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Ma D, Du G, Fang H, Li R, Zhang D. Advances and prospects in microbial production of biotin. Microb Cell Fact 2024; 23:135. [PMID: 38735926 PMCID: PMC11089781 DOI: 10.1186/s12934-024-02413-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/30/2024] [Indexed: 05/14/2024] Open
Abstract
Biotin, serving as a coenzyme in carboxylation reactions, is a vital nutrient crucial for the natural growth, development, and overall well-being of both humans and animals. Consequently, biotin is widely utilized in various industries, including feed, food, and pharmaceuticals. Despite its potential advantages, the chemical synthesis of biotin for commercial production encounters environmental and safety challenges. The burgeoning field of synthetic biology now allows for the creation of microbial cell factories producing bio-based products, offering a cost-effective alternative to chemical synthesis for biotin production. This review outlines the pathway and regulatory mechanism involved in biotin biosynthesis. Then, the strategies to enhance biotin production through both traditional chemical mutagenesis and advanced metabolic engineering are discussed. Finally, the article explores the limitations and future prospects of microbial biotin production. This comprehensive review not only discusses strategies for biotin enhancement but also provides in-depth insights into systematic metabolic engineering approaches aimed at boosting biotin production.
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Affiliation(s)
- Donghan Ma
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Guangqing Du
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Huan Fang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Rong Li
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China.
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China.
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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2
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Abstract
The accurate and precise determination of binding interactions plays a central role in fields such as drug discovery where structure-activity relationships guide the selection and optimization of drug leads. Binding is often assessed by monitoring the response caused by varying one of the binding partners in a functional assay or by using methods where the concentrations of free and/or bound ligand can be directly determined. In addition, there are also many approaches where binding leads to a change in the properties of the binding partner(s) that can be directly quantified such as an alteration in mass or in a spectroscopic signal. The analysis of data resulting from these techniques invariably relies on computer software that enable rapid fitting of the data to nonlinear multiparameter equations. The objective of this Perspective is to serve as a reminder of the basic assumptions that are used in deriving these equations and thus that should be considered during assay design and subsequent data analysis. The result is a set of guidelines for authors considering submitting their work to journals such as ACS Infectious Diseases.
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Affiliation(s)
- Peter J. Tonge
- Center for Advanced Study of Drug Action, Departments of Chemistry and Radiology, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
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3
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Singh S, Khare G, Bahal RK, Ghosh PC, Tyagi AK. Identification of Mycobacterium tuberculosis BioA inhibitors by using structure-based virtual screening. DRUG DESIGN DEVELOPMENT AND THERAPY 2018; 12:1065-1079. [PMID: 29750019 PMCID: PMC5935190 DOI: 10.2147/dddt.s144240] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Background 7,8-Diaminopelargonic acid synthase (BioA), an enzyme of biotin biosynthesis pathway, is a well-known promising target for anti-tubercular drug development. Methods In this study, structure-based virtual screening was employed against the active site of BioA to identify new chemical entities for BioA inhibition and top ranking compounds were evaluated for their ability to inhibit BioA enzymatic activity. Results Seven compounds inhibited BioA enzymatic activity by greater than 60% at 100 μg/mL with most potent compounds being A36, A35 and A65, displaying IC50 values of 10.48 μg/mL (28.94 μM), 33.36 μg/mL (88.16 μM) and 39.17 μg/mL (114.42 μM), respectively. Compounds A65 and A35 inhibited Mycobacterium tuberculosis (M. tuberculosis) growth with MIC90 of 20 μg/mL and 80 μg/mL, respectively, whereas compound A36 exhibited relatively weak inhibition of M. tuberculosis growth (83% inhibition at 200 μg/mL). Compound A65 emerged as the most potent compound identified in our study that inhibited BioA enzymatic activity and growth of the pathogen and possessed drug-like properties. Conclusion Our study has identified a few hit molecules against M. tuberculosis BioA that can act as potential candidates for further development of potent anti-tubercular therapeutic agents.
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Affiliation(s)
- Swati Singh
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Garima Khare
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Ritika Kar Bahal
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Prahlad C Ghosh
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Anil K Tyagi
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India.,Guru Gobind Singh Indraprastha University, New Delhi, India
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4
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Eiden CG, Aldrich CC. Synthesis of a 3-Amino-2,3-dihydropyrid-4-one and Related Heterocyclic Analogues as Mechanism-Based Inhibitors of BioA, a Pyridoxal Phosphate-Dependent Enzyme. J Org Chem 2017; 82:7806-7819. [PMID: 28682613 DOI: 10.1021/acs.joc.7b00847] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Amiclenomycin (ACM) is a chemically unstable antibiotic with selective activity against Mycobacterium tuberculosis (Mtb) due to mechanism-based inhibition of BioA, a pyridoxal 5'-phosphate (PLP)-dependent aminotransferase. The first-generation ACM analogue dihydro-2-pyridone 1 maintains a similar bioactivation mechanism concluding with covalent labeling of the PLP cofactor. To improve on 1, we report the synthesis of dihydro-4-pyranone 2, dihydro-4-pyridone 3, and dihydro-4-thiopyranone 13, which were rationally designed to boost the rate of enzyme inactivation by lowering the pKa of their α-protons. We employed a unified synthetic strategy for construction of the desired heterocycles featuring α-amino ynone generation followed by 6-endo-dig cyclization. However, competitive 5-exo-dig cyclization, β-elimination of the ynone, and dimerization of the resultant α-amino carbonyls all complicated the syntheses of the dihydro-4-pyranone and dihydro-4-pyridone scaffolds. These obstacles were overcome by Teoc protection of the β-amino group in the assembly of 3 and Boc-MOM protection of the α-amino group in the synthesis of 2, enabling the efficient construction of 2 and 3 in seven steps from commercially available starting materials. Dihydro-4-pyridone 3 possessed improved enzyme inhibition as measured by its kinact value against BioA.
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Affiliation(s)
- Carter G Eiden
- Department of Medicinal Chemistry, University of Minnesota , 308 Harvard Street SE, 8-174 WDH, Minneapolis, Minnesota 55455, United States
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota , 308 Harvard Street SE, 8-174 WDH, Minneapolis, Minnesota 55455, United States
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5
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Liu F, Dawadi S, Maize KM, Dai R, Park SW, Schnappinger D, Finzel BC, Aldrich CC. Structure-Based Optimization of Pyridoxal 5'-Phosphate-Dependent Transaminase Enzyme (BioA) Inhibitors that Target Biotin Biosynthesis in Mycobacterium tuberculosis. J Med Chem 2017; 60:5507-5520. [PMID: 28594172 DOI: 10.1021/acs.jmedchem.7b00189] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The pyridoxal 5'-phosphate (PLP)-dependent transaminase BioA catalyzes the second step in the biosynthesis of biotin in Mycobacterium tuberculosis (Mtb) and is an essential enzyme for bacterial survival and persistence in vivo. A promising BioA inhibitor 6 containing an N-aryl, N'-benzoylpiperazine scaffold was previously identified by target-based whole-cell screening. Here, we explore the structure-activity relationships (SAR) through the design, synthesis, and biological evaluation of a systematic series of analogues of the original hit using a structure-based drug design strategy, which was enabled by cocrystallization of several analogues with BioA. To confirm target engagement and discern analogues with off-target activity, each compound was evaluated against wild-type (WT) Mtb in biotin-free and -containing medium as well as BioA under- and overexpressing Mtb strains. Conformationally constrained derivative 36 emerged as the most potent analogue with a KD of 76 nM against BioA and a minimum inhibitory concentration of 1.7 μM (0.6 μg/mL) against Mtb in biotin-free medium.
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Affiliation(s)
- Feng Liu
- Department of Medicinal Chemistry, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Surendra Dawadi
- Department of Medicinal Chemistry, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Kimberly M Maize
- Department of Medicinal Chemistry, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Ran Dai
- Department of Medicinal Chemistry, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Sae Woong Park
- Department of Microbiology and Immunology, Weill Cornell Medical College , New York, New York 10065, United States
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College , New York, New York 10065, United States
| | - Barry C Finzel
- Department of Medicinal Chemistry, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota , Minneapolis, Minnesota 55455, United States
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6
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Akgün E, Javed MI, Lunzer MM, Powers MD, Sham YY, Watanabe Y, Portoghese PS. Inhibition of Inflammatory and Neuropathic Pain by Targeting a Mu Opioid Receptor/Chemokine Receptor5 Heteromer (MOR-CCR5). J Med Chem 2015; 58:8647-57. [PMID: 26451468 DOI: 10.1021/acs.jmedchem.5b01245] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Chemokine release promotes cross-talk between opioid and chemokine receptors that in part leads to reduced efficacy of morphine in the treatment of chronic pain. On the basis of the possibility that a MOR-CCR5 heteromer is involved in such cross-talk, we have synthesized bivalent ligands (MCC series) that contain mu opioid agonist and CCR5 antagonist pharmacophores linked through homologous spacers (14-24 atoms). When tested on lipopolysaccharide-inflamed mice, a member of the series (MCC22; 3e) with a 22-atom spacer exhibited profound antinociception (i.t. ED50 = 0.0146 pmol/mouse) that was 2000× greater than morphine. Moreover, MCC22 was ~3500× more potent than a mixture of mu agonist and CCR5 antagonist monovalent ligands. These data strongly suggest that MCC22 acts by bridging the protomers of a MOR-CCR5 heteromer having a TM5,6 interface. Molecular simulation studies are consistent with such bridging. This study supports the MOR-CCR5 heteromer as a novel target for the treatment of chronic pain.
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Affiliation(s)
- Eyup Akgün
- Department of Medicinal Chemistry, and ‡Center for Drug Design, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Muhammad I Javed
- Department of Medicinal Chemistry, and ‡Center for Drug Design, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Mary M Lunzer
- Department of Medicinal Chemistry, and ‡Center for Drug Design, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Michael D Powers
- Department of Medicinal Chemistry, and ‡Center for Drug Design, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Yuk Y Sham
- Department of Medicinal Chemistry, and ‡Center for Drug Design, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Yoshikazu Watanabe
- Department of Medicinal Chemistry, and ‡Center for Drug Design, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Philip S Portoghese
- Department of Medicinal Chemistry, and ‡Center for Drug Design, University of Minnesota , Minneapolis, Minnesota 55455, United States
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7
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Dai R, Geders TW, Liu F, Park SW, Schnappinger D, Aldrich CC, Finzel BC. Fragment-based exploration of binding site flexibility in Mycobacterium tuberculosis BioA. J Med Chem 2015; 58:5208-17. [PMID: 26068403 DOI: 10.1021/acs.jmedchem.5b00092] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The PLP-dependent transaminase (BioA) of Mycobacterium tuberculosis and other pathogens that catalyzes the second step of biotin biosynthesis is a now well-validated target for antibacterial development. Fragment screening by differential scanning fluorimetry has been performed to discover new chemical scaffolds and promote optimization of existing inhibitors. Calorimetry confirms binding of six molecules with high ligand efficiency. Thermodynamic data identifies which molecules bind with the enthalpy driven stabilization preferred in compounds that represent attractive starting points for future optimization. Crystallographic characterization of complexes with these molecules reveals the dynamic nature of the BioA active site. Different side chain conformational states are stabilized in response to binding by different molecules. A detailed analysis of conformational diversity in available BioA structures is presented, resulting in the identification of two states that might be targeted with molecular scaffolds incorporating well-defined conformational attributes. This new structural data can be used as part of a scaffold hopping strategy to further optimize existing inhibitors or create new small molecules with improved therapeutic potential.
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Affiliation(s)
- Ran Dai
- †Department of Medicinal Chemistry, University of Minnesota, 8-101 Weaver-Densford, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Todd W Geders
- †Department of Medicinal Chemistry, University of Minnesota, 8-101 Weaver-Densford, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Feng Liu
- †Department of Medicinal Chemistry, University of Minnesota, 8-101 Weaver-Densford, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Sae Woong Park
- ‡Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
| | - Dirk Schnappinger
- ‡Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
| | - Courtney C Aldrich
- †Department of Medicinal Chemistry, University of Minnesota, 8-101 Weaver-Densford, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Barry C Finzel
- †Department of Medicinal Chemistry, University of Minnesota, 8-101 Weaver-Densford, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
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8
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Salaemae W, Yap MY, Wegener KL, Booker GW, Wilce MCJ, Polyak SW. Nucleotide triphosphate promiscuity in Mycobacterium tuberculosis dethiobiotin synthetase. Tuberculosis (Edinb) 2015; 95:259-66. [PMID: 25801336 DOI: 10.1016/j.tube.2015.02.046] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 02/26/2015] [Indexed: 11/29/2022]
Abstract
Dethiobiotin synthetase (DTBS) plays a crucial role in biotin biosynthesis in microorganisms, fungi, and plants. Due to its importance in bacterial pathogenesis, and the absence of a human homologue, DTBS is a promising target for the development of new antibacterials desperately needed to combat antibiotic resistance. Here we report the first X-ray structure of DTBS from Mycobacterium tuberculosis (MtDTBS) bound to a nucleotide triphosphate (CTP). The nucleoside base is stabilized in its pocket through hydrogen-bonding interactions with the protein backbone, rather than amino acid side chains. This resulted in the unexpected finding that MtDTBS could utilise ATP, CTP, GTP, ITP, TTP, or UTP with similar Km and kcat values, although the enzyme had the highest affinity for CTP in competitive binding and surface plasmon resonance assays. This is in contrast to other DTBS homologues that preferentially bind ATP primarily through hydrogen-bonds between the purine base and the carboxamide side chain of a key asparagine. Mutational analysis performed alongside in silico experiments revealed a gate-keeper role for Asn175 in Escherichia coli DTBS that excludes binding of other nucleotide triphosphates. Here we provide evidence to show that MtDTBS has a broad nucleotide specificity due to the absence of the gate-keeper residue.
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Affiliation(s)
- Wanisa Salaemae
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Min Y Yap
- Department of Biochemistry and Molecular Biology, School of Biomedical Science, Monash University, Victoria, 3800, Australia
| | - Kate L Wegener
- 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
| | - Matthew C J Wilce
- Department of Biochemistry and Molecular Biology, School of Biomedical Science, Monash University, Victoria, 3800, Australia
| | - Steven W Polyak
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia.
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9
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Park SW, Casalena DE, Wilson DJ, Dai R, Nag PP, Liu F, Boyce JP, Bittker JA, Schreiber SL, Finzel BC, Schnappinger D, Aldrich CC. Target-based identification of whole-cell active inhibitors of biotin biosynthesis in Mycobacterium tuberculosis. CHEMISTRY & BIOLOGY 2015; 22:76-86. [PMID: 25556942 PMCID: PMC4305006 DOI: 10.1016/j.chembiol.2014.11.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/29/2014] [Accepted: 11/18/2014] [Indexed: 12/31/2022]
Abstract
Biotin biosynthesis is essential for survival and persistence of Mycobacterium tuberculosis (Mtb) in vivo. The aminotransferase BioA, which catalyzes the antepenultimate step in the biotin pathway, has been established as a promising target due to its vulnerability to chemical inhibition. We performed high-throughput screening (HTS) employing a fluorescence displacement assay and identified a diverse set of potent inhibitors including many diversity-oriented synthesis (DOS) scaffolds. To efficiently select only hits targeting biotin biosynthesis, we then deployed a whole-cell counterscreen in biotin-free and biotin-containing medium against wild-type Mtb and in parallel with isogenic bioA Mtb strains that possess differential levels of BioA expression. This counterscreen proved crucial to filter out compounds whose whole-cell activity was off target as well as identify hits with weak, but measurable whole-cell activity in BioA-depleted strains. Several of the most promising hits were cocrystallized with BioA to provide a framework for future structure-based drug design efforts.
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Affiliation(s)
- Sae Woong Park
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA
| | | | - Daniel J Wilson
- Center for Drug Design, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ran Dai
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Partha P Nag
- The Broad Institute Probe Development Center, Cambridge, MA 02142, USA
| | - Feng Liu
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jim P Boyce
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-6604, USA
| | - Joshua A Bittker
- The Broad Institute Probe Development Center, Cambridge, MA 02142, USA
| | | | - Barry C Finzel
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA.
| | - Courtney C Aldrich
- Center for Drug Design, University of Minnesota, Minneapolis, MN 55455, USA; Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
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10
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Šenica L, Grošelj U, Kasunič M, Kočar D, Stanovnik B, Svete J. Synthesis of Enaminone-Based Vinylogous Peptides. European J Org Chem 2014. [DOI: 10.1002/ejoc.201402033] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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11
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Dai R, Wilson DJ, Geders TW, Aldrich CC, Finzel BC. Inhibition of Mycobacterium tuberculosis transaminase BioA by aryl hydrazines and hydrazides. Chembiochem 2014; 15:575-86. [PMID: 24482078 PMCID: PMC4020011 DOI: 10.1002/cbic.201300748] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Indexed: 01/22/2023]
Abstract
7,8-Diaminopelargonic acid synthase (BioA) of Mycobacterium tuberculosis is a recently validated target for therapeutic intervention in the treatment of tuberculosis (TB). Using biophysical fragment screening and structural characterization of compounds, we have identified a potent aryl hydrazine inhibitor of BioA that reversibly modifies the pyridoxal-5'-phosphate (PLP) cofactor, forming a stable quinonoid. Analogous hydrazides also form covalent adducts that can be observed crystallographically but are incapable of inactivating the enzyme. In the X-ray crystal structures, small molecules induce unexpected conformational remodeling in the substrate binding site. We compared these conformational changes to those induced upon binding of the substrate (7-keto-8-aminopelargonic acid), and characterized the inhibition kinetics and the X-ray crystal structures of BioA with the hydrazine compound and analogues to unveil the mechanism of this reversible covalent modification.
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Affiliation(s)
- Ran Dai
- Department of Medicinal Chemistry University of Minnesota 308 Harvard St. SE, Minneapolis, MN 55455, United States
| | - Daniel J. Wilson
- Center for Drug Design University of Minnesota Academic Health Center, U of Minnesota, MN, 55455, United States
| | - Todd W. Geders
- Department of Medicinal Chemistry University of Minnesota 308 Harvard St. SE, Minneapolis, MN 55455, United States
| | - Courtney C. Aldrich
- Department of Medicinal Chemistry University of Minnesota 308 Harvard St. SE, Minneapolis, MN 55455, United States
| | - Barry C. Finzel
- Department of Medicinal Chemistry University of Minnesota 308 Harvard St. SE, Minneapolis, MN 55455, United States
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12
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Mann S, Eveleigh L, Lequin O, Ploux O. A microplate fluorescence assay for DAPA aminotransferase by detection of the vicinal diamine 7,8-diaminopelargonic acid. Anal Biochem 2013; 432:90-6. [DOI: 10.1016/j.ab.2012.09.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2012] [Revised: 09/26/2012] [Accepted: 09/29/2012] [Indexed: 10/27/2022]
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13
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Shi C, Aldrich CC. Design and synthesis of potential mechanism-based inhibitors of the aminotransferase BioA involved in biotin biosynthesis. J Org Chem 2012; 77:6051-8. [PMID: 22724679 DOI: 10.1021/jo3008435] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BioA, a pyridoxal 5'-phosphate (PLP) dependent aminotransferase, catalyzes the second step of biotin biosynthesis, converting 7-keto-8-aminopelargonic acid (KAPA) into 7,8-diaminopelargonic acid (DAPA). Amiclenomycin (ACM) isolated from cultures of different Streptomyces strains is a potent mechanism-based inhibitor of BioA that operates via an aromatization mechanism, irreversibly labeling the PLP cofactor. However, ACM is plagued by inherent chemical stability. Herein we describe the synthesis of four inhibitors, inspired by ACM but containing an allylic amine as the chemical warhead, designed to both improve stability and operate via a complementary Michael addition-pathway upon enzymatic oxidation of the allylic amine substrate to an enimine. Acyclic analogue M-1 contains a terminal olefin as the pro-Michael acceptor. The synthesis of M-1 features an alkyne-zipper reaction and the Overman rearrangement as key synthetic operations. The cyclic analogues M-2/3/4 contain either an endocyclic or exocyclic olefin as the pro-Michael acceptor. These were all prepared using a common strategy employing DIBAL reduction of a precursor bicyclic lactam, followed by in situ Horner-Wadsworth-Emmons (HWE) olefination as the key synthetic steps.
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Affiliation(s)
- Ce Shi
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
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14
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Geders TW, Gustafson K, Finzel BC. Use of differential scanning fluorimetry to optimize the purification and crystallization of PLP-dependent enzymes. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:596-600. [PMID: 22691796 PMCID: PMC3374521 DOI: 10.1107/s1744309112012912] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 03/24/2012] [Indexed: 11/10/2022]
Abstract
Differential scanning fluorimetry (DSF) is a practical and accessible technique that allows the assessment of multiphasic unfolding behavior resulting from subsaturating binding of ligands. Multiphasic unfolding is indicative of a heterogenous protein solution, which frequently interferes with crystallization and complicates functional characterization of proteins of interest. Along with UV-Vis spectroscopy, DSF was used to guide purification and crystallization improvements for the pyridoxal 5'-phosphate (PLP) dependent transaminase BioA from Mycobacterium tuberculosis. The incompatibility of the primary amine-containing buffer 2-amino-2-(hydroxymethyl)-1,3-propanediol (Tris) and PLP was identified as a significant contributor to heterogeneity. It is likely that the utility of DSF for ligand-binding assessment is not limited to the cofactor PLP but will be applicable to a variety of ligand-dependent enzymes.
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Affiliation(s)
- Todd W. Geders
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kathryn Gustafson
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Barry C. Finzel
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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15
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Shi C, Geders TW, Park SW, Wilson DJ, Boshoff HI, Orisadipe A, Barry CE, Schnappinger D, Finzel BC, Aldrich CC. Mechanism-based inactivation by aromatization of the transaminase BioA involved in biotin biosynthesis in Mycobaterium tuberculosis. J Am Chem Soc 2011; 133:18194-201. [PMID: 21988601 PMCID: PMC3222238 DOI: 10.1021/ja204036t] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
BioA catalyzes the second step of biotin biosynthesis, and this enzyme represents a potential target to develop new antitubercular agents. Herein we report the design, synthesis, and biochemical characterization of a mechanism-based inhibitor (1) featuring a 3,6-dihydropyrid-2-one heterocycle that covalently modifies the pyridoxal 5'-phosphate (PLP) cofactor of BioA through aromatization. The structure of the PLP adduct was confirmed by MS/MS and X-ray crystallography at 1.94 Å resolution. Inactivation of BioA by 1 was time- and concentration-dependent and protected by substrate. We used a conditional knock-down mutant of M. tuberculosis to demonstrate the antitubercular activity of 1 correlated with BioA expression, and these results provide support for the designed mechanism of action.
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Affiliation(s)
- Ce Shi
- Center for Drug Design, Academic Health Center, University of Minnesota, MN, 55455, United States
| | - Todd W. Geders
- Department of Medicinal Chemistry, University of Minnesota, MN, 55455, United States
| | - Sae Woong Park
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, United States
| | - Daniel J. Wilson
- Center for Drug Design, Academic Health Center, University of Minnesota, MN, 55455, United States
| | - Helena I. Boshoff
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, United States
| | - Abayomi Orisadipe
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, United States
| | - Clifton E. Barry
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, United States
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, United States
| | - Barry C. Finzel
- Department of Medicinal Chemistry, University of Minnesota, MN, 55455, United States
| | - Courtney C. Aldrich
- Center for Drug Design, Academic Health Center, University of Minnesota, MN, 55455, United States
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Woong Park S, Klotzsche M, Wilson DJ, Boshoff HI, Eoh H, Manjunatha U, Blumenthal A, Rhee K, Barry CE, Aldrich CC, Ehrt S, Schnappinger D. Evaluating the sensitivity of Mycobacterium tuberculosis to biotin deprivation using regulated gene expression. PLoS Pathog 2011; 7:e1002264. [PMID: 21980288 PMCID: PMC3182931 DOI: 10.1371/journal.ppat.1002264] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2011] [Accepted: 07/28/2011] [Indexed: 12/04/2022] Open
Abstract
In the search for new drug targets, we evaluated the biotin synthetic pathway of Mycobacterium tuberculosis (Mtb) and constructed an Mtb mutant lacking the biotin biosynthetic enzyme 7,8-diaminopelargonic acid synthase, BioA. In biotin-free synthetic media, ΔbioA did not produce wild-type levels of biotinylated proteins, and therefore did not grow and lost viability. ΔbioA was also unable to establish infection in mice. Conditionally-regulated knockdown strains of Mtb similarly exhibited impaired bacterial growth and viability in vitro and in mice, irrespective of the timing of transcriptional silencing. Biochemical studies further showed that BioA activity has to be reduced by approximately 99% to prevent growth. These studies thus establish that de novo biotin synthesis is essential for Mtb to establish and maintain a chronic infection in a murine model of TB. Moreover, these studies provide an experimental strategy to systematically rank the in vivo value of potential drug targets in Mtb and other pathogens. We evaluated the biotin synthetic pathway of Mycobacterium tuberculosis (Mtb) as a new drug target by first generating an Mtb deletion mutant, ΔbioA, in which the biotin biosynthetic enzyme 7,8-diaminopelargonic acid synthase (BioA) has been inactivated. This mutant grew in the presence of biotin or des-thiobiotin, but not with an intermediate of the biotin biosynthesis pathway that requires BioA to be converted into biotin. Without exogenous biotin or des-thiobiotin, ΔbioA, was unable to produce biotinylated proteins, which are required for the biosynthesis of fatty acids, and thus died in biotin-free media. Using a regulatable promoter and different ribosome binding sequences we next constructed tightly controlled TetON mutants, in which expression of BioA could be induced with tetracyclines, but was inhibited in their absence. Characterization of these mutants during infections demonstrated that de novo biotin synthesis is not only required to establish infections but also to maintain bacterial persistence. Inhibition of BioA or other enzymes of the biotin biosynthesis pathways could thus be used to kill Mtb during both acute and chronic infections. Biochemical and immunological analyses of different Mtb mutants indicate that drugs targeting BioA would have to inactive approximately 99% of its activity to be effective.
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Affiliation(s)
- Sae Woong Park
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Marcus Klotzsche
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Daniel J. Wilson
- Center for Drug Design, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Helena I. Boshoff
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Hyungjin Eoh
- Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | | | - Antje Blumenthal
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Kyu Rhee
- Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Clifton E. Barry
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Courtney C. Aldrich
- Center for Drug Design, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
- * E-mail: (SE); (DS)
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
- * E-mail: (SE); (DS)
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