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Park JH, Reviello RE, Loll PJ. Crystal structure of vancomycin bound to the resistance determinant D-alanine-D-serine. IUCRJ 2024; 11:133-139. [PMID: 38277167 PMCID: PMC10916290 DOI: 10.1107/s2052252524000289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 01/08/2024] [Indexed: 01/27/2024]
Abstract
Vancomycin is a glycopeptide antibiotic that for decades has been a mainstay of treatment for persistent bacterial infections. However, the spread of antibiotic resistance threatens its continued utility. In particular, vancomycin-resistant enterococci (VRE) have become a pressing clinical challenge. Vancomycin acts by binding and sequestering the intermediate Lipid II in cell-wall biosynthesis, specifically recognizing a D-alanine-D-alanine dipeptide motif within the Lipid II molecule. VRE achieve resistance by remodeling this motif to either D-alanine-D-lactate or D-alanine-D-serine; the former substitution essentially abolishes recognition by vancomycin of Lipid II, whereas the latter reduces the affinity of the antibiotic by roughly one order of magnitude. The complex of vancomycin bound to D-alanine-D-serine has been crystallized, and its 1.20 Å X-ray crystal structure is presented here. This structure reveals that the D-alanine-D-serine ligand is bound in essentially the same position and same pose as the native D-alanine-D-alanine ligand. The serine-containing ligand appears to be slightly too large to be comfortably accommodated in this way, suggesting one possible contribution to the reduced binding affinity. In addition, two flexible hydroxyl groups - one from the serine side chain of the ligand, and the other from a glucose sugar on the antibiotic - are locked into single conformations in the complex, which is likely to contribute an unfavorable entropic component to the recognition of the serine-containing ligand.
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Affiliation(s)
- Jee Hoon Park
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, PA 19102, USA
| | - Rachel E. Reviello
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, PA 19102, USA
| | - Patrick J. Loll
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, PA 19102, USA
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2
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Hammond LR, White ML, Eswara PJ. Probing Bacterial Cell Division and Cell Envelope Biogenesis with Live-Cell Fluorescence Microscopy. Methods Mol Biol 2024; 2727:205-214. [PMID: 37815719 DOI: 10.1007/978-1-0716-3491-2_16] [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] [Indexed: 10/11/2023]
Abstract
The development of advanced microscopy techniques has ushered in a new era of research as it helps understand biological processes on a deeper, mechanistic, and molecular level like never before. Live-cell fluorescence microscopy has importantly allowed us to visualize subcellular protein localization and incorporation of various fluorophores compatible with living cells in real time. As such, this technique offers valuable insights at the single-cell level and enables us to monitor phenotypic differences that were easily overlooked at a population level. One area of research that has benefited greatly from these advances is the study of the bacterial cell envelope biogenesis and cell division process. In this report, we provide detailed protocols, optimized in our lab, for imaging these processes in the Gram-positive organisms Bacillus subtilis and Staphylococcus aureus.
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Affiliation(s)
- Lauren R Hammond
- Department of Molecular Biosciences, University of South Florida, Tampa, FL, USA
| | - Maria L White
- Department of Molecular Biosciences, University of South Florida, Tampa, FL, USA
| | - Prahathees J Eswara
- Department of Molecular Biosciences, University of South Florida, Tampa, FL, USA.
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3
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Rius J, Torrelles X. A new density-modification procedure extending the application of the recent |ρ|-based phasing algorithm to larger crystal structures. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2021; 77:339-347. [PMID: 34196295 PMCID: PMC8248888 DOI: 10.1107/s2053273321004915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/10/2021] [Indexed: 11/10/2022]
Abstract
The incorporation of the new peakness-enhancing fast Fourier transform compatible ipp procedure (ipp = inner-pixel preservation) into the recently published SM algorithm based on |ρ| [Rius (2020). Acta Cryst A76, 489-493] improves its phasing efficiency for larger crystal structures with atomic resolution data. Its effectiveness is clearly demonstrated via a collection of test crystal structures (taken from the Protein Data Bank) either starting from random phase values or by using the randomly shifted modulus function (a Patterson-type synthesis) as initial ρ estimate. It has been found that in the presence of medium scatterers (e.g. S or Cl atoms) crystal structures with 1500 × c atoms in the unit cell (c = number of centerings) can be routinely solved. In the presence of strong scatterers like Fe, Cu or Zn atoms this number increases to around 5000 × c atoms. The implementation of this strengthened SM algorithm is simple, since it only includes a few easy-to-adjust parameters.
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Affiliation(s)
- Jordi Rius
- Institut de Ciència de Materials de Barcelona, CSIC, Campus de la UAB, Bellaterra, Catalonia 08193, Spain
| | - Xavier Torrelles
- Institut de Ciència de Materials de Barcelona, CSIC, Campus de la UAB, Bellaterra, Catalonia 08193, Spain
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Izsépi L, Erdei R, Tevyashova AN, Grammatikova NE, Shchekotikhin AE, Herczegh P, Batta G. Bacterial Cell Wall Analogue Peptides Control the Oligomeric States and Activity of the Glycopeptide Antibiotic Eremomycin: Solution NMR and Antimicrobial Studies. Pharmaceuticals (Basel) 2021; 14:ph14020083. [PMID: 33499349 PMCID: PMC7911593 DOI: 10.3390/ph14020083] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/05/2021] [Accepted: 01/18/2021] [Indexed: 12/18/2022] Open
Abstract
For some time, glycopeptide antibiotics have been considered the last line of defense against Methicillin-resistant Staphylococcus aureus (MRSA). However, vancomycin resistance of Gram-positive bacteria is an increasingly emerging worldwide health problem. The mode of action of glycopeptide antibiotics is essentially the binding of peptidoglycan cell-wall fragments terminating in the d-Ala-d-Ala sequence to the carboxylate anion binding pocket of the antibiotic. Dimerization of these antibiotics in aqueous solution was shown to persist and even to enhance the antibacterial effect in a co-operative manner. Some works based on solid state (ss) Nuclear Magnetic Resonance (NMR) studies questioned the presence of dimers under the conditions of ssNMR while in a few cases, higher-order oligomers associated with contiguous back-to-back and face-to-face dimers were observed in the crystal phase. However, it is not proved if such oligomers persist in aqueous solutions. With the aid of 15N-labelled eremomycin using 15N relaxation and diffusion NMR methods, we observed tetramers and octamers when the N-Ac-d-Ala-d-Ala dipeptide was added. To the contrary, the N-Ac-d-Ala or (N-Ac)2-l-Lys-d-Ala-d-Ala tripeptide did not induce higher-order oligomers. These observations are interesting examples of tailored supramolecular self-organization. New antimicrobial tests have also been carried out with these self-assemblies against MRSA and VRE (resistant) strains.
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Affiliation(s)
- László Izsépi
- Doctoral School of Chemistry, University of Debrecen, H-4032 Debrecen, Egyetem tér 1., Hungary;
- Department of Organic Chemistry, University of Debrecen, H-4032 Debrecen, Egyetem tér 1., Hungary;
| | - Réka Erdei
- Department of Organic Chemistry, University of Debrecen, H-4032 Debrecen, Egyetem tér 1., Hungary;
| | - Anna N. Tevyashova
- Gause Institute of New Antibiotics, 11 B. Pirogovskaya, 119021 Moscow, Russia; (A.N.T.); (N.E.G.); (A.E.S.)
| | - Natalia E. Grammatikova
- Gause Institute of New Antibiotics, 11 B. Pirogovskaya, 119021 Moscow, Russia; (A.N.T.); (N.E.G.); (A.E.S.)
| | - Andrey E. Shchekotikhin
- Gause Institute of New Antibiotics, 11 B. Pirogovskaya, 119021 Moscow, Russia; (A.N.T.); (N.E.G.); (A.E.S.)
| | - Pál Herczegh
- Department of Pharmaceutical Chemistry, University of Debrecen, H-4032 Debrecen, Egyetem tér 1., Hungary;
| | - Gyula Batta
- Department of Organic Chemistry, University of Debrecen, H-4032 Debrecen, Egyetem tér 1., Hungary;
- Correspondence:
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5
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Yang X, Beroske LP, Kemmink J, Rijkers DT, Liskamp RM. Synthesis of bicyclic tripeptides inspired by the ABC-ring system of vancomycin through ruthenium-based cyclization chemistries. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.10.046] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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6
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Kiamco MM, Atci E, Khan QF, Mohamed A, Renslow RS, Abu-Lail N, Fransson BA, Call DR, Beyenal H. Vancomycin and maltodextrin affect structure and activity of Staphylococcus aureus biofilms. Biotechnol Bioeng 2015; 112:2562-70. [PMID: 26084588 DOI: 10.1002/bit.25681] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 06/05/2015] [Accepted: 06/09/2015] [Indexed: 01/15/2023]
Abstract
Hyperosmotic agents such as maltodextrin negatively impact bacterial growth through osmotic stress without contributing to drug resistance. We hypothesized that a combination of maltodextrin (osmotic agent) and vancomycin (antibiotic) would be more effective against Staphylococcus aureus biofilms than either alone. To test our hypothesis, S. aureus was grown in a flat plate flow cell reactor. Confocal laser scanning microscopy images were analyzed to quantify changes in biofilm structure. We used dissolved oxygen microelectrodes to quantify how vancomycin and maltodextrin affected the respiration rate and oxygen penetration into the biofilm. We found that treatment with vancomycin or maltodextrin altered biofilm structure. The effect on the structure was significant when they were used simultaneously to treat S. aureus biofilms. In addition, vancomycin treatment increased the oxygen respiration rate, while maltodextrin treatment caused an increase and then a decrease. An increased maltodextrin concentration decreased the diffusivity of the antibiotic. Overall, we conclude that (1) an increased maltodextrin concentration decreases vancomycin diffusion but increases the osmotic effect, leading to the optimum treatment condition, and (2) the combination of vancomycin and maltodextrin is more effective against S. aureus biofilms than either alone. Vancomycin and maltodextrin act together to increase the effectiveness of treatment against S. aureus biofilm growth.
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Affiliation(s)
- Mia Mae Kiamco
- The Gene and Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington
| | - Erhan Atci
- The Gene and Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington
| | - Qaiser Farid Khan
- The Gene and Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington
| | - Abdelrhman Mohamed
- The Gene and Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington
| | - Ryan S Renslow
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington
| | - Nehal Abu-Lail
- The Gene and Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington
| | - Boel A Fransson
- Department of Veterinary Clinical Sciences, Washington State University, Pullman, Washington
| | - Douglas R Call
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, Washington
| | - Haluk Beyenal
- The Gene and Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington.
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7
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Abstract
Chiral recognition phenomena play an important role in nature as well as analytical separation sciences. In separation sciences such as chromatography and capillary electrophoresis, enantiospecific interactions between the enantiomers of an analyte and the chiral selector are required in order to observe enantioseparations. Due to the large structural variety of chiral selectors applied, different mechanisms and structural features contribute to the chiral recognition process. This chapter briefly illustrates the current models of the enantiospecific recognition on the structural basics of various chiral selectors.
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Affiliation(s)
- Gerhard K E Scriba
- Department of Pharmaceutical/Medicinal Chemistry, Friedrich Schiller University Jena, Jena, Germany.
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8
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Abstract
Capillary electrophoresis (CE) has matured to one of the major liquid phase enantiodifferentiation techniques since the first report in 1985. This can be primarily attributed to the flexibility as well as the various modes available including electrokinetic chromatography (EKC), micellar electrokinetic chromatography (MEKC), and microemulsion electrokinetic chromatography (MEEKC). In contrast to chromatographic techniques, the chiral selector is mobile in the background electrolyte. Furthermore, a large variety of chiral selectors are available that can be easily combined in the same separation system. In addition, the migration order of the enantiomers can be adjusted by a number of approaches. In CE enantiodifferentiations the separation principle is comparable to chromatography while the principle of the movement of the analytes in the capillary is based on electrophoretic phenomena. The present chapter will focus on mechanistic aspects of CE enantioseparations including enantiomer migration order and the current understanding of selector-selectand structures. Selected examples of the basic enantioseparation modes EKC, MEKC, and MEEKC will be discussed.
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Affiliation(s)
- Gerhard K E Scriba
- Department of Pharmaceutical/Medicinal Chemistry, Friedrich Schiller University Jena, Philosophenweg 14, 07743, Jena, Germany,
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9
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Zhang J, Kemmink J, Rijkers DTS, Liskamp RMJ. Synthesis of 1,5-triazole bridged vancomycin CDE-ring bicyclic mimics using RuAAC macrocyclization. Chem Commun (Camb) 2013; 49:4498-500. [DOI: 10.1039/c3cc40628h] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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10
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Abstract
The incidence of antibiotic resistance among pathogenic microorganisms is increasing at an alarming rate. Resistance against front-line therapeutics such as the glycopeptide antibiotic vancomycin has emerged and has spread to highly virulent pathogens, including Staphylococcus aureus. Glycopeptide antibiotics are natural products from the Actinomycetes that have a characteristic heptapeptide core. The chemical diversity of the class is achieved through glycosylation, halogenation, methylation, and acylation of the core, modifications that are implicated in improved solubility, stability, or activity of the molecule. Sulfation is yet another modification observed infrequently in glycopeptides, but its role is not known. Although glycopeptide sulfotransferases are found in the environmental metagenome and must therefore serve an evolutionary purpose, all previous studies have reported decreased antibiotic activity with sulfation. We report that sulfation of glycopeptides has little effect on the compound's ability to bind its target, the d-Ala-d-Ala peptidoglycan precursors of the bacterial cell wall. However, sulfation does impact glycopeptide dimerization, and importantly, sulfated glycopeptides are significantly less potent inducers of the resistance gene cluster vanHAX in actinomycetes. Our results begin to unravel the mystery of the biological role of glycopeptide sulfation and offer a potential new strategy for the development of new antibiotics that avoid resistance.
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12
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Liskamp RMJ, Rijkers DTS, Kruijtzer JAW, Kemmink J. Peptides and proteins as a continuing exciting source of inspiration for peptidomimetics. Chembiochem 2011; 12:1626-53. [PMID: 21751324 DOI: 10.1002/cbic.201000717] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Indexed: 12/17/2022]
Abstract
Despite their enormous diversity in biological function and structure, peptides and proteins are endowed with properties that have induced and stimulated the development of peptidomimetics. Clearly, peptides can be considered as the "stem" of a phylogenetic molecular development tree from which branches of oligomeric peptidomimetics such as peptoids, peptidosulfonamides, urea peptidomimetics, as well as β-peptides have sprouted. It is still a challenge to efficiently synthesize these oligomeric species, and study their structural and biological properties. Combining peptides and peptidomimetics led to the emergence of peptide-peptidomimetic hybrids in which one or more (proteinogenic) amino acid residues have been replaced with these mimetic residues. In scan-like approaches, the influence of these replacements on biological activity can then be studied, to evaluate to what extent a peptide can be transformed into a peptidomimetic structure while maintaining, or even improving, its biological properties. A central issue, especially with the smaller peptides, is the lack of secondary structure. Important approaches to control secondary structure include the introduction of α,α-disubstituted amino acids, or (di)peptidomimetic structures such as the Freidinger lactam. Apart from intra-amino acid constraints, inter-amino acid constraints for formation of a diversity of cyclic peptides have shaped a thick branch. Apart from the classical disulfide bridges, the repertoire has been extended to include sulfide and triazole bridges as well as the single-, double- and even triple-bond replacements, accessible by the extremely versatile ring-closing alkene/alkyne metathesis approaches. The latter approach is now the method of choice for the secondary structure that presents the greatest challenge for structural stabilization: the α-helix.
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Affiliation(s)
- Rob M J Liskamp
- Medicinal Chemistry and Chemical Biology, Department of Pharmaceutical Sciences, Faculty of Science, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands.
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13
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Zhang J, Kemmink J, Rijkers DTS, Liskamp RMJ. Cu(I)- and Ru(II)-mediated "click" cyclization of tripeptides toward vancomycin-inspired mimics. Org Lett 2011; 13:3438-41. [PMID: 21615166 DOI: 10.1021/ol201184b] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Structural mimics comprising 1,4- and 1,5-disubstituted triazole-containing cyclic tripeptides with excellent resemblance toward the DE-ring of vancomycin are conveniently accessible using Cu(I)- or Ru(II)-assisted "click" cyclization.
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Affiliation(s)
- Jinqiang Zhang
- Division of Medicinal Chemistry & Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutical Sciences, Faculty of Science, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands
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14
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Kikuchi T, Karki S, Fujisawa I, Matsushima Y, Nitanai Y, Aoki K. Crystal Structures of Two Vancomycin Complexes with Phosphate andN-Acetyl–D-Ala. Structural Comparison between Low-Affinity and High-Affinity Ligand Complexes of Vancomycin. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2010. [DOI: 10.1246/bcsj.20090326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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15
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Kövér KE, Szilágyi L, Batta G, Uhrín D, Jiménez-Barbero J. Biomolecular Recognition by Oligosaccharides and Glycopeptides: The NMR Point of View. COMPREHENSIVE NATURAL PRODUCTS II 2010:197-246. [DOI: 10.1016/b978-008045382-8.00193-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
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16
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Highlighting the possible secondary interactions in the role of balhimycin and its analogues for enantiorecognition in capillary electrophoresis. J Chromatogr A 2009; 1217:1149-56. [PMID: 19782369 DOI: 10.1016/j.chroma.2009.09.035] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Revised: 09/10/2009] [Accepted: 09/14/2009] [Indexed: 11/23/2022]
Abstract
It is believed that the enantiorecognition mechanism based on macrocyclic antibiotics involves multimodal interactions via hydrogen bonding, pi-pi interaction, steric hindrance, hydrophobic interaction and so on. A variety of enantiomeric N-benzoylated amino acids were separated using balhimycin (A) or its analogues bromobalhimycin (B) and dechlorobalhimycin (C) as chiral mobile phase additive using a CE method, which combined the partial filling technique with the dynamic coating technique and the co-EOF electrophoresis technique. The enantioresolution and the migration time were highly relevant to the structure of analytes, especially to the substitutions on the N-tagged benzoyl moiety of the amino acids. A steric effect and pi-pi interaction based mechanism is proposed in order to explain some observed enantioresolution differences between positional isomers. Notably dechlorobalhimycin exhibited the best enantioresolution for several N-benzoylated derivatives of leucine, which was rarely observed for N-dansylated amino acid derivatives. The hydrophobicity difference of the aglycone pocket among three chiral selectors was assumed to account for this behaviour.
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Domenech O, Francius G, Tulkens PM, Van Bambeke F, Dufrêne Y, Mingeot-Leclercq MP. Interactions of oritavancin, a new lipoglycopeptide derived from vancomycin, with phospholipid bilayers: Effect on membrane permeability and nanoscale lipid membrane organization. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:1832-40. [DOI: 10.1016/j.bbamem.2009.05.003] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Revised: 04/25/2009] [Accepted: 05/05/2009] [Indexed: 11/25/2022]
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18
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Nahoum V, Spector S, Loll PJ. Structure of ristocetin A in complex with a bacterial cell-wall mimetic. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:832-8. [PMID: 19622867 DOI: 10.1107/s0907444909018344] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Accepted: 05/14/2009] [Indexed: 11/10/2022]
Abstract
Antimicrobial drug resistance is a serious public health problem and the development of new antibiotics has become an important priority. Ristocetin A is a class III glycopeptide antibiotic that is used in the diagnosis of von Willebrand disease and which has served as a lead compound for the development of new antimicrobial therapeutics. The 1.0 A resolution crystal structure of the complex between ristocetin A and a bacterial cell-wall peptide has been determined. As is observed for most other glycopeptide antibiotics, it is shown that ristocetin A forms a back-to-back dimer containing concave binding pockets that recognize the cell-wall peptide. A comparison of the structure of ristocetin A with those of class I glycopeptide antibiotics such as vancomycin and balhimycin identifies differences in the details of dimerization and ligand binding. The structure of the ligand-binding site reveals a likely explanation for ristocetin A's unique anticooperativity between dimerization and ligand binding.
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Affiliation(s)
- Virginie Nahoum
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
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19
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Nitanai Y, Kikuchi T, Kakoi K, Hanamaki S, Fujisawa I, Aoki K. Crystal Structures of the Complexes between Vancomycin and Cell-Wall Precursor Analogs. J Mol Biol 2009; 385:1422-32. [DOI: 10.1016/j.jmb.2008.10.026] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Revised: 10/06/2008] [Accepted: 10/08/2008] [Indexed: 11/29/2022]
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20
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Loll PJ, Derhovanessian A, Shapovalov MV, Kaplan J, Yang L, Axelsen PH. Vancomycin forms ligand-mediated supramolecular complexes. J Mol Biol 2008; 385:200-11. [PMID: 18983853 DOI: 10.1016/j.jmb.2008.10.049] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2008] [Revised: 10/10/2008] [Accepted: 10/11/2008] [Indexed: 11/28/2022]
Abstract
The emergence of resistance to vancomycin and related glycopeptide antibiotics is spurring efforts to develop new antimicrobial therapeutics. High-resolution structural information about antibiotic-ligand recognition should prove valuable in the rational design of improved drugs. We have determined the X-ray crystal structure of the complex of vancomycin with N-acetyl-D-Ala-D-Ala, a mimic of the natural muramyl peptide target, and refined this structure at a resolution of 1.3 A to R and R(free) values of 0.172 and 0.195, respectively. The crystal asymmetric unit contains three back-back vancomycin dimers; two of these dimers participate in ligand-mediated face-face interactions that produce an infinite chain of molecules running throughout the crystal. The third dimer packs against the side of a face-face interface in a tight "side-side" interaction that involves both polar contacts and burial of hydrophobic surface. The trimer of dimers found in the asymmetric unit is essentially identical to complexes seen in three other crystal structures of glycopeptide antibiotics complexed with peptide ligands. These four structures are derived from crystals belonging to different space groups, suggesting that the trimer of dimers may not be simply a crystal packing artifact and prompting us to ask if ligand-mediated oligomerization could be observed in solution. Using size-exclusion chromatography, dynamic light scattering, and small-angle X-ray scattering, we demonstrate that vancomycin forms discrete supramolecular complexes in the presence of tripeptide ligands. Size estimates for these complexes are consistent with assemblies containing four to six vancomycin monomers.
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Affiliation(s)
- Patrick J Loll
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA.
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21
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Bauvais C, Barbault F, Zhu Y, Petitjean M, Fan BT. Elucidation of chiral recognition processes of macrocyclic antibiotic vancomycin. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2006; 17:253-64. [PMID: 16815766 DOI: 10.1080/10659360600787783] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
A theoretical investigation was carried out on the retention and separation of enantiomeric molecules including nonsteroidal anti-inflammatory drugs, anti-neoplastic compounds and N-derivatized amino acids by capillary electrophoresis using macrocyclic antibiotics, a new class of chiral selectors, as stationary phase. Firstly docking methods were used to study the enantiorecognition in chiral electrophoresis. The molecular dynamics simulations of the two diastereoisomer complexes were then performed in order to understand how these antibiotics recognize the enantiomers. Another approach was applied in this study to establish a quantitative structure-enantioselectivity relationship (QSER) model, able to describe the resolution of a series of chiral compounds in capillary electrophoresis using vancomycin as the resolving agent.
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Affiliation(s)
- C Bauvais
- ITODYS, CNRS UMR 7086, Université Paris 7 - Denis Diderot, 1 rue Guy de la Brosse, 75005, Paris, France
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22
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Lee JG, Sagui C, Roland C. Quantum Simulations of the Structure and Binding of Glycopeptide Antibiotic Aglycons to Cell Wall Analogues. J Phys Chem B 2005; 109:20588-96. [PMID: 16853665 DOI: 10.1021/jp0548117] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The recent rise of vancomycin-resistant enterococci (VRE) and vancomycin-resistant Staphylococcus aureus (VRSA) has given new impetus to the study of the binding between glycopeptide antibiotics and bacterial cell wall termini. Here, we report on an extensive first principles investigation of the binding of vancomycin, avoparcin, teicoplanin, and ristocetin aglycons with dipetides, Ac-d-Ala-X, where X = d-Lac and d-Ser (characteristic of VREs) and X = d-Ala, Gly (characteristic of non-VREs), and a model "methylated d-Ala" CH(2)CH(CH(3))COO(-), in liquid as well as gas phase. The gas-phase ordering of the binding, from strongest to weakest, is Gly, d-Ala, d-Ser, CH(2)CH(CH(3))COO(-), and d-Lac. Calculations show that the order of the Gly and d-Ala binding is reversed in solution. The results are in good agreement with recent experimental findings.
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Affiliation(s)
- Jung-Goo Lee
- Center for High Performance Simulations (CHiPS) and Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
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Lee JG, Sagui C, Roland C. First Principles Investigation of Vancomycin and Teicoplanin Binding to Bacterial Cell Wall Termini. J Am Chem Soc 2004; 126:8384-5. [PMID: 15237988 DOI: 10.1021/ja048645c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The recent rise of vancomycin-resistant enterococci (VRE) has given new impetus to the study of the binding between glycopeptide antibiotics and bacterial cell wall termini. Here, we report on an extensive first principles investigation of the binding of vancomycin and teicoplanin with d-Ala-d-Lac (characteristic of VREs) and d-Ala-d-Ala (characteristic of non-VREs). Binding of both antibiotics to d-Ala-d-Ala was found to be stronger by about 3-5 kcal/mol and due primarily to the oxygen-oxygen lone-pair repulsion characteristic of the antibiotic/d-Ala-d-Lac complex. These results are in good agreement with recent experimental findings.
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Affiliation(s)
- Jung-Goo Lee
- Department of Physics, The North Carolina State University, Raleigh, North Carolina 27695-82802, USA
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