1
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Muduli S, Karmakar S, Mishra S. The coordinated action of the enzymes in the L-lysine biosynthetic pathway and how to inhibit it for antibiotic targets. Biochim Biophys Acta Gen Subj 2023; 1867:130320. [PMID: 36813209 DOI: 10.1016/j.bbagen.2023.130320] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 01/19/2023] [Accepted: 02/02/2023] [Indexed: 02/22/2023]
Abstract
BACKGROUND Antimicrobial resistance is a global health issue that requires immediate attention in terms of new antibiotics and new antibiotic targets. The l-lysine biosynthesis pathway (LBP) is a promising avenue for drug discovery as it is essential for bacterial growth and survival and is not required by human beings. SCOPE OF REVIEW The LBP involves a coordinated action of fourteen different enzymes distributed over four distinct sub-pathways. The enzymes involved in this pathway belong to different classes, such as aspartokinase, dehydrogenase, aminotransferase, epimerase, etc. This review provides a comprehensive account of the secondary and tertiary structure, conformational dynamics, active site architecture, mechanism of catalytic action, and inhibitors of all enzymes involved in LBP of different bacterial species. MAJOR CONCLUSIONS LBP offers a wide scope for novel antibiotic targets. The enzymology of a majority of the LBP enzymes is well understood, although these enzymes are less widely studied in the critical pathogens (according to the 2017 WHO report) that require immediate attention. In particular, the enzymes in the acetylase pathway, DapAT, DapDH, and Aspartokinase in critical pathogens have received little attention. High throughput screening for inhibitor design against the enzymes of lysine biosynthetic pathway is rather limited, both in number and in the extent of success. GENERAL SIGNIFICANCE This review can serve as a guide for the enzymology of LBP and help in identifying new drug targets and designing potential inhibitors.
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Affiliation(s)
- Sunita Muduli
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Soumyajit Karmakar
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Sabyashachi Mishra
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India.
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2
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Chooback L, Thomas LN, Blythe N, Karsten W. Kinetic and structural studies of the reaction of Escherichia coli dihydrodipicolinate synthase with ( S)-2-bromopropionate. Acta Crystallogr D Struct Biol 2022; 78:846-852. [DOI: 10.1107/s2059798322005125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/12/2022] [Indexed: 11/10/2022] Open
Abstract
Dihydrodipicolinate synthase (DHDPS) catalyzes the first committed step in the lysine-biosynthetic pathway converting pyruvate and L-aspartate-β-semialdehyde to dihydrodipicolinate. Kinetic studies indicate that the pyruvate analog (S)-2-bromopropionate inactivates the enzyme in a pseudo-first-order process. An initial velocity pattern indicates that (S)-2-bromopropionate is a competitive inhibitor versus pyruvate, with an inhibition constant of about 8 mM. Crystals of DHDPS complexed with (S)-2-bromopropionate formed in a solution consisting of 50 mM HEPES pH 7.5, 18% polyethylene glycol 3350, 8 mM spermidine, 0.2 M sodium tartrate and 5.0 mg ml−1 DHDPS. The crystals diffracted to 2.15 Å resolution and belonged to space group P1. The crystal structure confirms the displacement of bromine and the formation of a covalent attachment between propionate and Lys161 at the active site of the enzyme. Lys161 is the active-site nucleophile that attacks the carbonyl C atom of pyruvate and subsequently generates an imine adduct in the first half-reaction of the ping-pong enzymatic reaction. A comparison of the crystal structures of DHDPS complexed with pyruvate or (S)-2-bromopropionate indicates the covalent adduct formed from (S)-2-bromopropionate leads to a rotation of about 180° of the β–δ C atoms of Lys61 that aligns the covalently bound propionate fairly closely with the imine adduct formed with pyruvate.
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3
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Diaminopimelic acid and its analogues: Synthesis and biological perspective. Tetrahedron 2021. [DOI: 10.1016/j.tet.2021.132403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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4
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Lloyd MD, Yevglevskis M, Nathubhai A, James TD, Threadgill MD, Woodman TJ. Racemases and epimerases operating through a 1,1-proton transfer mechanism: reactivity, mechanism and inhibition. Chem Soc Rev 2021; 50:5952-5984. [PMID: 34027955 PMCID: PMC8142540 DOI: 10.1039/d0cs00540a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Indexed: 12/12/2022]
Abstract
Racemases and epimerases catalyse changes in the stereochemical configurations of chiral centres and are of interest as model enzymes and as biotechnological tools. They also occupy pivotal positions within metabolic pathways and, hence, many of them are important drug targets. This review summarises the catalytic mechanisms of PLP-dependent, enolase family and cofactor-independent racemases and epimerases operating by a deprotonation/reprotonation (1,1-proton transfer) mechanism and methods for measuring their catalytic activity. Strategies for inhibiting these enzymes are reviewed, as are specific examples of inhibitors. Rational design of inhibitors based on substrates has been extensively explored but there is considerable scope for development of transition-state mimics and covalent inhibitors and for the identification of inhibitors by high-throughput, fragment and virtual screening approaches. The increasing availability of enzyme structures obtained using X-ray crystallography will facilitate development of inhibitors by rational design and fragment screening, whilst protein models will facilitate development of transition-state mimics.
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Affiliation(s)
- Matthew D Lloyd
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK.
| | - Maksims Yevglevskis
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK. and CatSci Ltd., CBTC2, Capital Business Park, Wentloog, Cardiff CF3 2PX, UK
| | - Amit Nathubhai
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK. and University of Sunderland, School of Pharmacy & Pharmaceutical Sciences, Sciences Complex, Sunderland SR1 3SD, UK
| | - Tony D James
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK and School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, People's Republic of China
| | - Michael D Threadgill
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK. and Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Aberystwyth SY23 3BY, UK
| | - Timothy J Woodman
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK.
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5
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Karsten W, Thomas LM, Fleming C, Seabourn P, Bruxvoort C, Chooback L. Kinetic, spectral, and structural studies of the slow-binding inhibition of the Escherichia coli dihydrodipicolinate synthase by 2, 4-oxo-pentanoic acid. Arch Biochem Biophys 2021; 702:108819. [PMID: 33639104 PMCID: PMC8592399 DOI: 10.1016/j.abb.2021.108819] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 01/09/2023]
Abstract
Dihydrodipicolinate synthase (DHDPS) catalyzes the first step in the biosynthetic pathway for production of l-lysine in bacteria and plants. The enzyme has received interest as a potential drug target owing to the absence of the enzyme in mammals. The DHDPS reaction is the rate limiting step in lysine biosynthesis and involves the condensation of l-aspartate-β-semialdehyde and pyruvate to form 2, 3-dihydrodipicolinate. 2, 4-oxo-pentanoic acid (acetopyruvate) is a slow-binding inhibitor of DHDPS that is competitive versus pyruvate with an initial Ki of about 20 μM and a final inhibition constant of about 1.4 μM. The enzyme:acetopyruvate complex displays an absorbance spectrum with a λmax at 304 nm and a longer wavelength shoulder. The rate constant for formation of the complex is 86 M-1 s-1. The enzyme forms a covalent enamine complex with the first substrate pyruvate and can be observed spectrally with a λmax at 271 nm. The spectra of the enzyme in the presence of pyruvate and acetopyruvate shows the initial formation of the pyruvate enamine intermediate followed by the slower appearance of the E:acetopyruvate spectra with a rate constant of about 0.013 s-1. The spectral studies suggest the formation of a Schiff base between acetopyruvate and K161 on enzyme that subsequently deprotonates to form a resonance stabilized anion similar to the enamine intermediate formed with pyruvate. The crystal structure of the E:acetopyruvate complex confirms the formation of the Schiff base between acetopyruvate and K161.
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Affiliation(s)
- William Karsten
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Pkwy, Norman, OK 73019
| | - Leonard M. Thomas
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Pkwy, Norman, OK 73019
| | - Christian Fleming
- Department of Chemistry, University of Central Oklahoma, 100 North University Drive, Edmond, OK 73034
| | - Priscilla Seabourn
- Department of Chemistry, University of Central Oklahoma, 100 North University Drive, Edmond, OK 73034
| | - Christina Bruxvoort
- Department of Chemistry, University of Central Oklahoma, 100 North University Drive, Edmond, OK 73034,To whom correspondence should be addressed: Dr. Lilian Chooback, Department of Chemistry, University of Central Oklahoma, 100 North University Drive, Edmond, OK 73034, Telephone: (405) 974-5481; FAX:(405) 974-3862; E-mail:
| | - Lilian Chooback
- Department of Chemistry, University of Central Oklahoma, 100 North University Drive, Edmond, OK 73034
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6
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Fischer C, Ahn YC, Vederas JC. Catalytic mechanism and properties of pyridoxal 5'-phosphate independent racemases: how enzymes alter mismatched acidity and basicity. Nat Prod Rep 2020; 36:1687-1705. [PMID: 30994146 DOI: 10.1039/c9np00017h] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covering: up to March 2019 Amino acid racemases and epimerases are key enzymes that invert the configuration of common amino acids and supply many corresponding d-isomers in living organisms. Some d-amino acids are inherently bioactive, whereas others are building blocks for important biomolecules, for example lipid II, the bacterial cell wall precursor. Peptides containing them have enhanced proteolytic stability and can act as important recognition elements in mammalian systems. Selective inhibition of certain amino acid racemases (e.g. glutamate racemase) is believed to offer a promising target for new antibacterial drugs effective against pathogens resistant to current antibiotics. Many amino acid racemases employ imine formation with pyridoxal phosphate (PLP) as a cofactor to accelerate the abstraction of the alpha proton. However, the group reviewed herein achieves racemization of free amino acids without the use of cofactors or metals, and uses a thiol/thiolate pair for deprotonation and reprotonation. All bacteria and higher plants contain such enzymes, for example diaminopimelate epimerase, which is required for lysine biosynthesis in these organisms. This process cannot be accomplished without an enzyme catalyst as the acidities of a thiol and the substrate α-hydrogen are inherently mismatched by at least 10 orders of magnitude. This review describes the structural and mechanistic studies on PLP-independent racemases and the evolving view of key enzymatic machinery that accomplishes these remarkable transformations.
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Affiliation(s)
- Conrad Fischer
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, Canada T6G 2G2.
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7
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Usman M, Zhang XW, Wu D, Guan ZH, Liu WB. Application of dialkyl azodicarboxylate frameworks featuring multi-functional properties. Org Chem Front 2019. [DOI: 10.1039/c9qo00017h] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The application of dialkyl azodicarboxylates as versatile reagents in Mitsunobu, oxidation, electrophilic, amination and carbonylation reactions is reviewed.
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Affiliation(s)
- Muhammad Usman
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education
- Department of Chemistry & Materials Science
- Northwest University
- Xi'an 710127
- Shaanxi, China
| | - Xiao-Wen Zhang
- Engineering Research Center of Organosilicon Compounds & Materials
- Ministry of Education
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072
| | - Di Wu
- Engineering Research Center of Organosilicon Compounds & Materials
- Ministry of Education
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072
| | - Zheng-Hui Guan
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education
- Department of Chemistry & Materials Science
- Northwest University
- Xi'an 710127
- Shaanxi, China
| | - Wen-Bo Liu
- Engineering Research Center of Organosilicon Compounds & Materials
- Ministry of Education
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072
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8
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Wang H, Kellogg GE, Xu P, Zhang Y. Exploring the binding mechanisms of diaminopimelic acid analogs to meso-diaminopimelate dehydrogenase by molecular modeling. J Mol Graph Model 2018; 83:100-111. [PMID: 29885593 DOI: 10.1016/j.jmgm.2018.05.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/30/2018] [Accepted: 05/30/2018] [Indexed: 01/30/2023]
Abstract
Meso-Diaminopimelic acid (meso-2,6-diamino-heptanedioic acid, DAP) is an important component of the cell wall of many bacteria. Meso-diaminopimelate dehydrogenase (m-Ddh) is a critical enzyme in the process of converting tetrahydrodipicolinate to DAP. Here, we are proposing that DAP analogs targeting m-Ddh may be considered as potential antibiotics. Four DAP analogs without significant structural change from DAP have been obtained and their inhibitory potencies against m-Ddh from the P. gingivalis strain W83 show significant differences from that of DAP. However, their inhibitory mechanisms as for how simple structural change influences the inhibitory potency remain unknown. Therefore, we employed molecular modeling methods to obtain insight into the inhibitory mechanisms of DAP and analogs with m-Ddh. The predicted binding mode of DAP was highly consistent with the experimental structural data and disclosed the important roles played by the binding pocket residues. According to our predictions, the isoxazoline ring of compounds 1 and 2 and the double bonds in compounds 3 and 4 had distinct influences on these compounds' binding to m-Ddh. This enriched understanding of the inhibitory mechanisms of DAP and these four analogs to m-Ddh has provided new and relevant information for future rational development of potent inhibitors targeting m-Ddh.
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Affiliation(s)
- Huiqun Wang
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA
| | - Glen E Kellogg
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA
| | - Ping Xu
- VCU Philips Institute, Virginia Commonwealth University, Richmond, VA, USA; Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA; Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - Yan Zhang
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA.
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9
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Ma H, Stone VN, Wang H, Kellogg GE, Xu P, Zhang Y. Diaminopimelic acid (DAP) analogs bearing isoxazoline moiety as selective inhibitors against meso-diaminopimelate dehydrogenase (m-Ddh) from Porphyromonas gingivalis. Bioorg Med Chem Lett 2017; 27:3840-3844. [PMID: 28668193 PMCID: PMC5546221 DOI: 10.1016/j.bmcl.2017.06.056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 06/19/2017] [Accepted: 06/21/2017] [Indexed: 11/18/2022]
Abstract
Two diastereomeric analogs (1 and 2) of diaminopimelic acid (DAP) bearing an isoxazoline moiety were synthesized and evaluated for their inhibitory activities against meso-diaminopimelate dehydrogenase (m-Ddh) from the periodontal pathogen, Porphyromonas gingivalis. Compound 2 showed promising inhibitory activity against m-Ddh with an IC50 value of 14.9µM at pH 7.8. The two compounds were further tested for their antibacterial activities against a panel of periodontal pathogens, and compound 2 was shown to be selectively potent to P. gingivalis strains W83 and ATCC 33277 with minimum inhibitory concentration (MIC) values of 773µM and 1.875mM, respectively. Molecular modeling studies revealed that the inversion of chirality at the C-5 position of these compounds was the primary reason for their different biological profiles. Based on these preliminary results, we believe that compound 2 has properties consistent with it being a lead compound for developing novel pathogen selective antibiotics to treat periodontal diseases.
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Affiliation(s)
- Hongguang Ma
- Department of Medicinal Chemistry, Virginia Commonwealth University, 800 East Leigh Street, Richmond, VA 23298, USA
| | - Victoria N Stone
- Philips Institute for Oral Health Research, Virginia Commonwealth University, 521 North 11th Street, Richmond, VA 23298, USA; Department of Microbiology and Immunology, Virginia Commonwealth University, 1101 East Marshall Street, Richmond, VA 23298, USA
| | - Huiqun Wang
- Department of Medicinal Chemistry, Virginia Commonwealth University, 800 East Leigh Street, Richmond, VA 23298, USA
| | - Glen E Kellogg
- Department of Medicinal Chemistry, Virginia Commonwealth University, 800 East Leigh Street, Richmond, VA 23298, USA; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, 800 East Leigh Street, Richmond, VA 23298, USA
| | - Ping Xu
- Philips Institute for Oral Health Research, Virginia Commonwealth University, 521 North 11th Street, Richmond, VA 23298, USA; Department of Microbiology and Immunology, Virginia Commonwealth University, 1101 East Marshall Street, Richmond, VA 23298, USA
| | - Yan Zhang
- Department of Medicinal Chemistry, Virginia Commonwealth University, 800 East Leigh Street, Richmond, VA 23298, USA.
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10
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Liu Y, Frirdich E, Taylor JA, Chan ACK, Blair KM, Vermeulen J, Ha R, Murphy MEP, Salama NR, Gaynor EC, Tanner ME. A Bacterial Cell Shape-Determining Inhibitor. ACS Chem Biol 2016; 11:981-91. [PMID: 26735022 DOI: 10.1021/acschembio.5b01039] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Helicobacter pylori and Campylobacter jejuni are human pathogens and causative agents of gastric ulcers/cancer and gastroenteritis, respectively. Recent studies have uncovered a series of proteases that are responsible for maintaining the helical shape of these organisms. The H. pylori metalloprotease Csd4 and its C. jejuni homologue Pgp1 cleave the amide bond between meso-diaminopimelate and iso-d-glutamic acid in truncated peptidoglycan side chains. Deletion of either csd4 or pgp1 results in bacteria with a straight rod phenotype, a reduced ability to move in viscous media, and reduced pathogenicity. In this work, a phosphinic acid-based pseudodipeptide inhibitor was designed to act as a tetrahedral intermediate analog against the Csd4 enzyme. The phosphinic acid was shown to inhibit the cleavage of the alternate substrate, Ac-l-Ala-iso-d-Glu-meso-Dap, with a Ki value of 1.5 μM. Structural analysis of the Csd4-inhibitor complex shows that the phosphinic acid displaces the zinc-bound water and chelates the metal in a bidentate fashion. The phosphinate oxygens also interact with the key acid/base residue, Glu222, and the oxyanion-stabilizing residue, Arg86. The results are consistent with the "promoted-water pathway" mechanism for carboxypeptidase A catalysis. Studies on cultured bacteria showed that the inhibitor causes significant cell straightening when incubated with H. pylori at millimolar concentrations. A diminished, yet observable, effect on the morphology of C. jejuni was also apparent. Cell straightening was more pronounced with an acapsular C. jejuni mutant strain compared to the wild type, suggesting that the capsule impaired inhibitor accessibility. These studies demonstrate that a highly polar compound is capable of crossing the outer membrane and altering cell shape, presumably by inhibiting cell shape determinant proteases. Peptidoglycan proteases acting as cell shape determinants represent novel targets for the development of antimicrobials against these human pathogens.
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Affiliation(s)
- Yanjie Liu
- Contribution
from the Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Emilisa Frirdich
- Department
of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Jennifer A. Taylor
- Division
of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
- Department
of Microbiology, University of Washington School of Medicine, Seattle, Washington 98195, United States
| | - Anson C. K. Chan
- Department
of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Kris M. Blair
- Division
of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
- Program
in Molecular and Cellular Biology, University of Washington, Seattle, Washington 98195, United States
| | - Jenny Vermeulen
- Department
of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Reuben Ha
- Department
of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Michael E. P. Murphy
- Department
of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Nina R. Salama
- Division
of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
- Department
of Microbiology, University of Washington School of Medicine, Seattle, Washington 98195, United States
- Program
in Molecular and Cellular Biology, University of Washington, Seattle, Washington 98195, United States
| | - Erin C. Gaynor
- Department
of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Martin E. Tanner
- Contribution
from the Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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11
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Martínez-Muñoz A, Monge D, Martín-Zamora E, Marqués-López E, Álvarez E, Fernández R, Lassaletta JM. Asymmetric organocatalytic Strecker-type reactions of aliphatic N,N-dialkylhydrazones. Org Biomol Chem 2013; 11:8247-55. [DOI: 10.1039/c3ob41437j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Conti P, Tamborini L, Pinto A, Blondel A, Minoprio P, Mozzarelli A, De Micheli C. Drug Discovery Targeting Amino Acid Racemases. Chem Rev 2011; 111:6919-46. [DOI: 10.1021/cr2000702] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Paola Conti
- Dipartimento di Scienze Farmaceutiche “P. Pratesi”, via Mangiagalli 25, 20133 Milano, Italy
| | - Lucia Tamborini
- Dipartimento di Scienze Farmaceutiche “P. Pratesi”, via Mangiagalli 25, 20133 Milano, Italy
| | - Andrea Pinto
- Dipartimento di Scienze Farmaceutiche “P. Pratesi”, via Mangiagalli 25, 20133 Milano, Italy
| | - Arnaud Blondel
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS-URA 2185, Département de Biologie Structurale et Chimie, 25 rue du Dr. Roux, 75724 Paris, France
| | - Paola Minoprio
- Institut Pasteur, Laboratoire des Processus Infectieux à Trypanosoma; Département d’Infection et Epidémiologie; 25 rue du Dr. Roux, 75724 Paris, France
| | - Andrea Mozzarelli
- Dipartimento di Biochimica e Biologia Molecolare, via G. P. Usberti 23/A, 43100 Parma, Italy
- Istituto di Biostrutture e Biosistemi, viale Medaglie d’oro, Roma, Italy
| | - Carlo De Micheli
- Dipartimento di Scienze Farmaceutiche “P. Pratesi”, via Mangiagalli 25, 20133 Milano, Italy
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13
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Gehmayr V, Mollay C, Reith L, Müller N, Jilek A. Tight binding of transition-state analogues to a peptidyl-aminoacyl-L/D-isomerase from frog skin. Chembiochem 2011; 12:1996-2000. [PMID: 21739559 PMCID: PMC3195878 DOI: 10.1002/cbic.201100203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Indexed: 11/30/2022]
Affiliation(s)
- Verena Gehmayr
- Institute of Organic Chemistry, Johannes Kepler University LinzAltenberger Strasse 69, 4040 Linz (Austria)
| | - Christa Mollay
- Institute of Molecular Biology, Austrian Academy of SciencesBillrothstrasse 11, 5020 Salzburg (Austria)
| | - Lorenz Reith
- Institute of Organic Chemistry, Johannes Kepler University LinzAltenberger Strasse 69, 4040 Linz (Austria)
| | - Norbert Müller
- Institute of Organic Chemistry, Johannes Kepler University LinzAltenberger Strasse 69, 4040 Linz (Austria)
| | - Alexander Jilek
- Chair of Bioinformatics, Department of Biotechnology, University of Natural Resources and Life SciencesMuthgasse 18, 1190 Vienna (Austria)
- Institute of Organic Chemistry, Johannes Kepler University LinzAltenberger Strasse 69, 4040 Linz (Austria)
- Institute of Molecular Biology, Austrian Academy of SciencesBillrothstrasse 11, 5020 Salzburg (Austria)
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14
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Dobson RCJ, Girón I, Hudson AO. L,L-diaminopimelate aminotransferase from Chlamydomonas reinhardtii: a target for algaecide development. PLoS One 2011; 6:e20439. [PMID: 21633707 PMCID: PMC3102117 DOI: 10.1371/journal.pone.0020439] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 04/29/2011] [Indexed: 11/21/2022] Open
Abstract
In some bacterial species and photosynthetic cohorts, including algae, the enzyme
l,l-diaminopimelate aminotransferase
(DapL) (E.C. 2.6.1.83) is involved in the anabolism of the essential amino acid
L-lysine. DapL catalyzes the conversion of
tetrahydrodipicolinate (THDPA) to
l,l-diaminopimelate
(l,l-DAP), in one step bypassing the
DapD, DapC and DapE enzymatic reactions present in the acyl DAP pathways. Here
we present an in vivo and in vitro
characterization of the DapL ortholog from the alga Chlamydomonas
reinhardtii (Cr-DapL). The in
vivo analysis illustrated that the enzyme is able to functionally
complement the E. coli dap auxotrophs and was essential for
plant development in Arabidopsis. In vitro, the enzyme was able
to inter-convert THDPA and l,l-DAP, showing
strong substrate specificity. Cr-DapL was dimeric in both
solution and when crystallized. The structure of Cr-DapL was
solved in its apo form, showing an overall architecture of a
α/β protein with each monomer in the dimer adopting a pyridoxal
phosphate-dependent transferase-like fold in a V-shaped conformation. The active
site comprises residues from both monomers in the dimer and shows some
rearrangement when compared to the apo-DapL structure from
Arabidopsis. Since animals do not possess the enzymatic machinery necessary for
the de novo synthesis of the amino acid
l-lysine, enzymes involved in this pathway are
attractive targets for the development of antibiotics, herbicides and
algaecides.
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Affiliation(s)
- Renwick C. J. Dobson
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science
and Biotechnology Institute, The University of Melbourne, Parkville, Victoria,
Australia
- Biomolecular Interaction Centre, School of Biological Sciences,
University of Canterbury, Christchurch, New Zealand
- * E-mail: (RCJD); (AOH)
| | - Irma Girón
- School of Biological Sciences, Rochester Institute of Technology,
Rochester, New York, United States of America
| | - André O. Hudson
- School of Biological Sciences, Rochester Institute of Technology,
Rochester, New York, United States of America
- * E-mail: (RCJD); (AOH)
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15
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Zamfir A, Tsogoeva SB. Asymmetric Hydrocyanation of Hydrazones Catalyzed by in Situ Formed O-Silylated BINOL-Phosphate: A Convenient Access to Versatile α-Hydrazino Acids. Org Lett 2009; 12:188-91. [DOI: 10.1021/ol9025974] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexandru Zamfir
- Department of Chemistry and Pharmacy, Chair of Organic Chemistry I, University of Erlangen-Nuremberg, Henkestrasse 42, 91054, Erlangen, Germany
| | - Svetlana B. Tsogoeva
- Department of Chemistry and Pharmacy, Chair of Organic Chemistry I, University of Erlangen-Nuremberg, Henkestrasse 42, 91054, Erlangen, Germany
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16
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Pillai B, Cherney M, Diaper CM, Sutherland A, Blanchard JS, Vederas JC, James MNG. Dynamics of catalysis revealed from the crystal structures of mutants of diaminopimelate epimerase. Biochem Biophys Res Commun 2007; 363:547-53. [PMID: 17889830 DOI: 10.1016/j.bbrc.2007.09.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Accepted: 09/04/2007] [Indexed: 10/22/2022]
Abstract
Diaminopimelate (DAP) epimerase catalyzes the stereoinversion of ll-DAP to meso-DAP, a precursor of l-lysine and an essential component of the bacterial peptidoglycan. This function is vital to bacteria and the enzyme therefore represents an attractive target for the design of novel anti-bacterials. DAP epimerase belongs to the group of PLP-independent amino acid racemases that function through a rather unusual mechanism involving two cysteines acting in concert as a base (thiolate) and an acid (thiol). We have solved the crystal structures of the apo-forms of DAP epimerase mutants (C73S and C217S) from Haemophilus influenzae at 2.3A and 2.2A resolution, respectively. These structures provide a snapshot of the enzyme in the first step of the catalytic cycle. Comparisons with the structures of the inhibitor-bound form reveal that the enzyme adopts an 'open conformation' in the absence of substrates or inhibitors with the two active site cysteines existing as a thiol-thiolate pair. Substrate binding to the C-terminal domain triggers the closure of the N-terminal domain coupled with tight encapsulation of the ligand, stabilization of the conformation of an active site loop containing Cys73 and expulsion of water molecules with concomitant desolvation of the thiolate base. This structural rearrangement is critical for catalysis.
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Affiliation(s)
- Bindu Pillai
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alta, Canada T6G 2H7
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17
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Singh S, Singh KN. Superoxide‐Mediated Synthesis ofN‐Aminoaziridines fromN‐Aminoheterocycles and Olefins. SYNTHETIC COMMUN 2006. [DOI: 10.1080/00397910500214185] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- S. Singh
- a Department of Applied Chemistry , Institute of Technology, Banaras Hindu University , Varanasi , India
| | - K. N. Singh
- a Department of Applied Chemistry , Institute of Technology, Banaras Hindu University , Varanasi , India
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18
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Abstract
The first major step of cysteine catabolism, the oxidation of cysteine to cysteine sulfinic acid, is catalyzed by cysteine dioxygenase (CDO). In the present work, we utilize recombinant rat liver CDO and cysteine derivatives to elucidate structural parameters involved in substrate recognition and x-ray absorption spectroscopy to probe the interaction of the active site iron center with cysteine. Kinetic studies using cysteine structural analogs show that most are inhibitors and that a terminal functional group bearing a negative charge (e.g. a carboxylate) is required for binding. The substrate-binding site has no stringent restrictions with respect to the size of the amino acid. Lack of the amino or carboxyl groups at the alpha-carbon does not prevent the molecules from interacting with the active site. In fact, cysteamine is shown to be a potent activator of the enzyme without being a substrate. CDO was also rendered inactive upon complexation with the metal-binding inhibitors azide and cyanide. Unlike many non-heme iron dioxygenases that employ alpha-keto acids as cofactors, CDO was shown to be the only dioxygenase known to be inhibited by alpha-ketoglutarate.
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Affiliation(s)
- Sergio C Chai
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
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19
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Diaper CM, Sutherland A, Pillai B, James MNG, Semchuk P, Blanchard JS, Vederas JC. The stereoselective synthesis of aziridine analogues of diaminopimelic acid (DAP) and their interaction with dap epimerase. Org Biomol Chem 2005; 3:4402-11. [PMID: 16327902 DOI: 10.1039/b513409a] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aziridine analogues of diaminopimelic acid (DAP) have been prepared stereoselectively for the first time and evaluated as inhibitors of DAP epimerase. (2R,3S,3'S)-3-(3'-Aminopropane)aziridine-2,3'-dicarboxylate was synthesised and shown to be a reversible inhibitor of DAP epimerase with an IC(50) value of 2.88 mM. (2S,4S)- and (2S,4R)-2-(4-Amino-4-carboxybutyl)aziridine-2-carboxylic acid (ll-azi-DAP and dl-azi-DAP ) were made as pure diastereomers, and both were shown to be irreversible inhibitors of DAP epimerase. ll-Azi-DAP selectively binds to Cys-73 of the enzyme active site whereas dl-azi-DAP binds to Cys-217 via attack of sulfhydryl on the methylene of the inhibitor aziridine ring. These observations are consistent with the two base mechanism proposed for the epimerization of ll-DAP and meso-DAP by DAP epimerase.
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Affiliation(s)
- Christopher M Diaper
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
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20
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Bold G, Allmendinger T, Herold P, Moesch L, Schär HP, Duthaler RO. Stereoselektive Synthese von (2S,6S)-2,6-Diaminoheptandisäure und von unsymmetrischen Derivaten dermeso-2,6-Diaminoheptandisäure. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19920750321] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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21
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Stereocontrolled synthesis of enantiomerically pure unsaturated analogues of 2,6-DAP. Part 5. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s0957-4166(02)00834-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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22
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Oguz U, Guilbeau GG, McLaughlin ML. A facile stereospecific synthesis of α-hydrazino esters. Tetrahedron Lett 2002. [DOI: 10.1016/s0040-4039(02)00352-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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23
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Paradisi F, Piccinelli F, Porzi G, Sandri S. Enantioselective synthesis of 2,6-diaminopimelic acid derivatives. Part 3. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s0957-4166(02)00126-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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24
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Cox RJ, Sutherland A, Vederas JC. Bacterial diaminopimelate metabolism as a target for antibiotic design. Bioorg Med Chem 2000; 8:843-71. [PMID: 10881998 DOI: 10.1016/s0968-0896(00)00044-4] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- R J Cox
- School of Chemistry, University of Bristol, Clifton, UK.
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25
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26
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Wehrmann A, Phillipp B, Sahm H, Eggeling L. Different modes of diaminopimelate synthesis and their role in cell wall integrity: a study with Corynebacterium glutamicum. J Bacteriol 1998; 180:3159-65. [PMID: 9620966 PMCID: PMC107817 DOI: 10.1128/jb.180.12.3159-3165.1998] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In eubacteria, there are three slightly different pathways for the synthesis of m-diaminopimelate (m-DAP), which is one of the key linking units of peptidoglycan. Surprisingly, for unknown reasons, some bacteria use two of these pathways together. An example is Corynebacterium glutamicum, which uses both the succinylase and dehydrogenase pathways for m-DAP synthesis. In this study, we clone dapD and prove by enzyme experiments that this gene encodes the succinylase (M(r) = 24082), initiating the succinylase pathway of m-DAP synthesis. By using gene-directed mutation, dapD, as well as dapE encoding the desuccinylase, was inactivated, thereby forcing C. glutamicum to use only the dehydrogenase pathway of m-DAP synthesis. The mutants are unable to grow on organic nitrogen sources. When supplied with low ammonium concentrations but excess carbon, their morphology is radically altered and they are less resistant to mechanical stress than the wild type. Since the succinylase has a high affinity toward its substrate and uses glutamate as the nitrogen donor, while the dehydrogenase has a low affinity and incorporates ammonium directly, the m-DAP synthesis is another example of twin activities present in bacteria for access to important metabolites such as the well-known twin activities for the synthesis of glutamate or for the uptake of potassium.
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27
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Scapin G, Blanchard JS. Enzymology of bacterial lysine biosynthesis. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 1998; 72:279-324. [PMID: 9559056 DOI: 10.1002/9780470123188.ch8] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Bacteria have evolved three strategies for the synthesis of lysine from aspartate via formation of the intermediate diaminopimelate (DAP), a metabolite that is also involved in peptidoglycan formation. The objectives of this chapter are descriptions of mechanistic studies on the reactions catalyzed by dihydrodipicolinate synthase, dihydrodopicolinate reductase, tetrahydrodipicolinate N-succinyl-transferase, N-succinyl-L,L-DAP aminotransferase, N-succinyl-L,L-DAP desuccinylase, L,L-DAP epimerase, L,L-DAP decarboxylase, and DAP dehydrogenase. These enzymes are discussed in terms of kinetic, isotopic, and X-ray crystallographic data that allow one to infer the nature of interactions of each of these enzymes with its substrate(s), coenzymes, and inhibitors.
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Affiliation(s)
- G Scapin
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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28
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29
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Cativiela C, Díaz-de-Villegas MD, Gálvez JA. A chiral hydrazone derived from d-glyceraldehyde: a convenient starting material for the stereoselective synthesis of α-hydrazino acids. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s0957-4166(97)00128-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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30
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Auger G, van Heijenoort J, Vederas JC, Blanot D. Effect of analogues of diaminopimelic acid on the meso-diaminopimelate-adding enzyme from Escherichia coli. FEBS Lett 1996; 391:171-4. [PMID: 8706910 DOI: 10.1016/0014-5793(96)00619-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Several analogues of diaminopimelic acid (A2pm) were tested as substrates or inhibitors of the meso-diaminopimelate-adding enzyme from Escherichia coli. They included lanthionine derivatives, a phosphonic analogue, heterocyclic compounds, 3-fluoro-A2pm, 4-methylene-A2pm and N-hydroxy-A2pm. The best substrates were, in decreasing order of specific enzyme activity, (2S,3R,6S)-3-fluoro-A2pm, meso-lanthionine sulfoxide and N-hydroxy-A2pm (mixture of stereoisomers). In those cases where all the stereoisomers were available, the specificity could be described as meso > > DD approximately to LL. N-Hydroxy-A2pm (mixture of stereoisomers) strongly inhibited the addition of radioactive meso-A2pm to UDP-N-acetylmuramoyl-dipeptide.
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Affiliation(s)
- G Auger
- URA 1131 du CNRS, Biochimie Moléculaire et Cellulaire, Université de Paris-Sud, Orsay, France
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31
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Williams RM, Fegley GJ, Gallegos R, Schaefer F, Pruess DL. Asymmetric Syntheses of (2S,3S,6S)-, (2S,3S,6R)-, and (2R,3R,6S)-2,3-Methano-2,6-diaminopimelic Acids. Studies Directed to the Design of Novel Substrate-based Inhibitors of L,L-Diaminopimelate Epimerase. Tetrahedron 1996. [DOI: 10.1016/0040-4020(95)00976-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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32
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Asymmetric syntheses of α-amino acids. ACTA ACUST UNITED AC 1995. [DOI: 10.1016/s1874-5148(06)80005-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
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33
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Holcomb RC, Schow S, Ayral-Kaloustian S, Powell D. An asymmetric synthesis of differentially protected meso-2,6-diaminopimelic acid. Tetrahedron Lett 1994. [DOI: 10.1016/0040-4039(94)88210-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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34
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Amination with N-benzyloxycarbonyl-3-phenyloxaziridine as a route to sensitive chiral α-hydrazino acids: Synthesis of l-hydrazino serine. Tetrahedron Lett 1993. [DOI: 10.1016/s0040-4039(00)91814-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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35
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Kapron JT, Santarsiero BD, Vederas JC. N-phthalimidoaziridines by diastereoselective Addition to α,β-unsaturated amides: a route to chiral β-substituted α-hydrazino acid derivatives. ACTA ACUST UNITED AC 1993. [DOI: 10.1039/c39930001074] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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