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Tian G, Hu J, Qin C, Li L, Ning Y, Zhu S, Xie S, Zou X, Seeberger PH, Yin J. Chemical Synthesis and Antigenicity Evaluation of an Aminoglycoside Trisaccharide Repeating Unit of Pseudomonas aeruginosa Serotype O5 O-Antigen Containing a Rare Dimeric-Man pN3NA. J Am Chem Soc 2024; 146:18427-18439. [PMID: 38946080 DOI: 10.1021/jacs.4c03814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Pseudomonas aeruginosa bacteria are becoming increasingly resistant against multiple antibiotics. Therefore, the development of vaccines to prevent infections with these bacteria is an urgent medical need. While the immunological activity of lipopolysaccharide O-antigens in P. aeruginosa is well-known, the specific protective epitopes remain unidentified. Herein, we present the first chemical synthesis of highly functionalized aminoglycoside trisaccharide 1 and its acetamido derivative 2 found in the P. aeruginosa serotype O5 O-antigen. The synthesis of the trisaccharide targets is based on balancing the reactivity of disaccharide acceptors and monosaccharide donors. Glycosylations were analyzed by quantifying the reactivity of the hydroxyl group of the disaccharide acceptor using the orbital-weighted Fukui function and dual descriptor. The stereoselective formation of 1,2-cis-α-fucosylamine linkages was achieved through a combination of remote acyl participation and reagent modulation. The simultaneous SN2 substitution of azide groups at C2' and C2″ enabled the efficient synthesis of 1,2-cis-β-linkages for both 2,3-diamino-D-mannuronic acids. Through a strategic orthogonal modification, the five amino groups on target trisaccharide 1 were equipped with a rare acetamidino (Am) and four acetyl (Ac) groups. Glycan microarray analyses of sera from patients infected with P. aeruginosa indicated that trisaccharides 1 and 2 are key antigenic epitopes of the serotype O5 O-antigen. The acetamidino group is not an essential determinant of antibody binding. The β-D-ManpNAc3NAcA residue is a key motif for the antigenicity of serotype O5 O-antigen. These findings serve as a foundation for the development of glycoconjugate vaccines targeting P. aeruginosa serotype O5.
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Affiliation(s)
- Guangzong Tian
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Avenue 1800, Wuxi, Jiangsu 214122, P.R. China
- Biomolecular Systems Department, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, Potsdam 14476, Germany
| | - Jing Hu
- Wuxi School of Medicine, Jiangnan University, Lihu Avenue 1800, Wuxi, Jiangsu 214122, P.R. China
| | - Chunjun Qin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Avenue 1800, Wuxi, Jiangsu 214122, P.R. China
| | - Lingxin Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Avenue 1800, Wuxi, Jiangsu 214122, P.R. China
| | - Yunzhan Ning
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Avenue 1800, Wuxi, Jiangsu 214122, P.R. China
| | - Shengyong Zhu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Avenue 1800, Wuxi, Jiangsu 214122, P.R. China
| | - Suqing Xie
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Avenue 1800, Wuxi, Jiangsu 214122, P.R. China
| | - Xiaopeng Zou
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Avenue 1800, Wuxi, Jiangsu 214122, P.R. China
| | - Peter H Seeberger
- Biomolecular Systems Department, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, Potsdam 14476, Germany
| | - Jian Yin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Avenue 1800, Wuxi, Jiangsu 214122, P.R. China
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2
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Mohammadjani N, Ashengroph M, Abdollahzadeh J. Untargeted metabolomics and molecular docking studies on green silver nanoparticles synthesized by Sarocladium subulatum: Exploring antibacterial and antioxidant properties. CHEMOSPHERE 2024; 355:141836. [PMID: 38561160 DOI: 10.1016/j.chemosphere.2024.141836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/21/2024] [Accepted: 03/27/2024] [Indexed: 04/04/2024]
Abstract
The biological synthesis of silver nanoparticles (Ag-NPs) with fungi has shown promising results in antibacterial and antioxidant properties. Fungi generate metabolites (both primary and secondary) and proteins, which aid in the formation of metal nanoparticles as reducing or capping agents. While several studies have been conducted on the biological production of Ag-NPs, the exact mechanisms still need to be clarified. In this study, Ag-NPs are synthesized greenly using an unstudied fungal strain, Sarocladium subulatum AS4D. Three silver salts were used to synthesize the Ag-NPs for the first time, optimized using a cell-free extract (CFE) strategy. Additionally, these NPs were assessed for their antimicrobial and antioxidant properties. Various spectroscopic and microscopy techniques were utilized to confirm Ag-NP formation and analyze their morphology, crystalline properties, functional groups, size, stability, and concentrations. Untargeted metabolomics and proteome disruption were employed to explore the synthesis mechanism. Computational tools were applied to predict metabolite toxicity and antibacterial activity. The study identified 40 fungal metabolites capable of reducing silver ions, with COOH and OH functional groups playing a pivotal role. The silver salt type impacted the NPs' size and stability, with sizes ranging from 40 to 52 nm and zeta potentials from -0.9 to -30.4 mV. Proteome disruption affected size and stability but not shape. Biosynthesized Ag-NPs using protein-free extracts ranged from 55 to 62 nm, and zeta potentials varied from -18 to -27 mV. Molecular docking studies and PASS results found no role for the metabolome in antibacterial activity. This suggests the antibacterial activity comes from Ag-NPs, not capping or reducing agents. Overall, the research affirmed the vital role of specific reducing metabolites in the biosynthesis of Ag-NPs, while proteins derived from biological extracts were found to solely affect their size and stability.
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Affiliation(s)
- Navid Mohammadjani
- Department of Biological Science, Faculty of Science, University of Kurdistan, P.O. Box 416, Sanandaj, Iran
| | - Morahem Ashengroph
- Department of Biological Science, Faculty of Science, University of Kurdistan, P.O. Box 416, Sanandaj, Iran.
| | - Jafar Abdollahzadeh
- Department of Plant Protection, Agriculture Faculty, University of Kurdistan, P.O. Box 416, Sanandaj, Iran
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Manjunath A, Chinmayi GVA, Renganathan S, Chandramohan V, Sabat S. Antimicrobial activity of Geranyl acetate against cell wall synthesis proteins of P. aeruginosa and S. aureus using molecular docking and simulation. J Biomol Struct Dyn 2024; 42:3030-3050. [PMID: 37199273 DOI: 10.1080/07391102.2023.2212060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/01/2023] [Indexed: 05/19/2023]
Abstract
Incidences of Methicillin-Resistant Staphylococcus aureus and Multi-Drug Resistant Pseudomonas aeruginosa causing skin and soft tissue infections are becoming more prevalent due to repeated mutations and changes in the environment. Coriandrum sativum, a well-known Indian herbal medicinal plant, is shown to have antioxidant, antibacterial, and anti-inflammatory activity. This comparative study focuses on the molecular docking (PyRx v0.9.8) of ligand binding domains of WbpE Aminotransferase involved in O-antigen assembly in Pseudomonas aeruginosa (3NU7) and Beta-Lactamase found in Staphylococcus aureus (1BLC) with selected phytocompounds of Coriandrum sativum along with a known binder and a clinical reference drug. This was followed by molecular dynamics simulation studies (GROMACS v2019.4) for the docked complexes (with Geranyl acetate) with the best binding affinities (-23.4304 kJ/mol with Beta-Lactamase and -28.4512 kJ/mol with WbpE Aminotransferase) and maximum hydrogen bonds. Molecular dynamics simulation studies for both the proteins demonstrated that the complex with Geranyl acetate showed stability comparable to the complex with reference drug observed via Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF) and H-bond analyses. Changes in the secondary structural elements indicated that Geranyl acetate could possibly cause improper functioning of WbpE Aminotransferase leading to disrupted cell wall formation. Further, MM/PBSA analyses showed significant binding affinity of Geranyl acetate with WbpE Aminotransferase and Beta-Lactamase. This study aims to provide rationale for further studies of Coriandrum sativum as an antimicrobial, and to contextualise the results in the current scenario of growing antimicrobial resistance. HIGHLIGHTSPhytoconstituents present in Coriandrum sativum show significant binding affinity to the proteins in Pseudomonas aeruginosa and Staphylococcus aureus.Geranyl acetate exhibited the highest binding affinity with WbpE Aminotransferase involved in O-antigen assembly in Pseudomonas aeruginosa (PDB ID:3NU7) and Beta-Lactamase found in Staphylococcus aureus (PDB ID: 1BLC)Molecular dynamics simulation analyses show that the phytoconstituent, Geranyl acetate has an effect similar to the clinical reference drug, thus exhibiting potential antibacterial activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | | | - Vivek Chandramohan
- Department of Biotechnology, Siddaganga Institute of Technology, Tumakuru, India
| | - Sasmita Sabat
- Department of Biotechnology, PES University, Bengaluru, India
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Prasertanan T, Palmer DRJ, Sanders DAR. Snapshots along the catalytic path of KabA, a PLP-dependent aminotransferase required for kanosamine biosynthesis in Bacillus cereus UW85. J Struct Biol 2021; 213:107744. [PMID: 33984505 DOI: 10.1016/j.jsb.2021.107744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 10/21/2022]
Abstract
Kanosamine is an antibiotic and antifungal monosaccharide. The kanosamine biosynthetic pathway from glucose 6-phosphate in Bacillus cereus UW85 was recently reported, and the functions of each of the three enzymes in the pathway, KabA, KabB and KabC, were demonstrated. KabA, a member of a subclass of the VIβ family of PLP-dependent aminotransferases, catalyzes the second step in the pathway, generating kanosamine 6-phosphate (K6P) using l-glutamate as the amino-donor. KabA catalysis was shown to be extremely efficient, with a second-order rate constant with respect to K6P transamination of over 107 M-1s-1. Here we report the high-resolution structure of KabA in both the PLP- and PMP-bound forms. In addition, co-crystallization with K6P allowed the structure of KabA in complex with the covalent PLP-K6P adduct to be solved. Co-crystallization or soaking with glutamate or 2-oxoglutarate did not result in crystals with either substrate/product. Reduction of the PLP-KabA complex with sodium cyanoborohydride gave an inactivated enzyme, and crystals of the reduced KabA were soaked with the l-glutamate analog glutarate to mimic the KabA-PLP-l-glutamate complex. Together these four structures give a complete picture of how the active site of KabA recognizes substrates for each half-reaction. The KabA structure is discussed in the context of homologous aminotransferases.
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Affiliation(s)
| | - David R J Palmer
- Department of Chemistry, University of Saskatchewan, Saskatoon, SK S7N 5C9, Canada.
| | - David A R Sanders
- Department of Chemistry, University of Saskatchewan, Saskatoon, SK S7N 5C9, Canada.
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Kaundinya CR, Savithri HS, Rao KK, Balaji PV. EpsN from Bacillus subtilis 168 has UDP-2,6-dideoxy 2-acetamido 4-keto glucose aminotransferase activity in vitro. Glycobiology 2019; 28:802-812. [PMID: 29982582 DOI: 10.1093/glycob/cwy063] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/04/2018] [Indexed: 01/08/2023] Open
Abstract
The gene epsN of Bacillus subtilis 168 was cloned and overexpressed in Escherichia coli. Purified recombinant EpsN is shown to be a pyridoxal 5'-phosphate (PLP)-dependent aminotransferase by absorption spectroscopy, l-cycloserine inhibition and reverse phase HPLC studies. EpsN catalyzes the conversion of UDP-2,6-dideoxy 2-acetamido 4-keto glucose to UDP-2,6-dideoxy 2-acetamido 4-amino glucose. Lys190 was found by sequence comparison and site-directed mutagenesis to form Schiff base with PLP. Mutagenesis studies showed that, in addition to Lys190, Ser185, Glu164, Gly58 and Thr59 are essential for aminotransferase activity.
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Affiliation(s)
- Chinmayi R Kaundinya
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Handanahal S Savithri
- Department of Biochemistry, Indian Institute of Science, CV Raman Road, Bengaluru, India
| | - K Krishnamurthy Rao
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Petety V Balaji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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6
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Yu C, Chen H, Tian F, Yang F, Yuan X, Yang C, He C. A ten gene-containing genomic island determines flagellin glycosylation: implication for its regulatory role in motility and virulence of Xanthomonas oryzae pv. oryzae. MOLECULAR PLANT PATHOLOGY 2018; 19:579-592. [PMID: 28213905 PMCID: PMC6638077 DOI: 10.1111/mpp.12543] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 02/06/2017] [Accepted: 02/13/2017] [Indexed: 05/19/2023]
Abstract
Flagellin glycosylation plays a crucial role in flagellar assembly, motility and virulence in several pathogenic bacteria. However, little is known about the genetic determinants and biological functions of flagellin glycosylation in Xanthomonas oryzae pv. oryzae (Xoo), the causal pathogen of bacterial blight of rice. Here, the structure, regulation and functions of a ten-gene cluster gigX (glycosylation island genes of Xoo), which was embedded in a flagellar regulon, were characterized. gigX1 to gigX10 encoded putative enzymes or proteins involved in glycan biosynthesis and transfer, including a nucleotide sugar transaminase, an acyl-carrier protein (ACP), a 3-oxoacyl-ACP synthase, a 3-oxoacyl-ACP reductase, a dehydrogenase, an acetyltransferase, a ring hydroxylating dioxygenase, a hypothetical protein, a methyltransferanse and a glycosyltransferase, respectively. The gigX genes were co-transcribed in an operon and up-regulated by the upstream σ54 factor RpoN2 and transcriptional activator FleQ. In-frame deletion of each gigX gene affected flagellin glycosylation modification, meaning that the unglycosylated flagellin of the mutants was smaller than the glycosylated flagellin of the wild-type. No significant changes in flagellar filament and motility were observed in the ΔgigX mutants, among which only ΔgigX6 displayed increased swimming ability. Importantly, all mutants, except ΔgigX9, showed significantly increased virulence and bacterial growth in the susceptible rice cultivar IR24, and ΔgigX1 and ΔgigX10 showed enhanced type III secretion system (T3SS)-related gene expression. Moreover, the glycosylated flagellin of the wild-type induced higher H2 O2 levels in rice leaves than did the unglycosylated flagellins of ΔgigX1 or ΔgigX10. Taken together, this study reveals that the gigX cluster determines flagellin glycosylation, and implicates the regulatory role of post-translational modification with the glycosylation, acetylation and methylation of flagellin in the regulation of motility and virulence of Xoo.
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Affiliation(s)
- Chao Yu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100193China
| | - Huamin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100193China
| | - Fang Tian
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100193China
| | - Fenghuan Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100193China
| | - Xiaochen Yuan
- Department of Biological SciencesUniversity of Wisconsin‐MilwaukeeMilwaukeeWI53211USA
| | - Ching‐Hong Yang
- Department of Biological SciencesUniversity of Wisconsin‐MilwaukeeMilwaukeeWI53211USA
| | - Chenyang He
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100193China
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7
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Qin C, Schumann B, Zou X, Pereira CL, Tian G, Hu J, Seeberger PH, Yin J. Total Synthesis of a Densely Functionalized Plesiomonas shigelloides Serotype 51 Aminoglycoside Trisaccharide Antigen. J Am Chem Soc 2018; 140:3120-3127. [PMID: 29377682 DOI: 10.1021/jacs.8b00148] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Plesiomonas shigelloides, a pathogen responsible for frequent outbreaks of severe travelers' diarrhea, causes grave extraintestinal infections. Sepsis and meningitis due to P. shigelloides are associated with a high mortality rate as antibiotic resistance increases and vaccines are not available. Carbohydrate antigens expressed by pathogens are often structurally unique and are targets for developing vaccines and diagnostics. Here, we report a total synthesis of the highly functionalized trisaccharide repeating unit 2 from P. shigelloides serotype 51 from three monosaccharides. A judicious choice of building blocks and reaction conditions allowed for the four amino groups adorning the sugar rings to be installed with two N-acetyl (Ac) groups, rare acetamidino (Am), and d-3-hydroxybutyryl (Hb) groups. The strategy for the differentiation of amino groups in trisaccharide 2 will serve well for the syntheses of other complex glycans.
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Affiliation(s)
- Chunjun Qin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi, Jiangsu Province 214122, P.R. China.,Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces , Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Benjamin Schumann
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces , Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Xiaopeng Zou
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi, Jiangsu Province 214122, P.R. China.,Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces , Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Claney L Pereira
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces , Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Guangzong Tian
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi, Jiangsu Province 214122, P.R. China.,Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces , Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Jing Hu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi, Jiangsu Province 214122, P.R. China
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces , Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Jian Yin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi, Jiangsu Province 214122, P.R. China
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8
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Dow GT, Gilbert M, Thoden JB, Holden HM. Structural investigation on WlaRG from Campylobacter jejuni: A sugar aminotransferase. Protein Sci 2017; 26:586-599. [PMID: 28028852 DOI: 10.1002/pro.3109] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 12/22/2016] [Indexed: 12/12/2022]
Abstract
Campylobacter jejuni is a Gram-negative bacterium that represents a leading cause of human gastroenteritis worldwide. Of particular concern is the link between C. jejuni infections and the subsequent development of Guillain-Barré syndrome, an acquired autoimmune disorder leading to paralysis. All Gram-negative bacteria contain complex glycoconjugates anchored to their outer membranes, but in most strains of C. jejuni, this lipoglycan lacks the O-antigen repeating units. Recent mass spectrometry analyses indicate that the C. jejuni 81116 (Penner serotype HS:6) lipoglycan contains two dideoxyhexosamine residues, and enzymological assay data show that this bacterial strain can synthesize both dTDP-3-acetamido-3,6-dideoxy-d-glucose and dTDP-3-acetamido-3,6-dideoxy-d-galactose. The focus of this investigation is on WlaRG from C. jejuni, which plays a key role in the production of these unusual sugars by functioning as a pyridoxal 5'-phosphate dependent aminotransferase. Here, we describe the first three-dimensional structures of the enzyme in various complexes determined to resolutions of 1.7 Å or higher. Of particular significance are the external aldimine structures of WlaRG solved in the presence of either dTDP-3-amino-3,6-dideoxy-d-galactose or dTDP-3-amino-3,6-dideoxy-d-glucose. These models highlight the manner in which WlaRG can accommodate sugars with differing stereochemistries about their C-4' carbon positions. In addition, we present a corrected structure of WbpE, a related sugar aminotransferase from Pseudomonas aeruginosa, solved to 1.3 Å resolution.
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Affiliation(s)
- Garrett T Dow
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, 53706
| | - Michel Gilbert
- National Research Council Canada, Human Health Therapeutics, Ottawa, Ontario, K1A 0R6, Canada
| | - James B Thoden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, 53706
| | - Hazel M Holden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, 53706
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Jaing CJ, McLoughlin KS, Thissen JB, Zemla A, Gardner SN, Vergez LM, Bourguet F, Mabery S, Fofanov VY, Koshinsky H, Jackson PJ. Identification of Genome-Wide Mutations in Ciprofloxacin-Resistant F. tularensis LVS Using Whole Genome Tiling Arrays and Next Generation Sequencing. PLoS One 2016; 11:e0163458. [PMID: 27668749 PMCID: PMC5036845 DOI: 10.1371/journal.pone.0163458] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/08/2016] [Indexed: 11/19/2022] Open
Abstract
Francisella tularensis is classified as a Class A bioterrorism agent by the U.S. government due to its high virulence and the ease with which it can be spread as an aerosol. It is a facultative intracellular pathogen and the causative agent of tularemia. Ciprofloxacin (Cipro) is a broad spectrum antibiotic effective against Gram-positive and Gram-negative bacteria. Increased Cipro resistance in pathogenic microbes is of serious concern when considering options for medical treatment of bacterial infections. Identification of genes and loci that are associated with Ciprofloxacin resistance will help advance the understanding of resistance mechanisms and may, in the future, provide better treatment options for patients. It may also provide information for development of assays that can rapidly identify Cipro-resistant isolates of this pathogen. In this study, we selected a large number of F. tularensis live vaccine strain (LVS) isolates that survived in progressively higher Ciprofloxacin concentrations, screened the isolates using a whole genome F. tularensis LVS tiling microarray and Illumina sequencing, and identified both known and novel mutations associated with resistance. Genes containing mutations encode DNA gyrase subunit A, a hypothetical protein, an asparagine synthase, a sugar transamine/perosamine synthetase and others. Structural modeling performed on these proteins provides insights into the potential function of these proteins and how they might contribute to Cipro resistance mechanisms.
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Affiliation(s)
- Crystal J. Jaing
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
- * E-mail:
| | - Kevin S. McLoughlin
- Computations Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - James B. Thissen
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - Adam Zemla
- Computations Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - Shea N. Gardner
- Computations Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - Lisa M. Vergez
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - Feliza Bourguet
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - Shalini Mabery
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | | | | | - Paul J. Jackson
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
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10
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Wang F, Singh S, Xu W, Helmich KE, Miller MD, Cao H, Bingman CA, Thorson JS, Phillips GN. Structural Basis for the Stereochemical Control of Amine Installation in Nucleotide Sugar Aminotransferases. ACS Chem Biol 2015; 10:2048-56. [PMID: 26023720 DOI: 10.1021/acschembio.5b00244] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sugar aminotransferases (SATs) are an important class of tailoring enzymes that catalyze the 5'-pyridoxal phosphate (PLP)-dependent stereo- and regiospecific installation of an amino group from an amino acid donor (typically L-Glu or L-Gln) to a corresponding ketosugar nucleotide acceptor. Herein we report the strategic structural study of two homologous C4 SATs (Micromonospora echinospora CalS13 and Escherichia coli WecE) that utilize identical substrates but differ in their stereochemistry of aminotransfer. This study reveals for the first time a new mode of SAT sugar nucleotide binding and, in conjunction with previously reported SAT structural studies, provides the basis from which to propose a universal model for SAT stereo- and regiochemical control of amine installation. Specifically, the universal model put forth highlights catalytic divergence to derive solely from distinctions within nucleotide sugar orientation upon binding within a relatively fixed SAT active site where the available ligand bound structures of the three out of four representative C3 and C4 SAT examples provide a basis for the overall model. Importantly, this study presents a new predictive model to support SAT functional annotation, biochemical study and rational engineering.
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Affiliation(s)
| | - Shanteri Singh
- Center
for Pharmaceutical Research and Innovation, University of Kentucky College of Pharmacy, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | | | - Kate E. Helmich
- Department
of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | | | | | - Craig A. Bingman
- Department
of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Jon S. Thorson
- Center
for Pharmaceutical Research and Innovation, University of Kentucky College of Pharmacy, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - George N. Phillips
- Department
of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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11
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Singh S, Kim Y, Wang F, Bigelow L, Endres M, Kharel MK, Babnigg G, Bingman CA, Joachimiak A, Thorson JS, Phillips GN. Structural characterization of AtmS13, a putative sugar aminotransferase involved in indolocarbazole AT2433 aminopentose biosynthesis. Proteins 2015; 83:1547-54. [PMID: 26061967 DOI: 10.1002/prot.24844] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 05/25/2015] [Accepted: 05/27/2015] [Indexed: 11/08/2022]
Abstract
AT2433 from Actinomadura melliaura is an indolocarbazole antitumor antibiotic structurally distinguished by its unique aminodideoxypentose-containing disaccharide moiety. The corresponding sugar nucleotide-based biosynthetic pathway for this unusual sugar derives from comparative genomics where AtmS13 has been suggested as the contributing sugar aminotransferase (SAT). Determination of the AtmS13 X-ray structure at 1.50-Å resolution reveals it as a member of the aspartate aminotransferase fold type I (AAT-I). Structural comparisons of AtmS13 with homologous SATs that act upon similar substrates implicate potential active site residues that contribute to distinctions in sugar C5 (hexose vs. pentose) and/or sugar C2 (deoxy vs. hydroxyl) substrate specificity.
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Affiliation(s)
- Shanteri Singh
- Center for Pharmaceutical Research and Innovation, Pharmaceutical Sciences Division, University of Kentucky College of Pharmacy, Lexington, Kentucky, 40536-0596
| | - Youngchang Kim
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois, 60439
| | - Fengbin Wang
- Department of BioSciences, Rice University, Houston, Texas, 77005
| | - Lance Bigelow
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois, 60439
| | - Michael Endres
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois, 60439
| | - Madan K Kharel
- School of Pharmacy, Department of Pharmaceutical Sciences, University of Maryland Eastern Shore, Princess Anne, Maryland
| | - Gyorgy Babnigg
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois, 60439
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois, 60439
| | - Jon S Thorson
- Center for Pharmaceutical Research and Innovation, Pharmaceutical Sciences Division, University of Kentucky College of Pharmacy, Lexington, Kentucky, 40536-0596
| | - George N Phillips
- Department of BioSciences, Rice University, Houston, Texas, 77005.,Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706.,Department of Chemistry, Rice University, Houston, Texas, 77005
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12
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Jarrell KF, Ding Y, Meyer BH, Albers SV, Kaminski L, Eichler J. N-linked glycosylation in Archaea: a structural, functional, and genetic analysis. Microbiol Mol Biol Rev 2014; 78:304-41. [PMID: 24847024 PMCID: PMC4054257 DOI: 10.1128/mmbr.00052-13] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
N-glycosylation of proteins is one of the most prevalent posttranslational modifications in nature. Accordingly, a pathway with shared commonalities is found in all three domains of life. While excellent model systems have been developed for studying N-glycosylation in both Eukarya and Bacteria, an understanding of this process in Archaea was hampered until recently by a lack of effective molecular tools. However, within the last decade, impressive advances in the study of the archaeal version of this important pathway have been made for halophiles, methanogens, and thermoacidophiles, combining glycan structural information obtained by mass spectrometry with bioinformatic, genetic, biochemical, and enzymatic data. These studies reveal both features shared with the eukaryal and bacterial domains and novel archaeon-specific aspects. Unique features of N-glycosylation in Archaea include the presence of unusual dolichol lipid carriers, the use of a variety of linking sugars that connect the glycan to proteins, the presence of novel sugars as glycan constituents, the presence of two very different N-linked glycans attached to the same protein, and the ability to vary the N-glycan composition under different growth conditions. These advances are the focus of this review, with an emphasis on N-glycosylation pathways in Haloferax, Methanococcus, and Sulfolobus.
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Affiliation(s)
- Ken F Jarrell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Yan Ding
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Benjamin H Meyer
- Molecular Biology of Archaea, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Lina Kaminski
- Department of Life Sciences, Ben Gurion University, Beersheva, Israel
| | - Jerry Eichler
- Department of Life Sciences, Ben Gurion University, Beersheva, Israel
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13
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Morrison MJ, Imperiali B. The renaissance of bacillosamine and its derivatives: pathway characterization and implications in pathogenicity. Biochemistry 2014; 53:624-38. [PMID: 24383882 PMCID: PMC3951908 DOI: 10.1021/bi401546r] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
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Prokaryote-specific
sugars, including N,N′-diacetylbacillosamine
(diNAcBac) and pseudaminic
acid, have experienced a renaissance in the past decade because of
their discovery in glycans related to microbial pathogenicity. DiNAcBac
is found at the reducing end of oligosaccharides of N- and O-linked
bacterial protein glycosylation pathways of Gram-negative pathogens,
including Campylobacter jejuni and Neisseria
gonorrhoeae. Further derivatization of diNAcBac results in
the nonulosonic acid known as legionaminic acid, which was first characterized
in the O-antigen of the lipopolysaccharide (LPS) in Legionella
pneumophila. Pseudaminic acid, an isomer of legionaminic
acid, is also important in pathogenic bacteria such as Helicobacter
pylori because of its occurrence in O-linked glycosylation
of flagellin proteins, which plays an important role in flagellar
assembly and motility. Here, we present recent advances in the characterization
of the biosynthetic pathways leading to these highly modified sugars
and investigation of the roles that each plays in bacterial fitness
and pathogenicity.
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Affiliation(s)
- Michael J Morrison
- Departments of Chemistry and Biology, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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14
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van Straaten KE, Ko JB, Jagdhane R, Anjum S, Palmer DRJ, Sanders DAR. The structure of NtdA, a sugar aminotransferase involved in the kanosamine biosynthetic pathway in Bacillus subtilis, reveals a new subclass of aminotransferases. J Biol Chem 2013; 288:34121-34130. [PMID: 24097983 DOI: 10.1074/jbc.m113.500637] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
NtdA from Bacillus subtilis is a sugar aminotransferase that catalyzes the pyridoxal phosphate-dependent equatorial transamination of 3-oxo-α-D-glucose 6-phosphate to form α-D-kanosamine 6-phosphate. The crystal structure of NtdA shows that NtdA shares the common aspartate aminotransferase fold (Type 1) with residues from both monomers forming the active site. The crystal structures of NtdA alone, co-crystallized with the product α-D-kanosamine 6-phosphate, and incubated with the amine donor glutamate reveal three key structures in the mechanistic pathway of NtdA. The structure of NtdA alone reveals the internal aldimine form of NtdA with the cofactor pyridoxal phosphate covalently attached to Lys-247. The addition of glutamate results in formation of pyridoxamine phosphate. Co-crystallization with kanosamine 6-phosphate results in the formation of the external aldimine. Only α-D-kanosamine 6-phosphate is observed in the active site of NtdA, not the β-anomer. A comparison of the structure and sequence of NtdA with other sugar aminotransferases enables us to propose that the VIβ family of aminotransferases should be divided into subfamilies based on the catalytic lysine motif.
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Affiliation(s)
- Karin E van Straaten
- Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9, Canada
| | - Jong Bum Ko
- Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9, Canada
| | - Rajendra Jagdhane
- Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9, Canada
| | - Shazia Anjum
- Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9, Canada
| | - David R J Palmer
- Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9, Canada
| | - David A R Sanders
- Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9, Canada.
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15
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Genes required for and effects of alginate overproduction induced by growth of Pseudomonas aeruginosa on Pseudomonas isolation agar supplemented with ammonium metavanadate. J Bacteriol 2013; 195:4020-36. [PMID: 23794622 DOI: 10.1128/jb.00534-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that can adapt to changing environments and can secrete an exopolysaccharide known as alginate as a protection response, resulting in a colony morphology and phenotype referred to as mucoid. However, how P. aeruginosa senses its environment and activates alginate overproduction is not fully understood. Previously, we showed that Pseudomonas isolation agar supplemented with ammonium metavanadate (PIAAMV) induces P. aeruginosa to overproduce alginate. Vanadate is a phosphate mimic and causes protein misfolding by disruption of disulfide bonds. Here we used PIAAMV to characterize the pathways involved in inducible alginate production and tested the global effects of P. aeruginosa growth on PIAAMV by a mutant library screen, by transcriptomics, and in a murine acute virulence model. The PA14 nonredundant mutant library was screened on PIAAMV to identify new genes that are required for the inducible alginate stress response. A functionally diverse set of genes encoding products involved in cell envelope biogenesis, peptidoglycan remodeling, uptake of phosphate and iron, phenazine biosynthesis, and other processes were identified as positive regulators of the mucoid phenotype on PIAAMV. Transcriptome analysis of P. aeruginosa cultures growing in the presence of vanadate showed differential expression of genes involved in virulence, envelope biogenesis, and cell stress pathways. In this study, it was observed that growth on PIAAMV attenuates P. aeruginosa in a mouse pneumonia model. Induction of alginate overproduction occurs as a stress response to protect P. aeruginosa, but it may be possible to modulate and inhibit these pathways based on the new genes identified in this study.
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16
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Morrison MJ, Imperiali B. Biosynthesis of UDP-N,N'-diacetylbacillosamine in Acinetobacter baumannii: Biochemical characterization and correlation to existing pathways. Arch Biochem Biophys 2013; 536:72-80. [PMID: 23747578 DOI: 10.1016/j.abb.2013.05.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 05/30/2013] [Indexed: 01/11/2023]
Abstract
The Gram-negative, opportunistic pathogen Acinetobacter baumannii has recently captured headlines due to its ability to circumvent current antibiotic therapies. Herein we show that the multi-drug resistant (MDR) AYE strain of A. baumannii contains a gene locus that encodes three enzymes responsible for the biosynthesis of the highly-modified bacterial nucleotide sugar, UDP-N,N'-diacetylbacillosamine (UDP-diNAcBac). Previously, this UDP-sugar has been implicated in the pgl pathway of Campylobacter jejuni. Here we report the overexpression, purification, and biochemical characterization of the A. baumannii enzymes WeeK, WeeJ, and WeeI that are responsible for the production of UDP-diNAcBac. We also demonstrate the function of the phosphoglycosyltransferase (WeeH), which transfers the diNAcBac moiety to undecaprenyl-phosphate. UDP-diNAcBac biosynthesis in A. baumannii is also directly compared to the homologous pathways in the pathogens C. jejuni and Neisseria gonorrhoeae. This work demonstrates for the first time the ability of A. baumannii to generate the highly-modified, UDP-diNAcBac nucleotide sugar found previously in other bacteria adding to the growing list of pathogens that assemble glycoconjugates including bacillosamine. Additionally, characterization of these pathway enzymes highlights the opportunity for investigating the significance of highly-modified sugars in bacterial pathogenesis.
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Affiliation(s)
- Michael J Morrison
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
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17
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Mostafavi AZ, Troutman JM. Biosynthetic assembly of the Bacteroides fragilis capsular polysaccharide A precursor bactoprenyl diphosphate-linked acetamido-4-amino-6-deoxygalactopyranose. Biochemistry 2013; 52:1939-49. [PMID: 23458065 DOI: 10.1021/bi400126w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The sugar capsule capsular polysaccharide A (CPSA), which coats the surface of the mammalian symbiont Bacteroides fragilis, is a key mediator of mammalian immune system development. In addition, this sugar polymer has shown therapeutic potential in animal models of multiple sclerosis and other autoimmune disorders. The structure of the CPSA polymer includes a rare stereoconfiguration sugar acetamido-4-amino-6-deoxygalactopyranose (AADGal) that we propose is the first sugar linked to a bactoprenyl diphosphate scaffold in the production of CPSA. In this report, we have utilized a heterologous system to reconstitute bactoprenyl diphosphate-linked AADGal production. Construction of this system included a previously reported Campylobacter jejuni dehydratase, PglF, coupled to a B. fragilis-encoded aminotransferase (WcfR) and initiating hexose-1-phosphate transferase (WcfS). The function of the aminotransferase was confirmed by capillary electrophoresis and a novel high-performance liquid chromatography (HPLC) method. Production of the rare uridine diphosphate (UDP)-AADGal was confirmed through a series of one- and two-dimensional nuclear magnetic resonance experiments and high-resolution mass spectrometry. A spectroscopically unique analogue of bactoprenyl phosphate was utilized to characterize the transfer reaction catalyzed by WcfS and allowed HPLC-based isolation of the isoprenoid-linked sugar product. Importantly, the entire heterologous system was utilized in a single-pot reaction to biosynthesize the bactoprenyl-linked sugar. This work provides the first critical step in the in vitro reconstitution of CPSA biosynthesis.
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Affiliation(s)
- Anahita Z Mostafavi
- Department of Chemistry, University of North Carolina at Charlotte , 9201 University City Boulevard, Charlotte, North Carolina 28223-0001, United States
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18
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Stratford M, Plumridge A, Pleasants MW, Novodvorska M, Baker-Glenn CA, Pattenden G, Archer DB. Mapping the structural requirements of inducers and substrates for decarboxylation of weak acid preservatives by the food spoilage mould Aspergillus niger. Int J Food Microbiol 2012; 157:375-83. [DOI: 10.1016/j.ijfoodmicro.2012.06.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 06/06/2012] [Accepted: 06/10/2012] [Indexed: 10/28/2022]
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19
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Singh S, Phillips GN, Thorson JS. The structural biology of enzymes involved in natural product glycosylation. Nat Prod Rep 2012; 29:1201-37. [PMID: 22688446 DOI: 10.1039/c2np20039b] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The glycosylation of microbial natural products often dramatically influences the biological and/or pharmacological activities of the parental metabolite. Over the past decade, crystal structures of several enzymes involved in the biosynthesis and attachment of novel sugars found appended to natural products have emerged. In many cases, these studies have paved the way to a better understanding of the corresponding enzyme mechanism of action and have served as a starting point for engineering variant enzymes to facilitate to production of differentially-glycosylated natural products. This review specifically summarizes the structural studies of bacterial enzymes involved in biosynthesis of novel sugar nucleotides.
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Affiliation(s)
- Shanteri Singh
- Laboratory for Biosynthetic Chemistry, Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
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20
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Walvoort MTC, Moggré GJ, Lodder G, Overkleeft HS, Codée JDC, van der Marel GA. Stereoselective Synthesis of 2,3-Diamino-2,3-dideoxy-β-d-mannopyranosyl Uronates. J Org Chem 2011; 76:7301-15. [DOI: 10.1021/jo201179p] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marthe T. C. Walvoort
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Gert-Jan Moggré
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Gerrit Lodder
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Herman S. Overkleeft
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Jeroen D. C. Codée
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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21
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Reversible covalent chemistries compatible with the principles of constitutional dynamic chemistry: new reactions to create more diversity. Top Curr Chem (Cham) 2011; 322:291-314. [PMID: 22025070 DOI: 10.1007/128_2011_277] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
An approach to make chemical diversity space more manageable is to search for smaller molecules, or fragments, and then combine or elaborate these fragments. Dynamic Combinatorial Chemistry (DCC) is a powerful approach whereby a number of molecular elements each with binding potential can be reversibly combined via covalent or noncovalent linkages to generate a dynamic library of products under thermodynamic equilibrium. Once a target molecule has been added, the distribution of products can be shifted to favor products that bind to the target. Thus the approach can be employed to identify products that selectively recognize the target. Although the size of the repertoire of reversible covalent reactions suitable for DCC has increased significantly over the past 5-10 years, the discovery of new reactions that satisfy all the criteria of reversibility and biocompatibility remains an exciting challenge for chemists. Increasing the number of chemical reactions will enable the engineering of larger and more diverse DCLs, which remains a key step toward a broader use of DCC. In this review, we aim to provide a nonexhaustive list of reversible covalent reactions that are compatible with the concept of DCC, focusing mainly on the most recent examples that were reported in the literature in the past 5 years.
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