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Stylianaki EA, Mouchlis VD, Magkrioti C, Papavasileiou KD, Afantitis A, Matralis AN, Aidinis V. Identification of two novel chemical classes of Autotaxin (ATX) inhibitors using Enalos Asclepios KNIME nodes. Bioorg Med Chem Lett 2024; 103:129690. [PMID: 38447786 DOI: 10.1016/j.bmcl.2024.129690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/23/2024] [Accepted: 03/03/2024] [Indexed: 03/08/2024]
Abstract
Autotaxin is a secreted lysophospholipase D which is a member of the ectonucleotide pyrophosphatase/phosphodiesterase family converting extracellular lysophosphatidylcholine and other non-choline lysophospholipids, such as lysophosphatidylethanolamine and lysophosphatidylserine, to the lipid mediator lysophosphatidic acid. Autotaxin is implicated in various fibroproliferative diseases including interstitial lung diseases, such as idiopathic pulmonary fibrosis and hepatic fibrosis, as well as in cancer. In this study, we present an effort of identifying ATX inhibitors that bind to allosteric ATX binding sites using the Enalos Asclepios KNIME Node. All the available PDB crystal structures of ATX were collected, prepared, and aligned. Visual examination of these structures led to the identification of four crystal structures of human ATX co-crystallized with four known inhibitors. These inhibitors bind to five binding sites with five different binding modes. These five binding sites were thereafter used to virtually screen a compound library of 14,000 compounds to identify molecules that bind to allosteric sites. Based on the binding mode and interactions, the docking score, and the frequency that a compound comes up as a top-ranked among the five binding sites, 24 compounds were selected for in vitro testing. Finally, two compounds emerged with inhibitory activity against ATX in the low micromolar range, while their mode of inhibition and binding pattern were also studied. The two derivatives identified herein can serve as "hits" towards developing novel classes of ATX allosteric inhibitors.
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Affiliation(s)
| | - Varnavas D Mouchlis
- Department of ChemoInformatics, Novamechanics Ltd., Nicosia 1070, Cyprus; Department of Chemoinformatics, Novamechanics MIKE, Piraeus 18545, Greece; Division of Data Driven Innovation, Entelos Institute, Larnaca 6059, Cyprus
| | | | | | - Antreas Afantitis
- Department of ChemoInformatics, Novamechanics Ltd., Nicosia 1070, Cyprus; Department of Chemoinformatics, Novamechanics MIKE, Piraeus 18545, Greece; Division of Data Driven Innovation, Entelos Institute, Larnaca 6059, Cyprus.
| | - Alexios N Matralis
- Biomedical Sciences Research Center "Alexander Fleming", 16672 Vari, Greece.
| | - Vassilis Aidinis
- Biomedical Sciences Research Center "Alexander Fleming", 16672 Vari, Greece.
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Abstract
Water-soluble proteins as well as membrane-bound proteins associate with membrane surfaces and bind specific lipid molecules in specific sites on the protein. Membrane surfaces include the traditional bilayer membranes of cells and subcellular organelles formed by phospholipids. Monolayer membranes include the outer monolayer phospholipid surface of intracellular lipid droplets of triglycerides and various lipoproteins including HDL, LDL, VLDL, and chylomicrons. These lipoproteins circulate in our blood and lymph systems and contain triglycerides, cholesterol, cholesterol esters, and proteins in their interior, and these are sometimes interspersed on their surfaces. Similar lipid-water interfaces also occur in mixed micelles of phospholipids and bile acids in our digestive system, which may also include internalized triglycerides and cholesterol esters. Diacyl phospholipids constitute the defining molecules of biological membranes. Phospholipase A1 (PLA1) hydrolyzes phospholipid acyl chains at the sn-1 position of membrane phospholipids, phospholipase A2 (PLA2) hydrolyzes acyl chains at the sn-2 position, phospholipase C (PLC) hydrolyzes the glycerol-phosphodiester bond, and phospholipase D (PLD) hydrolyzes the polar group-phosphodiester bond. Of the phospholipases, the PLA2s have been the most well studied at the mechanistic level. The PLA2 superfamily consists of 16 groups and numerous subgroups, and each is generally described as one of 6 types. The most well studied of the PLA2s include extensive genetic and mutational studies, complete lipidomics specificity characterization, and crystallographic structures. This Account will focus principally on results from deuterium exchange mass spectrometric (DXMS) studies of PLA2 interactions with membranes and extensive molecular dynamics (MD) simulations of their interactions with membranes and specific phospholipids bound in their catalytic and allosteric sites. These enzymes either are membrane-bound or are water-soluble and associate with membranes before extracting their phospholipid substrate molecule into their active site to carry out their enzymatic hydrolytic reaction. We present evidence that when a PLA2 associates with a membrane, the membrane association can result in a conformational change in the enzyme whereby the membrane association with an allosteric site on the enzyme stabilizes the enzyme in an active conformation on the membrane. We sometimes refer to this transition from a "closed" conformation in aqueous solution to an "open" conformation when associated with a membrane. The enzyme can then extract a single phospholipid substrate into its active site, and catalysis occurs. We have also employed DXMS and MD simulations to characterize how PLA2s interact with specific inhibitors that could lead to potential therapeutics. The PLA2s constitute a paradigm for how membranes interact allosterically with proteins, causing conformational changes and activation of the proteins to enable them to extract and bind a specific phospholipid from a membrane for catalysis, which is probably generalizable to intracellular and extracellular transport and phospholipid exchange processes as well as other specific biological functions. We will focus on the four main types of PLA2, namely, the secreted (sPLA2), cytosolic (cPLA2), calcium-independent (iPLA2), and lipoprotein-associated PLA2 (Lp-PLA2) also known as platelet-activating factor acetyl hydrolase (PAF-AH). Studies on a well-studied specific example of each of the four major types of the PLA2 superfamily demonstrate clearly that protein subsites can show precise specificity for one of the phospholipid hydrophobic acyl chains, often the one at the sn-2 position, including exquisite sensitivity to the number and position of double bonds.
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Affiliation(s)
- Varnavas D. Mouchlis
- Department of Chemistry and Biochemistry
and Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, California 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, California 92093-0601 United States
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Hayashi D, Mouchlis VD, Okamoto S, Namba T, Wang L, Li S, Ueda S, Yamanoue M, Tachibana H, Arai H, Ashida H, Dennis EA, Shirai Y. Vitamin E functions by association with a novel binding site on the 67 kDa laminin receptor activating diacylglycerol kinase. J Nutr Biochem 2022; 110:109129. [PMID: 35977663 PMCID: PMC10243646 DOI: 10.1016/j.jnutbio.2022.109129] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 03/27/2022] [Accepted: 07/16/2022] [Indexed: 01/13/2023]
Abstract
It is generally recognized that the main function of α-tocopherol (αToc), which is the most active form of vitamin E, is its antioxidant effect, while non-antioxidant effects have also been reported. We previously found that αToc ameliorates diabetic nephropathy via diacylglycerol kinase alpha (DGKα) activation in vivo, and the activation was not related to the antioxidant effect. However, the underlying mechanism of how αToc activates DGKα have been enigmatic. We report that the membrane-bound 67 kDa laminin receptor (67LR), which has previously been shown to serve as a receptor for epigallocatechin gallate (EGCG), also contains a novel binding site for vitamin E, and its association with Vitamin E mediates DGKα activation by αToc. We employed hydrogen-deuterium exchange mass spectrometry (HDX/MS) and molecular dynamics (MD) simulations to identify the specific binding site of αToc on the 67LR and discovered the conformation of the specific hydrophobic pocket that accommodates αToc. Also, HDX/MS and MD simulations demonstrated the detailed binding of EGCG to a water-exposed hydrophilic site on 67LR, while in contrast αToc binds to a distinct hydrophobic site. We demonstrated that 67LR triggers an important signaling pathway mediating non-antioxidant effects of αToc, such as DGKα activation. This is the first evidence demonstrating a membrane receptor for αToc and one of the underlying mechanisms of a non-antioxidant function for αToc.
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Affiliation(s)
- Daiki Hayashi
- Department of Applied Chemistry in Bioscience, Graduate School of Agricultural Science, Faculty of Agriculture, Kobe University, Kobe, Japan; Department of Pharmacology, and Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
| | - Varnavas D Mouchlis
- Department of Pharmacology, and Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
| | - Seika Okamoto
- Department of Applied Chemistry in Bioscience, Graduate School of Agricultural Science, Faculty of Agriculture, Kobe University, Kobe, Japan
| | - Tomoka Namba
- Department of Applied Chemistry in Bioscience, Graduate School of Agricultural Science, Faculty of Agriculture, Kobe University, Kobe, Japan
| | - Liuqing Wang
- Department of Applied Chemistry in Bioscience, Graduate School of Agricultural Science, Faculty of Agriculture, Kobe University, Kobe, Japan
| | - Sheng Li
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Shuji Ueda
- Department of Applied Chemistry in Bioscience, Graduate School of Agricultural Science, Faculty of Agriculture, Kobe University, Kobe, Japan
| | - Minoru Yamanoue
- Department of Applied Chemistry in Bioscience, Graduate School of Agricultural Science, Faculty of Agriculture, Kobe University, Kobe, Japan
| | - Hirofumi Tachibana
- Division of Applied Biological Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Hiroyuki Arai
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo Japan
| | - Hitoshi Ashida
- Department of Applied Chemistry in Bioscience, Graduate School of Agricultural Science, Faculty of Agriculture, Kobe University, Kobe, Japan
| | - Edward A Dennis
- Department of Pharmacology, and Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
| | - Yasuhito Shirai
- Department of Applied Chemistry in Bioscience, Graduate School of Agricultural Science, Faculty of Agriculture, Kobe University, Kobe, Japan.
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Hayashi D, Mouchlis VD, Dennis EA. Each phospholipase A 2 type exhibits distinct selectivity toward sn-1 ester, alkyl ether, and vinyl ether phospholipids. Biochim Biophys Acta Mol Cell Biol Lipids 2022; 1867:159067. [PMID: 34634490 PMCID: PMC9188868 DOI: 10.1016/j.bbalip.2021.159067] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/28/2021] [Accepted: 10/05/2021] [Indexed: 01/03/2023]
Abstract
Glycerophospholipids are major components of cell membranes and have enormous variation in the composition of fatty acyl chains esterified on the sn-1 and sn-2 position as well as the polar head groups on the sn-3 position of the glycerol backbone. Phospholipase A2 (PLA2) enzymes constitute a superfamily of enzymes which play a critical role in metabolism and signal transduction by hydrolyzing the sn-2 acyl chains of glycerophospholipids. In human cell membranes, in addition to the conventional diester phospholipids, a significant amount is the sn-1 ether-linked phospholipids which play a critical role in numerous biological activities. However, precisely how PLA2s distinguish the sn-1 acyl chain linkage is not understood. In the present study, we expanded the technique of lipidomics to determine the unique in vitro specificity of three major human PLA2s, including Group IVA cytosolic cPLA2, Group VIA calcium-independent iPLA2, and Group V secreted sPLA2 toward the linkage at the sn-1 position. Interestingly, cPLA2 prefers sn-1 vinyl ether phospholipids known as plasmalogens over conventional ester phospholipids and the sn-1 alkyl ether phospholipids. iPLA2 showed similar activity toward vinyl ether and ester phospholipids at the sn-1 position. Surprisingly, sPLA2 preferred ester phospholipids over alkyl and vinyl ether phospholipids. By taking advantage of molecular dynamics simulations, we found that Trp30 in the sPLA2 active site dominates its specificity for diester phospholipids.
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Hayashi D, Mouchlis VD, Dennis EA. Omega-3 versus Omega-6 fatty acid availability is controlled by hydrophobic site geometries of phospholipase A 2s. J Lipid Res 2021; 62:100113. [PMID: 34474084 PMCID: PMC8551542 DOI: 10.1016/j.jlr.2021.100113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/24/2021] [Accepted: 08/27/2021] [Indexed: 11/12/2022] Open
Abstract
Human phospholipase A2s (PLA2) constitute a superfamily of enzymes that hydrolyze the sn-2 acyl-chain of glycerophospholipids, producing lysophospholipids and free fatty acids. Each PLA2 enzyme type contributes to specific biological functions based on its expression, subcellular localization, and substrate specificity. Among the PLA2 superfamily, the cytosolic cPLA2 enzymes, calcium-independent iPLA2 enzymes, and secreted sPLA2 enzymes are implicated in many diseases, but a central issue is the preference for double-bond positions in polyunsaturated fatty acids (PUFAs) occupying the sn-2 position of membrane phospholipids. We demonstrate that each PLA2 has a unique preference between the specific omega-3 fatty acids eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) and the omega-6 arachidonic acid (AA), which are the precursors of most proinflammatory and anti-inflammatory or resolving eicosanoids and related oxylipins. Surprisingly, we discovered that human cPLA2 selectively prefers AA, whereas iPLA2 prefers EPA, and sPLA2 prefers DHA as substrate. We determined the optimal binding of each phospholipid substrate in the active site of each PLA2 to explain these specificities. To investigate this, we utilized recently developed lipidomics-based LC-MS/MS and GC/MS assays to determine the sn-2 acyl chain specificity in mixtures of phospholipids. We performed μs timescale molecular dynamics (MD) simulations to reveal unique active site properties, especially how the precise hydrophobic cavity accommodation of the sn-2 acyl chain contributes to the stability of substrate binding and the specificity of each PLA2 for AA, EPA, or DHA. This study provides the first comprehensive picture of the unique substrate selectivity of each PLA2 for omega-3 and omega-6 fatty acids.
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Affiliation(s)
- Daiki Hayashi
- Department of Chemistry and Biochemistry and Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Varnavas D Mouchlis
- Department of Chemistry and Biochemistry and Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Edward A Dennis
- Department of Chemistry and Biochemistry and Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA.
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Mouchlis VD, Afantitis A, Serra A, Fratello M, Papadiamantis AG, Aidinis V, Lynch I, Greco D, Melagraki G. Advances in de Novo Drug Design: From Conventional to Machine Learning Methods. Int J Mol Sci 2021; 22:1676. [PMID: 33562347 PMCID: PMC7915729 DOI: 10.3390/ijms22041676] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/31/2021] [Accepted: 01/31/2021] [Indexed: 12/11/2022] Open
Abstract
. De novo drug design is a computational approach that generates novel molecular structures from atomic building blocks with no a priori relationships. Conventional methods include structure-based and ligand-based design, which depend on the properties of the active site of a biological target or its known active binders, respectively. Artificial intelligence, including machine learning, is an emerging field that has positively impacted the drug discovery process. Deep reinforcement learning is a subdivision of machine learning that combines artificial neural networks with reinforcement-learning architectures. This method has successfully been employed to develop novel de novo drug design approaches using a variety of artificial networks including recurrent neural networks, convolutional neural networks, generative adversarial networks, and autoencoders. This review article summarizes advances in de novo drug design, from conventional growth algorithms to advanced machine-learning methodologies and highlights hot topics for further development.
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Affiliation(s)
| | - Antreas Afantitis
- Department of ChemoInformatics, NovaMechanics Ltd., Nicosia 1046, Cyprus;
| | - Angela Serra
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (A.S.); (M.F.); (D.G.)
- BioMEdiTech Institute, Tampere University, 33520 Tampere, Finland
| | - Michele Fratello
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (A.S.); (M.F.); (D.G.)
- BioMEdiTech Institute, Tampere University, 33520 Tampere, Finland
| | - Anastasios G. Papadiamantis
- Department of ChemoInformatics, NovaMechanics Ltd., Nicosia 1046, Cyprus;
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK;
| | - Vassilis Aidinis
- Institute for Bioinnovation, Biomedical Sciences Research Center Alexander Fleming, Fleming 34, 16672 Athens, Greece;
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK;
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (A.S.); (M.F.); (D.G.)
- BioMEdiTech Institute, Tampere University, 33520 Tampere, Finland
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
- Finnish Center for Alternative Methods (FICAM), Tampere University, 33520 Tampere, Finland
| | - Georgia Melagraki
- Division of Physical Sciences & Applications, Hellenic Military Academy, 16672 Vari, Greece
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Koutoulogenis GS, Kokotou MG, Hayashi D, Mouchlis VD, Dennis EA, Kokotos G. 2-Oxoester Phospholipase A 2 Inhibitors with Enhanced Metabolic Stability. Biomolecules 2020; 10:biom10030491. [PMID: 32213911 PMCID: PMC7175278 DOI: 10.3390/biom10030491] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 12/21/2022] Open
Abstract
2-Oxoesters constitute an important class of potent and selective inhibitors of human cytosolic phospholipase A2 (GIVA cPLA2) combining an aromatic scaffold or a long aliphatic chain with a short aliphatic chain containing a free carboxylic acid. Although highly potent 2-oxoester inhibitors of GIVA cPLA2 have been developed, their rapid degradation in human plasma limits their pharmaceutical utility. In an effort to address this problem, we designed and synthesized two new 2-oxoesters introducing a methyl group either on the α-carbon to the oxoester functionality or on the carbon carrying the ester oxygen. We studied the in vitro plasma stability of both derivatives and their in vitro inhibitory activity on GIVA cPLA2. Both derivatives exhibited higher plasma stability in comparison with the unsubstituted compound and both derivatives inhibited GIVA cPLA2, however to different degrees. The 2-oxoester containing a methyl group on the α-carbon atom to the oxoester functionality exhibits enhancement of the metabolic stability and retains considerable inhibitory potency.
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Affiliation(s)
- Giorgos S. Koutoulogenis
- Department of Chemistry, National and Kapodistrian University of Athens, Athens 15771, Greece; (G.S.K.); (M.G.K.)
| | - Maroula G. Kokotou
- Department of Chemistry, National and Kapodistrian University of Athens, Athens 15771, Greece; (G.S.K.); (M.G.K.)
| | - Daiki Hayashi
- Department of Chemistry and Biochemistry and Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0601, USA; (D.H.); (V.D.M.)
| | - 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, USA; (D.H.); (V.D.M.)
| | - 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, USA; (D.H.); (V.D.M.)
- Correspondence: (E.A.D.); (G.K.); Tel.: +1-858-534-3055 (E.A.D.); +30-210-7274462 (G.K.)
| | - George Kokotos
- Department of Chemistry, National and Kapodistrian University of Athens, Athens 15771, Greece; (G.S.K.); (M.G.K.)
- Correspondence: (E.A.D.); (G.K.); Tel.: +1-858-534-3055 (E.A.D.); +30-210-7274462 (G.K.)
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Mouchlis VD, Mu C, Hammons R, Dennis EA. Lipidomics-based assays coupled with computational approaches can identify novel phospholipase A 2 inhibitors. Adv Biol Regul 2020; 76:100719. [PMID: 32199750 DOI: 10.1016/j.jbior.2020.100719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/02/2020] [Accepted: 03/05/2020] [Indexed: 10/24/2022]
Abstract
Phospholipase A2 (PLA2) enzymes play a major role in many diseases including the inflammatory cascade and specific potent small molecule inhibitors could be useful in studying their physiological role as well as for the development of drugs. In order to discover novel small molecule inhibitor platforms for members of the PLA2 superfamily of enzymes, we have applied computational approaches to determine the binding mode of potent inhibitors specific for particular PLA2s to the screening of chemical libraries. This has including the U.S. National Institutes of Health (NIH) National Cancer Institute (NCI) Diversity Set V and the ChemBridge commercial compound libraries. We have then subjected identified inhibitor structures to recently developed lipidomics based screening assays to determine the XI(50) and specificity of the identified compounds for specific PLA2s. Herein we review this approach and report the identity of initial hits for both the Group IVA cytosolic PLA2 and the Group VIA calcium-independent PLA2 that are worthy of further structural modification to develop novel platforms for inhibitor development.
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Affiliation(s)
- 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, USA.
| | - Carol Mu
- Department of Chemistry and Biochemistry and Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA, 92093-0601, USA
| | - Renee Hammons
- Department of Chemistry and Biochemistry and Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA, 92093-0601, USA
| | - 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, USA.
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Mouchlis VD, Melagraki G, Zacharia LC, Afantitis A. Computer-Aided Drug Design of β-Secretase, γ-Secretase and Anti-Tau Inhibitors for the Discovery of Novel Alzheimer's Therapeutics. Int J Mol Sci 2020; 21:E703. [PMID: 31973122 PMCID: PMC7038192 DOI: 10.3390/ijms21030703] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 12/14/2022] Open
Abstract
Aging-associated neurodegenerative diseases, which are characterized by progressive neuronal death and synapses loss in human brain, are rapidly growing affecting millions of people globally. Alzheimer's is the most common neurodegenerative disease and it can be caused by genetic and environmental risk factors. This review describes the amyloid-β and Tau hypotheses leading to amyloid plaques and neurofibrillary tangles, respectively which are the predominant pathways for the development of anti-Alzheimer's small molecule inhibitors. The function and structure of the druggable targets of these two pathways including β-secretase, γ-secretase, and Tau are discussed in this review article. Computer-Aided Drug Design including computational structure-based design and ligand-based design have been employed successfully to develop inhibitors for biomolecular targets involved in Alzheimer's. The application of computational molecular modeling for the discovery of small molecule inhibitors and modulators for β-secretase and γ-secretase is summarized. Examples of computational approaches employed for the development of anti-amyloid aggregation and anti-Tau phosphorylation, proteolysis and aggregation inhibitors are also reported.
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Affiliation(s)
| | - Georgia Melagraki
- Division of Physical Sciences & Applications, Hellenic Military Academy, Vari 16672, Greece;
| | - Lefteris C. Zacharia
- Department of Life and Health Sciences, University of Nicosia, Nicosia 1700, Cyprus;
| | - Antreas Afantitis
- Department of ChemoInformatics, NovaMechanics Ltd., Nicosia 1046, Cyprus
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Psarra A, Kokotou MG, Galiatsatou G, Mouchlis VD, Dennis EA, Kokotos G. Correction to "Highly Potent 2-Oxoester Inhibitors of Cytosolic Phospholipase A 2 (GIVA cPLA 2)". ACS Omega 2019; 4:10714. [PMID: 31460169 PMCID: PMC6648946 DOI: 10.1021/acsomega.9b01662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Indexed: 06/10/2023]
Abstract
[This corrects the article DOI: 10.1021/acsomega.8b01214.].
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Dedaki C, Kokotou MG, Mouchlis VD, Limnios D, Lei X, Mu CT, Ramanadham S, Magrioti V, Dennis EA, Kokotos G. β-Lactones: A Novel Class of Ca 2+-Independent Phospholipase A 2 (Group VIA iPLA 2) Inhibitors with the Ability To Inhibit β-Cell Apoptosis. J Med Chem 2019; 62:2916-2927. [PMID: 30798607 DOI: 10.1021/acs.jmedchem.8b01216] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Ca2+-independent phospholipase A2 (GVIA iPLA2) has gained increasing interest recently as it has been recognized as a participant in biological processes underlying diabetes development and autoimmune-based neurological disorders. The development of potent GVIA iPLA2 inhibitors is of great importance because only a few have been reported so far. We present a novel class of GVIA iPLA2 inhibitors based on the β-lactone ring. This functionality in combination with a four-carbon chain carrying a phenyl group at position-3 and a linear propyl group at position-4 of the lactone ring confers excellent potency. trans-3-(4-Phenylbutyl)-4-propyloxetan-2-one (GK563) was identified as being the most potent GVIA iPLA2 inhibitor ever reported ( XI(50) 0.0000021, IC50 1 nM) and also one that is 22 000 times more active against GVIA iPLA2 than GIVA cPLA2. It was found to reduce β-cell apoptosis induced by proinflammatory cytokines, raising the possibility that it can be beneficial in countering autoimmune diseases, such as type 1 diabetes.
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Affiliation(s)
- Christina Dedaki
- Laboratory of Organic Chemistry, Department of Chemistry , National and Kapodistrian University of Athens , Panepistimiopolis, Athens 15771 , Greece
| | - Maroula G Kokotou
- Laboratory of Organic Chemistry, Department of Chemistry , National and Kapodistrian University of Athens , Panepistimiopolis, Athens 15771 , Greece.,Department of Chemistry and Biochemistry and Department of Pharmacology, School of Medicine , University of California, San Diego , La Jolla, San Diego , California 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, San Diego , California 92093-0601 , United States
| | - Dimitris Limnios
- Laboratory of Organic Chemistry, Department of Chemistry , National and Kapodistrian University of Athens , Panepistimiopolis, Athens 15771 , Greece.,Department of Chemistry and Biochemistry and Department of Pharmacology, School of Medicine , University of California, San Diego , La Jolla, San Diego , California 92093-0601 , United States
| | | | - Carol T Mu
- Department of Chemistry and Biochemistry and Department of Pharmacology, School of Medicine , University of California, San Diego , La Jolla, San Diego , California 92093-0601 , United States
| | | | - Victoria Magrioti
- Laboratory of Organic Chemistry, Department of Chemistry , National and Kapodistrian University of Athens , Panepistimiopolis, Athens 15771 , Greece
| | - Edward A Dennis
- Department of Chemistry and Biochemistry and Department of Pharmacology, School of Medicine , University of California, San Diego , La Jolla, San Diego , California 92093-0601 , United States
| | - George Kokotos
- Laboratory of Organic Chemistry, Department of Chemistry , National and Kapodistrian University of Athens , Panepistimiopolis, Athens 15771 , Greece
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13
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Mouchlis VD, Armando A, Dennis EA. Substrate-Specific Inhibition Constants for Phospholipase A 2 Acting on Unique Phospholipid Substrates in Mixed Micelles and Membranes Using Lipidomics. J Med Chem 2019; 62:1999-2007. [PMID: 30615445 PMCID: PMC6398150 DOI: 10.1021/acs.jmedchem.8b01568] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Assaying lipolytic enzymes is extremely challenging because they act on water-insoluble lipid substrates, which are normally components of micelles, vesicles, and cellular membranes. We extended a new lipidomics-based liquid chromatographic-mass spectrometric assay for phospholipases A2 to perform inhibition analysis using a variety of commercially available synthetic and natural phospholipids as substrates. Potent and selective inhibitors of three recombinant human enzymes, including cytosolic, calcium-independent, and secreted phospholipases A2 were used to establish and validate this assay. This is a novel use of dose-response curves with a mixture of phospholipid substrates, not previously feasible using traditional radioactive assays. The new application of lipidomics to developing assays for lipolytic enzymes revolutionizes in vitro testing for the discovery of potent and selective inhibitors using mixtures of membranelike substrates.
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Affiliation(s)
- Varnavas D Mouchlis
- Department of Chemistry and Biochemistry and Department of Pharmacology, School of Medicine , University of California, San Diego , La Jolla , California 92093-0601 , United States
| | - Aaron Armando
- Department of Chemistry and Biochemistry and Department of Pharmacology, School of Medicine , University of California, San Diego , La Jolla , California 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 , California 92093-0601 , United States
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14
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Psarra A, Kokotou MG, Galiatsatou G, Mouchlis VD, Dennis EA, Kokotos G. Highly Potent 2-Oxoester Inhibitors of Cytosolic Phospholipase A 2 (GIVA cPLA 2). ACS Omega 2018; 3:8843-8853. [PMID: 30197994 PMCID: PMC6120731 DOI: 10.1021/acsomega.8b01214] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 07/26/2018] [Indexed: 05/05/2023]
Abstract
Cytosolic phospholipase A2 (GIVA cPLA2) has attracted great interest as a medicinal target because it initiates the eicosanoid cascade and is involved in a number of inflammatory diseases. As a consequence, the development of potent synthetic inhibitors is of great importance. We have developed highly potent 2-oxoester inhibitors of GIVA cPLA2 presenting XI(50) values between 0.000019 and 0.000066. We demonstrate that the 2-oxoester functionality is essential for in vitro inhibitory activity, making these inhibitors useful research reagents. However, their high reactivity results in rapid degradation of the inhibitors in human plasma, limiting their pharmaceutical utility without further modification.
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Affiliation(s)
- Anastasia Psarra
- 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
| | - Gerasimia Galiatsatou
- Department
of Chemistry, National and Kapodistrian
University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Varnavas D. Mouchlis
- Department
of Pharmacology and Department of Chemistry and Biochemistry, School
of Medicine, University of California San
Diego, La Jolla, California 92093-0601, United States
| | - Edward A. Dennis
- Department
of Pharmacology and Department of Chemistry and Biochemistry, School
of Medicine, University of California San
Diego, La Jolla, California 92093-0601, United States
- E-mail: .
Phone: +1 858 534 3055 (E.A.D.)
| | - George Kokotos
- Department
of Chemistry, National and Kapodistrian
University of Athens, Panepistimiopolis, Athens 15771, Greece
- E-mail: . Phone: +30 210 7274462. Fax: +30 210 7274761 (G.K.)
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15
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Mouchlis VD, McCammon JA, Dennis EA. Membrane Allostery and Hydrophobic Binding Sites Control Substrate Specificity of Lipolytic Enzymes. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.528.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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16
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Abstract
![]()
We
demonstrate that lipidomics coupled with molecular dynamics
reveal unique phospholipase A2 specificity toward membrane
phospholipid substrates. We discovered unexpected headgroup and acyl-chain
specificity for three major human phospholipases A2. The
differences between each enzyme’s specificity, coupled with
molecular dynamics-based structural and binding studies, revealed
unique binding sites and interfacial surface binding moieties for
each enzyme that explain the observed specificity at a hitherto inaccessible
structural level. Surprisingly, we discovered that a unique hydrophobic
binding site for the cleaved fatty acid dominates each enzyme’s
specificity rather than its catalytic residues and polar headgroup
binding site. Molecular dynamics simulations revealed the optimal
phospholipid binding mode leading to a detailed understanding of the
preference of cytosolic phospholipase A2 for cleavage of
proinflammatory arachidonic acid, calcium-independent phospholipase
A2, which is involved in membrane remodeling for cleavage
of linoleic acid and for antibacterial secreted phospholipase A2 favoring linoleic acid, saturated fatty acids, and phosphatidylglycerol.
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Affiliation(s)
- Varnavas D Mouchlis
- Department of Chemistry and Biochemistry and Department of Pharmacology, School of Medicine , University of California , San Diego, La Jolla , California 92093-0601 , United States
| | - Yuan Chen
- Department of Chemistry and Biochemistry and Department of Pharmacology, School of Medicine , University of California , San Diego, La Jolla , California 92093-0601 , United States
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry and Department of Pharmacology, School of Medicine , University of California , San Diego, La Jolla , California 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 , California 92093-0601 , United States
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17
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Mouchlis VD, McCammon JA, Dennis EA. Allosteric Regulation by Membranes Controls Specificity of Lipolytic Enzymes through Recruitment of Unique Hydrophobic Binding Pockets. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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18
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Smyrniotou A, Kokotou MG, Mouchlis VD, Barbayianni E, Kokotos G, Dennis EA, Constantinou-Kokotou V. 2-Oxoamides based on dipeptides as selective calcium-independent phospholipase A 2 inhibitors. Bioorg Med Chem 2016; 25:926-940. [PMID: 28034646 DOI: 10.1016/j.bmc.2016.12.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 12/04/2016] [Accepted: 12/05/2016] [Indexed: 11/18/2022]
Abstract
Calcium-independent phospholipase A2 (GVIA iPLA2) has recently attracted interest as a medicinal target. The number of known GVIA iPLA2 inhibitors is limited to a handful of synthetic compounds (bromoenol lactone and polyfluoroketones). To expand the chemical diversity, a variety of 2-oxoamides based on dipeptides and ether dipeptides were synthesized and studied for their in vitro inhibitory activity on human GVIA iPLA2 and their selectivity over the other major intracellular GIVA cPLA2 and the secreted GV sPLA2. Structure-activity relationship studies revealed the first 2-oxoamide derivative (GK317), which presents potent inhibition of GVIA iPLA2 (XI(50) value of 0.007) and at the same time significant selectivity over GIVA cPLA2 and GV sPLA2.
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Affiliation(s)
- Anneta Smyrniotou
- Chemical Laboratories, Agricultural University of Athens, Iera Odos 75, Athens 11855, Greece
| | - Maroula G Kokotou
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece; Department of Pharmacology and Department of Chemistry and Biochemistry, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0601, USA
| | - Varnavas D Mouchlis
- Department of Pharmacology and Department of Chemistry and Biochemistry, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0601, USA
| | - Efrosini Barbayianni
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - George Kokotos
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Edward A Dennis
- Department of Pharmacology and Department of Chemistry and Biochemistry, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0601, USA.
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19
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Antonopoulou G, Magrioti V, Kokotou MG, Nikolaou A, Barbayianni E, Mouchlis VD, Dennis EA, Kokotos G. 2-Oxoamide inhibitors of cytosolic group IVA phospholipase A2 with reduced lipophilicity. Bioorg Med Chem 2016; 24:4544-4554. [PMID: 27522578 PMCID: PMC5014611 DOI: 10.1016/j.bmc.2016.07.057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 07/25/2016] [Accepted: 07/26/2016] [Indexed: 12/31/2022]
Abstract
Cytosolic GIVA phospholipase A2 (GIVA cPLA2) initiates the eicosanoid pathway of inflammation and thus inhibitors of this enzyme constitute novel potential agents for the treatment of inflammatory diseases. Traditionally, GIVA cPLA2 inhibitors have suffered systemically from high lipophilicity. We have developed a variety of long chain 2-oxoamides as inhibitors of GIVA PLA2. Among them, AX048 was found to produce a potent analgesic effect. We have now reduced the lipophilicity of AX048 by replacing the long aliphatic chain with a chain containing an ether linked aromatic ring with in vitro inhibitory activities similar to AX048.
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Affiliation(s)
- Georgia Antonopoulou
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece; Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Victoria Magrioti
- 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
| | - Aikaterini Nikolaou
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Efrosini Barbayianni
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Varnavas D Mouchlis
- Department of Chemistry and Biochemistry, School of Medicine, MC 0601, University of California, San Diego, La Jolla, CA 92093-0601, USA; Department of Pharmacology, School of Medicine, MC 0601, University of California, San Diego, La Jolla, CA 92093-0601, USA
| | - Edward A Dennis
- Department of Chemistry and Biochemistry, School of Medicine, MC 0601, University of California, San Diego, La Jolla, CA 92093-0601, USA; Department of Pharmacology, School of Medicine, MC 0601, University of California, San Diego, La Jolla, CA 92093-0601, USA.
| | - George Kokotos
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece.
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20
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Mouchlis VD, Limnios D, Kokotou MG, Barbayianni E, Kokotos G, McCammon JA, Dennis EA. Development of Potent and Selective Inhibitors for Group VIA Calcium-Independent Phospholipase A2 Guided by Molecular Dynamics and Structure-Activity Relationships. J Med Chem 2016; 59:4403-14. [PMID: 27087127 DOI: 10.1021/acs.jmedchem.6b00377] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The development of inhibitors for phospholipase A2 (PLA2) is important in elucidating the enzymes implication in various biological pathways. PLA2 enzymes are an important pharmacological target implicated in various inflammatory diseases. Computational chemistry, organic synthesis, and in vitro assays were employed to develop potent and selective inhibitors for group VIA calcium-independent PLA2. A set of fluoroketone inhibitors was studied for their binding mode with two human cytosolic PLA2 enzymes: group IVA cPLA2 and group VIA iPLA2. New compounds were synthesized and assayed toward three major PLA2s. This study led to the development of four potent and selective thioether fluoroketone inhibitors as well as a thioether keto-1,2,4-oxadiazole inhibitor for GVIA iPLA2, which will serve as lead compounds for future development and studies. The keto-1,2,4-oxadiazole functionality with a thioether is a novel structure, and it will be used as a lead to develop inhibitors with higher potency and selectivity toward GVIA iPLA2.
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Affiliation(s)
- Varnavas D Mouchlis
- Department of Pharmacology and Department of Chemistry and Biochemistry, School of Medicine, University of California, San Diego , La Jolla, California 92093-0601, United States
| | - Dimitris Limnios
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens , Panepistimiopolis, Athens 15771, Greece
| | - Maroula G Kokotou
- 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
| | - George Kokotos
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens , Panepistimiopolis, Athens 15771, Greece
| | - J Andrew McCammon
- Department of Pharmacology and Department of Chemistry and Biochemistry, School of Medicine, University of California, San Diego , La Jolla, California 92093-0601, United States
| | - Edward A Dennis
- Department of Pharmacology and Department of Chemistry and Biochemistry, School of Medicine, University of California, San Diego , La Jolla, California 92093-0601, United States
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21
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Mouchlis VD, Bucher D, McCammon JA, Dennis EA. Membranes serve as allosteric activators of phospholipase A2, enabling it to extract, bind, and hydrolyze phospholipid substrates. Proc Natl Acad Sci U S A 2015; 112:E516-25. [PMID: 25624474 PMCID: PMC4330758 DOI: 10.1073/pnas.1424651112] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Defining the molecular details and consequences of the association of water-soluble proteins with membranes is fundamental to understanding protein-lipid interactions and membrane functioning. Phospholipase A2 (PLA2) enzymes, which catalyze the hydrolysis of phospholipid substrates that compose the membrane bilayers, provide the ideal system for studying protein-lipid interactions. Our study focuses on understanding the catalytic cycle of two different human PLA2s: the cytosolic Group IVA cPLA2 and calcium-independent Group VIA iPLA2. Computer-aided techniques guided by deuterium exchange mass spectrometry data, were used to create structural complexes of each enzyme with a single phospholipid substrate molecule, whereas the substrate extraction process was studied using steered molecular dynamics simulations. Molecular dynamic simulations of the enzyme-substrate-membrane systems revealed important information about the mechanisms by which these enzymes associate with the membrane and then extract and bind their phospholipid substrate. Our data support the hypothesis that the membrane acts as an allosteric ligand that binds at the allosteric site of the enzyme's interfacial surface, shifting its conformation from a closed (inactive) state in water to an open (active) state at the membrane interface.
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Affiliation(s)
| | | | - J Andrew McCammon
- Departments of Pharmacology and Chemistry and Biochemistry, and Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093-0601
| | - Edward A Dennis
- Departments of Pharmacology and Chemistry and Biochemistry, and
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22
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Bucher D, Mouchlis VD, Dennis EA, McCammon JA. Modeling and Inhibitor Design of Ca(2+)-Independent Phospholipase A2. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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23
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Zhang L, Sedykh A, Tripathi A, Zhu H, Afantitis A, Mouchlis VD, Melagraki G, Rusyn I, Tropsha A. Identification of putative estrogen receptor-mediated endocrine disrupting chemicals using QSAR- and structure-based virtual screening approaches. Toxicol Appl Pharmacol 2013; 272:67-76. [PMID: 23707773 PMCID: PMC3775906 DOI: 10.1016/j.taap.2013.04.032] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 04/16/2013] [Accepted: 04/17/2013] [Indexed: 12/24/2022]
Abstract
Identification of endocrine disrupting chemicals is one of the important goals of environmental chemical hazard screening. We report on the development of validated in silico predictors of chemicals likely to cause estrogen receptor (ER)-mediated endocrine disruption to facilitate their prioritization for future screening. A database of relative binding affinity of a large number of ERα and/or ERβ ligands was assembled (546 for ERα and 137 for ERβ). Both single-task learning (STL) and multi-task learning (MTL) continuous quantitative structure-activity relationship (QSAR) models were developed for predicting ligand binding affinity to ERα or ERβ. High predictive accuracy was achieved for ERα binding affinity (MTL R(2)=0.71, STL R(2)=0.73). For ERβ binding affinity, MTL models were significantly more predictive (R(2)=0.53, p<0.05) than STL models. In addition, docking studies were performed on a set of ER agonists/antagonists (67 agonists and 39 antagonists for ERα, 48 agonists and 32 antagonists for ERβ, supplemented by putative decoys/non-binders) using the following ER structures (in complexes with respective ligands) retrieved from the Protein Data Bank: ERα agonist (PDB ID: 1L2I), ERα antagonist (PDB ID: 3DT3), ERβ agonist (PDB ID: 2NV7), and ERβ antagonist (PDB ID: 1L2J). We found that all four ER conformations discriminated their corresponding ligands from presumed non-binders. Finally, both QSAR models and ER structures were employed in parallel to virtually screen several large libraries of environmental chemicals to derive a ligand- and structure-based prioritized list of putative estrogenic compounds to be used for in vitro and in vivo experimental validation.
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Affiliation(s)
- Liying Zhang
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC
| | - Alexander Sedykh
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC
| | - Ashutosh Tripathi
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC
| | - Hao Zhu
- The Rutgers Center for Computational and Integrative Biology, Rutgers University, Camden, NJ
- Department of Chemistry, Rutgers University, Camden, NJ
| | | | | | | | - Ivan Rusyn
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC
| | - Alexander Tropsha
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC
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24
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Bucher D, Hsu YH, Mouchlis VD, Dennis EA, McCammon JA. Insertion of the Ca²⁺-independent phospholipase A₂ into a phospholipid bilayer via coarse-grained and atomistic molecular dynamics simulations. PLoS Comput Biol 2013; 9:e1003156. [PMID: 23935474 PMCID: PMC3723492 DOI: 10.1371/journal.pcbi.1003156] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 06/11/2013] [Indexed: 01/19/2023] Open
Abstract
Group VI Ca²⁺-independent phospholipase A₂ (iPLA₂) is a water-soluble enzyme that is active when associated with phospholipid membranes. Despite its clear pharmaceutical relevance, no X-ray or NMR structural information is currently available for the iPLA₂ or its membrane complex. In this paper, we combine homology modeling with coarse-grained (CG) and all-atom (AA) molecular dynamics (MD) simulations to build structural models of iPLA₂ in association with a phospholipid bilayer. CG-MD simulations of the membrane insertion process were employed to provide a starting point for an atomistic description. Six AA-MD simulations were then conducted for 60 ns, starting from different initial CG structures, to refine the membrane complex. The resulting structures are shown to be consistent with each other and with deuterium exchange mass spectrometry (DXMS) experiments, suggesting that our approach is suitable for the modeling of iPLA₂ at the membrane surface. The models show that an anchoring region (residues 710-724) forms an amphipathic helix that is stabilized by the membrane. In future studies, the proposed iPLA₂ models should provide a structural basis for understanding the mechanisms of lipid extraction and drug-inhibition. In addition, the dual-resolution approach discussed here should provide the means for the future exploration of the impact of lipid diversity and sequence mutations on the activity of iPLA₂ and related enzymes.
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Affiliation(s)
- Denis Bucher
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, United States of America.
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25
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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27
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Mouchlis VD, Barbayianni E, Mavromoustakos TM, Kokotos G. The application of rational design on phospholipase A(2) inhibitors. Curr Med Chem 2011; 18:2566-82. [PMID: 21568891 DOI: 10.2174/092986711795933678] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Accepted: 05/12/2011] [Indexed: 11/22/2022]
Abstract
The phospholipase A(2) (PLA(2)) superfamily consists of different groups of enzymes which are characterized by their ability to catalyze the hydrolysis of the sn-2 ester bond in a variety of phospholipid molecules. The products of PLA(2s) activity play divergent roles in a variety of physiological processes. There are four main types of PLA(2s): the secreted PLA(2s) (sPLA(2s)), the cytosolic PLA(2s) (cPLA(2s)), the calcium-independent PLA(2s) (iPLA(2)) and the lipoprotein-associated PLA(2s) (LpPLA(2s)). Various potent and selective PLA2 inhibitors have been reported up to date and have provided outstanding support in understanding the mechanism of action and elucidating the function of these enzymes. The current review focuses on the implementation of rational design through computer-aided drug design (CADD) on the discovery and development of new PLA(2) inhibitors.
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Affiliation(s)
- V D Mouchlis
- Laboratory of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis, Athens 15771, Greece
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28
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Mouchlis VD, Magrioti V, Barbayianni E, Cermak N, Oslund RC, Mavromoustakos TM, Gelb MH, Kokotos G. Inhibition of secreted phospholipases A₂ by 2-oxoamides based on α-amino acids: Synthesis, in vitro evaluation and molecular docking calculations. Bioorg Med Chem 2010; 19:735-43. [PMID: 21216150 DOI: 10.1016/j.bmc.2010.12.030] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 12/07/2010] [Accepted: 12/13/2010] [Indexed: 10/18/2022]
Abstract
Group IIA secreted phospholipase A₂ (GIIA sPLA₂) is a member of the mammalian sPLA₂ enzyme family and is associated with various inflammatory conditions. In this study, the synthesis of 2-oxoamides based on α-amino acids and the in vitro evaluation against three secreted sPLA₂s (GIIA, GV and GX) are described. The long chain 2-oxoamide GK126 based on the amino acid (S)-leucine displayed inhibition of human and mouse GIIA sPLA₂s (IC₅₀ 300nM and 180nM, respectively). It also inhibited human GV sPLA₂ with similar potency, while it did not inhibit human GX sPLA₂. The elucidation of the stereoelectronic characteristics that affect the in vitro activity of these compounds was achieved by using a combination of simulated annealing to sample low-energy conformations before the docking procedure, and molecular docking calculations.
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Mouchlis VD, Mavromoustakos TM, Kokotos G. Molecular Docking and 3D-QSAR CoMFA Studies on Indole Inhibitors of GIIA Secreted Phospholipase A2. J Chem Inf Model 2010; 50:1589-601. [PMID: 20795712 DOI: 10.1021/ci100217k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Varnavas D. Mouchlis
- Laboratory of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Thomas M. Mavromoustakos
- Laboratory of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - George Kokotos
- Laboratory of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis, Athens 15771, Greece
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Mouchlis VD, Mavromoustakos TM, Kokotos G. Design of new secreted phospholipase A2 inhibitors based on docking calculations by modifying the pharmacophore segments of the FPL67047XX inhibitor. J Comput Aided Mol Des 2010; 24:107-15. [DOI: 10.1007/s10822-010-9319-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Accepted: 01/21/2010] [Indexed: 10/19/2022]
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