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Alabugin IV, Kuhn L, Medvedev MG, Krivoshchapov NV, Vil' VA, Yaremenko IA, Mehaffy P, Yarie M, Terent'ev AO, Zolfigol MA. Stereoelectronic power of oxygen in control of chemical reactivity: the anomeric effect is not alone. Chem Soc Rev 2021; 50:10253-10345. [PMID: 34263287 DOI: 10.1039/d1cs00386k] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Although carbon is the central element of organic chemistry, oxygen is the central element of stereoelectronic control in organic chemistry. Generally, a molecule with a C-O bond has both a strong donor (a lone pair) and a strong acceptor (e.g., a σ*C-O orbital), a combination that provides opportunities to influence chemical transformations at both ends of the electron demand spectrum. Oxygen is a stereoelectronic chameleon that adapts to the varying situations in radical, cationic, anionic, and metal-mediated transformations. Arguably, the most historically important stereoelectronic effect is the anomeric effect (AE), i.e., the axial preference of acceptor groups at the anomeric position of sugars. Although AE is generally attributed to hyperconjugative interactions of σ-acceptors with a lone pair at oxygen (negative hyperconjugation), recent literature reports suggested alternative explanations. In this context, it is timely to evaluate the fundamental connections between the AE and a broad variety of O-functional groups. Such connections illustrate the general role of hyperconjugation with oxygen lone pairs in reactivity. Lessons from the AE can be used as the conceptual framework for organizing disjointed observations into a logical body of knowledge. In contrast, neglect of hyperconjugation can be deeply misleading as it removes the stereoelectronic cornerstone on which, as we show in this review, the chemistry of organic oxygen functionalities is largely based. As negative hyperconjugation releases the "underutilized" stereoelectronic power of unshared electrons (the lone pairs) for the stabilization of a developing positive charge, the role of orbital interactions increases when the electronic demand is high and molecules distort from their equilibrium geometries. From this perspective, hyperconjugative anomeric interactions play a unique role in guiding reaction design. In this manuscript, we discuss the reactivity of organic O-functionalities, outline variations in the possible hyperconjugative patterns, and showcase the vast implications of AE for the structure and reactivity. On our journey through a variety of O-containing organic functional groups, from textbook to exotic, we will illustrate how this knowledge can predict chemical reactivity and unlock new useful synthetic transformations.
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Affiliation(s)
- Igor V Alabugin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA.
| | - Leah Kuhn
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA.
| | - Michael G Medvedev
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., 119991 Moscow, Russian Federation.,A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilova St., 119991 Moscow, Russian Federation
| | - Nikolai V Krivoshchapov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., 119991 Moscow, Russian Federation.,Lomonosov Moscow State University, Leninskie Gory 1 (3), Moscow, 119991, Russian Federation
| | - Vera A Vil'
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., 119991 Moscow, Russian Federation
| | - Ivan A Yaremenko
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., 119991 Moscow, Russian Federation
| | - Patricia Mehaffy
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA.
| | - Meysam Yarie
- Department of Organic Chemistry, Faculty of Chemistry, Bu-Ali Sina University, Hamedan 65167, Iran
| | - Alexander O Terent'ev
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., 119991 Moscow, Russian Federation
| | - Mohammad Ali Zolfigol
- Department of Organic Chemistry, Faculty of Chemistry, Bu-Ali Sina University, Hamedan 65167, Iran
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2
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Nothling MD, Xiao Z, Hill NS, Blyth MT, Bhaskaran A, Sani MA, Espinosa-Gomez A, Ngov K, White J, Buscher T, Separovic F, O’Mara ML, Coote ML, Connal LA. A multifunctional surfactant catalyst inspired by hydrolases. SCIENCE ADVANCES 2020; 6:eaaz0404. [PMID: 32270041 PMCID: PMC7112759 DOI: 10.1126/sciadv.aaz0404] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/08/2020] [Indexed: 05/04/2023]
Abstract
The remarkable power of enzymes to undertake catalysis frequently stems from their grouping of multiple, complementary chemical units within close proximity around the enzyme active site. Motivated by this, we report here a bioinspired surfactant catalyst that incorporates a variety of chemical functionalities common to hydrolytic enzymes. The textbook hydrolase active site, the catalytic triad, is modeled by positioning the three groups of the triad (-OH, -imidazole, and -CO2H) on a single, trifunctional surfactant molecule. To support this, we recreate the hydrogen bond donating arrangement of the oxyanion hole by imparting surfactant functionality to a guanidinium headgroup. Self-assembly of these amphiphiles in solution drives the collection of functional headgroups into close proximity around a hydrophobic nano-environment, affording hydrolysis of a model ester at rates that challenge α-chymotrypsin. Structural assessment via NMR and XRD, paired with MD simulation and QM calculation, reveals marked similarities of the co-micelle catalyst to native enzymes.
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Affiliation(s)
- Mitchell D. Nothling
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Zeyun Xiao
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
| | - Nicholas S. Hill
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Mitchell T. Blyth
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Ayana Bhaskaran
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Marc-Antoine Sani
- School of Chemistry, Bio21 Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Andrea Espinosa-Gomez
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Kevin Ngov
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Jonathan White
- School of Chemistry, Bio21 Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Tim Buscher
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Frances Separovic
- School of Chemistry, Bio21 Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Megan L. O’Mara
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Michelle L. Coote
- ARC Centre of Excellence for Electromaterials Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Luke A. Connal
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- Corresponding author.
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3
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In vitro studies of dermally absorbed Cu(II) tripeptide complexes as potential anti-inflammatory drugs. Polyhedron 2017. [DOI: 10.1016/j.poly.2016.10.048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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4
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Sharipov BT, Pershin AA, Salikhov SM, Valeev FA. Eleuthesides and their analogs: XI. Final stage of the synthesis of sarcodictyin A analog with 14-methylcyclohex-12-ene ring A. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2016. [DOI: 10.1134/s1070428016050171] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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D’Ascenzo L, Auffinger P. A comprehensive classification and nomenclature of carboxyl-carboxyl(ate) supramolecular motifs and related catemers: implications for biomolecular systems. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2015; 71:164-75. [PMID: 25827369 PMCID: PMC4383392 DOI: 10.1107/s205252061500270x] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 02/08/2015] [Indexed: 05/13/2023]
Abstract
Carboxyl and carboxylate groups form important supramolecular motifs (synthons). Besides carboxyl cyclic dimers, carboxyl and carboxylate groups can associate through a single hydrogen bond. Carboxylic groups can further form polymeric-like catemer chains within crystals. To date, no exhaustive classification of these motifs has been established. In this work, 17 association types were identified (13 carboxyl-carboxyl and 4 carboxyl-carboxylate motifs) by taking into account the syn and anti carboxyl conformers, as well as the syn and anti lone pairs of the O atoms. From these data, a simple rule was derived stating that only eight distinct catemer motifs involving repetitive combinations of syn and anti carboxyl groups can be formed. Examples extracted from the Cambridge Structural Database (CSD) for all identified dimers and catemers are presented, as well as statistical data related to their occurrence and conformational preferences. The inter-carboxyl(ate) and carboxyl(ate)-water hydrogen-bond properties are described, stressing the occurrence of very short (strong) hydrogen bonds. The precise characterization and classification of these supramolecular motifs should be of interest in crystal engineering, pharmaceutical and also biomolecular sciences, where similar motifs occur in the form of pairs of Asp/Glu amino acids or motifs involving ligands bearing carboxyl(ate) groups. Hence, we present data emphasizing how the analysis of hydrogen-containing small molecules of high resolution can help understand structural aspects of larger and more complex biomolecular systems of lower resolution.
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Affiliation(s)
- Luigi D’Ascenzo
- Architecture et Réactivité de l’ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg, France
| | - Pascal Auffinger
- Architecture et Réactivité de l’ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg, France
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Matsumoto M, Lee SJ, Waters ML, Gagné MR. A catalyst selection protocol that identifies biomimetic motifs from β-hairpin libraries. J Am Chem Soc 2014; 136:15817-20. [PMID: 25347708 DOI: 10.1021/ja503012g] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Assaying a solid-phase library of histidine-containing β-hairpin peptides by a reactive tagging scheme in organic solvents selects for catalysts that reproduce the strategies used by His-based enzyme active sites to accelerate acyl- and phosphonyl-transfer reactions. Rate accelerations (k(rel)) in organic solvents of up to 2.4 × 10(8) are observed.
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Affiliation(s)
- Masaomi Matsumoto
- Department of Chemistry, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-3290, United States
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Potentiometric and Thermodynamic Studies of Binary and Ternary Transition Metal(II) Complexes of Imidazole-4-acetic Acid and Some Bio-relevant Ligands. J SOLUTION CHEM 2013. [DOI: 10.1007/s10953-013-0015-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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8
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Fedotova MV, Kruchinin SE. Hydration of acetic acid and acetate ion in water studied by 1D-RISM theory. J Mol Liq 2011. [DOI: 10.1016/j.molliq.2011.09.015] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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9
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Protodynamic intracellular acidification by cis-urocanic acid promotes apoptosis of melanoma cells in vitro and in vivo. J Invest Dermatol 2010; 130:2431-9. [PMID: 20520626 DOI: 10.1038/jid.2010.151] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The extracellular tumor microenvironment is acidified, whereas the intracellular pH of tumor and stromal cells is neutral. cis-Urocanic acid (cis-UCA), an endogenous compound of the skin, can acidify the cytosol by transporting protons into the cells. This phenomenon, termed the protodynamic concept, was studied here in human cancer cells. cis-UCA dose-dependently reduced the number of viable human melanoma, cervical carcinoma, and fibrosarcoma cells at weakly acidic extracellular pH. The intracellular pH decreased by up to 0.5 pH units in a concentration-dependent manner with 0.3-30 m cis-UCA at extracellular pH 6.5 but not at pH 7.4. Under the same conditions, 30 mM cis-UCA induced annexin-V binding and activation of caspase-3 in A2058 melanoma cells as signs of apoptotic cell death. Finally, growth of human melanoma xenografts in SCID mice was suppressed by 60% following intratumoral injection of cis-UCA. Accordingly, the percentage of tumor necrosis and active caspase-3-immunopositive cells increased, whereas proliferation activity decreased. These results identify cis-UCA as an anticancer agent inhibiting melanoma growth by immediate intracellular acidification followed by apoptotic cell death in vivo.
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Juusola P, Minkkinen P, Leino L, Laihia JK. Determination of the Dissociation Constants of Urocanic Acid Isomers in Aqueous Solutions. MONATSHEFTE FUR CHEMIE 2007. [DOI: 10.1007/s00706-007-0687-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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O'Neill DJ, Shen L, Prouty C, Conway BR, Westover L, Xu JZ, Zhang HC, Maryanoff BE, Murray WV, Demarest KT, Kuo GH. Design, synthesis, and biological evaluation of novel 7-azaindolyl-heteroaryl-maleimides as potent and selective glycogen synthase kinase-3beta (GSK-3beta) inhibitors. Bioorg Med Chem 2005; 12:3167-85. [PMID: 15158785 DOI: 10.1016/j.bmc.2004.04.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2004] [Accepted: 04/06/2004] [Indexed: 01/31/2023]
Abstract
Two approaches were developed to synthesize the novel 7-azaindolyl-heteroarylmaleimides. The first approach was based upon the palladium-catalyzed Suzuki cross-coupling or Stille cross-coupling of 2-chloro-maleimide 5 with various arylboronic acids or arylstannanes. The second approach was based upon the condensation of ethyl 7-azaindolyl-3-glyoxylate 12 with various acetamides. The hydroxypropyl-substituted 7-azaindolylmaleimide template was first used to screen different heteroaryls attached to the maleimide. Replacement of hydroxypropyl with different chain lengths and different functional groups were studied next. Many compounds synthesized were demonstrated to have high potency at GSK-3beta, good GS activity in HEK293 cells and good to excellent metabolic stability in human liver microsomes. Three representative compounds (21, 33, and 34) were demonstrated to have good selectivity against a panel of 80 kinase assays. Among them, compound 33 exhibited very weak inhibitions at the other 79 kinase assays, and behaved as a highly selective GSK-3beta inhibitor.
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Affiliation(s)
- David J O'Neill
- Drug Discovery Division, Johnson and Johnson Pharmaceutical Research and Development, L.L.C., Raritan, NJ 08869-0602, USA
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12
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13
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Madder A, Li L, De Muynck H, Farcy N, Van Haver D, Fant F, Vanhoenacker G, Sandra P, Davis AP, De Clercq PJ. Evaluation of a two-stage screening procedure in the combinatorial search for serine protease-like activity. JOURNAL OF COMBINATORIAL CHEMISTRY 2002; 4:552-62. [PMID: 12425599 DOI: 10.1021/cc020016g] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of peptidosteroid derivatives containing two independent peptide chains in which Ser and His are incorporated were synthesized by solid-phase peptide synthesis. The activity of the different compounds in the hydrolysis of the activated substrate NF31 was assessed in a stepwise fashion. First, the different resin-bound derivatives 6a-l and 6x-z were individually assayed for serine esterification in the absence of water. The use of a colored substrate allowed for a visual identification of the most active compounds. Through the inclusion of control substances, the involvement of histidine in the mechanism for serine acylation was shown. Second, the hydrolysis and methanolysis of the different acylated derivatives 8a-l and 8x were evaluated using UV spectroscopy, again indicating the involvement of histidine. The feasibility of applying the above procedures in a combinatorial context was proven via the screening of artificial libraries, created by mixing the different resin-bound peptidosteroid compounds. In this respect, the use of a photocleavable linker allowed for the unambiguous structural characterization of the selected members via application of single-bead electrospray tandem mass spectrometry.
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Affiliation(s)
- Annemieke Madder
- Laboratory of Organic Synthesis, Department of Organic Chemistry, Ghent University, Krijgslaan 281, B-9000 Gent, Belgium
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14
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Hermida-Ramón JM, Karlström G, Lindh R. Analysis of the Relative Stability of cis-Urocanic Acid in Condensed Phase. The Use of Langevin Dipoles. J Phys Chem B 2002. [DOI: 10.1021/jp025893r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jose Manuel Hermida-Ramón
- Department of Theoretical Chemistry and Department of Chemical Physics, Chemical Center, University of Lund, P.O.B. 124, S-221 00 Lund, Sweden
| | - Gunnar Karlström
- Department of Theoretical Chemistry and Department of Chemical Physics, Chemical Center, University of Lund, P.O.B. 124, S-221 00 Lund, Sweden
| | - Roland Lindh
- Department of Theoretical Chemistry and Department of Chemical Physics, Chemical Center, University of Lund, P.O.B. 124, S-221 00 Lund, Sweden
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15
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Vicentini CB, Guarneri M, Andrisano V, Guccione S, Langer T, Marschhofer R, Chabin R, Edison AM, Huang X, Knight WB, Giori P. Potential of pyrazolooxadiazinone derivatives as serine protease inhibitors. JOURNAL OF ENZYME INHIBITION 2001; 16:15-34. [PMID: 11496832 DOI: 10.1080/14756360109162352] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
As a part of an investigation on molecular hybrids as new serine protease inhibitors, the pyrazolo [4,3-c][1,2,5]oxadiazin-3(5H)-one ring system was selected as a model of potential mechanism-based inhibitors. Due to the inherent reactivity of this system an optimal balance between susceptibility to nucleophilic attack and stability in solvents was sought prior to development as therapeutic agents. Substitutions on N5 and C7 of the supporting pyrazole ring with either aliphatic or aromatic groups (compounds 2 a-m) and the replacement of the carbonyl oxygen on the reactive oxadiazinone ring with sulfur (compounds 3a,i) were explored. Two members (2i and 2k) of this class of inhibitors displayed time-dependent inhibition of HLE suggesting mechanism-based inhibition. The observation that HLE generated a product(s) from compound 2i which displayed an identical UV-Visible spectrum to that observed during non-enzymatic hydrolysis further supports this proposal. FlexX-based docking of these compounds into a model of the human leukocyte elastase (HLE) active site produced a molecular model of the inhibitor-enzyme interaction.
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Affiliation(s)
- C B Vicentini
- Dipartimento di Scienze Farmaceutiche, Università di Ferrara, Italy
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16
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De Muynck H, Madder A, Farcy N, De Clercq PJ, Pérez-Payán MN, Öhberg LM, Davis AP. Application of Combinatorial Procedures in the Search for Serine-Protease-Like Activity with Focus on the Acyl Transfer Step. Angew Chem Int Ed Engl 2000. [DOI: 10.1002/(sici)1521-3757(20000103)112:1<149::aid-ange149>3.0.co;2-n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Azami H, Barrett D, Matsuda K, Tsutsumi H, Washizuka K, Sakurai M, Kuroda S, Shirai F, Chiba T, Kamimura T, Murata M. Synthesis and antibacterial activity of novel 4-pyrrolidinylthio carbapenems. Part III: Novel 2-alkyl substituents containing cationic heteroaromatics linked via a C-N bond. Bioorg Med Chem 1999; 7:1665-82. [PMID: 10482459 DOI: 10.1016/s0968-0896(99)00085-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The synthesis and biological activity of a novel series of 2-alkyl-4-pyrrolidinylthio-beta-methylcarbapenems containing a variety of cationic heteroaromatic substituents is described. As a result of these studies, we uncovered a relationship between in vitro antibacterial activity and the length of the alkyl spacer part, and discovered FR20950 (1c), containing a two methylene spacer moiety and an imidazolio group, which possesses a balanced spectrum of antibacterial activity, including Pseudomonas aeruginosa and Methicillin-resistant Staphylococcus aureus (MRSA). Furthermore, FR20950 exhibited excellent urinary recovery, and comparable stability against renal dehydropeptidase-I (DHP-I) to Biapenem. DHP-I stability could be improved by introduction of a substituent on to the imidazole ring.
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Affiliation(s)
- H Azami
- Medicinal Chemistry Research Laboratories, Fujisawa Pharmaceutical Co. Ltd., Osaka, Japan.
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18
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Steric Enhancement of Imidazole Basicity incis-Urocanic Acid Derivatives: Models for the Action of Chymotrypsin. Bioorg Chem 1998. [DOI: 10.1006/bioo.1998.1115] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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19
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Li GS, Maigret B, Rinaldi D, Ruiz-L�pez MF. Influence of environment on proton-transfer mechanisms in model triads from theoretical calculations. J Comput Chem 1998. [DOI: 10.1002/(sici)1096-987x(19981130)19:15<1675::aid-jcc1>3.0.co;2-k] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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20
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Lahti A, Hotokka M, Neuvonen K, Karlström G. Quantum chemical calculations on the intramolecular hydrogen bond of cis-urocanic acid. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s0166-1280(98)00150-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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21
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22
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Madder A, De Clercq PJ, Declercq JP. Stepwise Approach toward First Generation Nonenzymatic Hydrolases. J Org Chem 1998; 63:2548-2559. [PMID: 11672118 DOI: 10.1021/jo971935+] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The synthesis and reactivity study of a first generation serine protease mimic is described. Central in the design stands the possibility of stabilization of the transition state by an amino triol such as 8t. En route to 8t, a series of amino alcohols (4-8) was obtained, the reactivity of which was studied toward esterification by acetylimidazole (AcIm) and by p-nitro-2,2,2-trifluoroacetanilide (PNTFA). Interesting reactivity differences were observed between the cis- and the trans-series, especially between 7c and 7t (AcIm), and between 8c and 8t (PNTFA). In both cases the results are explained by invoking extra stabilization of the tetrahedral oxyanion.
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Affiliation(s)
- Annemieke Madder
- Laboratoire de Chimie Physique et de Cristallographie, Université Catholique de Louvain, 1 Place Louis Pasteur, B-1348 Louvain-la Neuve, Belgium
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23
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Wei Y, Schottel JL, Derewenda U, Swenson L, Patkar S, Derewenda ZS. A novel variant of the catalytic triad in the Streptomyces scabies esterase. NATURE STRUCTURAL BIOLOGY 1995; 2:218-23. [PMID: 7773790 DOI: 10.1038/nsb0395-218] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The crystal structure of a novel esterase from Streptomyces scabies, a causal agent of the potato scab disease, was solved at 2.1 A resolution. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases. The active site contains a dyad of Ser 14 and His 283, closely resembling two of the three components of typical Ser-His-Asp(Glu) triads from other serine hydrolases. Proper orientation of the active site imidazol is maintained by a hydrogen bond between the N delta-H group and a main chain oxygen. Thus, the enzyme constitutes the first known natural variation of the chymotrypsin-like triad in which a carboxylic acid is replaced by a neutral hydrogen-bond acceptor.
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Affiliation(s)
- Y Wei
- Medical Research Council of Canada Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton
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Abstract
Spectroscopic properties of chymotrypsin and model compounds indicate that a low-barrier hydrogen bond participates in the mechanism of serine protease action. A low-barrier hydrogen bond between N delta 1 of His57 and the beta-carboxyl group of Asp102 in chymotrypsin can facilitate the formation of the tetrahedral adduct, and the nuclear magnetic resonance properties of this proton indicate that it is a low-barrier hydrogen bond. These conclusions are supported by the chemical shift of this proton, the deuterium isotope effect on the chemical shift, and the properties of hydrogen-bonded model compounds in organic solvents, including the hydrogen bond in cis-urocanic acid, in which the imidazole ring is internally hydrogen-bonded to the carboxyl group.
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Affiliation(s)
- P A Frey
- Institute for Enzyme Research, Graduate School, University of Wisconsin at Madison 53705
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25
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Affiliation(s)
- Z S Derewenda
- MRC of Canada Group in Protein Structure and Function, University of Alberta, Edmonton, Canada
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26
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Derewenda ZS, Derewenda U, Dodson GG. The crystal and molecular structure of the Rhizomucor miehei triacylglyceride lipase at 1.9 A resolution. J Mol Biol 1992; 227:818-39. [PMID: 1404390 DOI: 10.1016/0022-2836(92)90225-9] [Citation(s) in RCA: 216] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The crystal and molecular structure of a triacylglyceride lipase (EC 3.1.1.3) from the fungus Rhizomucor miehei was analyzed using X-ray single crystal diffraction data to 1.9 A resolution. The structure was refined to an R-factor of 0.169 for all available data. The details of the molecular architecture and the crystal structure of the enzyme are described. A single polypeptide chain of 269 residues is folded into a rather unusual singly wound beta-sheet domain with predominantly parallel strands, connected by a variety of hairpins, loops and helical segments. All the loops are right-handed, creating an uncommon situation in which the central sheet is asymmetric in that all the connecting fragments are located on one side of the sheet. A single N-terminal alpha-helix provides the support for the other, distal, side of the sheet. Three disulfide bonds (residues 29-268, 40-43, 235-244) stabilize the molecule. There are four cis peptide bonds, all of which precede proline residues. In all, 230 ordered water molecules have been identified; 12 of them have a distinct internal character. The catalytic center of the enzyme is made up of a constellation of three residues (His257, Asp203 and Ser144) similar in structure and function to the analogous (but not homologous) triad found in both of the known families of serine proteinases. The fourth residue in this system equivalent to Thr/Ser in proteinases), hydrogen bonded to Asp, is Tyr260. The catalytic site is concealed under a short amphipatic helix (residues 85 to 91), which acts as "lid", opening the active site when the enzyme is adsorbed at the oil-water interface. In the native enzyme the "lid" is held in place by hydrophobic interactions.
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Affiliation(s)
- Z S Derewenda
- Department of Biochemistry, University of Alberta, Edmonton, Canada
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