centre for Nanoscale BioPhotonics (CNBP) and
Institute of Photonics and Advanced Sensing (IPAS), School of Biological
Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Stephanie Nguyen
- Department
of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Steven W. Polyak
- UniSA
Clinical and Health Sciences, University
of South Australia, Adelaide, SA 5005, Australia
| | - Blagojce Jovcevski
- Department
of Chemistry and Centre for Nanoscale BioPhotonics (CNBP) and
Institute of Photonics and Advanced Sensing (IPAS), School of Biological
Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - John B. Bruning
- Department
of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Andrew D. Abell
- Department
of Chemistry and Centre for Nanoscale BioPhotonics (CNBP) and
Institute of Photonics and Advanced Sensing (IPAS), School of Biological
Sciences, University of Adelaide, Adelaide, SA 5005, Australia
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3
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Sternicki LM, Nguyen S, Pacholarz KJ, Barran P, Pendini NR, Booker GW, Huet Y, Baltz R, Wegener KL, Pukala TL, Polyak SW. Biochemical characterisation of class III biotin protein ligases from Botrytis cinerea and Zymoseptoria tritici. Arch Biochem Biophys 2020; 691:108509. [PMID: 32717225 DOI: 10.1016/j.abb.2020.108509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 10/23/2022]
Abstract
Biotin protein ligase (BPL) is an essential enzyme in all kingdoms of life, making it a potential target for novel anti-infective agents. Whilst bacteria and archaea have simple BPL structures (class I and II), the homologues from certain eukaryotes such as mammals, insects and yeast (class III) have evolved a more complex structure with a large extension on the N-terminus of the protein in addition to the conserved catalytic domain. The absence of atomic resolution structures of any class III BPL hinders structural and functional analysis of these enzymes. Here, two new class III BPLs from agriculturally important moulds Botrytis cinerea and Zymoseptoria tritici were characterised alongside the homologue from the prototypical yeast Saccharomyces cerevisiae. Circular dichroism and ion mobility-mass spectrometry analysis revealed conservation of the overall tertiary and secondary structures of all three BPLs, corresponding with the high sequence similarity. Subtle structural differences were implied by the different thermal stabilities of the enzymes and their varied Michaelis constants for their interactions with ligands biotin, MgATP, and biotin-accepting substrates from different species. The three BPLs displayed different preferences for fungal versus bacterial protein substrates, providing further evidence that class III BPLs have a 'substrate validation' activity for selecting only appropriate proteins for biotinylation. Selective, potent inhibition of these three BPLs was demonstrated despite sequence and structural homology. This highlights the potential for targeting BPL for novel, selective antifungal therapies against B. cinerea, Z. tritici and other fungal species.
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Affiliation(s)
- Louise M Sternicki
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Stephanie Nguyen
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia; Institute for Photonics and Advanced Sensing (IPAS), The University of Adelaide, South Australia, 5005, Australia
| | - Kamila J Pacholarz
- Michael Barber Centre for Collaborative Mass Spectrometry, Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Perdita Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Nicole R Pendini
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Grant W Booker
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Yoann Huet
- Bayer SAS CropScience, La Dargoire Research Centre, Lyon, 69263 Cedex 09, France
| | - Rachel Baltz
- Bayer SAS CropScience, La Dargoire Research Centre, Lyon, 69263 Cedex 09, France
| | - Kate L Wegener
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia; Institute for Photonics and Advanced Sensing (IPAS), The University of Adelaide, South Australia, 5005, Australia
| | - Tara L Pukala
- School of Physical Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Steven W Polyak
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia; Institute for Photonics and Advanced Sensing (IPAS), The University of Adelaide, South Australia, 5005, Australia.
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4
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Bockman MR, Mishra N, Aldrich CC. The Biotin Biosynthetic Pathway in Mycobacterium tuberculosis is a Validated Target for the Development of Antibacterial Agents. Curr Med Chem 2020; 27:4194-4232. [PMID: 30663561 DOI: 10.2174/0929867326666190119161551] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/14/2018] [Accepted: 01/12/2019] [Indexed: 12/11/2022]
Abstract
Mycobacterium tuberculosis, responsible for Tuberculosis (TB), remains the leading cause of mortality among infectious diseases worldwide from a single infectious agent, with an estimated 1.7 million deaths in 2016. Biotin is an essential cofactor in M. tuberculosis that is required for lipid biosynthesis and gluconeogenesis. M. tuberculosis relies on de novo biotin biosynthesis to obtain this vital cofactor since it cannot scavenge sufficient biotin from a mammalian host. The biotin biosynthetic pathway in M. tuberculosis has been well studied and rigorously genetically validated providing a solid foundation for medicinal chemistry efforts. This review examines the mechanism and structure of the enzymes involved in biotin biosynthesis and ligation, summarizes the reported genetic validation studies of the pathway, and then analyzes the most promising inhibitors and natural products obtained from structure-based drug design and phenotypic screening.
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Affiliation(s)
- Matthew R Bockman
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
| | - Neeraj Mishra
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
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5
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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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6
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Wang J, Samanta R, Custer G, Look C, Matysiak S, Beckett D. Tuning Allostery through Integration of Disorder to Order with a Residue Network. Biochemistry 2020; 59:790-801. [PMID: 31899864 DOI: 10.1021/acs.biochem.9b01006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In allostery, a signal from one site in a protein is transmitted to a second site to alter its function. Due to its ubiquity in biology and the potential for its exploitation in drug and protein design, the molecular basis of allosteric communication continues to be the subject of intense research. Although allosterically coupled sites are frequently characterized by disorder, how communication between disordered segments occurs remains obscure. Allosteric activation of Escherichia coli BirA dimerization occurs via coupled distant disorder-to-order transitions. In this work, combined structural and computational studies reveal an extensive residue network in BirA. Substitution of several network residues yields large perturbations to allostery. Force distribution analysis reveals that disruptions to the disorder-to-order transitions through amino acid substitution are manifested in shifts in the energy experienced by network residues as well as alterations in packing of an α-helix that plays a critical role in allostery. The combined results reveal a highly distributed allosteric mechanism that is robust to sequence change.
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Affiliation(s)
- Jingheng Wang
- Department of Chemistry & Biochemistry , University of Maryland , College Park , Maryland 20742 , United States
| | - Riya Samanta
- Biophysics Graduate Program , University of Maryland , College Park , Maryland 20742 , United States
| | - Gregory Custer
- Fischell Department of Bioengineering , University of Maryland , College Park , Maryland 20742 , United States
| | - Christopher Look
- Fischell Department of Bioengineering , University of Maryland , College Park , Maryland 20742 , United States
| | - Silvina Matysiak
- Fischell Department of Bioengineering , University of Maryland , College Park , Maryland 20742 , United States
| | - Dorothy Beckett
- Department of Chemistry & Biochemistry , University of Maryland , College Park , Maryland 20742 , United States
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7
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Lux MC, Standke LC, Tan DS. Targeting adenylate-forming enzymes with designed sulfonyladenosine inhibitors. J Antibiot (Tokyo) 2019; 72:325-349. [PMID: 30982830 PMCID: PMC6594144 DOI: 10.1038/s41429-019-0171-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/19/2019] [Accepted: 02/26/2019] [Indexed: 02/07/2023]
Abstract
Adenylate-forming enzymes are a mechanistic superfamily that are involved in diverse biochemical pathways. They catalyze ATP-dependent activation of carboxylic acid substrates as reactive acyl adenylate (acyl-AMP) intermediates and subsequent coupling to various nucleophiles to generate ester, thioester, and amide products. Inspired by natural products, acyl sulfonyladenosines (acyl-AMS) that mimic the tightly bound acyl-AMP reaction intermediates have been developed as potent inhibitors of adenylate-forming enzymes. This simple yet powerful inhibitor design platform has provided a wide range of biological probes as well as several therapeutic lead compounds. Herein, we provide an overview of the nine structural classes of adenylate-forming enzymes and examples of acyl-AMS inhibitors that have been developed for each.
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Affiliation(s)
- Michaelyn C Lux
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Lisa C Standke
- Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Derek S Tan
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA. .,Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA. .,Chemical Biology Program, Sloan Kettering Institute, and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
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8
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Evans CE, Si Y, Matarlo JS, Yin Y, French JB, Tonge PJ, Tan DS. Structure-Based Design, Synthesis, and Biological Evaluation of Non-Acyl Sulfamate Inhibitors of the Adenylate-Forming Enzyme MenE. Biochemistry 2019; 58:1918-1930. [PMID: 30912442 PMCID: PMC6653581 DOI: 10.1021/acs.biochem.9b00003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
N-Acyl sulfamoyladenosines (acyl-AMS) have been used
extensively to inhibit adenylate-forming enzymes that are involved in a wide
range of biological processes. These acyl-AMS inhibitors are nonhydrolyzable
mimics of the cognate acyl adenylate intermediates that are bound tightly by
adenylate-forming enzymes. However, the anionic acyl sulfamate moiety presents a
pharmacological liability that may be detrimental to cell permeability and
pharmacokinetic profiles. We have previously developed the acyl sulfamate
OSB-AMS (1) as a potent inhibitor of the adenylate-forming enzyme
MenE, an o-succinylbenzoate-CoA (OSB-CoA) synthetase that is
required for bacterial menaquinone biosynthesis. Herein, we report the use of
computational docking to develop novel, non-acyl sulfamate inhibitors of MenE. A
m-phenyl ether-linked analogue (5) was found
to be the most potent inhibitor (IC50 = 8 μM;
Kd = 244 nM), and its X-ray co-crystal structure
was determined to characterize its binding mode in comparison to the
computational prediction. This work provides a framework for the development of
potent non-acyl sulfamate inhibitors of other adenylate-forming enzymes in the
future.
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9
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Bockman MR, Engelhart CA, Dawadi S, Larson P, Tiwari D, Ferguson DM, Schnappinger D, Aldrich CC. Avoiding Antibiotic Inactivation in Mycobacterium tuberculosis by Rv3406 through Strategic Nucleoside Modification. ACS Infect Dis 2018; 4:1102-1113. [PMID: 29663798 DOI: 10.1021/acsinfecdis.8b00038] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
5'-[ N-(d-biotinoyl)sulfamoyl]amino-5'-deoxyadenosine (Bio-AMS, 1) possesses selective activity against Mycobacterium tuberculosis ( Mtb) and arrests fatty acid and lipid biosynthesis through inhibition of the Mycobacterium tuberculosis biotin protein ligase ( MtBPL). Mtb develops spontaneous resistance to 1 with a frequency of at least 1 × 10-7 by overexpression of Rv3406, a type II sulfatase that enzymatically inactivates 1. In an effort to circumvent this resistance mechanism, we describe herein strategic modification of the nucleoside at the 5'-position to prevent enzymatic inactivation. The new analogues retained subnanomolar potency to MtBPL ( KD = 0.66-0.97 nM), and 5' R- C-methyl derivative 6 exhibited identical antimycobacterial activity toward: Mtb H37Rv, MtBPL overexpression, and an isogenic Rv3406 overexpression strain (minimum inhibitory concentration, MIC = 1.56 μM). Moreover, 6 was not metabolized by recombinant Rv3406 and resistant mutants to 6 could not be isolated (frequency of resistance <1.4 × 10-10) demonstrating it successfully overcame Rv3406-mediated resistance.
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Affiliation(s)
- Matthew R. Bockman
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Curtis A. Engelhart
- Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, United States
| | - Surendra Dawadi
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Peter Larson
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Divya Tiwari
- Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, United States
| | - David M. Ferguson
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, United States
| | - Courtney C. Aldrich
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
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10
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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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11
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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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12
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Feng J, Paparella AS, Tieu W, Heim D, Clark S, Hayes A, Booker GW, Polyak SW, Abell AD. New Series of BPL Inhibitors To Probe the Ribose-Binding Pocket of Staphylococcus aureus Biotin Protein Ligase. ACS Med Chem Lett 2016; 7:1068-1072. [PMID: 27994739 DOI: 10.1021/acsmedchemlett.6b00248] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 10/10/2016] [Indexed: 01/11/2023] Open
Abstract
Replacing the labile adenosinyl-substituted phosphoanhydride of biotinyl-5'-AMP with a N1-benzyl substituted 1,2,3-triazole gave a new truncated series of inhibitors of Staphylococcus aureus biotin protein ligase (SaBPL). The benzyl group presents to the ribose-binding pocket of SaBPL based on in silico docking. Halogenated benzyl derivatives (12t, 12u, 12w, and 12x) proved to be the most potent inhibitors of SaBPL. These derivatives inhibited the growth of S. aureus ATCC49775 and displayed low cytotoxicity against HepG2 cells.
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Affiliation(s)
- Jiage Feng
- Department of Chemistry, §Department of Molecular and Cellular Biology, and ‡Centre for Nanoscale
BioPhotonics (CNBP), University of Adelaide, Adelaide, South Australia 5005, Australia
| | | | - William Tieu
- Department of Chemistry, §Department of Molecular and Cellular Biology, and ‡Centre for Nanoscale
BioPhotonics (CNBP), University of Adelaide, Adelaide, South Australia 5005, Australia
| | | | - Sarah Clark
- Department of Chemistry, §Department of Molecular and Cellular Biology, and ‡Centre for Nanoscale
BioPhotonics (CNBP), University of Adelaide, Adelaide, South Australia 5005, Australia
| | | | | | | | - Andrew D. Abell
- Department of Chemistry, §Department of Molecular and Cellular Biology, and ‡Centre for Nanoscale
BioPhotonics (CNBP), University of Adelaide, Adelaide, South Australia 5005, Australia
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13
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Design, synthesis, and biological evaluation of α-hydroxyacyl-AMS inhibitors of amino acid adenylation enzymes. Bioorg Med Chem Lett 2016; 26:5340-5345. [PMID: 27692545 DOI: 10.1016/j.bmcl.2016.09.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/09/2016] [Indexed: 11/22/2022]
Abstract
Biosynthesis of bacterial natural-product virulence factors is emerging as a promising antibiotic target. Many such natural products are produced by nonribosomal peptide synthetases (NRPS) from amino acid precursors. To develop selective inhibitors of these pathways, we have previously described aminoacyl-AMS (sulfamoyladenosine) macrocycles that inhibit NRPS amino acid adenylation domains but not mechanistically-related aminoacyl-tRNA synthetases. To improve the cell permeability of these inhibitors, we explore herein replacement of the α-amino group with an α-hydroxy group. In both macrocycles and corresponding linear congeners, this leads to decreased biochemical inhibition of the cysteine adenylation domain of the Yersina pestis siderophore synthetase HMWP2, which we attribute to loss of an electrostatic interaction with a conserved active-site aspartate. However, inhibitory activity can be regained by installing a cognate β-thiol moiety in the linear series. This provides a path forward to develop selective, cell-penetrant inhibitors of the biosynthesis of virulence factors to probe their biological functions and potential as therapeutic targets.
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14
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Biotin Protein Ligase Is a Target for New Antibacterials. Antibiotics (Basel) 2016; 5:antibiotics5030026. [PMID: 27463729 PMCID: PMC5039522 DOI: 10.3390/antibiotics5030026] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 12/02/2022] Open
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.
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15
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Abstract
Two vitamins, biotin and lipoic acid, are essential in all three domains of life. Both coenzymes function only when covalently attached to key metabolic enzymes. There they act as "swinging arms" that shuttle intermediates between two active sites (= covalent substrate channeling) of key metabolic enzymes. Although biotin was discovered over 100 years ago and lipoic acid 60 years ago, it was not known how either coenzyme is made until recently. In Escherichia coli the synthetic pathways for both coenzymes have now been worked out for the first time. The late steps of biotin synthesis, those involved in assembling the fused rings, were well described biochemically years ago, although recent progress has been made on the BioB reaction, the last step of the pathway in which the biotin sulfur moiety is inserted. In contrast, the early steps of biotin synthesis, assembly of the fatty acid-like "arm" of biotin were unknown. It has now been demonstrated that the arm is made by using disguised substrates to gain entry into the fatty acid synthesis pathway followed by removal of the disguise when the proper chain length is attained. The BioC methyltransferase is responsible for introducing the disguise, and the BioH esterase is responsible for its removal. In contrast to biotin, which is attached to its cognate proteins as a finished molecule, lipoic acid is assembled on its cognate proteins. An octanoyl moiety is transferred from the octanoyl acyl carrier protein of fatty acid synthesis to a specific lysine residue of a cognate protein by the LipB octanoyltransferase followed by sulfur insertion at carbons C-6 and C-8 by the LipA lipoyl synthetase. Assembly on the cognate proteins regulates the amount of lipoic acid synthesized, and, thus, there is no transcriptional control of the synthetic genes. In contrast, transcriptional control of the biotin synthetic genes is wielded by a remarkably sophisticated, yet simple, system, exerted through BirA, a dual-function protein that both represses biotin operon transcription and ligates biotin to its cognate proteins.
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16
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Abstract
Two vitamins, biotin and lipoic acid, are essential in all three domains of life. Both coenzymes function only when covalently attached to key metabolic enzymes. There they act as "swinging arms" that shuttle intermediates between two active sites (= covalent substrate channeling) of key metabolic enzymes. Although biotin was discovered over 100 years ago and lipoic acid was discovered 60 years ago, it was not known how either coenzyme is made until recently. In Escherichia coli the synthetic pathways for both coenzymes have now been worked out for the first time. The late steps of biotin synthesis, those involved in assembling the fused rings, were well described biochemically years ago, although recent progress has been made on the BioB reaction, the last step of the pathway, in which the biotin sulfur moiety is inserted. In contrast, the early steps of biotin synthesis, assembly of the fatty acid-like "arm" of biotin, were unknown. It has now been demonstrated that the arm is made by using disguised substrates to gain entry into the fatty acid synthesis pathway followed by removal of the disguise when the proper chain length is attained. The BioC methyltransferase is responsible for introducing the disguise and the BioH esterase for its removal. In contrast to biotin, which is attached to its cognate proteins as a finished molecule, lipoic acid is assembled on its cognate proteins. An octanoyl moiety is transferred from the octanoyl-ACP of fatty acid synthesis to a specific lysine residue of a cognate protein by the LipB octanoyl transferase, followed by sulfur insertion at carbons C6 and C8 by the LipA lipoyl synthetase. Assembly on the cognate proteins regulates the amount of lipoic acid synthesized, and thus there is no transcriptional control of the synthetic genes. In contrast, transcriptional control of the biotin synthetic genes is wielded by a remarkably sophisticated, yet simple, system exerted through BirA, a dual-function protein that both represses biotin operon transcription and ligates biotin to its cognate protein.
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17
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Bockman MR, Kalinda AS, Petrelli R, De la Mora-Rey T, Tiwari D, Liu F, Dawadi S, Nandakumar M, Rhee KY, Schnappinger D, Finzel BC, Aldrich CC. Targeting Mycobacterium tuberculosis Biotin Protein Ligase (MtBPL) with Nucleoside-Based Bisubstrate Adenylation Inhibitors. J Med Chem 2015; 58:7349-7369. [PMID: 26299766 PMCID: PMC4667793 DOI: 10.1021/acs.jmedchem.5b00719] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Mycobacterium tuberculosis (Mtb), responsible for both latent and symptomatic tuberculosis (TB), remains the second leading cause of mortality among infectious diseases worldwide. Mycobacterial biotin protein ligase (MtBPL) is an essential enzyme in Mtb and regulates lipid metabolism through the post-translational biotinylation of acyl coenzyme A carboxylases. We report the synthesis and evaluation of a systematic series of potent nucleoside-based inhibitors of MtBPL that contain modifications to the ribofuranosyl ring of the nucleoside. All compounds were characterized by isothermal titration calorimetry (ITC) and shown to bind potently with K(D)s ≤ 2 nM. Additionally, we obtained high-resolution cocrystal structures for a majority of the compounds. Despite fairly uniform biochemical potency, the whole-cell Mtb activity varied greatly with minimum inhibitory concentrations (MIC) ranging from 0.78 to >100 μM. Cellular accumulation studies showed a nearly 10-fold enhancement in accumulation of a C-2'-α analogue over the corresponding C-2'-β analogue, consistent with their differential whole-cell activity.
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Affiliation(s)
- Matthew R. Bockman
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Alvin S. Kalinda
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA,Center for Drug Design, Academic Health Center, University of Minnesota, MN 55455 USA
| | - Riccardo Petrelli
- Center for Drug Design, Academic Health Center, University of Minnesota, MN 55455 USA
| | - Teresa De la Mora-Rey
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Divya Tiwari
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Feng Liu
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Surrendra Dawadi
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Madhumitha Nandakumar
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Kyu Y. Rhee
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Barry C. Finzel
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Courtney C. Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA,Center for Drug Design, Academic Health Center, University of Minnesota, MN 55455 USA,Corresponding Author Footnote: To whom correspondence should be addressed. Phone 612-625-7956. Fax 612-626-3114.
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18
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Feng Y, Kumar R, Ravcheev DA, Zhang H. Paracoccus denitrificans possesses two BioR homologs having a role in regulation of biotin metabolism. Microbiologyopen 2015; 4:644-59. [PMID: 26037461 PMCID: PMC4554459 DOI: 10.1002/mbo3.270] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 05/04/2015] [Accepted: 05/12/2015] [Indexed: 11/05/2022] Open
Abstract
Recently, we determined that BioR, the GntR family of transcription factor, acts as a repressor for biotin metabolism exclusively distributed in certain species of α-proteobacteria, including the zoonotic agent Brucella melitensis and the plant pathogen Agrobacterium tumefaciens. However, the scenario is unusual in Paracoccus denitrificans, another closely related member of the same phylum α-proteobacteria featuring with denitrification. Not only does it encode two BioR homologs Pden_1431 and Pden_2922 (designated as BioR1 and BioR2, respectively), but also has six predictive BioR-recognizable sites (the two bioR homolog each has one site, whereas the two bio operons (bioBFDAGC and bioYB) each contains two tandem BioR boxes). It raised the possibility that unexpected complexity is present in BioR-mediated biotin regulation. Here we report that this is the case. The identity of the purified BioR proteins (BioR1 and BioR2) was confirmed with LC-QToF-MS. Phylogenetic analyses combined with GC percentage raised a possibility that the bioR2 gene might be acquired by horizontal gene transfer. Gel shift assays revealed that the predicted BioR-binding sites are functional for the two BioR homologs, in much similarity to the scenario seen with the BioR site of A. tumefaciens bioBFDAZ. Using the A. tumefaciens reporter system carrying a plasmid-borne LacZ fusion, we revealed that the two homologs of P. denitrificans BioR are functional repressors for biotin metabolism. As anticipated, not only does the addition of exogenous biotin stimulate efficiently the expression of bioYB operon encoding biotin transport/uptake system BioY, but also inhibits the transcription of the bioBFDAGC operon resembling the de novo biotin synthetic pathway. EMSA-based screening failed to demonstrate that the biotin-related metabolite is involved in BioR-DNA interplay, which is consistent with our former observation with Brucella BioR. Our finding defined a complex regulatory network for biotin metabolism in P. denitrificans by two BioR proteins.
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Affiliation(s)
- Youjun Feng
- Department of Medical Microbiology & Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China
| | - Ritesh Kumar
- Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas, 77030
| | - Dmitry A Ravcheev
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 2, avenue de l'Université, L-4365, Esch-sur-Alzette, Luxembourg
| | - Huimin Zhang
- Department of Medical Microbiology & Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China
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19
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Tieu W, Polyak SW, Paparella AS, Yap MY, Soares da Costa TP, Ng B, Wang G, Lumb R, Bell JM, Turnidge JD, Wilce MCJ, Booker GW, Abell AD. Improved Synthesis of Biotinol-5'-AMP: Implications for Antibacterial Discovery. ACS Med Chem Lett 2015; 6:216-20. [PMID: 25699152 DOI: 10.1021/ml500475n] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 12/11/2014] [Indexed: 11/30/2022] Open
Abstract
An improved synthesis of biotinol-5'-AMP, an acyl-AMP mimic of the natural reaction intermediate of biotin protein ligase (BPL), is reported. This compound was shown to be a pan inhibitor of BPLs from a series of clinically important bacteria, particularly Staphylococcus aureus and Mycobacterium tuberculosis, and kinetic analysis revealed it to be competitive against the substrate biotin. Biotinol-5'-AMP also exhibits antibacterial activity against a panel of clinical isolates of S. aureus and M. tuberculosis with MIC values of 1-8 and 0.5-2.5 μg/mL, respectively, while being devoid of cytotoxicity to human HepG2 cells.
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Affiliation(s)
- William Tieu
- School
of Chemistry and Physics, University of Adelaide, Adelaide, South Australia 5005, Australia
- Centre
for Molecular Pathology, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Steven W. Polyak
- School
of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
- Centre
for Molecular Pathology, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Ashleigh S. Paparella
- School
of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Min Y. Yap
- School
of Biomedical Science, Monash University, Victoria 3800, Australia
| | - Tatiana P. Soares da Costa
- School
of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Belinda Ng
- School
of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Geqing Wang
- School
of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Richard Lumb
- Microbiology
and Infectious Diseases Directorate, SA Pathology, Women’s and Children’s Hospital, Adelaide, South Australia 5006, Australia
| | - Jan M. Bell
- Microbiology
and Infectious Diseases Directorate, SA Pathology, Women’s and Children’s Hospital, Adelaide, South Australia 5006, Australia
| | - John D. Turnidge
- School
of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
- Microbiology
and Infectious Diseases Directorate, SA Pathology, Women’s and Children’s Hospital, Adelaide, South Australia 5006, Australia
| | | | - Grant W. Booker
- School
of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
- Centre
for Molecular Pathology, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Andrew D. Abell
- School
of Chemistry and Physics, University of Adelaide, Adelaide, South Australia 5005, Australia
- Centre
for Molecular Pathology, The University of Adelaide, Adelaide, South Australia 5005, Australia
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20
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Eginton C, Naganathan S, Beckett D. Sequence-function relationships in folding upon binding. Protein Sci 2014; 24:200-11. [PMID: 25407143 DOI: 10.1002/pro.2605] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 11/13/2014] [Indexed: 11/08/2022]
Abstract
Folding coupled to binding is ubiquitous in biology. Nevertheless, the relationship of sequence to function for protein segments that undergo coupled binding and folding remains to be determined. Specifically, it is not known if the well-established rules that govern protein folding and stability are relevant to ligand-linked folding transitions. Upon small ligand biotinoyl-5'-AMP (bio-5'-AMP) binding the Escherichia coli protein BirA undergoes a disorder-to-order transition that results in formation of a network of packed hydrophobic side chains. Ligand binding is also allosterically coupled to protein association, with bio-5'-AMP binding enhancing the dimerization free energy by -4.0 kcal/mol. Previous studies indicated that single alanine replacements in a three residue hydrophobic cluster that contributes to the larger network disrupt cluster formation, ligand binding, and allosteric activation of protein association. In this work, combined equilibrium and kinetic measurements of BirA variants with alanine substitutions in the entire hydrophobic network reveal large functional perturbations resulting from any single substitution and highly non-additive effects of multiple substitutions. These substitutions also disrupt ligand-linked folding. The combined results suggest that, analogous to protein folding, functional disorder-to-order linked to binding requires optimal packing of the relevant hydrophobic side chains that contribute to the transition. The potential for many combinations of residues to satisfy this requirement implies that, although functionally important, segments of homologous proteins that undergo folding linked to binding can exhibit sequence divergence.
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Affiliation(s)
- Christopher Eginton
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland, 20742
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21
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Sittiwong W, Cordonier EL, Zempleni J, Dussault PH. β-Keto and β-hydroxyphosphonate analogs of biotin-5'-AMP are inhibitors of holocarboxylase synthetase. Bioorg Med Chem Lett 2014; 24:5568-5571. [PMID: 25466176 DOI: 10.1016/j.bmcl.2014.11.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 10/29/2014] [Accepted: 11/03/2014] [Indexed: 11/15/2022]
Abstract
Holocarboxylase synthetase (HLCS) catalyzes the covalent attachment of biotin to cytoplasmic and mitochondrial carboxylases, nuclear histones, and over a hundred human proteins. Nonhydrolyzable ketophosphonate (β-ketoP) and hydroxyphosphonate (β-hydroxyP) analogs of biotin-5'-AMP inhibit holocarboxylase synthetase (HLCS) with IC50 values of 39.7 μM and 203.7 μM. By comparison, an IC50 value of 7 μM was observed with the previously reported biotinol-5'-AMP. The Ki values, 3.4 μM and 17.3 μM, respectively, are consistent with the IC50 results, and close to the Ki obtained for biotinol-5'-AMP (7 μM). The β-ketoP and β-hydroxyP molecules are competitive inhibitors of HLCS while biotinol-5'-AMP inhibited HLCS by a mixed mechanism.
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Affiliation(s)
- Wantanee Sittiwong
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Elizabeth L Cordonier
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583-0806, USA
| | - Janos Zempleni
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583-0806, USA.
| | - Patrick H Dussault
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
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22
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Liu DS, Nivón LG, Richter F, Goldman PJ, Deerinck TJ, Yao JZ, Richardson D, Phipps WS, Ye AZ, Ellisman MH, Drennan CL, Baker D, Ting AY. Computational design of a red fluorophore ligase for site-specific protein labeling in living cells. Proc Natl Acad Sci U S A 2014; 111:E4551-9. [PMID: 25313043 PMCID: PMC4217414 DOI: 10.1073/pnas.1404736111] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Chemical fluorophores offer tremendous size and photophysical advantages over fluorescent proteins but are much more challenging to target to specific cellular proteins. Here, we used Rosetta-based computation to design a fluorophore ligase that accepts the red dye resorufin, starting from Escherichia coli lipoic acid ligase. X-ray crystallography showed that the design closely matched the experimental structure. Resorufin ligase catalyzed the site-specific and covalent attachment of resorufin to various cellular proteins genetically fused to a 13-aa recognition peptide in multiple mammalian cell lines and in primary cultured neurons. We used resorufin ligase to perform superresolution imaging of the intermediate filament protein vimentin by stimulated emission depletion and electron microscopies. This work illustrates the power of Rosetta for major redesign of enzyme specificity and introduces a tool for minimally invasive, highly specific imaging of cellular proteins by both conventional and superresolution microscopies.
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Affiliation(s)
| | | | - Florian Richter
- Department of Biochemistry, Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA 98195
| | | | - Thomas J Deerinck
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems and
| | | | - Douglas Richardson
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | | | | | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems and Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093; and
| | - Catherine L Drennan
- Departments of Chemistry and Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - David Baker
- Department of Biochemistry, Howard Hughes Medical Institute, and
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23
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Tieu W, Jarrad AM, Paparella AS, Keeling KA, Soares da Costa TP, Wallace JC, Booker GW, Polyak SW, Abell AD. Heterocyclic acyl-phosphate bioisostere-based inhibitors of Staphylococcus aureus biotin protein ligase. Bioorg Med Chem Lett 2014; 24:4689-4693. [DOI: 10.1016/j.bmcl.2014.08.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 08/07/2014] [Accepted: 08/11/2014] [Indexed: 01/17/2023]
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24
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Shi C, Tiwari D, Wilson DJ, Seiler CL, Schnappinger D, Aldrich CC. Bisubstrate Inhibitors of Biotin Protein Ligase in Mycobacterium tuberculosis Resistant to Cyclonucleoside Formation. ACS Med Chem Lett 2013; 4. [PMID: 24363833 DOI: 10.1021/ml400328a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis, is the leading cause bacterial infectious diseases mortality. Biotin protein ligase (BirA) globally regulates lipid metabolism in Mtb through the posttranslational biotinylation of acyl coenzyme A carboxylases (ACCs) involved in lipid biosynthesis and is essential for Mtb survival. We previously developed a rationally designed bisubstrate inhibitor of BirA that displays potent enzyme inhibition and whole-cell activity against multidrug resistant and extensively drug resistant Mtb strains. Here we present the design, synthesis and evaluation of a focused series of inhibitors, which are resistant to cyclonucleoside formation, a key decomposition pathway of our initial analogue. Improved chemical stability is realized through replacement of the adenosyl N-3 nitrogen and C-5' oxygen atom with carbon as well as incorporation of bulky group on the nucleobase to prevent the required syn-conformation necessary for proper alignment of N-3 with C-5'.
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Affiliation(s)
- Ce Shi
- Center
for Drug Design, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Divya Tiwari
- Department
of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
| | - Daniel J. Wilson
- Center
for Drug Design, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Christopher L. Seiler
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Dirk Schnappinger
- Department
of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
| | - Courtney C. Aldrich
- Center
for Drug Design, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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25
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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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26
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Brucella BioR regulator defines a complex regulatory mechanism for bacterial biotin metabolism. J Bacteriol 2013; 195:3451-67. [PMID: 23729648 DOI: 10.1128/jb.00378-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The enzyme cofactor biotin (vitamin H or B7) is an energetically expensive molecule whose de novo biosynthesis requires 20 ATP equivalents. It seems quite likely that diverse mechanisms have evolved to tightly regulate its biosynthesis. Unlike the model regulator BirA, a bifunctional biotin protein ligase with the capability of repressing the biotin biosynthetic pathway, BioR has been recently reported by us as an alternative machinery and a new type of GntR family transcriptional factor that can repress the expression of the bioBFDAZ operon in the plant pathogen Agrobacterium tumefaciens. However, quite unusually, a closely related human pathogen, Brucella melitensis, has four putative BioR-binding sites (both bioR and bioY possess one site in the promoter region, whereas the bioBFDAZ [bio] operon contains two tandem BioR boxes). This raised the question of whether BioR mediates the complex regulatory network of biotin metabolism. Here, we report that this is the case. The B. melitensis BioR ortholog was overexpressed and purified to homogeneity, and its solution structure was found to be dimeric. Functional complementation in a bioR isogenic mutant of A. tumefaciens elucidated that Brucella BioR is a functional repressor. Electrophoretic mobility shift assays demonstrated that the four predicted BioR sites of Brucella plus the BioR site of A. tumefaciens can all interact with the Brucella BioR protein. In a reporter strain that we developed on the basis of a double mutant of A. tumefaciens (the ΔbioR ΔbioBFDA mutant), the β-galactosidase (β-Gal) activity of three plasmid-borne transcriptional fusions (bioBbme-lacZ, bioYbme-lacZ, and bioRbme-lacZ) was dramatically decreased upon overexpression of Brucella bioR. Real-time quantitative PCR analyses showed that the expression of bioBFDA and bioY is significantly elevated upon removal of bioR from B. melitensis. Together, we conclude that Brucella BioR is not only a negative autoregulator but also a repressor of expression of bioY and bio operons that separately function in biotin transport and the biosynthesis pathway.
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Ibarra JA, Pérez-Rueda E, Carroll RK, Shaw LN. Global analysis of transcriptional regulators in Staphylococcus aureus. BMC Genomics 2013; 14:126. [PMID: 23442205 PMCID: PMC3616918 DOI: 10.1186/1471-2164-14-126] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Accepted: 02/12/2013] [Indexed: 02/01/2023] Open
Abstract
Background Staphylococcus aureus is a widely distributed human pathogen capable of infecting almost every ecological niche of the host. As a result, it is responsible for causing many different diseases. S. aureus has a vast array of virulence determinants whose expression is modulated by an intricate regulatory network, where transcriptional factors (TFs) are the primary elements. In this work, using diverse sequence analysis, we evaluated the repertoire of TFs and sigma factors in the community-associated methicillin resistant S. aureus (CA-MRSA) strain USA300-FPR3757. Results A total of 135 TFs and sigma factors were identified and classified into 36 regulatory families. From these around 43% have been experimentally characterized to date, which demonstrates the significant work still at hand to unravel the regulatory network in place for this important pathogen. A comparison of the TF repertoire of S. aureus against 1209 sequenced bacterial genomes was carried out allowing us to identify a core set of orthologous TFs for the Staphylococacceae, and also allowing us to assign potential functions to previously uncharacterized TFs. Finally, the USA300 TFs were compared to those in eleven other S. aureus strains including: Newman, COL, JH1, JH9, MW2, Mu3, Mu50, N315, RF122, MRSA252 and MSSA476. We identify conserved TFs among these strains and suggest possible regulatory interactions. Conclusions The analysis presented herein highlights the complexity of regulatory networks in S. aureus strains, identifies key conserved TFs among the Staphylococacceae, and offers unique insights into several as yet uncharacterized TFs.
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Affiliation(s)
- Jose Antonio Ibarra
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 East Fowler Avenue, ISA 2015, Tampa, FL 33620-5150, USA.
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Duckworth BP, Nelson KM, Aldrich CC. Adenylating enzymes in Mycobacterium tuberculosis as drug targets. Curr Top Med Chem 2012; 12:766-96. [PMID: 22283817 DOI: 10.2174/156802612799984571] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 11/08/2011] [Indexed: 11/22/2022]
Abstract
Adenylation or adenylate-forming enzymes (AEs) are widely found in nature and are responsible for the activation of carboxylic acids to intermediate acyladenylates, which are mixed anhydrides of AMP. In a second reaction, AEs catalyze the transfer of the acyl group of the acyladenylate onto a nucleophilic amino, alcohol, or thiol group of an acceptor molecule leading to amide, ester, and thioester products, respectively. Mycobacterium tuberculosis encodes for more than 60 adenylating enzymes, many of which represent potential drug targets due to their confirmed essentiality or requirement for virulence. Several strategies have been used to develop potent and selective AE inhibitors including highthroughput screening, fragment-based screening, and the rationale design of bisubstrate inhibitors that mimic the acyladenylate. In this review, a comprehensive analysis of the mycobacterial adenylating enzymes will be presented with a focus on the identification of small molecule inhibitors. Specifically, this review will cover the aminoacyl tRNAsynthetases (aaRSs), MenE required for menaquinone synthesis, the FadD family of enzymes including the fatty acyl- AMP ligases (FAAL) and the fatty acyl-CoA ligases (FACLs) involved in lipid metabolism, and the nonribosomal peptide synthetase adenylation enzyme MbtA that is necessary for mycobactin synthesis. Additionally, the enzymes NadE, GuaA, PanC, and MshC involved in the respective synthesis of NAD, guanine, pantothenate, and mycothiol will be discussed as well as BirA that is responsible for biotinylation of the acyl CoA-carboxylases.
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Cross-neutralization of influenza A viruses mediated by a single antibody loop. Nature 2012; 489:526-32. [PMID: 22982990 DOI: 10.1038/nature11414] [Citation(s) in RCA: 368] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 07/13/2012] [Indexed: 11/08/2022]
Abstract
Immune recognition of protein antigens relies on the combined interaction of multiple antibody loops, which provide a fairly large footprint and constrain the size and shape of protein surfaces that can be targeted. Single protein loops can mediate extremely high-affinity binding, but it is unclear whether such a mechanism is available to antibodies. Here we report the isolation and characterization of an antibody called C05, which neutralizes strains from multiple subtypes of influenza A virus, including H1, H2 and H3. X-ray and electron microscopy structures show that C05 recognizes conserved elements of the receptor-binding site on the haemagglutinin surface glycoprotein. Recognition of the haemagglutinin receptor-binding site is dominated by a single heavy-chain complementarity-determining region 3 loop, with minor contacts from heavy-chain complementarity-determining region 1, and is sufficient to achieve nanomolar binding with a minimal footprint. Thus, binding predominantly with a single loop can allow antibodies to target small, conserved functional sites on otherwise hypervariable antigens.
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Dreyfus C, Laursen NS, Kwaks T, Zuijdgeest D, Khayat R, Ekiert DC, Lee JH, Metlagel Z, Bujny MV, Jongeneelen M, van der Vlugt R, Lamrani M, Korse HJWM, Geelen E, Sahin Ö, Sieuwerts M, Brakenhoff JPJ, Vogels R, Li OTW, Poon LLM, Peiris M, Koudstaal W, Ward AB, Wilson IA, Goudsmit J, Friesen RHE. Highly conserved protective epitopes on influenza B viruses. Science 2012; 337:1343-8. [PMID: 22878502 DOI: 10.1126/science.1222908] [Citation(s) in RCA: 608] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Identification of broadly neutralizing antibodies against influenza A viruses has raised hopes for the development of monoclonal antibody-based immunotherapy and "universal" vaccines for influenza. However, a substantial part of the annual flu burden is caused by two cocirculating, antigenically distinct lineages of influenza B viruses. Here, we report human monoclonal antibodies, CR8033, CR8071, and CR9114, that protect mice against lethal challenge from both lineages. Antibodies CR8033 and CR8071 recognize distinct conserved epitopes in the head region of the influenza B hemagglutinin (HA), whereas CR9114 binds a conserved epitope in the HA stem and protects against lethal challenge with influenza A and B viruses. These antibodies may inform on development of monoclonal antibody-based treatments and a universal flu vaccine for all influenza A and B viruses.
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Affiliation(s)
- Cyrille Dreyfus
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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Böttcher C, Dennis EG, Booker GW, Polyak SW, Boss PK, Davies C. A novel tool for studying auxin-metabolism: the inhibition of grapevine indole-3-acetic acid-amido synthetases by a reaction intermediate analogue. PLoS One 2012; 7:e37632. [PMID: 22649546 PMCID: PMC3359377 DOI: 10.1371/journal.pone.0037632] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 04/27/2012] [Indexed: 02/03/2023] Open
Abstract
An important process for the regulation of auxin levels in plants is the inactivation of indole-3-acetic acid (IAA) by conjugation to amino acids. The conjugation reaction is catalysed by IAA-amido synthetases belonging to the family of GH3 proteins. Genetic approaches to study the biological significance of these enzymes have been hampered by large gene numbers and a high degree of functional redundancy. To overcome these difficulties a chemical approach based on the reaction mechanism of GH3 proteins was employed to design a small molecule inhibitor of IAA-amido synthetase activity. Adenosine-5'-[2-(1H-indol-3-yl)ethyl]phosphate (AIEP) mimics the adenylated intermediate of the IAA-conjugation reaction and was therefore proposed to compete with the binding of MgATP and IAA in the initial stages of catalysis. Two grapevine IAA-amido synthetases with different catalytic properties were chosen to test the inhibitory effects of AIEP in vitro. GH3-1 has previously been implicated in the grape berry ripening process and is restricted to two amino acid substrates, whereas GH3-6 conjugated IAA to 13 amino acids. AIEP is the most potent inhibitor of GH3 enzymes so far described and was shown to be competitive against MgATP and IAA binding to both enzymes with K(i)-values 17-68-fold lower than the respective K(m)-values. AIEP also exhibited in vivo activity in an ex planta test system using young grape berries. Exposure to 5-20 µM of the inhibitor led to decreased levels of the common conjugate IAA-Asp and reduced the accumulation of the corresponding Asp-conjugate upon treatment with a synthetic auxin. AIEP therefore represents a novel chemical probe with which to study IAA-amido synthetase function.
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Bisubstrate adenylation inhibitors of biotin protein ligase from Mycobacterium tuberculosis. ACTA ACUST UNITED AC 2012; 18:1432-41. [PMID: 22118677 DOI: 10.1016/j.chembiol.2011.08.013] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 08/05/2011] [Accepted: 08/24/2011] [Indexed: 10/15/2022]
Abstract
The mycobacterial biotin protein ligase (MtBPL) globally regulates lipid metabolism in Mtb through the posttranslational biotinylation of acyl coenzyme A carboxylases involved in lipid biosynthesis that catalyze the first step in fatty acid biosynthesis and pyruvate coenzyme A carboxylase, a gluconeogenic enzyme vital for lipid catabolism. Here we describe the design, development, and evaluation of a rationally designed bisubstrate inhibitor of MtBPL. This inhibitor displays potent subnanomolar enzyme inhibition and antitubercular activity against multidrug resistant and extensively drug resistant Mtb strains. We show that the inhibitor decreases in vivo protein biotinylation of key enzymes involved in fatty acid biosynthesis and that the antibacterial activity is MtBPL dependent. Additionally, the gene encoding BPL was found to be essential in M. smegmatis. Finally, the X-ray cocrystal structure of inhibitor bound MtBPL was solved providing detailed insight for further structure-activity analysis. Collectively, these data suggest that MtBPL is a promising target for further antitubercular therapeutic development.
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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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Wang Z, Liu L, Xu Y, Sun L, Li G. Simulation and assay of protein biotinylation with electrochemical technique. Biosens Bioelectron 2011; 26:4610-3. [DOI: 10.1016/j.bios.2011.04.052] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 04/25/2011] [Accepted: 04/28/2011] [Indexed: 10/18/2022]
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Tungtur S, Skinner H, Zhan H, Swint-Kruse L, Beckett D. In vivo tests of thermodynamic models of transcription repressor function. Biophys Chem 2011; 159:142-51. [PMID: 21715082 DOI: 10.1016/j.bpc.2011.06.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 05/26/2011] [Accepted: 06/05/2011] [Indexed: 10/18/2022]
Abstract
One emphasis of the Gibbs Conference on Biothermodynamics is the value of thermodynamic measurements for understanding behaviors of biological systems. In this study, the correlation between thermodynamic measurements of in vitro DNA binding affinity with in vivo transcription repression was investigated for two transcription repressors. In the first system, which comprised an engineered LacI/GalR homolog, mutational changes altered the equilibrium constant for binding DNA. Changes correlated with altered repression, but estimates of in vivo repressor concentration suggest a ≥25-fold discrepancy with in vitro conditions. In the second system, changes in ligand binding to BirA altered dimerization and subsequent DNA occupancy. Again, these changes correlate with altered in vivo repression, but comparison with in vitro measurements reveals a ~10-fold discrepancy. Further analysis of each system suggests that the observed discrepancies between in vitro and in vivo results reflect the contributions of additional equilibria to the transcription repression process.
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Affiliation(s)
- Sudheer Tungtur
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, United States
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37
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Ingaramo M, Beckett D. Biotinylation, a post-translational modification controlled by the rate of protein-protein association. J Biol Chem 2011; 286:13071-8. [PMID: 21343300 DOI: 10.1074/jbc.m110.183624] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Biotin protein ligases catalyze specific covalent linkage of the coenzyme biotin to biotin-dependent carboxylases. The reaction proceeds in two steps, including synthesis of an adenylated intermediate followed by biotin transfer to the carboxylase substrate. In this work specificity in the transfer reaction was investigated using single turnover stopped-flow and quench-flow assays. Cognate and noncognate reactions were measured using the enzymes and minimal biotin acceptor substrates from Escherichia coli, Pyrococcus horikoshii, and Homo sapiens. The kinetic analysis demonstrates that for all enzyme-substrate pairs the bimolecular rate of association of enzyme with substrate limits post-translational biotinylation. In addition, in noncognate reactions the three enzymes displayed a range of selectivities. These results highlight the importance of protein-protein binding kinetics for specific biotin addition to carboxylases and provide one mechanism for determining biotin distribution in metabolism.
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Affiliation(s)
- Maria Ingaramo
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742, USA
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38
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Tron CM, McNae IW, Nutley M, Clarke DJ, Cooper A, Walkinshaw MD, Baxter RL, Campopiano DJ. Structural and functional studies of the biotin protein ligase from Aquifex aeolicus reveal a critical role for a conserved residue in target specificity. J Mol Biol 2009; 387:129-46. [PMID: 19385043 DOI: 10.1016/j.jmb.2008.12.086] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Biotin protein ligase (BPL; EC 6.3.4.15) catalyses the formation of biotinyl-5'-AMP from biotin and ATP, and the succeeding biotinylation of the biotin carboxyl carrier protein. We describe the crystal structures, at 2.4 A resolution, of the class I BPL from the hyperthermophilic bacteria Aquifex aeolicus (AaBPL) in its ligand-free form and in complex with biotin and ATP. The solvent-exposed beta- and gamma-phosphates of ATP are located in the inter-subunit cavity formed by the N- and C-terminal domains. The Arg40 residue from the conserved GXGRXG motif is shown to interact with the carboxyl group of biotin and to stabilise the alpha- and beta-phosphates of the nucleotide. The structure of the mutant AaBPL R40G in both the ligand-free and biotin-bound forms reveals that the mutated loop has collapsed, thus hindering ATP binding. Isothermal titration calorimetry indicated that the presence of biotin is not required for ATP binding to wild-type AaBPL in the absence of Mg(2+), and the binding of biotin and ATP has been determined to occur via a random but cooperative process. The affinity for biotin is relatively unaffected by the R40G mutation. In contrast, the thermodynamic data indicate that binding of ATP to AaBPL R40G is very weak in the absence or in the presence of biotin. The AaBPL R40G mutant remains catalytically active but shows poor substrate specificity; mass spectrometry and Western blot studies revealed that the mutant biotinylates both the target A. aeolicus BCCPDelta67 fragment and BSA, and is subject to self-biotinylation.
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Affiliation(s)
- Cecile M Tron
- School of Chemistry, EaStCHEM, The University of Edinburgh, West Mains Road, King's Buildings, Edinburgh, Scotland, UK
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Zhao H, Naganathan S, Beckett D. Thermodynamic and structural investigation of bispecificity in protein-protein interactions. J Mol Biol 2009; 389:336-48. [PMID: 19361526 DOI: 10.1016/j.jmb.2009.04.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Revised: 03/17/2009] [Accepted: 04/04/2009] [Indexed: 11/15/2022]
Abstract
The ability of a single protein to interact with multiple protein partners is central to many biological processes. However, the physical-chemical and structural basis of the multispecificity is not understood. In Escherichia coli, the protein BirA can self-associate to a homodimer or form a heterodimer with the biotin carboxyl carrier protein of the biotin-dependent carboxylase, acetyl coenzyme A carboxylase. The first interaction results in binding of BirA to the biotin operator sequence to repress transcription initiation at the biotin biosynthetic operon and the second is a prerequisite to posttranslational biotin addition to the carrier protein for use in metabolism. A single surface on BirA is used for both interactions and previous studies indicate that, despite the structural differences between the alternative partners, the two dimerization reactions are isoenergetic. In this work, the underlying thermodynamic driving forces and the sequence determinants of the two interactions were investigated in order to elucidate the energetic and structural underpinnings of the dual specificity. Combined measurements of the temperature and salt dependencies of heterodimerization indicate a modest unfavorable enthalpy and no dependence on salt concentration. By contrast, homodimerization is characterized by a very large unfavorable enthalpy and a modest dependence on salt concentration. Measurements of the function of BirA variants with single amino acid replacements in the alternative dimerization reactions indicate that although considerable overlap in structural determinants for both interactions exists, hotspots specific for one but not the other were detected.
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Affiliation(s)
- Huaying Zhao
- Department of Chemistry & Biochemistry, Center for Biological Structure and Organization, College of Chemical & Life Sciences, University of Maryland, College Park, MD 20742, USA
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40
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Purushothaman S, Gupta G, Srivastava R, Ramu VG, Surolia A. Ligand specificity of group I biotin protein ligase of Mycobacterium tuberculosis. PLoS One 2008; 3:e2320. [PMID: 18509457 PMCID: PMC2384007 DOI: 10.1371/journal.pone.0002320] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2008] [Accepted: 03/25/2008] [Indexed: 11/19/2022] Open
Abstract
Background Fatty acids are indispensable constituents of mycolic acids that impart toughness & permeability barrier to the cell envelope of M. tuberculosis. Biotin is an essential co-factor for acetyl-CoA carboxylase (ACC) the enzyme involved in the synthesis of malonyl-CoA, a committed precursor, needed for fatty acid synthesis. Biotin carboxyl carrier protein (BCCP) provides the co-factor for catalytic activity of ACC. Methodology/Principal Findings BPL/BirA (Biotin Protein Ligase), and its substrate, biotin carboxyl carrier protein (BCCP) of Mycobacterium tuberculosis (Mt) were cloned and expressed in E. coli BL21. In contrast to EcBirA and PhBPL, the ∼29.5 kDa MtBPL exists as a monomer in native, biotin and bio-5′AMP liganded forms. This was confirmed by molecular weight profiling by gel filtration on Superdex S-200 and Dynamic Light Scattering (DLS). Computational docking of biotin and bio-5′AMP to MtBPL show that adenylation alters the contact residues for biotin. MtBPL forms 11 H-bonds with biotin, relative to 35 with bio-5′AMP. Docking simulations also suggest that bio-5′AMP hydrogen bonds to the conserved ‘GRGRRG’ sequence but not biotin. The enzyme catalyzed transfer of biotin to BCCP was confirmed by incorporation of radioactive biotin and by Avidin blot. The Km for BCCP was ∼5.2 µM and ∼420 nM for biotin. MtBPL has low affinity (Kb = 1.06×10−6 M) for biotin relative to EcBirA but their Km are almost comparable suggesting that while the major function of MtBPL is biotinylation of BCCP, tight binding of biotin/bio-5′AMP by EcBirA is channeled for its repressor activity. Conclusions/Significance These studies thus open up avenues for understanding the unique features of MtBPL and the role it plays in biotin utilization in M. tuberculosis.
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Affiliation(s)
| | - Garima Gupta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Richa Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | | | - Avadhesha Surolia
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
- * E-mail:
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Laine O, Streaker ED, Nabavi M, Fenselau CC, Beckett D. Allosteric signaling in the biotin repressor occurs via local folding coupled to global dampening of protein dynamics. J Mol Biol 2008; 381:89-101. [PMID: 18586268 DOI: 10.1016/j.jmb.2008.05.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Revised: 05/09/2008] [Accepted: 05/10/2008] [Indexed: 11/18/2022]
Abstract
The biotin repressor is an allosterically regulated, site-specific DNA-binding protein. Binding of the small ligand bio-5'-AMP activates repressor dimerization, which is a prerequisite to DNA binding. Multiple disorder-to-order transitions, some of which are known to be important for the functional allosteric response, occur in the vicinity of the ligand-binding site concomitant with effector binding to the repressor monomer. In this work, the extent to which these local changes are coupled to additional changes in the structure/dynamics of the repressor was investigated using hydrogen/deuterium exchange coupled to mass spectrometry. Measurements were performed on the apo-protein and on complexes of the protein bound to four different effectors that elicit a range of thermodynamic responses in the repressor. Global exchange measurements indicate that binding of any effector to the intact protein is accompanied by protection from exchange. Mass spectrometric analysis of pepsin-cleavage products generated from the exchanged complexes reveals that the protection is distributed throughout the protein. Furthermore, the magnitude of the level of protection in each peptide from hydrogen/deuterium exchange correlates with the magnitude of the functional allosteric response elicited by a ligand. These results indicate that local structural changes in the binding site that occur concomitant with effector binding nucleate global dampening of dynamics. Moreover, the magnitude of dampening of repressor dynamics tracks with the magnitude of the functional response to effector binding.
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Affiliation(s)
- Olli Laine
- Department of Chemistry and Biochemistry and Center for Biological Structure and Organization, College of Chemical and Life Sciences, University of Maryland, College Park, MD 20742, USA
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42
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Zhao H, Beckett D. Kinetic partitioning between alternative protein-protein interactions controls a transcriptional switch. J Mol Biol 2008; 380:223-36. [PMID: 18508076 DOI: 10.1016/j.jmb.2008.04.068] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2008] [Revised: 04/24/2008] [Accepted: 04/29/2008] [Indexed: 01/14/2023]
Abstract
Proteins can perform completely distinct functions in response to the particular partners that they bind to. Consequently, determination of the mechanism of functional regulation in such systems requires elucidation of the mechanism switching between binding partners. The central protein of the Escherichia coli biotin regulatory system, BirA, switches between its function as a metabolic enzyme or a transcriptional repressor in response to binding either the biotin carboxyl carrier protein subunit of acetyl-CoA carboxylase or a second BirA monomer. These two protein-protein interactions are structurally mutually exclusive. The results of earlier studies suggest that the system is regulated by kinetic partitioning between the two protein-protein interactions. In this work, sedimentation velocity was employed to monitor the partitioning directly. The results indicate similar equilibrium parameters governing formation of the two protein-protein interactions. Kinetic analysis of the sedimentation velocity data indicated that holoBirA dimerization is governed by very slow forward and reverse rate constants. The slow kinetics of holoBirA dimerization combined with fluctuations in the intracellular apoBCCP pool are critical determinants in partitioning BirA between its distinct biological functions.
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Affiliation(s)
- Huaying Zhao
- Department of Chemistry and Biochemistry, Center for Biological Structure and Organization, University of Maryland, College Park, MD 20742, USA
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Zhao H, Streaker E, Pan W, Beckett D. Protein−Protein Interactions Dominate the Assembly Thermodynamics of a Transcription Repression Complex. Biochemistry 2007; 46:13667-76. [DOI: 10.1021/bi7013097] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Huaying Zhao
- Department of Chemistry & Biochemistry, College of Chemical & Life Sciences, Center for Biological Structure & Organization, University of Maryland, College Park, Maryland 20742
| | - Emily Streaker
- Department of Chemistry & Biochemistry, College of Chemical & Life Sciences, Center for Biological Structure & Organization, University of Maryland, College Park, Maryland 20742
| | - Weilan Pan
- Department of Chemistry & Biochemistry, College of Chemical & Life Sciences, Center for Biological Structure & Organization, University of Maryland, College Park, Maryland 20742
| | - Dorothy Beckett
- Department of Chemistry & Biochemistry, College of Chemical & Life Sciences, Center for Biological Structure & Organization, University of Maryland, College Park, Maryland 20742
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Naganathan S, Beckett D. Nucleation of an allosteric response via ligand-induced loop folding. J Mol Biol 2007; 373:96-111. [PMID: 17765263 PMCID: PMC2792881 DOI: 10.1016/j.jmb.2007.07.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2007] [Revised: 06/30/2007] [Accepted: 07/12/2007] [Indexed: 10/23/2022]
Abstract
The Escherichia coli biotin repressor BirA is an allosteric transcription regulatory protein to which binding of the small ligand corepressor biotinyl-5'-AMP promotes homodimerization and subsequent DNA binding. Structural data indicate that the apo or unliganded repressor is characterized by four partially disordered loops that are ordered in the ligand-bound dimer. While three of these loops participate directly in the dimerization, the fourth, consisting of residues 212-234 is distal to the interface. This loop, which is ordered around the adenine ring of the adenylate moiety in the BirA.adenylate structure, is referred to as the adenylate-binding loop (ABL). Although residues in the loop do not interact directly with the ligand, a hydrophobic cluster consisting of a tryptophan and two valine side-chains assembles over the adenine base. Results of previous measurements suggest that folding of the ABL is integral to the allosteric response. This idea and the role of the hydrophobic cluster in the process were investigated by systematic replacement of each side-chain in the cluster with alanine and analysis of the mutant proteins for small ligand binding and dimerization. Isothermal titration calorimetry measurements indicate defects in adenylate binding for all ABL variants. Additionally, sedimentation equilibrium measurements reveal that coupling between adenylate binding and dimerization is compromised in each mutant. Partial proteolysis measurements indicate that the mutants are defective in ligand-linked folding of the ABL. These results indicate that the hydrophobic cluster is critical to the ligand-induced disorder-to-order transition in the ABL and that this transition is integral to the allosteric response in the biotin repressor.
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Streaker ED, Beckett D. The biotin regulatory system: kinetic control of a transcriptional switch. Biochemistry 2006; 45:6417-25. [PMID: 16700552 DOI: 10.1021/bi052599r] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An organism's response to environmental and metabolic cues requires communication between transcription regulatory processes and "other" cellular events. In a number of biological control circuits, the communication is carried out by a single multifunctional protein that participates directly in transcription initiation and in at least one other cellular process. Structural studies suggest that the function of these proteins is dictated by the formation of mutually exclusive protein-protein interactions. However, the rules that govern partner, and thus functional switching, are not known. In the Escherichia coli Biotin Regulatory System, the bifunctional protein, BirA, catalyzes post-translational biotin addition to a biotin-dependent carboxylase and binds sequence-specifically to DNA to repress transcription initiation at the biotin biosynthetic operon. Previous structural and modeling studies suggest that BirA function is determined by formation of alternative homo- and heterodimeric protein-protein interactions. In this work, the BirA functional switch is investigated using DNaseI footprinting and MALDI-TOF mass spectrometry. Results of these measurements indicate that BirA can be selectively targeted toward its enzymatic function simply by increasing the kinetic probability of heterodimerization relative to that of homodimerization. Subsequent shifting to the DNA binding function occurs as the pool of heterodimer partner is depleted and homodimerization dominates. The data support a switching mechanism in which BirA's function is dictated by its probability of encountering a particular protein partner.
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Affiliation(s)
- Emily D Streaker
- Department of Chemistry and Biochemistry and Center for Biological Structure and Organization, University of Maryland, College Park, Maryland 20742, USA
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Streaker ED, Beckett D. Nonenzymatic biotinylation of a biotin carboxyl carrier protein: unusual reactivity of the physiological target lysine. Protein Sci 2006; 15:1928-35. [PMID: 16823034 PMCID: PMC2242587 DOI: 10.1110/ps.062187306] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Enzyme-catalyzed addition of biotin to proteins is highly specific. In any single organism one or a small number of proteins are biotinylated and only a single lysine on each of these proteins is modified. A detailed understanding of the structural basis for the selective biotinylation process has not yet been elucidated. Recently certain mutants of the Escherichia coli biotin protein ligase have been shown to mediate "promiscuous" biotinylation of proteins. It was suggested that the reaction involved diffusion of a reactive activated biotin intermediate, biotinoyl-5'-AMP, with nonspecific proteins. In this work the reactivity of this chemically synthesized intermediate toward the natural target of enzymatic biotinylation, the biotin carboxyl carrier protein, was investigated. The results indicate that the intermediate does, indeed, react with target protein, albeit at a significantly slower rate than the enzyme-catalyzed process. Surprisingly, analysis of the products of nonenzymatic biotinylation indicates that of five lysine residues in the protein only the physiological target side chain is modified. These results indicate that either the environment of this lysine residue or its intrinsic properties render it highly reactive to nonenzymatic biotinylation mediated by biotinoyl-5'-AMP. This reactivity may be important for its selective biotinylation in vivo.
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Affiliation(s)
- Emily D Streaker
- Department of Chemistry & Biochemistry and Center for Biological Structure and Organization, University of Maryland, College Park, 20742, USA
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Wood ZA, Weaver LH, Brown PH, Beckett D, Matthews BW. Co-repressor induced order and biotin repressor dimerization: a case for divergent followed by convergent evolution. J Mol Biol 2006; 357:509-23. [PMID: 16438984 DOI: 10.1016/j.jmb.2005.12.066] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2005] [Revised: 12/15/2005] [Accepted: 12/18/2005] [Indexed: 11/19/2022]
Abstract
BirA catalyzes the adenylation and subsequent covalent attachment of biotin to the biotin carboxyl carrier protein (BCCP). In the absence of apo-BCCP, biotin-5'-AMP acts as a co-repressor that induces BirA dimerization and binding to the bio operator to repress biotin biosynthesis. The crystal structures of apo-BirA, and BirA in complex with biotin have been reported. We here describe the 2.8A resolution crystal structure of BirA in complex with the co-repressor analog biotinol-5'-AMP. It was previously shown that the structure of apo-BirA is monomeric and that binding of biotin weakly induces a dimeric structure in which three disordered surface loops become organized to form the dimer interface. The structure of the co-repressor complex is also a dimer, clearly related to the BirA.biotin structure, but with several significant conformational changes. A hitherto disordered "adenylate binding loop" forms a well-defined structure covering the co-repressor. The co-repressor buttresses the dimer interface, resulting in improved packing and a 12 degrees change in the hinge-bending angle along the dimer interface relative to the BirA.biotin structure. This helps explain why the binding of the co-repressor is necessary to optimize the binding of BirA to the bioO operator. The structure reveals an unexpected use of the nucleotide-binding motif GXGXXG in binding adenylate and controlling the repressor function. Finally, based on structural analysis we propose that the class of adenylating enzymes represented by BirA, lipoate protein ligase and class II tRNA synthetases diverged early and were selected based on their ability to sequester co-factors or amino acid residues, and adenylation activity arose independently through functional convergence.
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Affiliation(s)
- Zachary A Wood
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403-1229, USA
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48
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Bagautdinov B, Kuroishi C, Sugahara M, Kunishima N. Crystal structures of biotin protein ligase from Pyrococcus horikoshii OT3 and its complexes: structural basis of biotin activation. J Mol Biol 2005; 353:322-33. [PMID: 16169557 DOI: 10.1016/j.jmb.2005.08.032] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2005] [Revised: 08/12/2005] [Accepted: 08/17/2005] [Indexed: 11/19/2022]
Abstract
Biotin protein ligase (EC 6.3.4.15) catalyses the synthesis of an activated form of biotin, biotinyl-5'-AMP, from substrates biotin and ATP followed by biotinylation of the biotin carboxyl carrier protein subunit of acetyl-CoA carboxylase. The three-dimensional structure of biotin protein ligase from Pyrococcus horikoshii OT3 has been determined by X-ray diffraction at 1.6A resolution. The structure reveals a homodimer as the functional unit. Each subunit contains two domains, a larger N-terminal catalytic domain and a smaller C-terminal domain. The structural feature of the active site has been studied by determination of the crystal structures of complexes of the enzyme with biotin, ADP and the reaction intermediate biotinyl-5'-AMP at atomic resolution. This is the first report of the liganded structures of biotin protein ligase with nucleotide and biotinyl-5'-AMP. The structures of the unliganded and the liganded forms are isomorphous except for an ordering of the active site loop upon ligand binding. Catalytic binding sites are suitably arranged to minimize the conformational changes required during the reaction, as the pockets for biotin and nucleotide are located spatially adjacent to each other in a cleft of the catalytic domain and the pocket for biotinyl-5'-AMP binding mimics the combination of those of the substrates. The exact locations of the ligands and the active site residues allow us to propose a general scheme for the first step of the reaction carried out by biotin protein ligase in which the positively charged epsilon-amino group of Lys111 facilitates the nucleophilic attack on the ATP alpha-phosphate group by the biotin carboxyl oxygen atom and stabilizes the negatively charged intermediates.
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Affiliation(s)
- Bagautdin Bagautdinov
- Advanced Protein Crystallography Research Group, RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan
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Pérez-Vázquez V, Uribe S, Velázquez-Arellano A. Effects of biotin on growth and protein biotinylation in Saccharomyces cerevisiae. J Nutr Biochem 2005; 16:438-40. [PMID: 15992687 DOI: 10.1016/j.jnutbio.2005.03.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2005] [Revised: 03/30/2005] [Accepted: 03/30/2005] [Indexed: 11/27/2022]
Abstract
In mammals, biotin, well known for its role as the cofactor of carboxylases, also controls the expression not only of proteins involved in this function, but also of a large number and variety of other different proteins. As a first step towards looking for a rationale for these phenomena, we intend to compare these regulatory functions of biotin between the rat and the much less evolutionized eukaryote, Saccharomyces cerevisiae. Thus far, we have measured growth in yeast cultured on different concentrations of biotin to choose the experimental conditions to be used (2, 200 and 2000 microM) and have found that a band corresponding to the biotinylated S. cerevisiae Arc1p protein appears at streptavidin Western blots at a biotin concentration above 2000 muM, its density increasing with higher biotin amounts. We will now study changes in yeast transcriptome with these varying concentrations and compare them with changes observed in the rat.
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Affiliation(s)
- Victoriano Pérez-Vázquez
- Unidad de Genética de la Nutrición, Instituto de Investigaciones Biomédicas, UNAM, Mexico, DF 04530, Mexico.
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50
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Abstract
The Escherichia coli biotin repressor is an allosteric DNA binding protein and is activated by the small molecule bio-5'-AMP. Binding of this small molecule promotes transcription repression complex assembly between the repressor and the biotin operator of the biotin biosynthetic operon. The ability of the adenylate to activate the assembly process reflects its effect on biotin repressor dimerization. Thus concomitant with small molecule binding the free energy of repressor dimerization becomes more favorable by approximately -4 kcal/mol. The structural, dynamic, and energetic changes in the repressor monomer that accompany allosteric activation are not known. In this work the thermodynamics of binding of four allosteric activators to the repressor have been characterized by isothermal titration calorimetry. While binding of two of the effectors results in relatively modest activation of the dimerization process, binding of the other two small molecules, including the physiological effector, leads to large changes in repressor dimerization energetics. Results of the calorimetric measurements indicate that strong effector binding is accompanied by an enthalpically costly transition in the protein. This transition is "paid for" by the enthalpy that would have otherwise been realized from the formation of noncovalent bonds between the ligand and repressor monomer.
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Affiliation(s)
- Patrick H Brown
- Department of Chemistry and Biochemistry, College of Life Sciences, University of Maryland, College Park, Maryland 20742, USA
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