1
|
Benzyl (R)-2-(Acetylthio)Propanoate: A Promising Sulfur Isoster of (R)-Lactic Acid and Ester Precursors. MOLBANK 2018. [DOI: 10.3390/m1010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In this paper, an accessible chiral pool synthesis of benzyl (R)-2-(acetylthio)propanoate (acetylthiolactate), which is less odorous than the methyl or ethyl analogue, was performed through a clean SN2 displacement reaction using available AcSK with tris[2-(2-methoxyethoxy)]ethylamine (TDA-1), starting from commercially available benzyl (S)-lactate in 76%, 94% ee (2 steps). Deprotection of the acetyl group using N,N-dimethylethylenediamine afforded benzyl (R)-2-sulfanylpropanoate in 93% yield with 90% ee. These two sulfur-containing benzyl esters were sufficiently odorless to be purified by column chromatography. Direct HPLC analysis was applied to determine the enantiomeric excess without thiazolidin-4-one derivatizations. A complementary debenzylation of benzyl (R)-2-(acetylthio)propanoate was also performed using HBr/AcOH to afford (R)-2-(acetylthio)propanoic acid without critical racemization in 92% yield with 92% ee.
Collapse
|
2
|
Sasaki R, Tanabe Y. Chiral syntheses of methyl (R)-2-Sulfanylcarboxylic esters and acids with optical purity determination using HPLC. Chirality 2018; 30:816-827. [PMID: 29659053 DOI: 10.1002/chir.22860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/06/2018] [Accepted: 02/08/2018] [Indexed: 12/16/2022]
Abstract
Accessible chiral syntheses of 3 types of (R)-2-sulfanylcarboxylic esters and acids were performed: (R)-2-sulfanylpropanoic (thiolactic) ester (53%, 98%ee) and acid (39%, 96%ee), (R)-2-sulfanylsucciinic diester (59%, 96%ee), and (R)-2-mandelic ester (78%, 90%ee) and acid (59%, 96%ee). The present practical and robust method involves (i) clean SN 2 displacement of methanesulfonates of (S)-2-hydroxyesters by using commercially available AcSK with tris(2-[2-methoxyethoxy])ethylamine and (ii) sufficiently mild deacetylation. The optical purity was determined by the corresponding (2R,5R)-trans-thiazolidin-4-one and (2S,5R)-cis-thiazolidin-4-one derivatives based on accurate high-performance liquid chromatography analysis with high-resolution efficiency. Compared with the reported method utilizing AcSCs (generated from AcSH and CsCO3 ), the present method has several advantages, that is, the use of odorless AcCOSK reagent, reasonable reaction velocity, isolation procedure, and accurate, reliable optical purity determination. The use of accessible AcSK has advantages because of easy-to-handle odorless and hygroscopic solid that can be used in a bench-top procedure. The Ti(OiPr)4 catalyst promoted smooth trans-cyclo-condensation to afford (2R,5R)-trans-thiazolidin-4-one formation of (R)-2-sulfanylcarboxylic esters with available N-(benzylidene)methylamine under neutral conditions without any racemization, whereas (2S,5R)-cis-thiazollidin-4-ones were obtained via cis-cyclo-condensation and no catalysts. Direct high-performance liquid chromatography analysis of methyl (R)-mandelate was also performed; however, the resolution efficiency was inferior to that of the thaizolidin-4-one derivatizations.
Collapse
Affiliation(s)
- Ryosuke Sasaki
- Department of Chemistry, School of Science & Technology, Kwansei Gakuin University, Sanda, Japan
| | - Yoo Tanabe
- Department of Chemistry, School of Science & Technology, Kwansei Gakuin University, Sanda, Japan
| |
Collapse
|
3
|
Adediran SA, Sarkar KS, Pratt RF. Kinetic Evidence for a Second Ligand Binding Site on Streptococcus pneumoniae Penicillin-Binding Protein 2x. Biochemistry 2018; 57:1758-1766. [PMID: 29485264 DOI: 10.1021/acs.biochem.7b01209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
High molecular mass penicillin-binding proteins (PBPs, DD-peptidases) of class B, such as Streptococcus pneumoniae PBP2x, catalyze the cross-linking of peptidoglycan in bacterial cell wall biosynthesis and are thus important antibiotic targets. Despite their importance in this regard, structure-function studies of ligands of these enzymes have been impeded by the absence of useful substrates. In vitro, these enzymes do not catalyze peptide hydrolysis or aminolysis, their in vivo reaction, but some, such as PBP2x, do catalyze these reactions of certain thioesters such as PhCH2CONHCH2COSCH(D-Me)CO2- (2). We have now prepared several peptidoglycan-mimetic thioesters that we expected to more closely resemble the natural substrates of these enzymes. To our surprise, however, these compounds, although indeed substrates of PBP2x, did not, unlike 2, appear to form an acyl-enzyme intermediate during hydrolysis, and their turnover was inhibited by certain peptides and N-acylamino acids much more weakly than that of 2. An inhibitor of this type, N-benzyloxycarbonyl-d-glutamic acid, also quenched the fluorescence of PBP2x that had been labeled at the DD-peptidase active site by 6-dansylamidopenicillanic acid. These results were interpreted in terms of a model where the peptidoglycan-mimetic thioesters preferentially bound to and hydrolyzed at a site other than the classical DD-peptidase active site. This second site is likely to represent part of an extended binding site that accommodates a peptidoglycan substrate or regulator in vivo. Such a site may be a target for future inhibitor/antibiotic design.
Collapse
Affiliation(s)
- S A Adediran
- Department of Chemistry , Wesleyan University , Lawn Avenue , Middletown , Connecticut 06459 , United States
| | - Kumar Subarno Sarkar
- Department of Chemistry , Wesleyan University , Lawn Avenue , Middletown , Connecticut 06459 , United States
| | - R F Pratt
- Department of Chemistry , Wesleyan University , Lawn Avenue , Middletown , Connecticut 06459 , United States
| |
Collapse
|
4
|
Affiliation(s)
- R. F. Pratt
- Department
of Chemistry, Wesleyan University, Lawn Avenue, Middletown, Connecticut 06459, United States
| |
Collapse
|
5
|
Avan I, Hall CD, Katritzky AR. Peptidomimetics via modifications of amino acids and peptide bonds. Chem Soc Rev 2014; 43:3575-94. [DOI: 10.1039/c3cs60384a] [Citation(s) in RCA: 183] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
6
|
Schreiber A, Schiller SM. Nanobiotechnology of protein-based compartments: steps toward nanofactories. BIOINSPIRED BIOMIMETIC AND NANOBIOMATERIALS 2013. [DOI: 10.1680/bbn.13.00008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
7
|
Nemmara VV, Adediran SA, Dave K, Duez C, Pratt RF. Dual substrate specificity of Bacillus subtilis PBP4a. Biochemistry 2013; 52:2627-37. [PMID: 23560856 DOI: 10.1021/bi400211q] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial dd-peptidases are the targets of the β-lactam antibiotics. The sharp increase in bacterial resistance toward these antibiotics in recent years has stimulated the search for non-β-lactam alternatives. The substrates of dd-peptidases are elements of peptidoglycan from bacterial cell walls. Attempts to base dd-peptidase inhibitor design on peptidoglycan structure, however, have not been particularly successful to date because the specific substrates for most of these enzymes are unknown. It is known, however, that the preferred substrates of low-molecular mass (LMM) class B and C dd-peptidases contain the free N-terminus of the relevant peptidoglycan. Two very similar LMMC enzymes, for example, the Actinomadura R39 dd-peptidase and Bacillus subtilis PBP4a, recognize a d-α-aminopimelyl terminus. The peptidoglycan of B. subtilis in the vegetative stage, however, has the N-terminal d-α-aminopimelyl carboxylic acid amidated. The question is, therefore, whether the dd-peptidases of B. subtilis are separately specific to carboxylate or carboxamide or have dual specificity. This paper describes an investigation of this issue with B. subtilis PBP4a. This enzyme was indeed found to have a dual specificity for peptide substrates, both in the acyl donor and in the acyl acceptor sites. In contrast, the R39 dd-peptidase, from an organism in which the peptidoglycan is not amidated, has a strong preference for a terminal carboxylate. It was also found that acyl acceptors, reacting with acyl-enzyme intermediates, were preferentially d-amino acid amides for PBP4a and the corresponding amino acids for the R39 dd-peptidase. Examination of the relevant crystal structures, aided by molecular modeling, suggested that the expansion of specificity in PBP4a accompanies a change of Arg351 in the R39 enzyme and most LMMC dd-peptidases to histidine in PBP4a and its orthologs in other Bacillus sp. This histidine, in neutral form at pH 7, appeared to be able to favorably interact with both carboxylate and carboxamide termini of substrates, in agreement with the kinetic data. It may still be possible, in specific cases, to combat bacteria with new antibiotics based on particular elements of their peptidoglycan structure.
Collapse
Affiliation(s)
- Venkatesh V Nemmara
- Department of Chemistry, Wesleyan University, Lawn Avenue, Middletown, Connecticut 06459, USA
| | | | | | | | | |
Collapse
|
8
|
Dzhekieva L, Kumar I, Pratt RF. Inhibition of Bacterial DD-Peptidases (Penicillin-Binding Proteins) in Membranes and in Vivo by Peptidoglycan-Mimetic Boronic Acids. Biochemistry 2012; 51:2804-11. [DOI: 10.1021/bi300148v] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Liudmila Dzhekieva
- Department of Chemistry, Wesleyan University, Lawn Avenue, Middletown, Connecticut 06459,
United
States
| | - Ish Kumar
- School of Natural
Sciences, Fairleigh Dickinson University, Teaneck, New Jersey 07666, United States
| | - R. F. Pratt
- Department of Chemistry, Wesleyan University, Lawn Avenue, Middletown, Connecticut 06459,
United
States
| |
Collapse
|
9
|
Nemmara VV, Dzhekieva L, Sarkar KS, Adediran SA, Duez C, Nicholas RA, Pratt RF. Substrate specificity of low-molecular mass bacterial DD-peptidases. Biochemistry 2011; 50:10091-101. [PMID: 22029692 DOI: 10.1021/bi201326a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bacterial DD-peptidases or penicillin-binding proteins (PBPs) catalyze the formation and regulation of cross-links in peptidoglycan biosynthesis. They are classified into two groups, the high-molecular mass (HMM) and low-molecular mass (LMM) enzymes. The latter group, which is subdivided into classes A-C (LMMA, -B, and -C, respectively), is believed to catalyze DD-carboxypeptidase and endopeptidase reactions in vivo. To date, the specificity of their reactions with particular elements of peptidoglycan structure has not, in general, been defined. This paper describes the steady-state kinetics of hydrolysis of a series of specific peptidoglycan-mimetic peptides, representing various elements of stem peptide structure, catalyzed by a range of LMM PBPs (the LMMA enzymes, Escherichia coli PBP5, Neisseria gonorrhoeae PBP4, and Streptococcus pneumoniae PBP3, and the LMMC enzymes, the Actinomadura R39 dd-peptidase, Bacillus subtilis PBP4a, and N. gonorrhoeae PBP3). The R39 enzyme (LMMC), like the previously studied Streptomyces R61 DD-peptidase (LMMB), specifically and rapidly hydrolyzes stem peptide fragments with a free N-terminus. In accord with this result, the crystal structures of the R61 and R39 enzymes display a binding site specific to the stem peptide N-terminus. These are water-soluble enzymes, however, with no known specific function in vivo. On the other hand, soluble versions of the remaining enzymes of those noted above, all of which are likely to be membrane-bound and/or associated in vivo and have been assigned particular roles in cell wall biosynthesis and maintenance, show little or no specificity for peptides containing elements of peptidoglycan structure. Peptidoglycan-mimetic boronate transition-state analogues do inhibit these enzymes but display notable specificity only for the LMMC enzymes, where, unlike peptide substrates, they may be able to effectively induce a specific active site structure. The manner in which LMMA (and HMM) DD-peptidases achieve substrate specificity, both in vitro and in vivo, remains unknown.
Collapse
Affiliation(s)
- Venkatesh V Nemmara
- Department of Chemistry, Wesleyan University, Lawn Avenue, Middletown, Connecticut 06459, USA
| | | | | | | | | | | | | |
Collapse
|
10
|
One-pot synthesis of diverse DL-configuration dipeptides by a Streptomyces D-stereospecific amidohydrolase. Appl Environ Microbiol 2011; 77:8209-18. [PMID: 21948842 DOI: 10.1128/aem.05543-11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The synthesis of diverse DL-configuration dipeptides in a one-pot reaction was demonstrated by using a function of the aminolysis reaction of a D-stereospecific amidohydrolase from Streptomyces sp., a clan SE, S12 family peptidase categorized as a peptidase with D-stereospecificity. The enzyme was able to use various aminoacyl derivatives, including L-aminoacyl derivatives, as acyl donors and acceptors. Investigations of the specificity of the peptide synthetic activity revealed that the enzyme preferentially used D-aminoacyl derivatives as acyl donors. In contrast, L-amino acids and their derivatives were preferentially used as acyl acceptors. Consequently, the synthesized dipeptides had a DL-configuration when D- and L-aminoacyl derivatives were mixed in a one-pot reaction. This report also describes that the enzyme produced cyclo(D-Pro-L-Arg), a specific inhibitor of family 18 chitinase, with a conversion rate for D-Pro benzyl ester and L-Arg methyl ester to cyclo(D-Pro-L-Arg) of greater than 65%. Furthermore, based on results of cyclo(D-Pro-L-Arg) synthesis, we propose a reaction mechanism for cyclo(D-Pro-L-Arg) production.
Collapse
|
11
|
Arima J, Ito H, Hatanaka T, Mori N. Aminolytic reaction catalyzed by d-stereospecific amidohydrolases from Streptomyces spp. Biochimie 2011; 93:1460-9. [DOI: 10.1016/j.biochi.2011.04.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 04/25/2011] [Indexed: 10/18/2022]
|
12
|
Lupoli TJ, Tsukamoto H, Doud EH, Wang TSA, Walker S, Kahne D. Transpeptidase-mediated incorporation of D-amino acids into bacterial peptidoglycan. J Am Chem Soc 2011; 133:10748-51. [PMID: 21682301 DOI: 10.1021/ja2040656] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The β-lactams are the most important class of antibiotics in clinical use. Their lethal targets are the transpeptidase domains of penicillin binding proteins (PBPs), which catalyze the cross-linking of bacterial peptidoglycan (PG) during cell wall synthesis. The transpeptidation reaction occurs in two steps, the first being formation of a covalent enzyme intermediate and the second involving attack of an amine on this intermediate. Here we use defined PG substrates to dissect the individual steps catalyzed by a purified E. coli transpeptidase. We demonstrate that this transpeptidase accepts a set of structurally diverse D-amino acid substrates and incorporates them into PG fragments. These results provide new information on donor and acceptor requirements as well as a mechanistic basis for previous observations that noncanonical D-amino acids can be introduced into the bacterial cell wall.
Collapse
Affiliation(s)
- Tania J Lupoli
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | | | | | | | | | | |
Collapse
|
13
|
Shi Q, Meroueh SO, Fisher JF, Mobashery S. A computational evaluation of the mechanism of penicillin-binding protein-catalyzed cross-linking of the bacterial cell wall. J Am Chem Soc 2011; 133:5274-83. [PMID: 21417389 DOI: 10.1021/ja1074739] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Penicillin-binding protein 1b (PBP 1b) of the gram-positive bacterium Streptococcus pneumoniae catalyzes the cross-linking of adjacent peptidoglycan strands, as a critical event in the biosynthesis of its cell wall. This enzyme is representative of the biosynthetic PBP structures of the β-lactam-recognizing enzyme superfamily and is the target of the β-lactam antibiotics. In the cross-linking reaction, the amide between the -D-Ala-D-Ala dipeptide at the terminus of a peptide stem acts as an acyl donor toward the ε-amino group of a lysine found on an adjacent stem. The mechanism of this transpeptidation was evaluated using explicit-solvent molecular dynamics simulations and ONIOM quantum mechanics/molecular mechanics calculations. Sequential acyl transfer occurs to, and then from, the active site serine. The resulting cross-link is predicted to have a cis-amide configuration. The ensuing and energetically favorable cis- to trans-amide isomerization, within the active site, may represent the key event driving product release to complete enzymatic turnover.
Collapse
Affiliation(s)
- Qicun Shi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | | | | | | |
Collapse
|
14
|
Extracellular production and characterization of Streptomyces X-prolyl dipeptidyl aminopeptidase. Appl Biochem Biotechnol 2011; 164:475-86. [PMID: 21207186 DOI: 10.1007/s12010-010-9149-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Accepted: 12/16/2010] [Indexed: 10/18/2022]
Abstract
X-prolyl dipeptidyl aminopeptidases (X-PDAPs) are useful in various food industries. In this study, we performed sequence-based screening to obtain a stable X-PDAP enzyme from thermophilic Streptomyces strains. We found three genes that encoded X-PDAP from Streptomyces thermoluteus subsp. fuscus NBRC 14270 (14270 X-PDAP), Streptomyces thermocyaneoviolaceus NBRC 14271 (14271 X-PDAP), and Streptomyces thermocoerulescens NBRC 14273, which were subsequently cloned and sequenced. The deduced amino acid sequences of these genes showed high similarity, with ~80% identity with each other. The isolated X-PDAPs and an X-PDAP from Streptomyces coelicolor were expressed in Streptomyces lividans using a hyperexpression vector: pTONA5a. Among these genes, only 14270 and 14271 X-PDAPs caused overexpression and extracellular production without artificial signal peptides. We also characterized the biochemical properties of purified 14271 X-PDAP. In addition, we found that, in peptide synthesis via an aminolysis reaction, this enzyme recognized D-amino acid derivatives as acyl acceptors, similar to L-amino acid derivatives.
Collapse
|
15
|
Adediran SA, Kumar I, Nagarajan R, Sauvage E, Pratt RF. Kinetics of Reactions of the Actinomadura R39 dd-Peptidase with Specific Substrates. Biochemistry 2010; 50:376-87. [DOI: 10.1021/bi101760p] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- S. A. Adediran
- Department of Chemistry, Wesleyan University, Lawn Avenue, Middletown, Connecticut 06459, United States
| | - Ish Kumar
- Department of Chemistry, Wesleyan University, Lawn Avenue, Middletown, Connecticut 06459, United States
| | - Rajesh Nagarajan
- Department of Chemistry, Wesleyan University, Lawn Avenue, Middletown, Connecticut 06459, United States
| | - Eric Sauvage
- Centre d’Ingéniere des Proteines, Université de Liège, B-4000 Sart Tilman, Liège, Belgium
| | - R. F. Pratt
- Department of Chemistry, Wesleyan University, Lawn Avenue, Middletown, Connecticut 06459, United States
| |
Collapse
|
16
|
Sauvage E, Powell AJ, Heilemann J, Josephine HR, Charlier P, Davies C, Pratt RF. Crystal structures of complexes of bacterial DD-peptidases with peptidoglycan-mimetic ligands: the substrate specificity puzzle. J Mol Biol 2008; 381:383-93. [PMID: 18602645 DOI: 10.1016/j.jmb.2008.06.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Revised: 05/28/2008] [Accepted: 06/01/2008] [Indexed: 10/22/2022]
Abstract
The X-ray crystal structures of covalent complexes of the Actinomadura R39 dd-peptidase and Escherichia coli penicillin-binding protein (PBP) 5 with beta-lactams bearing peptidoglycan-mimetic side chains have been determined. The structure of the hydrolysis product of an analogous peptide bound noncovalently to the former enzyme has also been obtained. The R39 DD-peptidase structures reveal the presence of a specific binding site for the D-alpha-aminopimelyl side chain, characteristic of the stem peptide of Actinomadura R39. This binding site features a hydrophobic cleft for the pimelyl methylene groups and strong hydrogen bonding to the polar terminus. Both of these active site elements are provided by amino acid side chains from two separate domains of the protein. In contrast, no clear electron density corresponding to the terminus of the peptidoglycan-mimetic side chains is present when these beta-lactams are covalently bound to PBP5. There is, therefore, no indication of a specific side-chain binding site in this enzyme. These results are in agreement with those from kinetics studies published earlier and support the general prediction made at the time of a direct correlation between kinetics and structural evidence. The essential high-molecular-mass PBPs have demonstrated, to date, no specific reactivity with peptidoglycan-mimetic peptide substrates and beta-lactam inhibitors and, thus, probably do not possess a specific substrate-binding site of the type demonstrated here with the R39 DD-peptidase. This striking deficiency may represent a sophisticated defense mechanism against low-molecular-mass substrate-analogue inhibitors/antibiotics; its discovery should focus new inhibitor design.
Collapse
Affiliation(s)
- Eric Sauvage
- Centre d'Ingéniere des Proteines, Université de Liège, B-4000 Sart Tilman, Liège, Belgium
| | | | | | | | | | | | | |
Collapse
|
17
|
Crystal structures of biapenem and tebipenem complexed with penicillin-binding proteins 2X and 1A from Streptococcus pneumoniae. Antimicrob Agents Chemother 2008; 52:2053-60. [PMID: 18391040 DOI: 10.1128/aac.01456-07] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biapenem is a parenteral carbapenem antibiotic that exhibits wide-ranging antibacterial activity, remarkable chemical stability, and extensive stability against human renal dehydropeptidase-I. Tebipenem is the active form of tebipenem pivoxil, a novel oral carbapenem antibiotic that has a high level of bioavailability in humans, in addition to the above-mentioned features. beta-lactam antibiotics, including carbapenems, target penicillin-binding proteins (PBPs), which are membrane-associated enzymes that play essential roles in peptidoglycan biosynthesis. To envisage the binding of carbapenems to PBPs, we determined the crystal structures of the trypsin-digested forms of both PBP 2X and PBP 1A from Streptococcus pneumoniae strain R6, each complexed with biapenem or tebipenem. The structures of the complexes revealed that the carbapenem C-2 side chains form hydrophobic interactions with Trp374 and Thr526 of PBP 2X and with Trp411 and Thr543 of PBP 1A. The Trp and Thr residues are conserved in PBP 2B. These results suggest that interactions between the C-2 side chains of carbapenems and the conserved Trp and Thr residues in PBPs play important roles in the binding of carbapenems to PBPs.
Collapse
|
18
|
Buynak JD. Cutting and stitching: the cross-linking of peptidoglycan in the assembly of the bacterial cell wall. ACS Chem Biol 2007; 2:602-5. [PMID: 17894443 DOI: 10.1021/cb700182u] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The machinery responsible for bacterial cell wall synthesis has proven to be an invaluable antibiotic target. Nearly 80 years after the discovery of penicillin, some of the mysteries surrounding this process are finally being unraveled.
Collapse
Affiliation(s)
- John D Buynak
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, USA.
| |
Collapse
|
19
|
Magnet S, Arbeloa A, Mainardi JL, Hugonnet JE, Fourgeaud M, Dubost L, Marie A, Delfosse V, Mayer C, Rice LB, Arthur M. Specificity of L,D-transpeptidases from gram-positive bacteria producing different peptidoglycan chemotypes. J Biol Chem 2007; 282:13151-9. [PMID: 17311917 DOI: 10.1074/jbc.m610911200] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We report here the first direct assessment of the specificity of a class of peptidoglycan cross-linking enzymes, the L,D-transpeptidases, for the highly diverse structure of peptidoglycan precursors of Gram-positive bacteria. The lone functionally characterized member of this new family of active site cysteine peptidases, Ldt(fm) from Enterococcus faecium, was previously shown to bypass the D,D-transpeptidase activity of the classical penicillin-binding proteins leading to high level cross-resistance to glycopeptide and beta-lactam antibiotics. Ldt(fm) homologues from Bacillus subtilis (Ldt(Bs)) and E. faecalis (Ldt(fs)) were found here to cross-link their cognate disaccharide-peptide subunits containing meso-diaminopimelic acid (mesoDAP(3)) and L-Lys(3)-L-Ala-L-Ala at the third position of the stem peptide, respectively, instead of L-Lys(3)-d-iAsn in E. faecium. Ldt(fs) differed from Ldt(fm) and Ldt(Bs) by its capacity to hydrolyze the L-Lys(3)-D-Ala(4) bond of tetrapeptide (L,D-carboxypeptidase activity) and pentapeptide (L,D-endopeptidase activity) stems, in addition to the common cross-linking activity. The three enzymes were specific for their cognate acyl acceptors in the cross-linking reaction. In contrast to Ldt(fs), which was also specific for its cognate acyl donor, Ldt(fm) tolerated substitution of L-Lys(3)-D-iAsn by L-Lys(3)-L-Ala-L-Ala. Likewise, Ldt(Bs) tolerated substitution of mesoDAP(3) by L-Lys(3)-D-iAsn and L-Lys(3)-L-Ala-L-Ala in the acyl donor. Thus, diversification of the structure of peptidoglycan precursors associated with speciation has led to a parallel evolution of the substrate specificity of the L,D-transpeptidases affecting mainly the recognition of the acyl acceptor. Blocking the assembly of the side chain could therefore be used to combat antibiotic resistance involving L,D-transpeptidases.
Collapse
|
20
|
Abstract
Beta-lactam antibiotics restrict bacterial growth by inhibiting DD-peptidases. These enzymes catalyze the final transpeptidation step in bacterial cell wall biosynthesis. Although much structural information is now available for these enzymes, the mechanism of the actual transpeptidation reaction has not been studied in detail. The reaction is known to involve a double-displacement mechanism with an acyl-enzyme intermediate, which can be attacked by water, specific amino acids, peptides, and other acyl acceptors. We describe in this paper an investigation of acyl acceptor specificity and assess the need for general base catalysis in the deacylation transition state of the Streptomyces R61 DD-peptidase. We show, by the criterion of solvent deuterium kinetic isotope effect measurements and proton inventories, that the transition states of specific and nonspecific substrates are very similar, at least with respect to proton motion. The transition states for attack (tetrahedral intermediate formation) by d-amino acids and Gly-l-Xaa dipeptides do not include a general base catalyst, while such catalysis is essential for reaction with water and d-alpha-hydroxy acids. D-Alpha-hydroxy acids act as acyl acceptors for glycyl substrates but not for more specific d-alanyl substrates; hydroxy acids actually behave, more generally, as mixed inhibitors of the DD-peptidase. The structural and mechanistic bases of these observations are discussed; they should inform transition state analogue design.
Collapse
Affiliation(s)
| | | | - R.F. Pratt
- Corresponding Author: Dr. R.F. Pratt, address above, telephone 860-685-2629; e-mail: ; Fax: 860-685-2211
| |
Collapse
|