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Kim RR, Chen Z, J. Mann T, Bastard K, F. Scott K, Church WB. Structural and Functional Aspects of Targeting the Secreted Human Group IIA Phospholipase A 2. Molecules 2020; 25:molecules25194459. [PMID: 32998383 PMCID: PMC7583969 DOI: 10.3390/molecules25194459] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/20/2020] [Accepted: 09/25/2020] [Indexed: 12/11/2022] Open
Abstract
Human group IIA secretory phospholipase A2 (hGIIA) promotes the proliferation of cancer cells, making it a compelling therapeutic target, but it is also significant in other inflammatory conditions. Consequently, suitable inhibitors of hGIIA have always been sought. The activation of phospholipases A2 and the catalysis of glycerophospholipid substrates generally leads to the release of fatty acids such as arachidonic acid (AA) and lysophospholipid, which are then converted to mediator compounds, including prostaglandins, leukotrienes, and the platelet-activating factor. However, this ability of hGIIA to provide AA is not a complete explanation of its biological role in inflammation, as it has now been shown that it also exerts proinflammatory effects by a catalysis-independent mechanism. This mechanism is likely to be highly dependent on key specific molecular interactions, and the full mechanistic descriptions of this remain elusive. The current candidates for the protein partners that may mediate this catalysis-independent mechanism are also introduced in this review. A key discovery has been that selective inhibition of the catalysis-independent activity of hGIIA is achieved with cyclised derivatives of a pentapeptide, FLSYK, derived from the primary sequence of hGIIA. The effects of hGIIA on cell function appear to vary depending on the pathology studied, and so its mechanism of action is complex and context-dependent. This review is comprehensive and covers the most recent developments in the understanding of the many facets of hGIIA function and inhibition and the insight they provide into their clinical application for disease treatment. A cyclic analogue of FLSYK, c2, the most potent analogue known, has now been taken into clinical trials targeting advanced prostate cancer.
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Affiliation(s)
- Ryung Rae Kim
- School of Pharmacy, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia; (R.R.K.); (Z.C.); (K.B.)
| | - Zheng Chen
- School of Pharmacy, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia; (R.R.K.); (Z.C.); (K.B.)
| | - Timothy J. Mann
- School of Medicine, Western Sydney University, Centre for Oncology, Education and Research Translation and The Ingham Institute, Liverpool, NSW 2170, Australia;
| | - Karine Bastard
- School of Pharmacy, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia; (R.R.K.); (Z.C.); (K.B.)
| | - Kieran F. Scott
- School of Medicine, Western Sydney University, Centre for Oncology, Education and Research Translation and The Ingham Institute, Liverpool, NSW 2170, Australia;
- Correspondence: (K.F.S.); (W.B.C.); Tel.: +61-2-8738-9026 (K.F.S.); +61-2-9036-6569 (W.B.C.)
| | - W. Bret Church
- School of Pharmacy, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia; (R.R.K.); (Z.C.); (K.B.)
- Correspondence: (K.F.S.); (W.B.C.); Tel.: +61-2-8738-9026 (K.F.S.); +61-2-9036-6569 (W.B.C.)
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Sobrinho J, Francisco A, Simões-Silva R, Kayano A, Ruiz Diaz JA, Garay AG, Arruda A, Ferreira A, Santos A, Luiz M, Teles C, Pereira S, Zanchi F, Calderon L, Zuliani J, Soares A. Antimyotoxic Activity of Synthetic Peptides Derived from Bothrops atrox Snake Gamma Phospholipase A2 Inhibitor Selected by Virtual Screening. Curr Top Med Chem 2019; 19:1952-1961. [DOI: 10.2174/1568026619666190725102812] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/13/2019] [Accepted: 07/04/2019] [Indexed: 11/22/2022]
Abstract
Background:
Several studies have aimed to identify molecules that inhibit the toxic actions
of snake venom phospholipases A2 (PLA2s). Studies carried out with PLA2 inhibitors (PLIs) have been
shown to be efficient in this assignment.
Objective:
This work aimed to analyze the interaction of peptides derived from Bothrops atrox PLIγ
(atPLIγ) with a PLA2 and to evaluate the ability of these peptides to reduce phospholipase and myotoxic
activities.
Methods:
Peptides were subjected to molecular docking with a homologous Lys49 PLA2 from B. atrox
venom modeled by homology. Phospholipase activity neutralization assay was performed with BthTX-II
and different ratios of the peptides. A catalytically active and an inactive PLA2 were purified from the B.
atrox venom and used together in the in vitro myotoxic activity neutralization experiments with the peptides.
Results:
The peptides interacted with amino acids near the PLA2 hydrophobic channel and the loop that
would be bound to calcium in Asp49 PLA2. They were able to reduce phospholipase activity and peptides
DFCHNV and ATHEE reached the highest reduction levels, being these two peptides the best that
also interacted in the in silico experiments. The peptides reduced the myotubes cell damage with a highlight
for the DFCHNV peptide, which reduced by about 65%. It has been suggested that myotoxic activity
reduction is related to the sites occupied in the PLA2 structure, which could corroborate the results
observed in molecular docking.
Conclusion:
This study should contribute to the investigation of the potential of PLIs to inhibit the toxic
effects of PLA2s.
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Affiliation(s)
- J.C. Sobrinho
- Centro de Estudos de Biomoléculas Aplicadas à Saúde, CEBio, Fundação Oswaldo Cruz, FIOCRUZ, Fiocruz Rondônia, Brazil
| | - A.F. Francisco
- Centro de Estudos de Biomoléculas Aplicadas à Saúde, CEBio, Fundação Oswaldo Cruz, FIOCRUZ, Fiocruz Rondônia, Brazil
| | - R. Simões-Silva
- Centro de Estudos de Biomoléculas Aplicadas à Saúde, CEBio, Fundação Oswaldo Cruz, FIOCRUZ, Fiocruz Rondônia, Brazil
| | - A.M. Kayano
- Centro de Estudos de Biomoléculas Aplicadas à Saúde, CEBio, Fundação Oswaldo Cruz, FIOCRUZ, Fiocruz Rondônia, Brazil
| | - J.J. Alfonso Ruiz Diaz
- Centro de Estudos de Biomoléculas Aplicadas à Saúde, CEBio, Fundação Oswaldo Cruz, FIOCRUZ, Fiocruz Rondônia, Brazil
| | - A.F. Gomez Garay
- Centro de Estudos de Biomoléculas Aplicadas à Saúde, CEBio, Fundação Oswaldo Cruz, FIOCRUZ, Fiocruz Rondônia, Brazil
| | - A. Arruda
- Laboratório de Engenharia de Anticorpos, Fiocruz Rondônia, Porto Velho-RO, Brazil
| | - A.S. Ferreira
- Laboratório da Plataforma de Bioensaios de Malária e Leishmaniose, Fiocruz Rondônia, Porto Velho-RO, Brazil
| | - A.P.A. Santos
- Laboratório da Plataforma de Bioensaios de Malária e Leishmaniose, Fiocruz Rondônia, Porto Velho-RO, Brazil
| | - M.B. Luiz
- Laboratório de Engenharia de Anticorpos, Fiocruz Rondônia, Porto Velho-RO, Brazil
| | - C.B.G. Teles
- Laboratório da Plataforma de Bioensaios de Malária e Leishmaniose, Fiocruz Rondônia, Porto Velho-RO, Brazil
| | - S.S. Pereira
- Laboratório de Engenharia de Anticorpos, Fiocruz Rondônia, Porto Velho-RO, Brazil
| | - F.B. Zanchi
- Centro de Estudos de Biomoléculas Aplicadas à Saúde, CEBio, Fundação Oswaldo Cruz, FIOCRUZ, Fiocruz Rondônia, Brazil
| | - L.A. Calderon
- Centro de Estudos de Biomoléculas Aplicadas à Saúde, CEBio, Fundação Oswaldo Cruz, FIOCRUZ, Fiocruz Rondônia, Brazil
| | - J.P. Zuliani
- Centro de Estudos de Biomoléculas Aplicadas à Saúde, CEBio, Fundação Oswaldo Cruz, FIOCRUZ, Fiocruz Rondônia, Brazil
| | - A.M. Soares
- Centro de Estudos de Biomoléculas Aplicadas à Saúde, CEBio, Fundação Oswaldo Cruz, FIOCRUZ, Fiocruz Rondônia, Brazil
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Zhu B, He H, Hou T. A Comprehensive Review of Corn Protein-derived Bioactive Peptides: Production, Characterization, Bioactivities, and Transport Pathways. Compr Rev Food Sci Food Saf 2018; 18:329-345. [DOI: 10.1111/1541-4337.12411] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 10/29/2018] [Accepted: 10/29/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Biyang Zhu
- College of Food Science and Technology; Huazhong Agricultural Univ.; Wuhan 430070 China
- Key Lab of Environment Correlative Dietology (Huazhong Agricultural Univ.); Ministry of Education; Wuhan 43000 China
| | - Hui He
- College of Food Science and Technology; Huazhong Agricultural Univ.; Wuhan 430070 China
- Key Lab of Environment Correlative Dietology (Huazhong Agricultural Univ.); Ministry of Education; Wuhan 43000 China
| | - Tao Hou
- College of Food Science and Technology; Huazhong Agricultural Univ.; Wuhan 430070 China
- Key Lab of Environment Correlative Dietology (Huazhong Agricultural Univ.); Ministry of Education; Wuhan 43000 China
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Kim RR, Malde AK, Nematollahi A, Scott KF, Church WB. Molecular dynamics simulations reveal structural insights into inhibitor binding modes and functionality in human Group IIA phospholipase A 2. Proteins 2017; 85:827-842. [PMID: 28056488 DOI: 10.1002/prot.25235] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 12/14/2016] [Accepted: 12/21/2016] [Indexed: 11/09/2022]
Abstract
Human Group IIA phospholipase A2 (hGIIA) promotes inflammation in immune-mediated pathologies by regulating the arachidonic acid pathway through both catalysis-dependent and -independent mechanisms. The hGIIA crystal structure, both alone and inhibitor-bound, together with structures of closely related snake-venom-derived secreted phospholipase enzymes has been well described. However, differentiation of biological and nonbiological contacts and the relevance of structures determined from snake venom enzymes to human enzymes are not clear. We employed molecular dynamics (MD) and docking approaches to understand the binding of inhibitors that selectively or nonselectively block the catalysis-independent mechanism of hGIIA. Our results indicate that hGIIA behaves as a monomer in the solution environment rather than a dimer arrangement that is in the asymmetric unit of some crystal structures. The binding mode of a nonselective inhibitor, KH064, was validated by a combination of the experimental electron density and MD simulations. The binding mode of the selective pentapeptide inhibitor FLSYK to hGIIA was stipulated to be different to that of the snake venom phospholipases A2 of Daboia russelli pulchella (svPLA2 ). Our data suggest that the application of MD approaches to crystal structure data is beneficial in evaluating the robustness of conclusions drawn based on crystal structure data alone. Proteins 2017; 85:827-842. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ryung Rae Kim
- Group in Biomolecular Structure and Informatics, Faculty of Pharmacy, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Alpeshkumar K Malde
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia, 4072
| | - Alireza Nematollahi
- Group in Biomolecular Structure and Informatics, Faculty of Pharmacy, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Kieran F Scott
- School of Medicine, Western Sydney University, The Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia, 2170.,Centre for Oncology Education and Research Translation (CONCERT), The Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia, 2170
| | - W Bret Church
- Group in Biomolecular Structure and Informatics, Faculty of Pharmacy, The University of Sydney, Sydney, NSW, 2006, Australia
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Viperatoxin-II: A novel viper venom protein as an effective bactericidal agent. FEBS Open Bio 2015; 5:928-41. [PMID: 26793432 PMCID: PMC4688439 DOI: 10.1016/j.fob.2015.10.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 10/12/2015] [Accepted: 10/14/2015] [Indexed: 12/19/2022] Open
Abstract
Two novel viperatoxins (VipTx-I and VipTx-II) from Indian Russell’s viper snake venom were purified and characterized. VipTx-II but not VipTx-I showed strong antimicrobial effects against S. aureus and Burkholderia pseudomallei (strains KHW/TES), Proteus vulgaris and P. mirabilis. In broth dilution assays, VipTx-II had a potent bactericidal effect at the lowest dilutions against B. pseudomallei (strains KHW/TES), S. aureus and P. mirabilis. Protein-induced bactericidal potency was closely associated with pore formation and membrane damage. These proteins showed a low level of cytotoxic effects on human cells.
Infections caused by methicillin-resistant Staphylococcus aureus (MRSA) have become a rising threat to public health. There is an urgent need for development of promising new therapeutic agents against drug resistant bacteria like S. aureus. This report discusses purification and characterization of proteins from Indian Russell’s viper snake venom. Novel 15-kDa proteins called “Viperatoxin” (VipTx-I and VipTx-II) were extracted from the whole venom and evaluated using in vitro antimicrobial experiments. The N-terminal amino acid sequence of “Viperatoxin” showed high sequence homology to daboiatoxin isolated from the same venom and also matched phospholipase A2 (PLA2) enzymes isolated from other snake venoms. In an in vitro plate assay, VipTx-II but not VipTx-I showed strong antimicrobial effects against S. aureus and Burkholderia pseudomallei (KHW & TES), Proteus vulgaris and P. mirabilis. The VipTx-II was further tested by a broth-dilution assay at 100–3.1 μg/ml concentrations. The most potent bactericidal effect was found at the lowest dilutions (MICs of 6.25 μg/ml) against B. pseudomallei, S. aureus and P. vulgaris (MICs of 12.25 μg/ml). Electron microscopic investigation revealed that the protein-induced bactericidal potency was closely associated with pore formation and membrane damage, even at the lowest concentrations (<20 μg/ml). The toxin caused a low level of cytotoxic effects as observed in human (THP-1) cells at higher concentrations. Molecular weight determinations of VipTx-II by sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed one major, along with a few minor bands. The results indicate that VipTx-II plays a significant role in bactericidal and membrane damaging effects in vitro. Non-cytotoxic properties on human cells highlight it as a promising candidate for further evaluation of antimicrobial potential in vivo.
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Key Words
- Bactericidal
- Daboia russelli russelli
- MALDI-TOF/MS, matrix-assisted laser desorption ionization-time of flight/mass spectrometer
- MDR, multi-drug resistant
- MH, Mueller Hinton
- MICs, minimum inhibitory concentrations
- MRSA, methicillin-resistant Staphylococcus aureus
- MTXs, myotoxins
- PLA2, phospholipase A2
- Phospholipase A2
- SEM, scanning electron microscopy
- TEM, transmission electron microscopy
- TS, Tryptic Soya
- VipTx-I and VipTx-II, viperatoxins I and II
- Viperatoxin-I
- Viperatoxin-II
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Zhan C, Li S, Zhong Q, Zhou D. Structure-Based Grafting, Mutation, and Optimization of Peptide Inhibitors to Fit in the Active Pocket of Human Secreted Phospholipase A2: Find New Use of Old Peptide Agents with Anti-Inflammatory Activity. Chem Biol Drug Des 2014; 85:418-26. [PMID: 25187416 DOI: 10.1111/cbdd.12424] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 08/02/2014] [Accepted: 08/26/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Chengye Zhan
- Department of ICU; Tongji Hospital; Tongji Medical College; Huazhong University of Science and Technology; Wuhan 430030 China
| | - Shusheng Li
- Department of ICU; Tongji Hospital; Tongji Medical College; Huazhong University of Science and Technology; Wuhan 430030 China
| | - Qiang Zhong
- Department of ICU; Tongji Hospital; Tongji Medical College; Huazhong University of Science and Technology; Wuhan 430030 China
| | - Daixing Zhou
- Department of ICU; Tongji Hospital; Tongji Medical College; Huazhong University of Science and Technology; Wuhan 430030 China
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Ramakrishnan C, Joshi V, Joseph JM, Vishwanath BS, Velmurugan D. Identification of Novel Inhibitors ofDaboia russelliPhospholipase A2Using the Combined Pharmacophore Modeling Approach. Chem Biol Drug Des 2014; 84:379-92. [DOI: 10.1111/cbdd.12332] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 03/26/2014] [Accepted: 03/28/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Chandrasekaran Ramakrishnan
- Centre of Advanced Study in Crystallography and Biophysics; University of Madras; Maraimalai (Guindy) Campus Chennai 600025 India
| | - Vikram Joshi
- Department of Studies in Biochemistry; University of Mysore; Manasagangotri Mysore Karnataka 570006 India
| | - Joseph Mavelithuruthel Joseph
- Centre of Advanced Study in Crystallography and Biophysics; University of Madras; Maraimalai (Guindy) Campus Chennai 600025 India
| | - Bannikuppe S. Vishwanath
- Department of Studies in Biochemistry; University of Mysore; Manasagangotri Mysore Karnataka 570006 India
| | - Devadasan Velmurugan
- Centre of Advanced Study in Crystallography and Biophysics; University of Madras; Maraimalai (Guindy) Campus Chennai 600025 India
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Wadood A, Ali SA, Sattar R, Lodhi MA, Ul-Haq Z. A novel pharmacophore model to identify leads for simultaneous inhibition of anti-coagulation and anti-inflammatory activities of snake venom phospholipase A(2). Chem Biol Drug Des 2012; 79:431-41. [PMID: 22136624 DOI: 10.1111/j.1747-0285.2011.01281.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In addition to catalytic action, snake venom phospholipase A(2) induces several pharmacological effects including neurotoxicity, cardiotoxicity as well as anti-coagulant and anti-platelet aggregation effects. Therefore, strategy to identify dual inhibitor for this enzyme will be of much importance in medical research. In this paper, structure-based pharmacophore mapping, molecular docking, protein-ligand interaction fingerprints, binding energy calculations, and binding affinity predictions were employed in a virtual screening strategy to identify new hits for dual inhibition of anti-coagulation and inflammation of phospholipase A(2) . A structure-based pharmacophore map was modeled which comprised of important interactions as observed in co-crystal of phospholipase A(2) and its dual inhibitor indomethacin. The generated model was used to retrieve molecules from ChemBridge, a free database of commercially available compounds. A total of 381 molecules mapped on the developed pharmacophore model from ChemBridge database. The hits retrieved were further screened by molecular docking, protein-ligand interaction fingerprints, binding energy calculations, and binding affinity predictions using Genetic Optimization for Ligand Docking and moe. Based on these results, 32 chemo-types molecules were predicted as potential lead scaffolds for developing novel, potent and structurally diverse dual inhibitor of phospholipase A(2.).
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Affiliation(s)
- Abdul Wadood
- Dr Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
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Perumal Samy R, Gopalakrishnakone P, Chow VTK. Therapeutic application of natural inhibitors against snake venom phospholipase A(2). Bioinformation 2012; 8:48-57. [PMID: 22359435 PMCID: PMC3282276 DOI: 10.6026/97320630008048] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Accepted: 12/17/2011] [Indexed: 02/07/2023] Open
Abstract
Natural inhibitors occupy an important place in the potential to neutralize the toxic effects caused by snake venom proteins and enzymes. It has been well recognized for several years that animal sera, some of the plant and marine extracts are the most potent in neutralizing snake venom phospholipase A(2) (svPLA(2)). The implication of this review to update the latest research work which has been accomplished with svPLA(2) inhibitors from various natural sources like animal, marine organisms presents a compilation of research in this field over the past decade and revisiting the previous research report including those found in plants. In addition to that the bioactive compounds/inhibitor molecules from diverse sources like aristolochic alkaloid, flavonoids and neoflavonoids from plants, hydrocarbones -2, 4 dimethyl hexane, 2 methylnonane, and 2, 6 dimethyl heptane obtained from traditional medicinal plants Tragia involucrata (Euphorbiaceae) member of natural products involved for the inhibitory potential of phospholipase A(2) (PLA(2)) enzymes in vitro and also decrease both oedema induced by snake venom as well as human synovial fluid PLA(2). Besides marine natural products that inhibit PLA(2) are manoalide and its derivatives such as scalaradial and related compounds, pseudopterosins and vidalols, tetracylne from synthetic chemicals etc. There is an overview of the role of PLA(2) in inflammation that provides a rationale for seeking inhibitors of PLA(2) as anti-inflammatory agents. However, more studies should be considered to evaluate antivenom efficiency of sera and other agents against a variety of snake venoms found in various parts of the world. The implications of these new groups of svPLA(2) toxin inhibitors in the context of our current understanding of snake biology as well as in the development of new novel antivenoms therapeutics agents in the efficient treatment of snake envenomations are discussed.
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Affiliation(s)
- Ramar Perumal Samy
- Infectious Disease Programme, Department of Microbiology
- Venom and Toxin Research Programme, Department of Anatomy; Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597
| | - Ponnampalam Gopalakrishnakone
- Venom and Toxin Research Programme, Department of Anatomy; Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597
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Huang WN, Chen YH, Chen CL, Wu W. Surface pressure-dependent interactions of secretory phospholipase A2 with zwitterionic phospholipid membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:7034-7041. [PMID: 21557547 DOI: 10.1021/la200255r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The hydrolytic activity of secretory phospholipase A(2) (PLA(2)) is regulated by many factors, including the physical state of substrate aggregates and the chemical nature of phospholipid molecules. In order to achieve strong binding of PLA(2) on its substrates, many previous works have used anionic lipid dispersion to characterize the orientation and penetration depth of PLA(2) molecules on membrane surfaces. In this study, we applied monolayer technique with controllable surface area to investigate the PLA(2)s of Taiwan cobra venom and bee venom on zwitterionic phophatidylcholine monolayers and demonstrated an optimum hydrolytic activity at a surface pressure of 18 and 24 mN/m, respectively. By combining polarized attenuated total reflection Fourier-transform infrared spectroscopy and monolayer-binding experiments, we found that the amount of membrane-bound PLA(2) decreased markedly as the surface pressure of the monolayer was increased. Interestingly, the insertion area of the PLA(2)s decreased to near zero as the surface pressure increased to the optimum pressure for hydrolytic activity. On the basis of the measured infrared dichroic ratio, the orientation of the PLA(2)s bound to zwitterionic membranes was similar to that observed on a negatively charged membrane and was independent of the surface pressure. Our findings suggest that both PLA(2)s were located on the membrane surface rather than penetrating the membrane bilayer and that the deeply inserted mode is not a favorable condition for the hydrolysis of phospholipids in zwitterionic phospholipid membranes. The results are discussed in terms of the easy access of catalytic water for the PLA(2) activity and the mobilization of its substrate and product to facilitate the catalytic process.
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Affiliation(s)
- Wei-Ning Huang
- Department of Biotechnology, Yuanpei University, Hsinchu, Taiwan.
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Kang TS, Georgieva D, Genov N, Murakami MT, Sinha M, Kumar RP, Kaur P, Kumar S, Dey S, Sharma S, Vrielink A, Betzel C, Takeda S, Arni RK, Singh TP, Kini RM. Enzymatic toxins from snake venom: structural characterization and mechanism of catalysis. FEBS J 2011; 278:4544-76. [PMID: 21470368 DOI: 10.1111/j.1742-4658.2011.08115.x] [Citation(s) in RCA: 185] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Snake venoms are cocktails of enzymes and non-enzymatic proteins used for both the immobilization and digestion of prey. The most common snake venom enzymes include acetylcholinesterases, l-amino acid oxidases, serine proteinases, metalloproteinases and phospholipases A(2) . Higher catalytic efficiency, thermal stability and resistance to proteolysis make these enzymes attractive models for biochemists, enzymologists and structural biologists. Here, we review the structures of these enzymes and describe their structure-based mechanisms of catalysis and inhibition. Some of the enzymes exist as protein complexes in the venom. Thus we also discuss the functional role of non-enzymatic subunits and the pharmacological effects of such protein complexes. The structures of inhibitor-enzyme complexes provide ideal platforms for the design of potent inhibitors which are useful in the development of prototypes and lead compounds with potential therapeutic applications.
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Affiliation(s)
- Tse Siang Kang
- Department of Pharmacy, National University of Singapore, Singapore
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Structural analysis of a group III Glu62-phospholipase A2 from the scorpion, Mesobuthus tamulus: Targeting and reversible inhibition by native peptides. Int J Biol Macromol 2011; 48:423-31. [PMID: 21238479 DOI: 10.1016/j.ijbiomac.2011.01.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 12/22/2010] [Accepted: 01/04/2011] [Indexed: 11/22/2022]
Abstract
Group III phospholipase A(2) enzyme transcript from the Mesobuthus tamulus (Indian red scorpion) codes for three distinct products that include a large enzymatic subunit, a pentameric peptide and a small non-enzymatic subunit. The structures of these two subunits were modeled based on their sequence identity to bee venom PLA(2) and the partial sequence of MU2 adaptin subunit of AP2 clathrin adaptor, respectively. The enzymatic subunit comprises of three helices, the calcium binding loop and a substrate binding hydrophobic channel where the structure is stabilized by four disulfide bonds. The active site of the enzyme shows a catalytic histidine residue. Interestingly, there is a conservative mutation of the conserved aspartic acid, a classical participant of catalysis in this enzyme family, to glutamic acid. However, the side chain oxygen atoms of this glutamate are oriented away from the catalytic histidine implicating the non-participation of this residue in stabilizing the tautomeric conformation of the histidine. The acidic non-enzymatic subunit comprises of extensive hydrophobic residues with a conformation of an anti-parallel β-sheets making it ideal for tissue specific targeting. The native pentapeptide with the sequence Alanine-Arginine-Serine-Alanine-Arginine was docked to the enzymatic subunit. The peptide ligand occupies the hydrophobic cavity and makes a plethora of interactions with the residues in the channel, including a hydrogen bond with the crucial catalytic histidine and coordinate bond with the calcium ion. This ligand has a binding constant (K(D)) of 1.5μM. This makes the ligand a potential reversible inhibitor, ideal to prevent the enzyme from interacting with non-specific molecules enroute to the target. The enzyme-ligand complex also provides a model to understand the stereochemistry required for the design of more potent drug molecules against such enzyme drug targets.
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Thwin M, Samy RP, Satyanarayanajois SD, Gopalakrishnakone P. Venom neutralization by purified bioactive molecules: Synthetic peptide derivatives of the endogenous PLA2 inhibitory protein PIP (a mini-review). Toxicon 2010; 56:1275-83. [DOI: 10.1016/j.toxicon.2009.12.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Revised: 12/17/2009] [Accepted: 12/21/2009] [Indexed: 01/06/2023]
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14
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Singh N, Kumar RP, Kumar S, Sharma S, Mir R, Kaur P, Srinivasan A, Singh TP. Simultaneous inhibition of anti-coagulation and inflammation: crystal structure of phospholipase A2 complexed with indomethacin at 1.4 A resolution reveals the presence of the new common ligand-binding site. J Mol Recognit 2009; 22:437-45. [PMID: 19462410 DOI: 10.1002/jmr.960] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A novel ligand-binding site with functional implications has been identified in phospholipase A(2) (PLA(2)). The binding of non-steroidal anti-inflammatory agent indomethacin at this site blocks both catalytic and anti-coagulant actions of PLA(2). A group IIA PLA(2) has been isolated from Daboia russelli pulchella (Russell's viper) which is enzymatically active as well as induces a strong anti-coagulant action. The binding studies have shown that indomethacin reduces the effects of both anti-coagulant and pro-inflammatory actions of PLA(2). A group IIA PLA(2) was co-crystallized with indomethacin and the structure of the complex has been determined at 1.4 A resolution. The structure determination has revealed the presence of an indomethacin molecule in the structure of PLA(2) at a site which is distinct from the conventional substrate-binding site. One of the carboxylic group oxygen atoms of indomethacin interacts with Asp 49 and His 48 through the catalytically important water molecule OW 18 while the second carboxylic oxygen atom forms an ionic interaction with the side chain of Lys 69. It is well known that the residues, His 48 and Asp 49 are essential for catalysis while Lys 69 is a part of the anti-coagulant loop (residues, 54-77). Indomethacin binds in such a manner that it blocks the access to both, it works as a dual inhibitor for catalytic and anti-coagulant actions of PLA(2). This new binding site in PLA(2) has been observed for the first time and indomethacin is the first compound that has been shown to bind at this novel site resulting in the prevention of anti-coagulation and inflammation.
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Affiliation(s)
- Nagendra Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110 029, India
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15
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Kumar V, Hassan MI, Singh AK, Dey S, Singh TP, Yadav S. Strategy for sensitive and specific detection of molecular forms of PSA based on 2DE and kinetic analysis: A step towards diagnosis of prostate cancer. Clin Chim Acta 2009; 403:17-22. [DOI: 10.1016/j.cca.2008.11.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Revised: 11/04/2008] [Accepted: 11/07/2008] [Indexed: 11/29/2022]
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16
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Taneja B, Yadav J, Chakraborty TK, Brahmachari SK. An Indian effort towards affordable drugs: “Generic to designer drugs”. Biotechnol J 2009; 4:348-60. [DOI: 10.1002/biot.200900031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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17
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Somvanshi RK, Singh AK, Saxena M, Mishra B, Dey S. Development of novel peptide inhibitor of Lipoxygenase based on biochemical and BIAcore evidences. BIOCHIMICA ET BIOPHYSICA ACTA 2008; 1784:1812-7. [PMID: 18691678 DOI: 10.1016/j.bbapap.2008.07.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2008] [Revised: 06/19/2008] [Accepted: 07/07/2008] [Indexed: 10/21/2022]
Abstract
Lipoxygenase (LOX) are enzymes implicated in a broad range of inflammatory diseases, cancer, asthma and atherosclerosis. These diverse biological properties lead to the interesting target for the inhibition of this metabolic pathway of LOX. The drugs available in the market against LOX reported to have various side effects. To develop potent and selective therapeutic agents against LOX, it is essential to have the knowledge of its active site. Due to the lack of structural data of human LOX, researchers are using soybean LOX (sLOX) because of their availability and similarities in the active site structure. Based on the crystal structure of sLOX-3 and its complex with known inhibitors, we have designed a tripeptide, FWY which strongly inhibits sLOX-3 activity. The inhibition by peptide has been tested with purified sLOX-3 and with LOX present in blood serum of breast cancer patients in the presence of substrate linoleic acid and arachidonic acid respectively. The dissociation constant (K(D)) of the peptide with sLOX-3 as determined by Surface Plasmon Resonance (SPR) was 3.59x10(-9) M. The kinetic constant (K(i)) and IC(50), as determined biochemical methods were 7.41x10(-8) M and 0.15x10(-6) M respectively.
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Affiliation(s)
- Rishi Kumar Somvanshi
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110 029, India
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18
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Singh N, Jabeen T, Pal A, Sharma S, Perbandt M, Betzel C, Singh TP. Crystal structures of the complexes of a group IIA phospholipase A2with two natural anti‐inflammatory agents, anisic acid, and atropine reveal a similar mode of binding. Proteins 2006; 64:89-100. [PMID: 16596639 DOI: 10.1002/prot.20970] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Secretory low molecular weight phospholipase A(2)s (PLA(2)s) are believed to be involved in the release of arachidonic acid, a precursor for the biosynthesis of pro-inflammatory eicosanoids. Therefore, the specific inhibitors of these enzymes may act as potent anti-inflammatory agents. Similarly, the compounds with known anti-inflammatory properties should act as specific inhibitors. Two plant compounds, (a) anisic acid (4-methoxy benzoic acid) and (b) atropine (8-methyl-8-azabicyclo oct-3-hydroxy-2-phenylpropanoate), have been used in various inflammatory disorders. Both compounds (a) and (b) have been found to inhibit PLA(2) activity having binding constants of 4.5 x 10(-5) M and 2.1 x 10(-8) M, respectively. A group IIA PLA(2) was isolated and purified from the venom of Daboia russelli pulchella (DRP) and its complexes were made with anisic acid and atropine. The crystal structures of the two complexes (i) and (ii) of PLA(2) with compounds (a) and (b) have been determined at 1.3 and 1.2 A resolutions, respectively. The high-quality observed electron densities for the two compounds allowed the accurate determinations of their atomic positions. The structures revealed that these compounds bound to the enzyme at the substrate - binding cleft and their positions were stabilized by networks of hydrogen bonds and hydrophobic interactions. The most characteristic interactions involving Asp 49 and His 48 were clearly observed in both complexes, although the residues that formed hydrophobic interactions with these compounds were not identical because their positions did not exactly superimpose in the large substrate-binding hydrophobic channel. Owing to a relatively small size, the structure of anisic acid did not alter upon binding to PLA(2), while that of atropine changed significantly when compared with its native crystal structure. The conformation of the protein also did not show notable changes upon the bindings of these ligands. The mode of binding of anisic acid to the present group II PLA(2) is almost identical to its binding with bovine pancreatic PLA(2) of group I. On the other hand, the binding of atropine to PLA(2) is similar to that of another plant alkaloid aristolochic acid.
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Affiliation(s)
- Nagendra Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
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19
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Jabeen T, Singh N, Singh RK, Ethayathulla AS, Sharma S, Srinivasan A, Singh TP. Crystal structure of a novel phospholipase A2 from Naja naja sagittifera with a strong anticoagulant activity. Toxicon 2005; 46:865-75. [PMID: 16269164 DOI: 10.1016/j.toxicon.2005.08.008] [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] [Received: 02/25/2005] [Revised: 08/10/2005] [Accepted: 08/10/2005] [Indexed: 11/19/2022]
Abstract
This is the first PLA(2) crystal structure from group I that shows a strong anticoagulant property. The monomeric PLA(2) was purified from the venom of Naja naja sagittifera (Indian cobra). Its amino acid sequence has been determined using cDNA technique. The amino acid sequence of sPLA(2) contains three positively charged and two negatively charged residues in the segment 54-71 (numbering scheme of sPLA(2)) thus giving this region an overall cationic amphiphilic surface. This suggested the presence of an anticoagulant activity in sPLA(2). The enzyme was crystallized using hanging drop vapour diffusion method in the presence of calcium chloride. The crystals belong to space group P4(1) with cell dimensions of a=b=42.0A, c=65.9A. The X-ray crystal structure was determined at 1.8A resolution using molecular replacement method and refined to an R value of 0.179 for 10,023 reflections. The overall scaffolding of sPLA(2) is essentially similar to those observed for other group I PLA(2)s. However, the conformations of various surface loops were found to be significantly different. The most significant observation pertains to the anticoagulant loop in which both the acidic residues are engaged in intramolecular interactions whereas all the three basic residues are free to interact with other molecules. This makes the sPLA(2) a potentially strong anticoagulating molecule.
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Affiliation(s)
- Talat Jabeen
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
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20
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Balasubramanya R, Chandra V, Kaur P, Singh TP. Crystal structure of the complex of the secretory phospholipase A2 from Daboia russelli pulchella with an endogenic indole derivative, 2-carbamoylmethyl-5-propyl-octahydro-indol-7-yl-acetic acid at 1.8 A resolution. BIOCHIMICA ET BIOPHYSICA ACTA 2005; 1752:177-85. [PMID: 16122995 DOI: 10.1016/j.bbapap.2005.07.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2005] [Revised: 07/25/2005] [Accepted: 07/27/2005] [Indexed: 10/25/2022]
Abstract
Phospholipase A2 (PLA2) enzymes from snake venoms are approximately 14 kDa secretory proteins and catalyze the release of arachidonic acid which is the precursor of proinflammatory mediators such as prostaglandins, leukotrienes, thromboxanes and platelet-activating factors. The structure of the PLA2 enzyme purified from the venom of Daboia russelli pulchella was determined using molecular replacement method and refined to an R value of 18.3% for all the reflections to 1.8 A resolution. The structure contains two crystallographically independent molecules A and B which form an asymmetric homodimer. The Ca2+ ion was not detected in the present structure, however, a characteristic non-protein high quality electron density was observed at the substrate-binding site of molecule A which allowed a clear interpretation of a natural ligand identified as a derivative of indole, 2-carbamoylmethyl-5-propyl-octahydro-indol-7-yl)-acetic acid. The corresponding substrate-binding site in molecule B was empty. The ligand present in molecule A is involved in extensive interactions with the protein atoms including important catalytic residues such as Asp-49 and His-48. The results also show that the indole derivatives act as potent inhibitors of secretory group II PLA2 enzymes that can be further modified to be used as potential therapeutic agents.
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Affiliation(s)
- R Balasubramanya
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110 029, India
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21
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Singh G, Jasti J, Saravanan K, Sharma S, Kaur P, Srinivasan A, Singh TP. Crystal structure of the complex formed between a group I phospholipase A2 and a naturally occurring fatty acid at 2.7 A resolution. Protein Sci 2005; 14:395-400. [PMID: 15659372 PMCID: PMC2253428 DOI: 10.1110/ps.041115505] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
This is the first evidence of a naturally bound fatty acid to a group I Phospholipase A(2) (PLA(2)) and also to a PLA(2) with Asp 49. The fatty acid identified as n-tridecanoic acid is observed at the substrate recognition site of PLA(2) hydrophobic channel. The complex was isolated from the venom of Bungarus caeruleus (Common Indian Krait). The primary sequence of the PLA(2) was determined using the cDNA method. Three-dimensional structure has been solved by the molecular replacement method and refined using the CNS package to a final R factor of 19.8% for the data in the resolution range from 20.0 to 2.7 A. The final refined model is comprised of 912 protein atoms, one sodium ion, one molecule of n-tridecanoic acid, and 60 water molecules. The sodium ion is located in the calcium-binding loop with a sevenfold coordination. A characteristic extra electron density was observed in the hydrophobic channel of the enzyme, into which a molecule of n-tridecanoic acid was clearly fitted. The MALDI-TOF measurements of the crystals had earlier indicated an increase in the molecular mass of PLA(2) by 212 Da over the native PLA(2). A major part of the ligand fits well in the binding pocket and interacts directly with His 48 and Asp 49. Although the overall structure of PLA(2) in the present complex is similar to the native structure reported earlier, it differs significantly in the folding of its calcium-binding loop.
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Affiliation(s)
- Garima Singh
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
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22
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Singh G, Gourinath S, Sarvanan K, Sharma S, Bhanumathi S, Betzel C, Yadav S, Srinivasan A, Singh TP. Crystal structure of a carbohydrate induced homodimer of phospholipase A2 from Bungarus caeruleus at 2.1Å resolution. J Struct Biol 2005; 149:264-72. [PMID: 15721580 DOI: 10.1016/j.jsb.2004.11.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2004] [Revised: 11/15/2004] [Indexed: 11/22/2022]
Abstract
This is the first crystal structure of a carbohydrate induced dimer of phospholipase A(2) (PLA(2)). This is an endogenous complex formed between two PLA(2) molecules and two mannoses. It was isolated from Krait venom (Bungarus caeruleus) and crystallized as such. The complete amino acid sequence of PLA(2) was determined using cDNA method. Three-dimensional structure of the complex has been solved with molecular replacement method and refined to a final R-factor of 0.192 for all the data in the resolution range 20.0-2.1A. The presence of mannose molecules in the protein crystals was confirmed using dinitrosalicylic acid test and the molecular weight of the dimer was verified with MALDI-TOF. As indicated by dynamic light scattering and analytical ultracentrifugation the dimer was also stable in solution. The good quality non-protein electron density at the interface of two PLA(2) molecules enabled us to model two mannoses. The mannoses are involved extensively in interactions with protein atoms of both PLA(2) molecules. Some of the critical amino acid residues such as Asp 49 and Tyr 31, which are part of the substrate-binding site, are found facing the interface and interacting with mannoses. The structure of the complex clearly shows that the dimerization is caused by mannoses and it results in the loss of enzymatic activity.
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Affiliation(s)
- Garima Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110 029, India
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23
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Singh N, Jabeen T, Sharma S, Roy I, Gupta MN, Bilgrami S, Somvanshi RK, Dey S, Perbandt M, Betzel C, Srinivasan A, Singh TP. Detection of native peptides as potent inhibitors of enzymes. FEBS J 2004; 272:562-72. [PMID: 15654893 DOI: 10.1111/j.1742-4658.2004.04499.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Chymotrypsin is a prominent member of the family of serine proteases. The present studies demonstrate the presence of a native fragment containing 14 residues from Ile16 to Trp29 in alpha-chymotrypsin that binds to chymotrypsin at the active site with an exceptionally high affinity of 2.7 +/- 0.3 x 10(-11) M and thus works as a highly potent competitive inhibitor. The commercially available alpha-chymotrypsin was processed through a three phase partitioning system (TPP). The treated enzyme showed considerably enhanced activity. The 14 residue fragment was produced by autodigestion of a TPP-treated alpha-chymotrypsin during a long crystallization process that lasted more than four months. The treated enzyme was purified and kept for crystallization using vapour the diffusion method at 295 K. Twenty milligrams of lyophilized protein were dissolved in 1 mL of 25 mM sodium acetate buffer, pH 4.8. It was equilibrated against the same buffer containing 1.2 M ammonium sulfate. The rectangular crystals of small dimensions of 0.24 x 0.15 x 0.10 mm(3) were obtained. The X-ray intensity data were collected at 2.2 angstroms resolution and the structure was refined to an R-factor of 0.192. An extra electron density was observed at the binding site of alpha-chymotrypsin, which was readily interpreted as a 14 residue fragment of alpha-chymotrypsin corresponding to Ile-Val-Asn-Gly-Glu-Glu-Ala-Val-Pro-Gly-Ser-Trp-Pro-Trp(16-29). The electron density for the eight residues of the C-terminus, i.e. Ala22-Trp29, which were completely buried in the binding cleft of the enzyme, was of excellent quality and all the side chains of these eight residues were clearly modeled into it. However, the remaining six residues from the N-terminus, Ile16-Glu21 were poorly defined although the backbone density was good. There was a continuous electron density at 3.0 sigma between the active site Ser195 Ogamma and the carbonyl carbon atom of Trp29 of the fragment. The final refined coordinates showed a distance of 1.35 angstroms between Ser195 Ogamma and Trp29 C indicating the presence of a covalent linkage between the enzyme and the native fragment. This meant that the enzyme formed an acyl intermediate with the autodigested fragment Ile16-Trp29. In addition to the O-C covalent bond, there were several hydrogen bonds and hydrophobic interactions between the enzyme and the native fragment. The fragment showed a high complementarity with the binding site of alpha-chymotrypsin and the buried part of the fragment matched excellently with the corresponding buried part of Turkey ovomucoid inhibitor of alpha-chymotrypsin.
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Affiliation(s)
- Nagendra Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110 029, India
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Smart BP, Pan YH, Weeks AK, Bollinger JG, Bahnson BJ, Gelb MH. Inhibition of the complete set of mammalian secreted phospholipases A2 by indole analogues. Bioorg Med Chem 2004; 12:1737-49. [PMID: 15028265 DOI: 10.1016/j.bmc.2004.01.022] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2003] [Accepted: 01/07/2004] [Indexed: 11/24/2022]
Abstract
Structure-guided design was employed in a search for potent and selective inhibitors of mammalian secreted phospholipases A(2) (sPLA(2)s). Using the X-ray structures of human groups IIA and X sPLA(2)s (hGIIA and hGX) as templates, homology structural models were made for the other human and mouse sPLA(2)s (hGIB, mGIB, mGIIA, mGIIC, hGIID, mGIID, hGIIE, mGIIE, hGIIF, mGIIF, hGV, mGV, and mGX). Me-Indoxam is a previously discovered indole analogue that binds tightly to many sPLA(2)s, and the X-ray structure of the hGX-Me-Indoxam complex was determined at a resolution of 2.0 A. Modeling suggests that the residues near the N(1)-substituent of Me-Indoxam vary significantly among the mammalian sPLA(2)s, and therefore a library of 83N(1)-variants was prepared by parallel synthesis. Several Me-Indoxam analogues bearing a 4-(2-oxy-ethanoic acid) side chain were potent inhibitors (IC(50) <0.05 microM) of hGIIA, mGIIA, mGIIC, hGIIE, mGIIE, hGV, and mGV, while they displayed intermediate potency (0.05-5 microM) against hGIB, mGIB, hGX, and mGX, and poorly inhibited (>5 microM) hGIID, mGIID, hGIIF, and mGIIF. Me-Indoxam analogues bearing a 5-(4-oxy-butanoic acid) side chain were generally less potent inhibitors. Although no compounds were found to be highly specific for a single human or mouse sPLA(2), combinations of Me-Indoxam analogues were discovered that could be used to distinguish the action of various sPLA(2)s in cellular events. For example, Me-Indoxam and compound 5 are approximately 5-fold more potent on hGIIA than on hGV, and compound 21 is 10-fold more potent on hGV versus hGIIA.
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Affiliation(s)
- Brian P Smart
- Departments of Chemistry and Biochemistry, University of Washington, Seattle, WA 98195, USA
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