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Vasilakaki S, Vathiotis I, Panagiotou E, Dimakakos E, Gomatou G, Kotteas E. Molecular interactions of antibodies with PD-1/PD-L1 proteins. Immunotherapy 2024; 16:21-28. [PMID: 38054258 DOI: 10.2217/imt-2023-0165] [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] [Indexed: 12/07/2023] Open
Abstract
Aim: To compare the protein-protein interactions of antibodies targeting PD-1 and its ligand (PD-L1) with their targets in an attempt to explain the antibodies' binding affinity. Materials & methods: The structural features of complexes between pembrolizumab, nivolumab, durvalumab, atezolizumab, avelumab and PD-1/PD-L1 are described, with the use of software and based on crystallographic data. Results: Pembrolizumab has more structural features, including the number and type of the bonds and total binding surface area, which could rationalize its different clinical behavior compared with nivolumab. Similarly, protein-protein interactions with PD-L1 differ among durvalumab, atezolizumab and avelumab. Conclusion: Differential protein-protein interactions between antibodies and PD-1/PD-L1 may indicate differential clinical activity; however, further research is needed to provide evidence.
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Affiliation(s)
- Sofia Vasilakaki
- Chemistry Department, National & Kapodistrian University of Athens, Panepistimiopolis, Athens, 15771, Greece
| | - Ioannis Vathiotis
- Oncology Unit, Third Department of Medicine, Sotiria General Hospital, 152 Mesogeion Avenue, Athens, 11527, Greece
| | - Emmanouil Panagiotou
- Oncology Unit, Third Department of Medicine, Sotiria General Hospital, 152 Mesogeion Avenue, Athens, 11527, Greece
| | - Evangelos Dimakakos
- Oncology Unit, Third Department of Medicine, Sotiria General Hospital, 152 Mesogeion Avenue, Athens, 11527, Greece
| | - Georgia Gomatou
- Oncology Unit, Third Department of Medicine, Sotiria General Hospital, 152 Mesogeion Avenue, Athens, 11527, Greece
| | - Elias Kotteas
- Oncology Unit, Third Department of Medicine, Sotiria General Hospital, 152 Mesogeion Avenue, Athens, 11527, Greece
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Mantzourani C, Vasilakaki S, Gerogianni VE, Kokotos G. The discovery and development of transmembrane serine protease 2 (TMPRSS2) inhibitors as candidate drugs for the treatment of COVID-19. Expert Opin Drug Discov 2022; 17:231-246. [PMID: 35072549 PMCID: PMC8862169 DOI: 10.1080/17460441.2022.2029843] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/12/2022] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused the devastating pandemic named coronavirus disease 2019 (COVID-19). Unfortunately, the discovery of antiviral agents to combat COVID-19 is still an unmet need. Transmembrane serine protease 2 (TMPRSS2) is an important mediator in viral infection and thus, TMPRRS2 inhibitors may be attractive agents for COVID-19 treatment. AREAS COVERED This review article discusses the role of TMPRSS2 in SARS-CoV-2 cell entry and summarizes the inhibitors of TMPRSS2 and their potential anti-SARS activity. Two known TMPRSS2 inhibitors, namely camostat and nafamostat, approved drugs for the treatment of pancreatitis, are under clinical trials as potential drugs against COVID-19. EXPERT OPINION Due to the lack of the crystal structure of TMPRSS2, homology models have been developed to study the interactions of known inhibitors, including repurposed drugs, with the enzyme. However, novel TMPRSS2 inhibitors have been identified through high-throughput screening, and appropriate assays studying their in vitro activity have been set up. The discovery of TMPRSS2's crystal structure will facilitate the rational design of novel inhibitors and in vivo studies and clinical trials will give a clear answer if TMPRSS2 inhibitors could be a new weapon against COVID-19.
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Affiliation(s)
- Christiana Mantzourani
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens, Greece
- Center of Excellence for Drug Design and Discovery, National and Kapodistrian University of Athens, Athens, Greece
| | - Sofia Vasilakaki
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens, Greece
- Center of Excellence for Drug Design and Discovery, National and Kapodistrian University of Athens, Athens, Greece
| | - Velisaria-Eleni Gerogianni
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens, Greece
- Center of Excellence for Drug Design and Discovery, National and Kapodistrian University of Athens, Athens, Greece
| | - George Kokotos
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens, Greece
- Center of Excellence for Drug Design and Discovery, National and Kapodistrian University of Athens, Athens, Greece
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Machairiotis N, Vasilakaki S, Minns L, Malakasis A. Nutrients that modulate gestational diabetes mellitus: A systematic review of cohort studies Jan 2019-Jan 2020. Int J Clin Pract 2021; 75:e14033. [PMID: 33480127 DOI: 10.1111/ijcp.14033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 01/17/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The role of eating habits of pregnant women in the development and treatment of gestational diabetes mellitus (GDM) is well established. OBJECTIVES To estimate the contribution of specific nutrients and dietary patterns in the development or privation of GDM in pregnant women. DATA SOURCES A systematic review of cohort studies, published between January 2019 and January 2020, of English articles using PubMed, Scopus and Europe PMC databases. Search terms included diabetes, pregnancy, dietary, food, and nutrients. STUDY SELECTION Only cohort studies about the association between eating habits before and during pregnancy and the risk of GDM in English were included. The studies used dietary patterns, specific nutrients or records of food intake of the participants using a questionnaire. DATA EXTRACTION Two authors independently extracted data from articles-including dietary patterns, food intake, nutrients, number and demographic data of participants, data about pregnancies-using predefined criteria. RESULTS In total, 28 cohort studies were organised to examine the correlation between dietary patterns and the prevention of GDM. Studies were conducted in 13 countries and included 3 058 242 participants. Of those, 13 (46%) studies focused on the consumption of vitamins, probiotics, micronutrients, folate, vegetables and fruits. Moreover, seven (25%) studies focused on what is considered to be "unhealthy" eating habits, including prudent and Western dietary patterns. The mediterranean pattern was used in three (11%) studies. CONCLUSIONS Ongoing studies support advice to adhere to a healthy balanced diet, with the addition of folic acid and a multi-vitamin suitable for pregnancy. There is new evidence suggesting probiotics and cod-liver oil supplementation may improve glycaemic control and also the important consideration of the psychological influences of eating.
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Affiliation(s)
- Nikolaos Machairiotis
- Department of Obstetrics and Gynaecology, Accredited Endometriosis Centre, Northwick Park Hospital, London North West Healthcare NHS Trust, Harrow, London, UK
| | - Sofia Vasilakaki
- Pharmacy Department, University of Athens, Panepistimiopolis of Zographou, Athens, Greece
| | - Laura Minns
- Department of Obstetrics and Gynaecology, Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich, UK
| | - Anastasios Malakasis
- Department of Obstetrics and Gynaecology, Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich, UK
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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: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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Bantzi M, Augsburger F, Loup J, Berset Y, Vasilakaki S, Myrianthopoulos V, Mikros E, Szabo C, Bochet CG. Novel Aryl-Substituted Pyrimidones as Inhibitors of 3-Mercaptopyruvate Sulfurtransferase with Antiproliferative Efficacy in Colon Cancer. J Med Chem 2021; 64:6221-6240. [PMID: 33856792 DOI: 10.1021/acs.jmedchem.1c00260] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The enzyme 3-mercaptopyruvate sulfurtransferase (3-MST) is one of the more recently identified mammalian sources of H2S. A recent study identified several novel 3-MST inhibitors with micromolar potency. Among those, (2-[(4-hydroxy-6-methylpyrimidin-2-yl)sulfanyl]-1-(naphthalen-1-yl)ethan-1-one) or HMPSNE was found to be the most potent and selective. We now took the central core of this compound and modified the pyrimidone and the arylketone sides independently. A 63-compound library was synthesized; compounds were tested for H2S generation from recombinant 3-MST in vitro. Active compounds were subsequently tested to elucidate their potency and selectivity. Computer modeling studies have delineated some of the key structural features necessary for binding to the 3-MST's active site. Six novel 3-MST inhibitors were tested in cell-based assays: they exerted inhibitory effects in murine MC38 and CT26 colon cancer cell proliferation; the antiproliferative effect of the compound with the highest potency and best cell-based activity (1b) was also confirmed on the growth of MC38 tumors in mice.
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Affiliation(s)
- Marina Bantzi
- Department of Chemistry, University of Fribourg, 1700 Fribourg, Switzerland.,Chair of Pharmacology, Faculty of Science and Medicine University of Fribourg, 1700 Fribourg, Switzerland
| | - Fiona Augsburger
- Chair of Pharmacology, Faculty of Science and Medicine University of Fribourg, 1700 Fribourg, Switzerland
| | - Jérémie Loup
- Department of Chemistry, University of Fribourg, 1700 Fribourg, Switzerland
| | - Yan Berset
- Department of Chemistry, University of Fribourg, 1700 Fribourg, Switzerland
| | - Sofia Vasilakaki
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Athens, 15772 Athens, Greece
| | - Vassilios Myrianthopoulos
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Athens, 15772 Athens, Greece
| | - Emmanuel Mikros
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Athens, 15772 Athens, Greece
| | - Csaba Szabo
- Chair of Pharmacology, Faculty of Science and Medicine University of Fribourg, 1700 Fribourg, Switzerland
| | - Christian G Bochet
- Department of Chemistry, University of Fribourg, 1700 Fribourg, Switzerland
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6
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Psarra A, Theodoropoulou MA, Erhardt M, Mertiri M, Mantzourani C, Vasilakaki S, Magrioti V, Huwiler A, Kokotos G. α-Ketoheterocycles Able to Inhibit the Generation of Prostaglandin E 2 (PGE 2) in Rat Mesangial Cells. Biomolecules 2021; 11:biom11020275. [PMID: 33668480 PMCID: PMC7918003 DOI: 10.3390/biom11020275] [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] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/28/2021] [Accepted: 02/10/2021] [Indexed: 02/07/2023] Open
Abstract
Prostaglandin E2 (PGE2) is a key mediator of inflammation, and consequently huge efforts have been devoted to the development of novel agents able to regulate its formation. In this work, we present the synthesis of various α-ketoheterocycles and a study of their ability to inhibit the formation of PGE2 at a cellular level. A series of α-ketobenzothiazoles, α-ketobenzoxazoles, α-ketobenzimidazoles, and α-keto-1,2,4-oxadiazoles were synthesized and chemically characterized. Evaluation of their ability to suppress the generation of PGE2 in interleukin-1β plus forskolin-stimulated mesangial cells led to the identification of one α-ketobenzothiazole (GK181) and one α-ketobenzoxazole (GK491), which are able to suppress the PGE2 generation at a nanomolar level.
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Affiliation(s)
- Anastasia Psarra
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, 15771 Athens, Greece; (A.P.); (M.A.T.); (M.M.); (C.M.); (S.V.); (V.M.)
| | - Maria A. Theodoropoulou
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, 15771 Athens, Greece; (A.P.); (M.A.T.); (M.M.); (C.M.); (S.V.); (V.M.)
| | - Martin Erhardt
- Institute of Pharmacology, University of Bern, CH-3010 Bern, Switzerland; (M.E.); (A.H.)
| | - Marina Mertiri
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, 15771 Athens, Greece; (A.P.); (M.A.T.); (M.M.); (C.M.); (S.V.); (V.M.)
| | - Christiana Mantzourani
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, 15771 Athens, Greece; (A.P.); (M.A.T.); (M.M.); (C.M.); (S.V.); (V.M.)
| | - Sofia Vasilakaki
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, 15771 Athens, Greece; (A.P.); (M.A.T.); (M.M.); (C.M.); (S.V.); (V.M.)
| | - Victoria Magrioti
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, 15771 Athens, Greece; (A.P.); (M.A.T.); (M.M.); (C.M.); (S.V.); (V.M.)
| | - Andrea Huwiler
- Institute of Pharmacology, University of Bern, CH-3010 Bern, Switzerland; (M.E.); (A.H.)
| | - George Kokotos
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, 15771 Athens, Greece; (A.P.); (M.A.T.); (M.M.); (C.M.); (S.V.); (V.M.)
- Correspondence: ; Tel.: +30-210-727-4462
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7
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Vasilakaki S, Kraml J, Schauperl M, Liedl KR, Kokotos G. Hydration thermodynamics of cytosolic phospholipase A 2 GIVA predict its membrane-associated parts and its highly hydrated binding site. J Biomol Struct Dyn 2020; 39:953-959. [PMID: 32085688 DOI: 10.1080/07391102.2020.1733665] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
During biological events, the water molecules associated with the protein are re-oriented to adapt to the new conditions, inducing changes in the system's free energy. The characterization of water structure and thermodynamics may facilitate the prediction of certain biological events, such as the binding of a ligand and the membrane-associated parts of a protein. In this computational study, we calculated the hydration thermodynamics of cytosolic phospholipase A2 group IV (GIVA cPLA2) to study the hydration properties of the protein's surface and binding pocket. Hydrophobicity scales and the Grid Inhomogeneous Solvation Theory (GIST) tool were employed for the calculations. The hydrophobic areas of the protein's surface were predicted more accurately with the GIST method rather than with the hydrophobicity scales. Based on this, a model of the protein-membrane complex was constructed. In addition, the calculation revealed the highly hydrated binding pocket that further contribute to our understanding of the ligands' binding. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sofia Vasilakaki
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Johannes Kraml
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Tyrol, Austria
| | - Michael Schauperl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Tyrol, Austria
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Tyrol, Austria
| | - George Kokotos
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
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8
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Machairiotis N, Vasilakaki S, Kouroutou P. Natural products: Potential lead compounds for the treatment of endometriosis. Eur J Obstet Gynecol Reprod Biol 2020; 245:7-12. [DOI: 10.1016/j.ejogrb.2019.11.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/18/2019] [Accepted: 11/20/2019] [Indexed: 12/15/2022]
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Nikolaou A, Kokotou MG, Vasilakaki S, Kokotos G. Corrigendum to "Small-molecule inhibitors as potential therapeutics and as tools to understand the role of phospholipases A2" [Biochim. Biophys. Acta Mol. Cell Biol. Lipids 1864/6 2019 941-956]. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1864:1681. [PMID: 31221540 PMCID: PMC8445307 DOI: 10.1016/j.bbalip.2019.06.009] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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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10
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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Sapalidis K, Machairiotis N, Zarogoulidis P, Vasilakaki S, Sardeli C, Koimtzis G, Pavlidis E, Katsaounis A, Giannakidis D, Michalopoulos N, Mantalobas S, Alexandrou V, Koulouris C, Amaniti A, Kesisoglou I. Genes' Interactions: A Major Contributor to the Malignant Transformation of Endometriosis. Int J Mol Sci 2019; 20:ijms20081842. [PMID: 31013963 PMCID: PMC6515388 DOI: 10.3390/ijms20081842] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/08/2019] [Accepted: 04/12/2019] [Indexed: 12/12/2022] Open
Abstract
The genetic and epigenetic factors that contribute to the malignant transformation of endometriosis are still under investigation. The objective of the present study was to investigate the genetic link between endometriosis and cancer by examining and correlating the latest clinical observations with biological experimental data. We collected updated evidence about the genetic relationship between endometriosis and cancers by conducting a comprehensive search of PubMed and Scopus databases, focusing on the papers published between January 2018 and January 2019. New insights into the mechanism of the malignant transformation of endometriosis have been published recently. The use of state-of-the-art techniques and methods, such as the genome-wide association study analysis and the weighted gene co-expression analysis, have significantly altered our understanding of the association between endometriosis and endometriosis-associated cancer development. Interestingly, the interactions formed between genes seem to play a pivotal role in the phenotypic expression of mutations. Therefore, the effect of single nucleotide polymorphisms and the function of the expression quantitative trait loci on genes’ expression have been the subject of many recent works. In addition, it has been discovered that genes, the mutations of which have been related to the development of endometriosis, play a role as hub genes. This may lead to new areas of research for understanding the mechanism of malignant transformation of the disease. Significant steps forward have been made towards the identification of factors that control the malignant transformation of endometriosis. Still, due to rarity of the event, a better-organized scheme for sampling on a global level should be adopted.
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Affiliation(s)
- Konstantinos Sapalidis
- Department of Obstetrics-Gynaecology, Royal Oldham Hospital, Pennine Accute Trust, Oldham OL12JH, UK.
- 3rd Department of Surgery, "AHEPA" University Hospital, Aristotle University of Thessaloniki, 55236 Thessaloniki, Greece.
| | - Nikolaos Machairiotis
- Department of Obstetrics-Gynaecology, Royal Oldham Hospital, Pennine Accute Trust, Oldham OL12JH, UK.
| | - Paul Zarogoulidis
- 3rd Department of Surgery, "AHEPA" University Hospital, Aristotle University of Thessaloniki, 55236 Thessaloniki, Greece.
| | - Sofia Vasilakaki
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, 15771 Athens, Greece.
| | - Chrysanthi Sardeli
- Department of Pharmacology & Clinical Pharmacology, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 52236 Thessaloniki, Greece.
| | - George Koimtzis
- 3rd Department of Surgery, "AHEPA" University Hospital, Aristotle University of Thessaloniki, 55236 Thessaloniki, Greece.
| | - Efstathios Pavlidis
- 3rd Department of Surgery, "AHEPA" University Hospital, Aristotle University of Thessaloniki, 55236 Thessaloniki, Greece.
| | - Athanasios Katsaounis
- 3rd Department of Surgery, "AHEPA" University Hospital, Aristotle University of Thessaloniki, 55236 Thessaloniki, Greece.
| | - Dimitrios Giannakidis
- 3rd Department of Surgery, "AHEPA" University Hospital, Aristotle University of Thessaloniki, 55236 Thessaloniki, Greece.
| | - Nikolaos Michalopoulos
- 3rd Department of Surgery, "AHEPA" University Hospital, Aristotle University of Thessaloniki, 55236 Thessaloniki, Greece.
| | - Stylianos Mantalobas
- 3rd Department of Surgery, "AHEPA" University Hospital, Aristotle University of Thessaloniki, 55236 Thessaloniki, Greece.
| | - Vyron Alexandrou
- 3rd Department of Surgery, "AHEPA" University Hospital, Aristotle University of Thessaloniki, 55236 Thessaloniki, Greece.
| | - Charilaos Koulouris
- 3rd Department of Surgery, "AHEPA" University Hospital, Aristotle University of Thessaloniki, 55236 Thessaloniki, Greece.
| | - Aikaterini Amaniti
- Anesthesiology Department, "AHEPA" University Hospital, Aristotle University of Thessaloniki, 52236 Thessaloniki, Greece.
| | - Isaak Kesisoglou
- 3rd Department of Surgery, "AHEPA" University Hospital, Aristotle University of Thessaloniki, 55236 Thessaloniki, Greece.
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Mavrogeni ME, Pronios F, Zareifi D, Vasilakaki S, Lozach O, Alexopoulos L, Meijer L, Myrianthopoulos V, Mikros E. A facile consensus ranking approach enhances virtual screening robustness and identifies a cell-active DYRK1α inhibitor. Future Med Chem 2018; 10:2411-2430. [PMID: 30325204 PMCID: PMC6479281 DOI: 10.4155/fmc-2018-0198] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [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: 05/27/2018] [Accepted: 08/16/2018] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Virtual screening is vital for contemporary drug discovery but striking performance fluctuations are commonly encountered, thus hampering error-free use. Results and Methodology: A conceptual framework is suggested for combining screening algorithms characterized by orthogonality (docking-scoring calculations, 3D shape similarity, 2D fingerprint similarity) into a simple, efficient and expansible python-based consensus ranking scheme. An original experimental dataset is created for comparing individual screening methods versus the novel approach. Its utilization leads to identification and phosphoproteomic evaluation of a cell-active DYRK1α inhibitor. CONCLUSION Consensus ranking considerably stabilizes screening performance at reasonable computational cost, whereas individual screens are heavily dependent on calculation settings. Results indicate that the novel approach, currently available as a free online tool, is highly suitable for prospective screening by nonexperts.
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Affiliation(s)
- Maria E Mavrogeni
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Athens, Panepistimiopolis Zografou, 157 71 Athens, Greece
| | - Filippos Pronios
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Athens, Panepistimiopolis Zografou, 157 71 Athens, Greece
| | - Danae Zareifi
- ProtATonce Ltd, Dimokritos Science Park, Agia Paraskevi, 153 43 Athens, Greece
| | - Sofia Vasilakaki
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Athens, Panepistimiopolis Zografou, 157 71 Athens, Greece
| | - Olivier Lozach
- Laboratoire Chimie Electrochimie Moléculaires et Chimie Analytique, University of Brest, 29238 Brest, France
| | - Leonidas Alexopoulos
- School of Mechanical Engineering, National Technical University of Athens, 157 80 Athens, Greece
| | - Laurent Meijer
- ManRos Therapeutics, Perharidy Research Center, 29680 Roscoff, Bretagne, France
| | - Vassilios Myrianthopoulos
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Athens, Panepistimiopolis Zografou, 157 71 Athens, Greece
- ‘Athena’ Research & Innovation Center, 151 25 Athens, Greece
| | - Emmanuel Mikros
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Athens, Panepistimiopolis Zografou, 157 71 Athens, Greece
- ‘Athena’ Research & Innovation Center, 151 25 Athens, Greece
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Athanasiou C, Vasilakaki S, Dellis D, Cournia Z. Using physics-based pose predictions and free energy perturbation calculations to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2. J Comput Aided Mol Des 2017; 32:21-44. [DOI: 10.1007/s10822-017-0075-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 10/09/2017] [Indexed: 01/21/2023]
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14
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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15
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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