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Ishida T. [Overview of structural study on conformations and intermolecular interactions of biomolecules]. YAKUGAKU ZASSHI 2012; 132:785-816. [PMID: 22790026 DOI: 10.1248/yakushi.132.785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Information on the conformational feature and specific intermolecular interaction of biomolecules is important to understand the biological function and to develop device for treating disorder caused by the abnormal function. Thus the 3D structures of the biologically active molecules and the specific interactions with their target molecules at the atomic level have been investigated by various physicochemical approaches. Herein, the following five subjects are reviewed: (1) function-linked conformations of biomolecules including natural annular products, opioid peptides and neuropeptides; (2) π-π stacking interactions of tryptophan derivatives with coenzymes and nucleic acid bases; (3) mRNA cap recognition of eukaryotic initiation factor 4E and its regulation by 4E-binding protein; (4) conformational feature of histamine H2 receptor antagonists and design of cathepsin B inhibitors; (5) self-aggregation mechanism of tau protein and its inhibition.
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Affiliation(s)
- Toshimasa Ishida
- Laboratory of Physical Chemistry, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan.
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Shahlaei M, Fassihi A, Saghaie L, Arkan E, Madadkar-Sobhani A, Pourhossein A. Computational evaluation of some indenopyrazole derivatives as anticancer compounds; application of QSAR and docking methodologies. J Enzyme Inhib Med Chem 2011; 28:16-32. [DOI: 10.3109/14756366.2011.618991] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Mohsen Shahlaei
- Department of Medicinal Chemistry, School of Pharmacy and Isfahan Pharmaceutical Sciences Research Center, Isfahan University of Medical Sciences,
Isfahan, I.R. Iran
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kermanshah University of Medical Sciences,
Kermanshah, I.R.Iran
| | - Afshin Fassihi
- Department of Medicinal Chemistry, School of Pharmacy and Isfahan Pharmaceutical Sciences Research Center, Isfahan University of Medical Sciences,
Isfahan, I.R. Iran
| | - Lotfollah Saghaie
- Department of Medicinal Chemistry, School of Pharmacy and Isfahan Pharmaceutical Sciences Research Center, Isfahan University of Medical Sciences,
Isfahan, I.R. Iran
| | - Elham Arkan
- Department of Medical Nanotechnology, School of Advanced Medical Technologies
| | - Armin Madadkar-Sobhani
- Department of Life Sciences, Barcelona Supercomputing Center,
Edificio Nexus II, Barcelona, Spain
- Department of Bioinformatics, Institute of Biophysics and Biochemistry, University of Tehran,
Tehran, I.R.Iran
| | - Alireza Pourhossein
- Young Researchers Club, Kermanshah branch, Islamic Azad University,
Kermanshah, I.R.Iran
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Mouchlis VD, Magrioti V, Barbayianni E, Cermak N, Oslund RC, Mavromoustakos TM, Gelb MH, Kokotos G. Inhibition of secreted phospholipases A₂ by 2-oxoamides based on α-amino acids: Synthesis, in vitro evaluation and molecular docking calculations. Bioorg Med Chem 2010; 19:735-43. [PMID: 21216150 DOI: 10.1016/j.bmc.2010.12.030] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 12/07/2010] [Accepted: 12/13/2010] [Indexed: 10/18/2022]
Abstract
Group IIA secreted phospholipase A₂ (GIIA sPLA₂) is a member of the mammalian sPLA₂ enzyme family and is associated with various inflammatory conditions. In this study, the synthesis of 2-oxoamides based on α-amino acids and the in vitro evaluation against three secreted sPLA₂s (GIIA, GV and GX) are described. The long chain 2-oxoamide GK126 based on the amino acid (S)-leucine displayed inhibition of human and mouse GIIA sPLA₂s (IC₅₀ 300nM and 180nM, respectively). It also inhibited human GV sPLA₂ with similar potency, while it did not inhibit human GX sPLA₂. The elucidation of the stereoelectronic characteristics that affect the in vitro activity of these compounds was achieved by using a combination of simulated annealing to sample low-energy conformations before the docking procedure, and molecular docking calculations.
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Mouchlis VD, Mavromoustakos TM, Kokotos G. Molecular Docking and 3D-QSAR CoMFA Studies on Indole Inhibitors of GIIA Secreted Phospholipase A2. J Chem Inf Model 2010; 50:1589-601. [PMID: 20795712 DOI: 10.1021/ci100217k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Varnavas D. Mouchlis
- Laboratory of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Thomas M. Mavromoustakos
- Laboratory of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - George Kokotos
- Laboratory of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis, Athens 15771, Greece
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Mouchlis VD, Mavromoustakos TM, Kokotos G. Design of new secreted phospholipase A2 inhibitors based on docking calculations by modifying the pharmacophore segments of the FPL67047XX inhibitor. J Comput Aided Mol Des 2010; 24:107-15. [DOI: 10.1007/s10822-010-9319-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Accepted: 01/21/2010] [Indexed: 10/19/2022]
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Xu W, Yi L, Feng Y, Chen L, Liu J. Structural insight into the activation mechanism of human pancreatic prophospholipase A2. J Biol Chem 2009; 284:16659-16666. [PMID: 19297324 DOI: 10.1074/jbc.m808029200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pancreatic phospholipase A2 (phospholipase A2 group 1B, G1B) belongs to the superfamily of secreted phospholipase A2 (PLA2) enzymes. G1B has been proposed to be a potential target for diseases such as hypertension, obesity, and diabetes. Human pancreatic prophospholipase A2 (pro-hG1B) is activated by cleavage of the first seven-residue propeptide (phospholipase A2 propeptide, PROP). However, questions still remain on the mode of action for pro-hG1B. In this work, we expressed pro-hG1B in Pichia pastoris and determined the crystal structure at 1.55-A resolution. The x-ray structure demonstrates that pro-hG1B forms a trimer. In addition, PROP occupies the catalytic cavity and can be self-cleaved at 37 degrees C. A new membrane-bound surface and activation mechanism are proposed based on the trimeric model of pro-hG1B. We also propose a new autoproteolytic mechanism for pro-hG1B by the reaction triad Asp49-Arg0-Ser(-2) that is similar to the serine protease catalytic triad.
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Affiliation(s)
- Wei Xu
- From the Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510663, China; Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lina Yi
- From the Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510663, China
| | - Yumei Feng
- From the Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510663, China
| | - Ling Chen
- From the Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510663, China; School of Life Sciences, University of Science and Technology of China, Hefei 230027, China.
| | - Jinsong Liu
- From the Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510663, China; School of Life Sciences, University of Science and Technology of China, Hefei 230027, China.
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Prijatelj P, Vardjan N, Rowan EG, Krizaj I, Pungercar J. Binding to the high-affinity M-type receptor for secreted phospholipases A2 is not obligatory for the presynaptic neurotoxicity of ammodytoxin A. Biochimie 2006; 88:1425-33. [PMID: 16815622 DOI: 10.1016/j.biochi.2006.06.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Accepted: 06/05/2006] [Indexed: 01/19/2023]
Abstract
R180, isolated from porcine brain cortex, is a high-affinity membrane receptor for ammodytoxin A (AtxA), a secreted phospholipase A(2) (sPLA(2)) and presynaptically active neurotoxin from venom of the long-nosed viper (Vipera ammodytes ammodytes). As a member of the M-type sPLA(2) receptors, present on the mammalian plasma membrane, R180 has been proposed to be responsible for one of the first events in the process of presynaptic neurotoxicity, the binding of the toxin to the nerve cell. To test this hypothesis, we prepared and analyzed three N-terminal fusion proteins of AtxA possessing a 12 or 5 amino acid residue peptide. The presence of such an additional "propeptide" prevented interaction of the toxin with the M-type receptor but not its lethality in mouse and neurotoxic effects on a mouse phrenic nerve-hemidiaphragm preparation. In addition, antibodies raised against the sPLA(2)-binding C-type lectin-like domain 5 of the M-type sPLA(2) receptor were unable to abolish the neurotoxic action of AtxA on the neuromuscular preparation. The specific enymatic activities of the fusion AtxAs were two to three orders of magnitude lower from that of the wild type, yet resulting in a similar but less pronounced neurotoxic profile on the neuromuscular junction. This is in accordance with other data showing that a minimal enzymatic activity suffices for presynaptic toxicity of sPLA(2)s to occur. Our results indicate that the interaction of AtxA with the M-type sPLA(2) receptor at the plasma membrane is not essential for presynaptic activity of the toxin. Interaction of AtxA with two intracellular proteins, calmodulin and the R25 receptor, was affected but not prevented by the presence of the N-terminal fusion peptides, implying that these proteins may play a role in the sPLA(2) neurotoxicity.
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Affiliation(s)
- Petra Prijatelj
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Askerceva 5, SI-1000 Ljubljana, Slovenia
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Epstein TM, Yu BZ, Pan YH, Tutton SP, Maliwal BP, Jain MK, Bahnson BJ. The basis for k(cat) impairment in prophospholipase A(2) from the anion-assisted dimer structure. Biochemistry 2001; 40:11411-22. [PMID: 11560489 DOI: 10.1021/bi011228h] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Kinetic results in this paper show that, contrary to earlier reports, pig pancreatic prophospholipase A(2) (proPLA2) does not hydrolyze monodisperse short chain phosphatidylcholine below the critical micelle concentration. ProPLA2 is active on an anionic interface, but at a rate that is decreased by more than 100-fold compared to that of PLA2, the active form. Solution studies show that both proPLA2 and PLA2 bind to an anionic interface and also bind a tetrahedral intermediate mimic at the active site. The 1.5 A resolution crystal structure of the anion-assisted dimer of proPLA2 reported in this paper is compared with the corresponding structure for PLA2 [Pan, Y. H., et al. (2001) Biochemistry 40, 609-617]. As a mimic for the forms bound to the anionic interface, these structures provide insights into the possible structural basis for the impaired chemical step of the zymogen. The proPLA2 dimer contained within one crystallographic asymmetric unit has one molecule of the inhibitor 1-hexadecyl-3-(trifluoroethyl)-sn-glycero-2-phosphomethanol and is bridged by four coplanar sulfate anions. Relative to the structure of PLA2, the subunit contact surface in proPLA2 displays a tilted orientation, an altered mode of inhibitor binding, displacement of a mechanistically significant loop that includes Tyr69, and a critical active site water seen in PLA2 that is not seen in proPLA2. These differences are interpreted to suggest possible origins of the functional differences between the pro and active enzyme at an anionic interface. A structural origin of this difference is discussed in terms of the calcium-coordinated activated water mechanism of the esterolysis reaction. Together, a comparison of the structures of the anion-assisted dimers of PLA2 and proPLA2 not only offers an explanation of why the zymogen form is k(cat)-impaired and binds poorly even to the anionic interface but also supports a mechanism for the activated enzyme that includes a critical second-sphere assisting water bridging His48 and the calcium-coordinated catalytic water.
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Affiliation(s)
- T M Epstein
- Department of Chemistry and Biochemistry, University of Delaware, Newark 19716, USA
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Berg OG, Gelb MH, Tsai MD, Jain MK. Interfacial enzymology: the secreted phospholipase A(2)-paradigm. Chem Rev 2001; 101:2613-54. [PMID: 11749391 DOI: 10.1021/cr990139w] [Citation(s) in RCA: 266] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- O G Berg
- Evolutionary Biology Center, Uppsala University, Uppsala, Sweden
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Yuan C, Tsai M. Pancreatic phospholipase A(2): new views on old issues. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1441:215-22. [PMID: 10570249 DOI: 10.1016/s1388-1981(99)00156-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The recent development in the structure-function relationship of pancreatic phospholipase A(2) is reviewed. The results of extensive studies by a combination of site-directed mutagenesis, X-ray crystallography, and NMR have provided new insight into several old issues. In particular, we summarize current views on the active site, the interfacial binding site, the mechanism of interfacial activation, the roles of the hydrogen-bonding network and the catalytic dyad, and the conformational stability of the structure.
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Affiliation(s)
- C Yuan
- Department of Chemistry, Ohio State University, 100 West 18th Avenue, Columbus, OH 43210-1173, USA
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Kley JT, Unger C, Massing U. Inhibition of 14-kDa PLA2 by 2-acylamino-alkylphospholipids: the influence of amide acidity. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1392:193-201. [PMID: 9630626 DOI: 10.1016/s0005-2760(98)00033-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
2-Acylamino-alkyl phospholipids are potent competitive inhibitors of 14-kDa phospholipases A2 (e.g., human nonpancreatic secretory PLA2). As concluded from X-ray studies the amide hydrogen of these inhibitors forms a hydrogen bond to His-48 in the active site of the enzyme. We investigated the quantitative contribution of this hydrogen bond to inhibition using especially designed inhibitors that bear different acyl chains with and without electron withdrawing or donating substituents, thus differing in amide acidity. Relative free enthalpies DeltaDeltaG of enzyme-inhibitor complex formations were calculated from Xi(50) values determined by pH-stat titration using a mixed micelles assay and PLA2 from Naja mocambique mocambique. A quantitative relationship between amide acidity and DeltaDeltaG values is presented. Comparison of isoacidic and isosteric inhibitors reveals that (i) the hydrogen bond of the amide proton to His-48 is crucial for strong PLA2 inhibition, (ii) regardless of the headgroup unsubstituted N-acyl groups result in optimal amide acidity for PLA2 inhibition and (iii) the exceptionally strong inhibition by acetamides and the isosteric fluoroacetamides is due to an additional steric effect.
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Affiliation(s)
- J T Kley
- Tumor Biology Center, Department of Medical Oncology, Division of Medical Research, Breisacher Strasse 117, D-79106 Freiburg, Germany
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