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Sadhu SP, Yarla NS, Pragada RR, Konduri P. Anti-inflammatory Activity of PLA 2 Inhibitory Saccharumoside-B. Antiinflamm Antiallergy Agents Med Chem 2022; 21:121-134. [PMID: 35362396 DOI: 10.2174/1871523021666220330143058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/25/2022] [Accepted: 02/16/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Saccharumoside-B and its analogs were found to have anticancer potential in vitro. The present study reports acute toxicity, molecular docking, ADMET profile analysis, and in vitro and in vivo anti-inflammatory activity of saccharumoside-B for the first time. METHODS The in vitro enzyme inhibitory activity of saccharumoside-B on PLA2, COX-1, COX-2, and 5-LOX enzymes was evaluated by the cell-free method, and its effect on TNF-α, IL1β, and IL- 6 secretion levels in LPS stimulated THP-1 human monocytes was determined by ELISA-based methods. The anti-inflammatory activity was evaluated in vivo by carrageenan-induced rat paw edema model. To test its binding affinity at the active site pockets of PLA2 enzymes and assess drug-like properties, docking experiments and ADMET studies were performed. RESULTS Saccharumoside-B showed selective inhibition of the sPLA2 enzyme (IC50 = 7.53 ± 0.232 μM), and thioetheramide-PC was used as a positive control. It showed significant inhibition (P ≤ 0.05) of TNF-α, IL-1β, and IL-6 cytokines compared to the positive control dexamethasone. Saccharumoside-B showed a dose-dependent inhibition of carrageenan-induced rat paw edema, with a maximum inhibition (76.09 ± 0.75) observed at 3 hours after the phlogistic agent injection. Saccharumoside-B potentially binds to the active site pocket of sPLA2 crystal protein (binding energy -7.6 Kcal/Mol). It complies with Lipinski's Rule of Five, showing a promising safety profile. The bioactivity scores suggested it to be a better enzyme inhibitor. CONCLUSION Saccharumoside-B showed significant PLA2 inhibition. It can become a potential lead molecule in synthesizing a new class of selective PLA2 inhibitors with a high safety profile in the future.
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Affiliation(s)
- Surya Prabha Sadhu
- Department of AU College of Pharmaceutical Sciences and Pharmacology, Andhra University, Visakhapatnam, India
- Department of Pharmacology, Shri Vishnu College of Pharmacy, Bhimavaram, India
| | - Nagendra Sastry Yarla
- Department of Biochemistry, GITAM Institute of Science, GITAM University, Visakhapatnam, India
| | - Rajeswara Rao Pragada
- Department of AU College of Pharmaceutical Sciences, Pharmacology, Andhra University, Visakhapatnam, India
| | - Prasad Konduri
- Department of Pharmacology, Shri Vishnu College of Pharmacy, Bhimavaram, India
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2
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Batsika CS, Gerogiannopoulou ADD, Mantzourani C, Vasilakaki S, Kokotos G. The design and discovery of phospholipase A 2 inhibitors for the treatment of inflammatory diseases. Expert Opin Drug Discov 2021; 16:1287-1305. [PMID: 34143707 DOI: 10.1080/17460441.2021.1942835] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AREAS COVERED This review article summarizes the most important synthetic PLA2 inhibitors developed to target each one of the four major types of human PLA2 (cytosolic cPLA2, calcium-independent iPLA2, secreted sPLA2, and lipoprotein-associated Lp-PLA2), discussing their in vitro and in vivo activities as well as their recent applications and therapeutic properties. Recent findings on the role of PLA2 in the pathobiology of COVID-19 are also discussed. EXPERT OPINION Although a number of PLA2 inhibitors have entered clinical trials, none has reached the market yet. Lipoprotein-associated PLA2 is now considered a biomarker of vascular inflammation rather than a therapeutic target for inhibitors like darapladib. Inhibitors of cytosolic PLA2 may find topical applications for diseases like atopic dermatitis and psoriasis. Inhibitors of secreted PLA2, varespladib and varespladib methyl, are under investigation for repositioning in snakebite envenoming. A deeper understanding of PLA2 enzymes is needed for the development of novel selective inhibitors. Lipidomic technologies combined with medicinal chemistry approaches may be useful tools toward this goal.
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Affiliation(s)
| | | | - Christiana Mantzourani
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Greece
| | - Sofia Vasilakaki
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Greece
| | - George Kokotos
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Greece
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3
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Robello M, Barresi E, Baglini E, Salerno S, Taliani S, Settimo FD. The Alpha Keto Amide Moiety as a Privileged Motif in Medicinal Chemistry: Current Insights and Emerging Opportunities. J Med Chem 2021; 64:3508-3545. [PMID: 33764065 PMCID: PMC8154582 DOI: 10.1021/acs.jmedchem.0c01808] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Over the years, researchers in drug discovery have taken advantage of the use of privileged structures to design innovative hit/lead molecules. The α-ketoamide motif is found in many natural products, and it has been widely exploited by medicinal chemists to develop compounds tailored to a vast range of biological targets, thus presenting clinical potential for a plethora of pathological conditions. The purpose of this perspective is to provide insights into the versatility of this chemical moiety as a privileged structure in drug discovery. After a brief analysis of its physical-chemical features and synthetic procedures to obtain it, α-ketoamide-based classes of compounds are reported according to the application of this motif as either a nonreactive or reactive moiety. The goal is to highlight those aspects that may be useful to understanding the perspectives of employing the α-ketoamide moiety in the rational design of compounds able to interact with a specific target.
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Affiliation(s)
- Marco Robello
- Synthetic Bioactive Molecules Section, LBC, NIDDK, NIH, 8 Center Drive, Room 404, Bethesda, Maryland 20892, United States
| | - Elisabetta Barresi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Emma Baglini
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Silvia Salerno
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Sabrina Taliani
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Federico Da Settimo
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
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4
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Zhang Q, Jeanneau E, Queneau Y, Soulère L. (2R)- and (2S)- 2-hydroxy- hexanoyl and octanoyl-l-homoserine lactones: New highly potent Quorum Sensing modulators with opposite activities. Bioorg Chem 2020; 104:104307. [PMID: 33142422 DOI: 10.1016/j.bioorg.2020.104307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/15/2020] [Accepted: 09/21/2020] [Indexed: 11/28/2022]
Abstract
The synthesis and the QS modulation activity of diastereoisomerically pure 2-hydroxy-N-acyl-l-homoserine lactones (2-OH-AHLs) are unveiled. (2R)- and (2S)- 2-hydroxy-N-hexanoyl-l-homoserine lactone and 2-hydroxy-N-octanoyl-l-homoserine lactone have been identified as very potent QS agonists and antagonists on the Vibrio fischeri-quorum sensing system with opposite activities depending on the configuration of the carbon atom with the hydroxyl group. Flexible molecular docking showed that the (2R)-OH configuration in the antagonist isomer induces new hydrogen bonds with Tyr70 and Asp79, two importantly conserved residues in the LuxR protein family, while the (2S)-OH agonist configuration exhibits a binding mode comparable to the natural ligand 3-oxo-hexanoyl-l-homoserine lactone (OHHL). For the analogs with long alkyl chain 3a and 3b and aromatic analogs, all are antagonists with no effect of the configuration at C-2.
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Affiliation(s)
- Qiang Zhang
- Univ Lyon, Université Claude Bernard Lyon 1, INSA Lyon, CPE Lyon, UMR 5246, CNRS, ICBMS, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, Chimie Organique et Bioorganique, Bât. E. Lederer, 1 rue Victor Grignard, F-69622 Villeurbanne, France
| | - Erwann Jeanneau
- Univ Lyon, Université Claude Bernard Lyon 1, Centre de Diffractométrie Henri Longchambon, 5 rue de La Doua, 69100 Villeurbanne, France
| | - Yves Queneau
- Univ Lyon, Université Claude Bernard Lyon 1, INSA Lyon, CPE Lyon, UMR 5246, CNRS, ICBMS, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, Chimie Organique et Bioorganique, Bât. E. Lederer, 1 rue Victor Grignard, F-69622 Villeurbanne, France.
| | - Laurent Soulère
- Univ Lyon, Université Claude Bernard Lyon 1, INSA Lyon, CPE Lyon, UMR 5246, CNRS, ICBMS, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, Chimie Organique et Bioorganique, Bât. E. Lederer, 1 rue Victor Grignard, F-69622 Villeurbanne, France.
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5
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Sales TA, Marcussi S, Ramalho TC. Current Anti-Inflammatory Therapies and the Potential of Secretory Phospholipase A2 Inhibitors in the Design of New Anti-Inflammatory Drugs: A Review of 2012 - 2018. Curr Med Chem 2020; 27:477-497. [PMID: 30706775 DOI: 10.2174/0929867326666190201120646] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 11/12/2018] [Accepted: 12/11/2018] [Indexed: 01/30/2023]
Abstract
The inflammatory process is a natural self-defense response of the organism to damage agents and its action mechanism involves a series of complex reactions. However, in some cases, this process can become chronic, causing much harm to the body. Therefore, over the years, many anti-inflammatory drugs have been developed aiming to decrease the concentrations of inflammatory mediators in the organism, which is a way of controlling these abnormal chain reactions. The main target of conventional anti-inflammatory drugs is the cyclooxygenase (COX) enzyme, but its use implies several side effects. Thus, based on these limitations, many studies have been performed, aiming to create new drugs, with new action mechanisms. In this sense, the phospholipase A2 (PLA2) enzymes stand out. Among all the existing isoforms, secretory PLA2 is the major target for inhibitor development, since many studies have proven that this enzyme participates in various inflammatory conditions, such as cancer, Alzheimer and arthritis. Finally, for the purpose of developing anti-inflammatory drugs that are sPLA2 inhibitors, many molecules have been designed. Accordingly, this work presents an overview of inflammatory processes and mediators, the current available anti-inflammatory drugs, and it briefly covers the PLA2 enzymes, as well as the diverse structural array of the newest sPLA2 inhibitors as a possible target for the production of new anti-inflammatory drugs.
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Affiliation(s)
- Thais A Sales
- Molecular Modeling Laboratory, Chemistry Department, Federal University of Lavras, 37200-000 Lavras, Brazil
| | - Silvana Marcussi
- Biochemistry Laboratory, Chemistry Department, Federal University of Lavras, 37200-000 Lavras, Brazil
| | - Teodorico C Ramalho
- Molecular Modeling Laboratory, Chemistry Department, Federal University of Lavras, 37200-000 Lavras, Brazil.,Center for Basic and Applied Research, Faculty of Informatics and Management, University of Hradec Kralove, 62, 50003 Rokitanskeho, Czech Republic
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6
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Hu X, Maffucci I, Contini A. Advances in the Treatment of Explicit Water Molecules in Docking and Binding Free Energy Calculations. Curr Med Chem 2020; 26:7598-7622. [DOI: 10.2174/0929867325666180514110824] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 02/26/2018] [Accepted: 04/18/2018] [Indexed: 12/30/2022]
Abstract
Background:
The inclusion of direct effects mediated by water during the ligandreceptor
recognition is a hot-topic of modern computational chemistry applied to drug discovery
and development. Docking or virtual screening with explicit hydration is still debatable,
despite the successful cases that have been presented in the last years. Indeed, how to select
the water molecules that will be included in the docking process or how the included waters
should be treated remain open questions.
Objective:
In this review, we will discuss some of the most recent methods that can be used in
computational drug discovery and drug development when the effect of a single water, or of a
small network of interacting waters, needs to be explicitly considered.
Results:
Here, we analyse the software to aid the selection, or to predict the position, of water
molecules that are going to be explicitly considered in later docking studies. We also present
software and protocols able to efficiently treat flexible water molecules during docking, including
examples of applications. Finally, we discuss methods based on molecular dynamics
simulations that can be used to integrate docking studies or to reliably and efficiently compute
binding energies of ligands in presence of interfacial or bridging water molecules.
Conclusions:
Software applications aiding the design of new drugs that exploit water molecules,
either as displaceable residues or as bridges to the receptor, are constantly being developed.
Although further validation is needed, workflows that explicitly consider water will
probably become a standard for computational drug discovery soon.
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Affiliation(s)
- Xiao Hu
- Università degli Studi di Milano, Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica “A. Marchesini”, Via Venezian, 21 20133 Milano, Italy
| | - Irene Maffucci
- Pasteur, Département de Chimie, École Normale Supérieure, PSL Research University, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, 75005 Paris, France
| | - Alessandro Contini
- Università degli Studi di Milano, Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica “A. Marchesini”, Via Venezian, 21 20133 Milano, Italy
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7
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Nikolaou A, Kokotou MG, Vasilakaki S, Kokotos G. Small-molecule inhibitors as potential therapeutics and as tools to understand the role of phospholipases A 2. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1864:941-956. [PMID: 30905350 PMCID: PMC7106526 DOI: 10.1016/j.bbalip.2018.08.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/10/2018] [Accepted: 08/16/2018] [Indexed: 11/20/2022]
Abstract
Phospholipase A2 (PLA2) enzymes are involved in various inflammatory pathological conditions including arthritis, cardiovascular and autoimmune diseases. The regulation of their catalytic activity is of high importance and a great effort has been devoted in developing synthetic inhibitors. We summarize the most important small-molecule synthetic PLA2 inhibitors developed to target each one of the four major types of human PLA2 (cytosolic cPLA2, calcium-independent iPLA2, secreted sPLA2, and lipoprotein-associated LpPLA2). We discuss recent applications of inhibitors to understand the role of each PLA2 type and their therapeutic potential. Potent and selective PLA2 inhibitors have been developed. Although some of them have been evaluated in clinical trials, none reached the market yet. Apart from their importance as potential medicinal agents, PLA2 inhibitors are excellent tools to unveil the role that each PLA2 type plays in cells and in vivo. Modern medicinal chemistry approaches are expected to generate improved PLA2 inhibitors as new agents to treat inflammatory diseases.
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Affiliation(s)
- Aikaterini Nikolaou
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Maroula G Kokotou
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Sofia Vasilakaki
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - George Kokotos
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece.
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8
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Prasher P, Mudila H, Sharma M, Khati B. Developmental perspectives of the drugs targeting enzyme-instigated inflammation: a mini review. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02315-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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9
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Zhang S, Li Y, Qin Z, Tu G, Chen G, Yan A. SAR study on inhibitors of GIIA secreted phospholipase A
2
using machine learning methods. Chem Biol Drug Des 2019; 93:666-684. [DOI: 10.1111/cbdd.13470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 12/14/2018] [Accepted: 12/17/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Shengde Zhang
- State Key Laboratory of Chemical Resource EngineeringDepartment of Pharmaceutical EngineeringBeijing University of Chemical Technology Beijing China
| | - Yang Li
- Institute of Science and TechnologyShandong University of Traditional Chinese Medicine Ji'nan Shandong China
| | - Zijian Qin
- State Key Laboratory of Chemical Resource EngineeringDepartment of Pharmaceutical EngineeringBeijing University of Chemical Technology Beijing China
| | - Guipin Tu
- State Key Laboratory of Chemical Resource EngineeringDepartment of Pharmaceutical EngineeringBeijing University of Chemical Technology Beijing China
| | - Guang Chen
- College of Life Science and TechnologyBeijing University of Chemical Technology Beijing China
| | - Aixia Yan
- State Key Laboratory of Chemical Resource EngineeringDepartment of Pharmaceutical EngineeringBeijing University of Chemical Technology Beijing China
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10
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Elgazar AA, Knany HR, Ali MS. Insights on the molecular mechanism of anti-inflammatory effect of formula from Islamic traditional medicine: An in-silico study. J Tradit Complement Med 2018; 9:353-363. [PMID: 31453132 PMCID: PMC6702150 DOI: 10.1016/j.jtcme.2018.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 09/25/2018] [Accepted: 09/25/2018] [Indexed: 02/09/2023] Open
Abstract
Background and aim Traditional medicine is an important source for drug discovery. However, many challenges face the scientific community to develop novel drugs from it. To investigate the rationale behind the medical legacy of centuries of precious knowledge from traditional medicine, we aimed at performing virtual screening to identify potential leads from the middle-age textbook, The Canon of Medicine. Experimental procedure A database of chemical constituents of plants mentioned within the book was built and docked against different molecular targets associated with inflammation such as phospholipase A2, p38 alpha mitogen activated protein kinase, cyclooxygenase-2 and leukotriene B4 dehydrogenase, after that literature survey was done to determine the consistency of traditional uses and molecular docking results with the current knowledge obtained from previous studies and reports. Results and conclusion The in-silico study revealed the ability of several chemical constituents, in the plants under investigation, to bind effectively to different targets associated with inflammation, which was consistent with previous reports, indicating that Islamic traditional medicine can be considered as a reliable promising source for developing new anti-inflammatory agents with low toxicity and minimal side effects.
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Affiliation(s)
- Abdullah A Elgazar
- Department of Pharmacognosy, Faculty of Pharmacy, Kafrelsheikh University, Egypt
| | - Hamada Ramadan Knany
- Department of Pharmacognosy, Faculty of Pharmacy, Kafrelsheikh University, Egypt
| | - Mohammed Soliman Ali
- Department of Pharmacognosy, Faculty of Pharmacy, Kafrelsheikh University, Egypt
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11
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Phospholipase A 2 catalysis and lipid mediator lipidomics. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1864:766-771. [PMID: 30905345 DOI: 10.1016/j.bbalip.2018.08.010] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/10/2018] [Accepted: 08/16/2018] [Indexed: 01/09/2023]
Abstract
Phospholipase A2 (PLA2) enzymes are the upstream regulators of the eicosanoid pathway liberating free arachidonic acid from the sn-2 position of membrane phospholipids. Free intracellular arachidonic acid serves as a substrate for the eicosanoid biosynthetic enzymes including cyclooxygenases, lipoxygenases, and cytochrome P450s that lead to inflammation. The Group IVA cytosolic (cPLA2), Group VIA calcium-independent (iPLA2), and Group V secreted (sPLA2) are three well-characterized human enzymes that have been implicated in eicosanoid formation. In this review, we will introduce and summarize the regulation of catalytic activity and cellular localization, structural characteristics, interfacial activation and kinetics, substrate specificity, inhibitor binding and interactions, and the downstream implications for eicosanoid biosynthesis of these three important PLA2 enzymes.
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12
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Giordanetto F, Knerr L, Nordberg P, Pettersen D, Selmi N, Beisel HG, de la Motte H, Månsson Å, Dahlström M, Broddefalk J, Saarinen G, Klingegård F, Hurt-Camejo E, Rosengren B, Wikström J, Wågberg M, Brengdahl J, Rohman M, Sandmark J, Åkerud T, Roth RG, Jansen F, Ahlqvist M. Design of Selective sPLA 2-X Inhibitor (-)-2-{2-[Carbamoyl-6-(trifluoromethoxy)-1 H-indol-1-yl]pyridine-2-yl}propanoic Acid. ACS Med Chem Lett 2018; 9:600-605. [PMID: 30034586 DOI: 10.1021/acsmedchemlett.7b00507] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 06/23/2018] [Indexed: 11/28/2022] Open
Abstract
A lead generation campaign identified indole-based sPLA2-X inhibitors with a promising selectivity profile against other sPLA2 isoforms. Further optimization of sPLA2 selectivity and metabolic stability resulted in the design of (-)-17, a novel, potent, and selective sPLA2-X inhibitor with an exquisite pharmacokinetic profile characterized by high absorption and low clearance, and low toxicological risk. Compound (-)-17 was tested in an ApoE-/- murine model of atherosclerosis to evaluate the effect of reversible, pharmacological sPLA2-X inhibition on atherosclerosis development. Despite being well tolerated and achieving adequate systemic exposure of mechanistic relevance, (-)-17 did not significantly affect circulating lipid and lipoprotein biomarkers and had no effect on coronary function or histological markers of atherosclerosis.
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13
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Tiwari PK, Ballav H, Aidhen IS. Total Synthesis of Natural Product Piperodione and Its Analogues. ChemistrySelect 2018. [DOI: 10.1002/slct.201801427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Praveen Kumar Tiwari
- Department of ChemistryIndian Institute of Technology Madras Chennai 600036 India
| | - Hemkalyan Ballav
- Department of ChemistryIndian Institute of Technology Madras Chennai 600036 India
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14
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Li MM, Xu ZJ, Wu Y, Liu B. Synthesis, Structure and Configuration of Streptanoate. ChemistrySelect 2018. [DOI: 10.1002/slct.201702871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Mei-Mei Li
- Key Laboratory of Green Chemical Technology of College of Heilongjiang Province; School of Chemical and Environmental Engineering; Harbin University of Science and Technology; Harbin 150040 China
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Ze-Jun Xu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Yikang Wu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Bo Liu
- Key Laboratory of Green Chemical Technology of College of Heilongjiang Province; School of Chemical and Environmental Engineering; Harbin University of Science and Technology; Harbin 150040 China
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15
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Small Peptides Able to Suppress Prostaglandin E₂ Generation in Renal Mesangial Cells. Molecules 2018; 23:molecules23010158. [PMID: 29342835 PMCID: PMC6017359 DOI: 10.3390/molecules23010158] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/10/2018] [Accepted: 01/10/2018] [Indexed: 11/17/2022] Open
Abstract
Peptide drug discovery may play a key role in the identification of novel medicinal agents. Here, we present the development of novel small peptides able to suppress the production of PGE₂ in mesangial cells. The new compounds were generated by structural alterations applied on GK115, a novel inhibitor of secreted phospholipase A₂, which has been previously shown to reduce PGE₂ synthesis in rat renal mesangial cells. Among the synthesized compounds, the tripeptide derivative 11 exhibited a nice dose-dependent suppression of PGE₂ production, similar to that observed for GK115.
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16
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Vasquez AM, Mouchlis VD, Dennis EA. Review of four major distinct types of human phospholipase A 2. Adv Biol Regul 2018; 67:212-218. [PMID: 29248300 PMCID: PMC5807221 DOI: 10.1016/j.jbior.2017.10.009] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 10/20/2017] [Accepted: 10/20/2017] [Indexed: 12/18/2022]
Abstract
The phospholipase A2 superfamily of enzymes plays a significant role in the development and progression of numerous inflammatory diseases. Through their catalytic action on membrane phospholipids, phospholipases are the upstream regulators of the eicosanoid pathway releasing free fatty acids for cyclooxygenases, lipoxygenases, and cytochrome P450 enzymes which produce various well-known inflammatory mediators including leukotrienes, thromboxanes and prostaglandins. Elucidating the association of phospholipases A2 with the membrane, the extraction and binding of phospholipid substrates, and their interactions with small-molecule inhibitors is crucial for the development of new anti-inflammatory therapeutics. Studying phospholipases has been challenging because they act on the surface of cellular membranes and micelles. Multidisciplinary approaches including hydrogen/deuterium exchange mass spectrometry, molecular dynamics simulations, and other computer-aided drug design techniques have been successfully employed by our laboratory to study interactions of phospholipases with membranes, phospholipid substrates and inhibitors. This review summarizes the application of these techniques to study four human recombinant phospholipases A2.
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Affiliation(s)
- Alexis M Vasquez
- Department of Chemistry and Biochemistry and Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0601, United States
| | - Varnavas D Mouchlis
- Department of Chemistry and Biochemistry and Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0601, United States.
| | - Edward A Dennis
- Department of Chemistry and Biochemistry and Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0601, United States.
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17
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Synthesis, Antiphospholipase A₂, Antiprotease, Antibacterial Evaluation and Molecular Docking Analysis of Certain Novel Hydrazones. Molecules 2016; 21:molecules21121664. [PMID: 27918459 PMCID: PMC6272960 DOI: 10.3390/molecules21121664] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 11/20/2016] [Accepted: 11/28/2016] [Indexed: 11/22/2022] Open
Abstract
Some novel hydrazone derivatives 6a–o were synthesized from the key intermediate 4-Chloro-N-(2-hydrazinocarbonyl-phenyl)-benzamide 5 and characterized using IR, 1H-NMR, 13C-NMR, mass spectroscopy and elemental analysis. The inhibitory potential against two secretory phospholipase A2 (sPLA2), three protease enzymes and eleven bacterial strains were evaluated. The results revealed that all compounds showed preferential inhibition towards hGIIA isoform of sPLA2 rather than DrG-IB with compounds 6l and 6e being the most active. The tested compounds exhibited excellent antiprotease activity against proteinase K and protease from Bacillus sp. with compound 6l being the most active against both enzymes. Furthermore, the maximum zones of inhibition against bacterial growth were exhibited by compounds; 6a, 6m, and 6o against P. aeruginosa; 6a, 6b, 6d, 6f, 6l, 6m, 6n, and 6o against Serratia; 6k against S. mutans; and compounds 6a, 6d, 6e, 6m, and 6n against E. feacalis. The docking simulations of hydrazones 6a–o with GIIA sPLA2, proteinase K and hydrazones 6a–e with glutamine-fructose-6-phosphate transaminase were performed to obtain information regarding the mechanism of action.
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Vasilakaki S, Barbayianni E, Magrioti V, Pastukhov O, Constantinou-Kokotou V, Huwiler A, Kokotos G. Inhibitors of secreted phospholipase A2 suppress the release of PGE2 in renal mesangial cells. Bioorg Med Chem 2016; 24:3029-3034. [PMID: 27234891 DOI: 10.1016/j.bmc.2016.05.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/11/2016] [Indexed: 01/15/2023]
Abstract
The upregulation of PGE2 by mesangial cells has been observed under chronic inflammation condition. In the present work, renal mesangial cells were stimulated to trigger a huge increase of PGE2 synthesis and were treated in the absence or presence of known PLA2 inhibitors. A variety of synthetic inhibitors, mainly developed in our labs, which are known to selectively inhibit each of GIVA cPLA2, GVIA iPLA2, and GIIA/GV sPLA2, were used as tools in this study. Synthetic sPLA2 inhibitors, such as GK115 (an amide derivative based on the non-natural amino acid (R)-γ-norleucine) as well as GK126 and GK241 (2-oxoamides based on the natural (S)-α-amino acid leucine and valine, respectively) presented an interesting effect on the suppression of PGE2 formation.
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Affiliation(s)
- Sofia Vasilakaki
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Efrosini Barbayianni
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Victoria Magrioti
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece
| | | | | | - Andrea Huwiler
- Institute of Pharmacology, University of Bern, Bern 3010, Switzerland
| | - George Kokotos
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece.
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Vasilakaki S, Barbayianni E, Leonis G, Papadopoulos MG, Mavromoustakos T, Gelb MH, Kokotos G. Development of a potent 2-oxoamide inhibitor of secreted phospholipase A2 guided by molecular docking calculations and molecular dynamics simulations. Bioorg Med Chem 2016; 24:1683-95. [PMID: 26970660 DOI: 10.1016/j.bmc.2016.02.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 02/24/2016] [Accepted: 02/27/2016] [Indexed: 10/22/2022]
Abstract
Inhibition of group IIA secreted phospholipase A2 (GIIA sPLA2) has been an important objective for medicinal chemists. We have previously shown that inhibitors incorporating the 2-oxoamide functionality may inhibit human and mouse GIIA sPLA2s. Herein, the development of new potent inhibitors by molecular docking calculations using the structure of the known inhibitor 7 as scaffold, are described. Synthesis and biological evaluation of the new compounds revealed that the long chain 2-oxoamide based on (S)-valine GK241 led to improved activity (IC50=143 nM and 68 nM against human and mouse GIIA sPLA2, respectively). In addition, molecular dynamics simulations were employed to shed light on GK241 potent and selective inhibitory activity.
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Affiliation(s)
- Sofia Vasilakaki
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Efrosini Barbayianni
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Georgios Leonis
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece
| | - Manthos G Papadopoulos
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece
| | - Thomas Mavromoustakos
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Michael H Gelb
- Department of Chemistry and Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - George Kokotos
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece.
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20
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De Risi C, Pollini GP, Zanirato V. Recent Developments in General Methodologies for the Synthesis of α-Ketoamides. Chem Rev 2016; 116:3241-305. [DOI: 10.1021/acs.chemrev.5b00443] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Carmela De Risi
- Dipartimento
di Scienze Chimiche e Farmaceutiche, Università degli Studi di Ferrara, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Gian Piero Pollini
- Istituto Universitario
di Studi Superiori “IUSS−Ferrara 1391”, Via delle Scienze 41/b, 44121 Ferrara, Italy
| | - Vinicio Zanirato
- Dipartimento
di Scienze Chimiche e Farmaceutiche, Università degli Studi di Ferrara, Via Fossato di Mortara 17, 44121 Ferrara, Italy
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21
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Membrane and inhibitor interactions of intracellular phospholipases A2. Adv Biol Regul 2015; 61:17-24. [PMID: 26774606 DOI: 10.1016/j.jbior.2015.11.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 11/19/2015] [Accepted: 11/20/2015] [Indexed: 02/06/2023]
Abstract
Studying phospholipases A2 (PLA2s) is a challenging task since they act on membrane-like aggregated substrates and not on monomeric phospholipids. Multidisciplinary approaches that include hydrogen/deuterium exchange mass spectrometry (DXMS) and computational techniques have been employed with great success in order to address important questions about the mode of interactions of PLA2 enzymes with membranes, phospholipid substrates and inhibitors. Understanding the interactions of PLA2s is crucial since these enzymes are the upstream regulators of the eicosanoid pathway liberating free arachidonic acid (AA) and other polyunsaturated fatty acids (PUFA). The liberation of AA by PLA2 enzymes sets off a cascade of molecular events that involves downstream regulators such as cyclooxygenase (COX) and lipoxygenase (LOX) metabolites leading to inflammation. Aspirin and other nonsteroidal anti-inflammatory drugs (NSAIDs) work by inhibiting COX, while Zileuton inhibits LOX and both rely on PLA2 enzymes to provide them with AA. That means PLA2 enzymes can potentially also be targeted to diminish inflammation at an earlier point in the process. In this review we describe extensive efforts reported in the past to define the interactions of PLA2 enzymes with membranes, substrate phospholipids and inhibitors using DXMS, molecular docking, and molecular dynamics (MD) simulations.
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Sivaramakrishnan V, Ilamathi M, Ghosh KS, Sathish S, Gowda TV, Vishwanath BS, Rangappa KS, Dhananjaya BL. Virtual analysis of structurally diverse synthetic analogs as inhibitors of snake venom secretory phospholipase A2. J Mol Recognit 2015. [PMID: 26218369 DOI: 10.1002/jmr.2492] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Due to the toxic pathophysiological role of snake venom phospholipase A2 (PLA2 ), its compelling limitations to anti-venom therapy in humans and the need for alternative therapy foster considerable pharmacological interest towards search of PLA2 specific inhibitors. In this study, an integrated approach involving homology modeling, molecular dynamics and molecular docking studies on VRV-PL-V (Vipera russellii venom phospholipase A2 fraction-V) belonging to Group II-B secretory PLA2 from Daboia russelli pulchella is carried out in order to study the structure-based inhibitor design. The accuracy of the model was validated using multiple computational approaches. The molecular docking study of this protein was undertaken using different classes of experimentally proven, structurally diverse synthetic inhibitors of secretory PLA2 whose selection is based on IC50 value that ranges from 25 μM to 100 μM. Estimation of protein-ligand contacts by docking analysis sheds light on the importance of His 47 and Asp 48 within the VRV-PL-V binding pocket as key residue for hydrogen bond interaction with ligands. Our virtual analysis revealed that compounds with different scaffold binds to the same active site region. ADME analysis was also further performed to filter and identify the best potential specific inhibitor against VRV-PL-V. Additionally, the e-pharmacophore was generated for the best potential specific inhibitor against VRV-PL-V and reported here. The present study should therefore play a guiding role in the experimental design of VRV-PL-V inhibitors that may provide better therapeutic molecular models for PLA2 recognition and anti-ophidian activity.
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Affiliation(s)
- V Sivaramakrishnan
- Cardiomyocyte Toxicity and Oncology Research Lab, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA University, Thanjavur, 613401, India
| | - M Ilamathi
- Cardiomyocyte Toxicity and Oncology Research Lab, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA University, Thanjavur, 613401, India
| | - K S Ghosh
- Department of Chemistry, National Institute of Technology (NIT), Hamirpur, 177 005, India
| | - S Sathish
- Department of Studies in Biochemistry, University of Mysore, Mysore, 570006, India
| | - T V Gowda
- Department of Studies in Biochemistry, University of Mysore, Mysore, 570006, India
| | - B S Vishwanath
- Department of Studies in Biochemistry, University of Mysore, Mysore, 570006, India
| | - K S Rangappa
- Department of Chemistry, University of Mysore, Mysore, 570006, India
| | - B L Dhananjaya
- Toxinology/Toxicology and Drug Discovery Unit, Center for Emerging Technologies, Jain University, Jakkasandra post, Ramanagara, 562112, India
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23
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Ong WY, Farooqui T, Kokotos G, Farooqui AA. Synthetic and natural inhibitors of phospholipases A2: their importance for understanding and treatment of neurological disorders. ACS Chem Neurosci 2015; 6:814-31. [PMID: 25891385 DOI: 10.1021/acschemneuro.5b00073] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Phospholipases A2 (PLA2) are a diverse group of enzymes that hydrolyze membrane phospholipids into arachidonic acid and lysophospholipids. Arachidonic acid is metabolized to eicosanoids (prostaglandins, leukotrienes, thromboxanes), and lysophospholipids are converted to platelet-activating factors. These lipid mediators play critical roles in the initiation, maintenance, and modulation of neuroinflammation and oxidative stress. Neurological disorders including excitotoxicity; traumatic nerve and brain injury; cerebral ischemia; Alzheimer's disease; Parkinson's disease; multiple sclerosis; experimental allergic encephalitis; pain; depression; bipolar disorder; schizophrenia; and autism are characterized by oxidative stress, inflammatory reactions, alterations in phospholipid metabolism, accumulation of lipid peroxides, and increased activities of brain phospholipase A2 isoforms. Several old and new synthetic inhibitors of PLA2, including fatty acid trifluoromethyl ketones; methyl arachidonyl fluorophosphonate; bromoenol lactone; indole-based inhibitors; pyrrolidine-based inhibitors; amide inhibitors, 2-oxoamides; 1,3-disubstituted propan-2-ones and polyfluoroalkyl ketones as well as phytochemical based PLA2 inhibitors including curcumin, Ginkgo biloba and Centella asiatica extracts have been discovered and used for the treatment of neurological disorders in cell culture and animal model systems. The purpose of this review is to summarize information on selective and potent synthetic inhibitors of PLA2 as well as several PLA2 inhibitors from plants, for treatment of oxidative stress and neuroinflammation associated with the pathogenesis of neurological disorders.
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Affiliation(s)
- Wei-Yi Ong
- Department
of Anatomy, National University of Singapore, Singapore 119260, Singapore
| | - Tahira Farooqui
- Department
of Molecular and Cellular Biochemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - George Kokotos
- Laboratory
of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis,
Athens 15771, Greece
| | - Akhlaq A. Farooqui
- Department
of Molecular and Cellular Biochemistry, Ohio State University, Columbus, Ohio 43210, United States
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24
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Qiu S, Chen F, Liu Y, Lai L. Discovery of Novel Secretory Phospholipase A2Inhibitors Using Virtual Screen. Chem Biol Drug Des 2014; 84:216-22. [DOI: 10.1111/cbdd.12307] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 01/11/2014] [Accepted: 02/14/2014] [Indexed: 12/14/2022]
Affiliation(s)
- Shunchen Qiu
- BNLMS; State Key Laboratory of Structural Chemistry for Unstable and Stable Species; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Fangjin Chen
- Center for Quantitative Biology; Peking University; Beijing 100871 China
| | - Ying Liu
- BNLMS; State Key Laboratory of Structural Chemistry for Unstable and Stable Species; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Center for Quantitative Biology; Peking University; Beijing 100871 China
| | - Luhua Lai
- BNLMS; State Key Laboratory of Structural Chemistry for Unstable and Stable Species; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Center for Quantitative Biology; Peking University; Beijing 100871 China
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25
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Ton TMU, Himawan F, Chang JWW, Chan PWH. Copper(II) triflate catalyzed amination of 1,3-dicarbonyl compounds. Chemistry 2012; 18:12020-7. [PMID: 22890890 DOI: 10.1002/chem.201201219] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Indexed: 11/11/2022]
Abstract
A method to prepare α,α-acyl amino acid derivatives efficiently by Cu(OTf)(2)+1,10-phenanthroline (1,10-phen)-catalyzed amination of 1,3-dicarbonyl compounds with PhI=NSO(2) Ar is described. The mechanism is thought to initially involve aziridination of the enolic form of the substrate, formed in situ through coordination to the Lewis acidic metal catalyst, by the putative copper-nitrene/imido species generated from the reaction of the metal catalyst with the iminoiodane source. Subsequent ring opening of the resultant aziridinol adduct under the Lewis acidic conditions then provided the α-aminated product. The utility of this method was exemplified by the enantioselective synthesis of a precursor of 3-styryl-2-benzoyl-L-alanine.
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Affiliation(s)
- Thi My Uyen Ton
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
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26
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Potent and selective 2-oxoamide inhibitors of phospholipases A2 as novel medicinal agents for the treatment of inflammatory diseases. PURE APPL CHEM 2012. [DOI: 10.1351/pac-con-11-10-32] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Phospholipases A2 (PLA2s) are enzymes that are capable of catalyzing the hydrolysis of the sn-2 ester bond of glycerophospholipids, releasing free fatty acids, including arachidonic acid (AA), and lysophospholipids. Both products are precursor signaling molecules involved in inflammation. Among the various PLA2s, cytosolic GIVA cPLA2 is considered a major target for inflammatory diseases, while secreted GIIA sPLA2 is involved in cardiovascular diseases. We have developed lipophilic 2-oxoamides based on (S)-γ- or δ-amino acids as potent and selective inhibitors of GIVA cPLA2, which present interesting in vivo anti-inflammatory activity. 2-Oxoamides based on natural α-amino acids are selective inhibitors of GIIA sPLA2. The mode of binding of 2-oxoamides with either GIVA cPLA2 or GIIA sPLA2 has been studied by various techniques.
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27
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Mouchlis VD, Melagraki G, Mavromoustakos T, Kollias G, Afantitis A. Molecular Modeling on Pyrimidine-Urea Inhibitors of TNF-α Production: An Integrated Approach Using a Combination of Molecular Docking, Classification Techniques, and 3D-QSAR CoMSIA. J Chem Inf Model 2012; 52:711-23. [DOI: 10.1021/ci200579f] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
| | - Georgia Melagraki
- Department
of Chemoinformatics, NovaMechanics, Ltd., Nicosia, Cyprus
| | - Thomas Mavromoustakos
- Laboratory
of Organic Chemistry,
Department of Chemistry, University of Athens, Athens 15771, Greece
| | - George Kollias
- Institute
of Immunology, Biomedical Sciences Research Center “Alexander Fleming”, Athens, Greece
| | - Antreas Afantitis
- Department
of Chemoinformatics, NovaMechanics, Ltd., Nicosia, Cyprus
- Institute
of Immunology, Biomedical Sciences Research Center “Alexander Fleming”, Athens, Greece
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28
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Mouchlis VD, Michopoulou V, Constantinou-Kokotou V, Mavromoustakos T, Dennis EA, Kokotos G. Binding conformation of 2-oxoamide inhibitors to group IVA cytosolic phospholipase A2 determined by molecular docking combined with molecular dynamics. J Chem Inf Model 2012; 52:243-54. [PMID: 22196172 DOI: 10.1021/ci2005093] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The group IVA cytosolic phospholipase A(2) (GIVA cPLA(2)) plays a central role in inflammation. Long chain 2-oxoamides constitute a class of potent GIVA cPLA(2) inhibitors that exhibit potent in vivo anti-inflammatory and analgesic activity. We have now gained insight into the binding of 2-oxoamide inhibitors in the GIVA cPLA(2) active site through a combination of molecular docking calculations and molecular dynamics simulations. Recently, the location of the 2-oxoamide inhibitor AX007 within the active site of the GIVA cPLA(2) was determined using a combination of deuterium exchange mass spectrometry followed by molecular dynamics simulations. After the optimization of the AX007-GIVA cPLA(2) complex using the docking algorithm Surflex-Dock, a series of additional 2-oxoamide inhibitors have been docked in the enzyme active site. The calculated binding affinity presents a good statistical correlation with the experimental inhibitory activity (r(2) = 0.76, N = 11). A molecular dynamics simulation of the docking complex of the most active compound has revealed persistent interactions of the inhibitor with the enzyme active site and proves the stability of the docking complex and the validity of the binding suggested by the docking calculations. The combination of molecular docking calculations and molecular dynamics simulations is useful in defining the binding of small-molecule inhibitors and provides a valuable tool for the design of new compounds with improved inhibitory activity against GIVA cPLA(2).
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Affiliation(s)
- Varnavas D Mouchlis
- Laboratory of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis, Athens 15771, Greece
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29
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Characterization of suramin binding sites on the human group IIA secreted phospholipase A2 by site-directed mutagenesis and molecular dynamics simulation. Arch Biochem Biophys 2012; 519:17-22. [PMID: 22248627 DOI: 10.1016/j.abb.2012.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2011] [Revised: 12/31/2011] [Accepted: 01/03/2012] [Indexed: 11/23/2022]
Abstract
Suramin is a polysulphonated naphthylurea with inhibitory activity against the human secreted group IIA phospholipase A(2) (hsPLA2GIIA), and we have investigated suramin binding to recombinant hsPLA2GIIA using site-directed mutagenesis and molecular dynamics (MD) simulations. The changes in suramin binding affinity of 13 cationic residue mutants of the hsPLA2GIIA was strongly correlated with alterations in the inhibition of membrane damaging activity of the protein. Suramin binding to hsPLA2GIIA was also studied by MD simulations, which demonstrated that altered intermolecular potential energy of the suramin/mutant complexes was a reliable indicator of affinity change. Although residues in the C-terminal region play a major role in the stabilization of the hsPLA2GIIA/suramin complex, attractive and repulsive hydrophobic and electrostatic interactions with residues throughout the protein together with the adoption of a bent suramin conformation, all contribute to the stability of the complex. Analysis of the hsPLA2GIIA/suramin interactions allows the prediction of the properties of suramin analogues with improved binding and higher affinities which may be candidates for novel phospholipase A(2) inhibitors.
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