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Zhao Y, Bai Y, Zhang Q, Chen Z, Dai Q, Ma C. A facile method for the synthesis of pyridazino[4,5-b][1,4]thiazine-diones via Smiles rearrangement. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.04.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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2
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Mechanisms mediating bactericidal properties and conditions that enhance the potency of a broad-spectrum oligo-acyl-lysyl. Antimicrob Agents Chemother 2010; 55:688-95. [PMID: 21078924 DOI: 10.1128/aac.00666-10] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Previous studies have established the potential of the oligo-acyl-lysyl (OAK) concept in generating simple chemical mimics of host defense peptides (HDPs) with improved antimicrobial properties. We investigated the antibacterial properties of such an OAK, C(16(ω7))-KK-C(12)-K(amide), to obtain a better understanding of the complex mode(s) of action of cationic antibacterial peptides. The average MIC, determined against a multispecies panel of 50 strains, was 6 ± 5 μg/ml. However, although the OAK exerted an essentially dose-dependent bactericidal effect (time-kill curves typically exhibited 99% death within 2 h), marked differences in the killing rates occurred among inter- and intraspecies strains. Mechanistic comparison between equally sensitive and related strains revealed death of one strain to stem from the OAK's capacity to breach the cell membrane permeability barrier, whereas the death of the related strain resulted from the OAK's direct interference with DNA functions in vivo, without detectable membrane damage. These findings therefore support the notion that the antibacterial mechanism of action of a single HDP can vary among inter- and intraspecies strains. In addition, we present data illustrating the differential effects of environmental conditions (pH, ionic strength and temperature), on the OAK's antibacterial properties, and ultimately demonstrate potency enhancement (by orders of magnitude) through selection of optimal incubation conditions. Such attributes might be useful in a variety of antibacterial applications.
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Rotem S, Mor A. Antimicrobial peptide mimics for improved therapeutic properties. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1788:1582-92. [PMID: 19028449 DOI: 10.1016/j.bbamem.2008.10.020] [Citation(s) in RCA: 203] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Revised: 10/16/2008] [Accepted: 10/21/2008] [Indexed: 01/04/2023]
Abstract
The relatively recent recognition of the major role played by antimicrobial peptides (AMPs) in sustaining an effective host response to immune challenges was greatly influenced by studies of amphibian peptides. AMPs are also widely regarded as a potential source of future antibiotics owing to a remarkable set of advantageous properties ranging from molecular simplicity to low-resistance swift-kill of a broad range of microbial cells. However, the peptide formula per se, represents less than ideal drug candidates, namely because of poor bioavailability issues, potential immunogenicity, optional toxicity and high production costs. To address these issues, synthetic peptides have been designed, reproducing the critical peptide biophysical characteristic in unnatural sequence-specific oligomers. Thus, the use of peptidomimetics to overcome the limitations inherent to peptides physical characteristics is becoming an important and promising approach for improving the therapeutic potential of AMPs. Here, we review most recent advances in the design strategies and the biophysical properties of the main classes of mimics to natural AMPs, emphasizing the importance of structure-activity relationship studies in fine-tuning of their physicochemical attributes for improved antimicrobial properties.
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Affiliation(s)
- Shahar Rotem
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Israel
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Tu S, Li C, Li G, Cao L, Shao Q, Zhou D, Jiang B, Zhou J, Xia M. Microwave-assisted combinatorial synthesis of polysubstituent imidazo[1,2-a]quinoline, pyrimido[1,2-a]quinoline and quinolino[1,2-a]quinazoline derivatives. ACTA ACUST UNITED AC 2007; 9:1144-8. [PMID: 17953448 DOI: 10.1021/cc700124g] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of unusual fused heterocyclic compound derivatives, consisting of a pyridine and a imidazole or pyrimidine core, with a bridgehead nitrogen, were successfully synthesized by a microwave-assisted, three-component domino reaction of aldehydes, enaminones, and malononnitrile. In this one-pot reaction, up to five new bonds were formed accompanied by generating the lactam group. This method has the advantages of short synthetic route, operational simplicity, increased safety for small-scale high-speed synthesis, and minimal environment impact.
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Affiliation(s)
- Shujiang Tu
- School of Chemistry and Chemical Engineering, Xuzhou Normal University, Key Laboratory of Biotechnology for Medicinal Plant, Xuzhou, Jiangsu, 221116, PR China.
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Abzalimov RR, Dubin PL, Kaltashov IA. Glycosaminoglycans as Naturally Occurring Combinatorial Libraries: Developing a Mass Spectrometry-Based Strategy for Characterization of Anti-Thrombin Interaction with Low Molecular Weight Heparin and Heparin Oligomers. Anal Chem 2007; 79:6055-63. [PMID: 17658885 DOI: 10.1021/ac0710432] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Heparin is a densely charged polysaccharide, which is best known for its anticoagulant activity, although it also modulates a plethora of other biological processes. Unlike biopolymers whose synthesis is strictly controlled by a unique genetic template, heparin molecules exhibit a remarkable degree of structural heterogeneity, which poses a serious challenge for studies of heparin-protein interactions. This analytical challenge is often dealt with by reducing the enormous structural repertoire of heparin to a model small molecule. In this paper, we describe a different approach inspired by the experimental methodologies from the arsenal of combinatorial chemistry. Interaction of anti-thrombin III (AT) with heparinoids is studied using a mixture of oligoheparin molecules of fixed degree of polymerization, but varying chemical composition (heparin hexasaccharides obtained by size exclusion chromatography of an enzymatic digest of porcine intestinal heparin with bacterial heparinase), as well as a heparin-derived pharmaceutical preparation Tinzaparin (heparin oligosaccharides up to a 22-mer). AT binders are identified based on the results of ESI MS measurements of complexes formed by protein-oligoheparin association. Additionally, differential depletion of free heparin oligomers in solution in the presence of AT is used to verify the binding preferences. ESI MS characterization of oligoheparin-AT interaction under partially denaturing conditions allowed the conformer specificity of the protein-polyanion binding to be monitored. A model emerging from these studies invokes the notion of a well-defined binding site on AT, to which a flexible partner (heparin) adapts to maximize favorable intermolecular electrostatic interactions. This study demonstrates the enormous potential of ESI MS as an analytical tool to study the interactions of highly heterogeneous glycosaminoglycans with their cognate proteins outside of the commonly accepted reductionist paradigm, which reduces the intrinsic complexity of heparin by using structurally defined homogeneous low molecular weight mimetics.
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Affiliation(s)
- Rinat R Abzalimov
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003, USA
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Hilpert K, Winkler DFH, Hancock REW. Cellulose-bound Peptide Arrays: Preparation and Applications. Biotechnol Genet Eng Rev 2007; 24:31-106. [DOI: 10.1080/02648725.2007.10648093] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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7
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Lee HK, Chui WK. Combinatorial mixture synthesis and biological evaluation of dihydrophenyl triazine antifolates. Bioorg Med Chem 1999; 7:1255-62. [PMID: 10428399 DOI: 10.1016/s0968-0896(99)00051-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The traditional 'one-pot' three component synthesis was adapted successfully for combinatorial mixtures synthesis of dihydrophenyl triazines, which are nonclassical, dihydrofolate reductase (DHFR) inhibitors. Each library was designed to comprise eight reaction mixture pots and in every pot there were three dihydrophenyl triazines. A total of three libraries were synthesized and the final number of compounds harvested was 64. The products precipitated out of the reaction mixture and could be collected easily and cleansed by washing. Solid supports and further purification processes were not required. The reactions were monitored by TLC and a HPLC method was developed to determine the number of products in each pot. All 24 pots were screened for inhibitory activity against the rat liver DHFR. Two pots showed good inhibitory activity and the products in them were individually synthesized, characterized and biologically tested again. One lead compound was identified amongst all the compounds synthesized, and would be further optimized.
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Affiliation(s)
- H K Lee
- Department of Pharmacy, Faculty of Science, National University of Singapore, Singapore
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Nefzi A, Ostresh JM, Giulianotti M, Houghten RA. Solid-Phase Synthesis of Trisubstituted 2-Imidazolidones and 2-Imidazolidinethiones. ACTA ACUST UNITED AC 1999. [DOI: 10.1021/cc980019m] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Adel Nefzi
- Torrey Pines Institute for Molecular Studies, 3550 General Atomics Court, San Diego, California 92121
| | - John M. Ostresh
- Torrey Pines Institute for Molecular Studies, 3550 General Atomics Court, San Diego, California 92121
| | - Marc Giulianotti
- Torrey Pines Institute for Molecular Studies, 3550 General Atomics Court, San Diego, California 92121
| | - Richard A. Houghten
- Torrey Pines Institute for Molecular Studies, 3550 General Atomics Court, San Diego, California 92121
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Kundu B, Khare SK, Rastogi SK. Combinatorial chemistry: Polymer supported synthesis of peptide and non-peptide libraries. PROGRESS IN DRUG RESEARCH 1999; 53:89-156. [PMID: 10616297 DOI: 10.1007/978-3-0348-8735-9_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
Abstract
In recent years, combinatorial chemistry has emerged as a powerful tool for accelerating drug discovery. While industry is rapidly embracing the technology, researchers continue to develop novel library methods including resins, linkers, tagging and deconvolution techniques. Newer strategies involving computer-customized combinatorial libraries offer enormous potential for the design of more "focused" and "smart" chemical libraries with maximal diversity. In addition, miniaturized systems for synthesizing chemical libraries are also being developed, which has made it possible to carry out reactions at submicroliter volumes.
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Affiliation(s)
- B Kundu
- Division of Medicinal Chemistry, Central Drug Research Institute, Lucknow, India
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Eliseev AV, Nelen MI. Use of Molecular Recognition To Drive Chemical Evolution: Mechanisms of an Automated Genetic Algorithm Implementation. Chemistry 1998. [DOI: 10.1002/(sici)1521-3765(19980515)4:5<825::aid-chem825>3.0.co;2-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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11
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Manual solid-phase syntheses of peptides on resins with high loading capacity requiring small volumes of solvents. J CHEM SCI 1997. [DOI: 10.1007/bf02875973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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12
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An H, Haly BD, Fraser AS, Guinosso CJ, Cook PD. Solution Phase Combinatorial Chemistry. Synthesis of Novel Linear Pyridinopolyamine Libraries with Potent Antibacterial Activity. J Org Chem 1997. [DOI: 10.1021/jo970535j] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Haoyun An
- Isis Pharmaceuticals, Inc., 2292 Faraday Avenue, Carlsbad, California 92008
| | - Becky D. Haly
- Isis Pharmaceuticals, Inc., 2292 Faraday Avenue, Carlsbad, California 92008
| | - Allister S. Fraser
- Isis Pharmaceuticals, Inc., 2292 Faraday Avenue, Carlsbad, California 92008
| | | | - P. Dan Cook
- Isis Pharmaceuticals, Inc., 2292 Faraday Avenue, Carlsbad, California 92008
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Combinatorial chemistry and natural products. Teicoplanin aglycone as a molecular scaffold for solid phase synthesis of combinatorial libraries. Tetrahedron Lett 1996. [DOI: 10.1016/0040-4039(96)01350-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Freier SM, Konings DA, Wyatt JR, Ecker DJ. 'Mutational SURF': a strategy for improving lead compounds identified from combinatorial libraries. Bioorg Med Chem 1996; 4:717-25. [PMID: 8804538 DOI: 10.1016/0968-0896(96)00068-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Synthesis and testing of mixtures of compounds in a combinatorial library offers the potential of much greater throughput than the 'one compound, one well' approach. When mixtures of compounds are screened, however, pooling and deconvolution strategies must be employed to identify the most active compound in the library. The possibility exists that the most active compound will not be identified. We have developed a theoretical model of library deconvolution using the well characterized properties of nucleic acid hybridization to calculate activities of individual molecules in libraries of more than 250,000 compounds. Calculations using this model have been employed to evaluate strategies for pooling and deconvolution. In the presence of errors in synthesis and testing, iterative deconvolution or position scanning sometimes identified a compound with sub-optimal activity. We describe a procedure called 'mutational SURF' in which 'mutants' of the selected compound are individually synthesized and tested. Simulations of mutational SURF using our model libraries suggest that mutational SURF provides an efficient method for improving the activity of lead compounds identified from combinatorial libraries.
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Affiliation(s)
- S M Freier
- ISIS Pharmaceuticals, Carlsbad, CA 92008, USA
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