1
|
Ozawa H, Miyazawa T, Burdeos GC, Miyazawa T. Biological Functions of Antioxidant Dipeptides. J Nutr Sci Vitaminol (Tokyo) 2022; 68:162-171. [PMID: 35768247 DOI: 10.3177/jnsv.68.162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In the history of modern nutritional science, understanding antioxidants is one of the major topics. In many cases, food-derived antioxidants have π conjugate or thiol group in their molecular structures because π conjugate stabilizes radical by its delocalization and two thiol groups form a disulfide bond in its antioxidative process. In recent years, antioxidant peptides have received much attention because for their ability to scavenge free radicals, inhibition of lipid peroxidation, chelation of transition metal ions, as well as their additional nutritional value. Among them, dipeptides are attracting much interest as post-amino acids, which have residues in common with amino acids, but also have different physiological properties and functions from those of amino acids. Especially, dipeptides containing moieties of several amino acid (tryptophan, tyrosine, histidine, cysteine, and methionine) possess potent antioxidant activity. This review summarizes previous details of structural property, radical scavenging activity, and biological activity of antioxidant dipeptide. Hopefully, this review will help provide a new insight into the study of the biological functions of antioxidant dipeptides.
Collapse
Affiliation(s)
- Hitoshi Ozawa
- New Industry Creation Hatchery Center (NICHe), Tohoku University
| | - Taiki Miyazawa
- New Industry Creation Hatchery Center (NICHe), Tohoku University
| | | | - Teruo Miyazawa
- New Industry Creation Hatchery Center (NICHe), Tohoku University
| |
Collapse
|
2
|
Brinkmann S, Semmler S, Kersten C, Patras MA, Kurz M, Fuchs N, Hammerschmidt SJ, Legac J, Hammann PE, Vilcinskas A, Rosenthal PJ, Schirmeister T, Bauer A, Schäberle TF. Identification, Characterization, and Synthesis of Natural Parasitic Cysteine Protease Inhibitors: Pentacitidins Are More Potent Falcitidin Analogues. ACS Chem Biol 2022; 17:576-589. [PMID: 35262340 DOI: 10.1021/acschembio.1c00861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protease inhibitors represent a promising therapeutic option for the treatment of parasitic diseases such as malaria and human African trypanosomiasis. Falcitidin was the first member of a new class of inhibitors of falcipain-2, a cysteine protease of the malaria parasite Plasmodium falciparum. Using a metabolomics dataset of 25 Chitinophaga strains for molecular networking enabled identification of over 30 natural analogues of falcitidin. Based on MS/MS spectra, they vary in their amino acid chain length, sequence, acyl residue, and C-terminal functionalization; therefore, they were grouped into the four falcitidin peptide families A-D. The isolation, characterization, and absolute structure elucidation of two falcitidin-related pentapeptide aldehyde analogues by extensive MS/MS spectrometry and NMR spectroscopy in combination with advanced Marfey's analysis was in agreement with the in silico analysis of the corresponding biosynthetic gene cluster. Total synthesis of chosen pentapeptide analogues followed by in vitro testing against a panel of proteases revealed selective parasitic cysteine protease inhibition and, additionally, low-micromolar inhibition of α-chymotrypsin. The pentapeptides investigated here showed superior inhibitory activity compared to falcitidin.
Collapse
Affiliation(s)
- Stephan Brinkmann
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen 35392, Germany
| | - Sandra Semmler
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen 35392, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Mainz 55128, Germany
| | - Maria A. Patras
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen 35392, Germany
| | - Michael Kurz
- Sanofi-Aventis Deutschland GmbH, R&D, Frankfurt am Main 65926, Germany
| | - Natalie Fuchs
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Mainz 55128, Germany
| | - Stefan J. Hammerschmidt
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Mainz 55128, Germany
| | - Jenny Legac
- Department of Medicine, University of California, San Francisco, California 94143, United States
| | | | - Andreas Vilcinskas
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen 35392, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen 35392, Germany
| | - Philip J. Rosenthal
- Department of Medicine, University of California, San Francisco, California 94143, United States
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Mainz 55128, Germany
| | - Armin Bauer
- Sanofi-Aventis Deutschland GmbH, R&D, Frankfurt am Main 65926, Germany
| | - Till F. Schäberle
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen 35392, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen 35392, Germany
| |
Collapse
|
3
|
Tomohara K, Adachi I, Horino Y, Kesamaru H, Abe H, Suyama K, Nose T. DMSO-Perturbing Assay for Identifying Promiscuous Enzyme Inhibitors. ACS Med Chem Lett 2019; 10:923-928. [PMID: 31223449 DOI: 10.1021/acsmedchemlett.9b00093] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/10/2019] [Indexed: 01/09/2023] Open
Abstract
In search for enzyme inhibitors, we often encounter "promiscuous" enzyme inhibitors exhibiting nonspecific binding property toward enzyme active site. Therefore, inhibitory candidates should be mechanistically characterized as early as possible in discovery processes. However, there remains a lack of highly reliable and readily available methodology to evaluate specificity of initial hits inhibitors. The present study developed and established a novel DMSO-perturbing assay to identify promiscuous enzyme inhibitors. The assay successfully identified nonspecific binding inhibitors with a broad scope, typically by the attenuation of inhibitory activity by the influence of DMSO-addition. This attenuation would be attributed to the nonspecific binding property of inhibitors toward both productive and nonproductive (nondenatured) states of enzymes in perturbation solution. This working hypothesis was supported by spectroscopic analyses of enzyme conformations and analyses of solvent effects on perturbation. Overall, these results provided a novel concept of the DMSO-perturbing assay.
Collapse
Affiliation(s)
- Keisuke Tomohara
- Faculty of Arts and Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Isao Adachi
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Yoshikazu Horino
- Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
| | - Hitoshi Kesamaru
- Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Hitoshi Abe
- Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
| | - Keitaro Suyama
- Faculty of Arts and Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Takeru Nose
- Faculty of Arts and Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| |
Collapse
|
4
|
Simões ICM, Coimbra JTS, Neves RPP, Costa IPD, Ramos MJ, Fernandes PA. Properties that rank protein:protein docking poses with high accuracy. Phys Chem Chem Phys 2018; 20:20927-20942. [DOI: 10.1039/c8cp03888k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The development of docking algorithms to predict near-native structures of protein:protein complexes from the structure of the isolated monomers is of paramount importance for molecular biology and drug discovery.
Collapse
Affiliation(s)
- Inês C. M. Simões
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - João T. S. Coimbra
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - Rui P. P. Neves
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - Inês P. D. Costa
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - Maria J. Ramos
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - Pedro A. Fernandes
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| |
Collapse
|
5
|
Gilles P, Wenck K, Stratmann I, Kirsch M, Smolin DA, Schaller T, de Groot H, Kraft A, Schrader T. High-Affinity Copolymers Inhibit Digestive Enzymes by Surface Recognition. Biomacromolecules 2017; 18:1772-1784. [DOI: 10.1021/acs.biomac.7b00162] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Arno Kraft
- Heriot-Watt University, Edinburgh, Scotland, United Kingdom EH14 4AS
| | | |
Collapse
|
6
|
Ono S, Nakai T, Kuroda H, Miyatake R, Horino Y, Abe H, Umezaki M, Oyama H. Site-selective chemical modification of chymotrypsin using peptidyl derivatives bearing optically active diphenyl 1-amino-2-phenylethylphosphonate: Stereochemical effect of the diphenyl phosphonate moiety. Biopolymers 2016; 106:521-30. [PMID: 26615968 DOI: 10.1002/bip.22790] [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: 08/30/2015] [Revised: 10/30/2015] [Accepted: 11/02/2015] [Indexed: 01/24/2023]
Abstract
Diphenyl (α-aminoalkyl)phosphonates act as mechanism-based inhibitors against serine proteases by forming a covalent bond with the hydroxy group of the active center Ser residue. Because the covalent bond was found to be broken and replaced by 2-pyridinaldoxime methiodide (2PAM), we employed a peptidyl derivative bearing diphenyl 1-amino-2-phenylethylphosphonate moiety (Phe(p) (OPh)2 ) to target the active site of chymotrypsin and to selectively anchor to Lys175 in the vicinity of the active site. Previously, it was reported that the configuration of the α-carbon of phosphorus in diphenyl (α-aminoalkyl)phosphonates affects the inactivation reaction of serine proteases, i.e., the (R)-enantiomeric diphenyl phosphonate is comparable to l-amino acids and it effectively reacts with serine proteases, whereas the (S)-enantiomeric form does not. In this study, we evaluated the stereochemical effect of the phosphonate moiety on the selective chemical modification. Epimeric dipeptidyl derivatives, Ala-(R or S)-Phe(p) (OPh)2 , were prepared by separation with RP-HPLC. A tripeptidyl (R)-epimer (Ala-Ala-(R)-Phe(p) (OPh)2 ) exhibited a more potent inactivation ability against chymotrypsin than the (S)-epimer. The enzyme inactivated by the (R)-epimer was more effectively reactivated with 2PAM than the enzyme inactivated by the (S)-epimer. Finally, N-succinimidyl (NHS) active ester derivatives, NHS-Suc-Ala-Ala- (R or S)-Phe(p) (OPh)2 , were prepared, and we evaluated their action when modifying Lys175 in chymotrypsin. We demonstrated that the epimeric NHS derivative that possessed the diphenyl phosphonate moiety with the (R)-configuration effectively modified Lys175 in chymotrypsin, whereas that with the (S)-configuration did not. These results demonstrate the utility of peptidyl derivatives that bear an optically active diphenyl phosphonate moiety as affinity labeling probes in protein bioconjugation. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 521-530, 2016.
Collapse
Affiliation(s)
- Shin Ono
- Genome Biotechnology Laboratory, Kanazawa Institute of Technology, Hakusan, 924-0838, Japan
| | - Takahiko Nakai
- Graduate School of Science and Engineering, University of Toyama, Toyama, 930-8555, Japan
| | - Hirofumi Kuroda
- Department of General Education, Ishikawa National College of Technology, Ishikawa, 929-0392, Japan
| | - Ryuta Miyatake
- Graduate School of Science and Engineering, University of Toyama, Toyama, 930-8555, Japan
| | - Yoshikazu Horino
- Graduate School of Science and Engineering, University of Toyama, Toyama, 930-8555, Japan
| | - Hitoshi Abe
- Graduate School of Science and Engineering, University of Toyama, Toyama, 930-8555, Japan
| | - Masahito Umezaki
- Institute of Natural Medicine, University of Toyama, Toyama, 930-0194, Japan
| | - Hiroshi Oyama
- Faculty of Science and Engineering, Setsunan University, Osaka, 572-8508, Japan
| |
Collapse
|
7
|
Tang AW, Kong X, Terskikh V, Wu G. Solid-State 17O NMR of Unstable Acyl-Enzyme Intermediates: A Direct Probe of Hydrogen Bonding Interactions in the Oxyanion Hole of Serine Proteases. J Phys Chem B 2016; 120:11142-11150. [PMID: 27731644 DOI: 10.1021/acs.jpcb.6b08798] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report preparation, trapping, and solid-state 17O NMR characterization of three unstable acyl-enzyme intermediates (≈ 26 kDa): p-N,N-dimethylamino-[17O]benzoyl-chymotrypsin, trans-o-methoxy-[17O]cinnamoyl-chymotrypsin, and trans-p-methoxy-[17O]cinnamoyl-chymotrypsin. We show that both the 17O chemical shifts and nuclear quadrupolar parameters obtained for these acyl-enzyme intermediates in the solid state are correlated with their deacylation rate constants measured in aqueous solution. With the aid of quantum mechanical calculations, the experimental 17O NMR parameters were interpreted as to reflect the hydrogen bonding interactions between the carbonyl (C═17O) functional group of the acyl moiety and the two NH groups from the protein backbone (Ser195 and Gly193) in the oxyanion hole, a general feature of all serine proteases. Our results further suggest that the 17O chemical shift and quadrupole coupling constant display distinctly different sensitivities toward different aspects of hydrogen bonding, such as hydrogen bond distance and direction. This work demonstrates the utility of 17O as a useful nuclear probe in NMR studies of enzymes.
Collapse
Affiliation(s)
- Aaron W Tang
- Department of Chemistry, Queen's University , 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada
| | - Xianqi Kong
- Department of Chemistry, Queen's University , 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada
| | - Victor Terskikh
- Department of Chemistry, Queen's University , 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada.,Department of Chemistry, University of Ottawa , Ottawa, Ontario K1N 6N5, Canada
| | - Gang Wu
- Department of Chemistry, Queen's University , 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada
| |
Collapse
|
8
|
Ono S, Murai J, Nakai T, Kuroda H, Horino Y, Yoshimura T, Oyama H, Umezaki M. Site-selective Chemical Modification of Chymotrypsin Using a Peptidyl Diphenyl 1-Amino-2-phenylethylphosphonate Derivative. CHEM LETT 2013. [DOI: 10.1246/cl.130244] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Shin Ono
- Graduate School of Science and Engineering, University of Toyama
| | - Junya Murai
- Graduate School of Science and Engineering, University of Toyama
| | - Takahiko Nakai
- Graduate School of Science and Engineering, University of Toyama
| | | | - Yoshikazu Horino
- Graduate School of Science and Engineering, University of Toyama
| | | | - Hiroshi Oyama
- Faculty of Science and Engineering, Setsunan University
| | | |
Collapse
|
9
|
Vulpetti A, Hommel U, Landrum G, Lewis R, Dalvit C. Design and NMR-Based Screening of LEF, a Library of Chemical Fragments with Different Local Environment of Fluorine. J Am Chem Soc 2009; 131:12949-59. [DOI: 10.1021/ja905207t] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Anna Vulpetti
- Novartis Institute for Biomedical Research, Novartis Pharma AG, CH-4002 Basel, Switzerland, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy
| | - Ulrich Hommel
- Novartis Institute for Biomedical Research, Novartis Pharma AG, CH-4002 Basel, Switzerland, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy
| | - Gregory Landrum
- Novartis Institute for Biomedical Research, Novartis Pharma AG, CH-4002 Basel, Switzerland, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy
| | - Richard Lewis
- Novartis Institute for Biomedical Research, Novartis Pharma AG, CH-4002 Basel, Switzerland, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy
| | - Claudio Dalvit
- Novartis Institute for Biomedical Research, Novartis Pharma AG, CH-4002 Basel, Switzerland, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy
| |
Collapse
|
10
|
Yuki H, Tanaka Y, Hata M, Ishikawa H, Neya S, Hoshino T. Implementation of π-π interactions in molecular dynamics simulation. J Comput Chem 2007; 28:1091-9. [PMID: 17279501 DOI: 10.1002/jcc.20557] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
No explicit pi-pi interaction term has been incorporated in the conventional molecular dynamics (MD) simulation programs in spite of its significant role in the folding of biomolecules and the clustering of organic chemicals. In this article, we propose a technique to emphasize the effect of pi-pi interactions using a function of energy and implement it into an MD simulation program. Several trial calculations show that the pi-pi incorporated program gives improved results consistent with experimental data on atom geometry and has no unfavorable interference with the conventional computational framework. This indicates an importance of the explicit consideration of pi-pi interactions in MD simulation.
Collapse
Affiliation(s)
- Hitomi Yuki
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan
| | | | | | | | | | | |
Collapse
|
11
|
Michalarias I, Gao X, Ford RC, Li J. Recent progress on our understanding of water around biomolecules. J Mol Liq 2005. [DOI: 10.1016/j.molliq.2004.08.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
12
|
Smoum R, Rubinstein A, Srebnik M. Noncovalent inhibition of the serine proteases, alpha-chymotrypsin and trypsin by trifluoro(organo)borates. Org Biomol Chem 2005; 3:941-4. [PMID: 15731882 DOI: 10.1039/b415957h] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of potassium organotrifluoroborates were synthesized. Their stability to hydrolysis was determined in D2O, TRIS and phosphate buffer. It was found that in both D2O and TRIS buffers, these compounds are quite stable, whereas in phosphate buffer rapid hydrolysis occurs. Based on these results, a study was undertaken to determine whether potassium organotrifluoroborates can serve as protease inhibitors. It was found that potassium organotrifluoroborates increased inhibition by at least an order of magnitude over the corresponding boronates. Dixon plots showed that these compounds are reversible competitive inhibitors of alpha-chymotrypsin and trypsin. Based on 19F NMR, we speculate that they inactivate the enzymes as a result of the formation of hydrogen-bonds between fluorine atoms of the inhibitors and the serine protease.
Collapse
Affiliation(s)
- Reem Smoum
- Department of Pharmaceutics, School of Pharmacy, Faculty of Medicine, Hebrew University of Jerusalem, POB 12065, 91120, Jerusalem, Israel
| | | | | |
Collapse
|
13
|
Olsen JA, Banner DW, Seiler P, Wagner B, Tschopp T, Obst-Sander U, Kansy M, Müller K, Diederich F. Fluorine Interactions at the Thrombin Active Site: Protein Backbone Fragments HCαCO Comprise a Favorable CF Environment and Interactions of CF with Electrophiles. Chembiochem 2004; 5:666-75. [PMID: 15122639 DOI: 10.1002/cbic.200300907] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In a systematic fluorine scan of a rigid inhibitor to map the fluorophilicity/fluorophobicity of the active site in thrombin, one or more F substituents were introduced into the benzyl ring reaching into the D pocket. The 4-fluorobenzyl inhibitor showed a five to tenfold higher affinity than ligands with other fluorination patterns. X-ray crystal-structure analysis of the protein-ligand complex revealed favorable C-F...H-C(alpha)-C=O and C-F...C=O interactions of the 4-F substituent of the inhibitor with the backbone H-C(alpha)-C=O unit of Asn98. The importance of these interactions was further corroborated by the analysis of small-molecule X-ray crystal-structure searches in the Protein Data Base (PDB) and the Cambridge Structural Database (CSD). In the C--F...C=O interactions that are observed for both aromatic and aliphatic C-F units and a variety of carbonyl and carboxyl derivatives, the F atom approaches the C=O C atom preferentially along the pseudotrigonal axis of the carbonyl system. Similar orientational preferences are also seen in the dipolar interactions C--F.C[triple chemical bond]N, C-F.C-F, and C-F...NO(2), in which the F atoms interact at sub-van der Waals distances with the electrophilic centers.
Collapse
Affiliation(s)
- Jacob A Olsen
- Laboratorium für Organische Chemie, ETH-Hönggerberg, HCI, 8093 Zürich, Switzerland
| | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Martyn DC, Vernall AJ, Clark BM, Abell AD. Ring-deactivated hydroxyalkylpyrrole-based inhibitors of alpha-chymotrypsin: synthesis and mechanism of action. Org Biomol Chem 2003; 1:2103-10. [PMID: 12945901 DOI: 10.1039/b302411c] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
13C NMR and mass spectrometry studies have been used to demonstrate that the inhibition of alpha-chymotrypsin by N-sulfonylhydroxymethylpyrrole inhibitors (10) is non-covalent. Hydroxyalkylpyrroles in which an electron-withdrawing group (acyl substituent) is introduced at the alternative C2 position have been synthesised and also shown to inactivate alpha-chymotrypsin. SAR studies on this class suggests that the incorporation of phenylalanine at C2 is favoured, however, there is little gain in introducing a hydrophobic substituent at C5.
Collapse
Affiliation(s)
- Derek C Martyn
- Department of Chemistry, University of Canterbury, Christchurch, New Zealand
| | | | | | | |
Collapse
|
15
|
Shimohigashi Y, Nose T, Yamauchi Y, Maeda I. Design of serine protease inhibitors with conformation restricted by amino acid side-chain-side-chain CH/pie interaction. Biopolymers 2000; 51:9-17. [PMID: 10380349 DOI: 10.1002/(sici)1097-0282(1999)51:1<9::aid-bip3>3.0.co;2-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A novel type of conformationally restricted peptides with the structure of H-D-Xaa-Phe-NH-CH2-C6H5 has been developed as inhibitors of serine proteinase chymotrypsin. The D-Xaa-alkyl and Phe-phenyl groups resulted in a formation of the hydrophobic core due to the side-chain-side-chain CH/pie interaction. Their spatial proximity was evidenced by 400 MHz 1H-nmr measurements, observing large upfield shifts of proton signals of D-Xaa-alkyl and nuclear Over-hauser effect (NOE) enhancements between the D-Xaa-alkyl and Phe-phenyl groups. This conformational restriction brought by CH/pie interaction produced an inhibitory structure, in which the C-terminal amide-benzyl group fits the chymotrypsin S1 site and the hydrophobic core binds to the S2 site. The inhibitory conformation was demonstrated crystallographically for the complex between the dipeptide H-D-Leu-Phe-NH-CH2-C6H4(p-F) and gamma-chymotrypsin. Detailed structure-activity studies have substantiated the structure of dipeptides in the active center of the enzyme.
Collapse
Affiliation(s)
- Y Shimohigashi
- Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka, Japan.
| | | | | | | |
Collapse
|
16
|
Goto M, Kawasaki M, Kometani T. Enzymatic resolution of 2-phenyl-1-propanol by enantioselective hydrolysis of its ester having a bulky group in an acyl moiety. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s1381-1177(99)00101-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
17
|
Pletnev VZ, Zamolodchikova TS, Pangborn WA, Duax WL. Crystal structure of bovine duodenase, a serine protease, with dual trypsin and chymotrypsin-like specificities. Proteins 2000. [DOI: 10.1002/1097-0134(20001001)41:1<8::aid-prot30>3.0.co;2-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
18
|
Peisach E, Wang J, de los Santos T, Reich E, Ringe D. Crystal structure of the proenzyme domain of plasminogen. Biochemistry 1999; 38:11180-8. [PMID: 10460175 DOI: 10.1021/bi991130r] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have solved the X-ray crystal structure of the proenzyme form of the catalytic domain of plasminogen, with the nonessential mutations M585Q, V673M, and M788L, to 2.0 A resolution. The structure presents an inactive protease characterized by Asp740 (chymotrypsinogen 194) hydrogen bonded to His586 (chymotrypsinogen 40), preventing proper formation of the oxyanion hole and S1 specificity pocket. In addition, the catalytic triad residues are misplaced relative to the active conformation adopted by serine proteases in the chymotrypsin family. Finally, a unique form of zymogen inactivation is observed, characterized by a "foot-in-mouth" mechanism in which Trp761 (chymotrypsinogen 215) is folded into the S1 specificity pocket preventing substrate binding.
Collapse
Affiliation(s)
- E Peisach
- Program in Biophysics and Structural Biology, Brandeis University, Waltham, Massachusetts 02454-9110, USA
| | | | | | | | | |
Collapse
|