1
|
Stamou C, Dechambenoit P, Lada ZG, Gkolfi P, Riga V, Raptopoulou CP, Psycharis V, Konidaris KF, Chasapis CT, Perlepes SP. Reactions of Cadmium(II) Halides and Di-2-Pyridyl Ketone Oxime: One-Dimensional Coordination Polymers. Molecules 2024; 29:509. [PMID: 38276587 PMCID: PMC10820575 DOI: 10.3390/molecules29020509] [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] [Received: 12/05/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
The coordination chemistry of 2-pyridyl ketoximes continues to attract the interest of many inorganic chemistry groups around the world for a variety of reasons. Cadmium(II) complexes of such ligands have provided models of solvent extraction of this toxic metal ion from aqueous environments using 2-pyridyl ketoxime extractants. Di-2-pyridyl ketone oxime (dpkoxH) is a unique member of this family of ligands because its substituent on the oxime carbon bears another potential donor site, i.e., a second 2-pyridyl group. The goal of this study was to investigate the reactions of cadmium(II) halides and dpkoxH in order to assess the structural role (if any) of the halogeno ligand and compare the products with their zinc(II) analogs. The synthetic studies provided access to complexes {[CdCl2(dpkoxH)∙2H2O]}n (1∙2H2O), {[CdBr2(dpkoxH)]}n (2) and {[CdI2(dpkoxH)]}n (3) in 50-60% yields. The structures of the complexes were determined by single-crystal X-ray crystallography. The compounds consist of structurally similar 1D zigzag chains, but only 2 and 3 are strictly isomorphous. Neighboring CdII atoms are alternately doubly bridged by halogeno and dpkoxH ligands, the latter adopting the η1:η1:η1:μ (or 2.0111 using Harris notation) coordination mode. A terminal halogeno group completes distorted octahedral coordination at each metal ion, and the coordination sphere of the CdII atoms is {CdII(η1 - X)(μ - X)2(Npyridyl)2(Noxime)} (X = Cl, Br, I). The trans-donor-atom pairs in 1∙2H2O are Clterminal/Noxime and two Clbridging/Npyridyl; on the contrary, these donor-atom pairs are Xterminal/Npyridyl, Xbridging/Noxime, and Xbridging/Npyridyl (X = Br, I). There are intrachain H-bonding interactions in the structures. The packing of the chains in 1∙2H2O is achieved via π-π stacking interactions, while the 3D architecture of the isomorphous 2 and 3 is built via C-H∙∙∙Cg (Cg is the centroid of one pyridyl ring) and π-π overlaps. The molecular structures of 1∙2H2O and 2 are different compared with their [ZnX2(dpkoxH)] (X = Cl, Br) analogs. The polymeric compounds were characterized by IR and Raman spectroscopies in the solid state, and the data were interpreted in terms of the known molecular structures. The solid-state structures of the complexes are not retained in DMSO, as proven via NMR (1H, 13C, and 113Cd NMR) spectroscopy and molar conductivity data. The complexes completely release the coordinated dpkoxH molecule, and the dominant species in solution seem to be [Cd(DMSO)6]2+ in the case of the chloro and bromo complexes and [CdI2(DMSO)4].
Collapse
Affiliation(s)
- Christina Stamou
- Department of Chemistry, University of Patras, 26504 Patras, Greece; (C.S.); (P.G.); (V.R.)
| | - Pierre Dechambenoit
- Centre de Recherche Paul Pascal, UMR 5031, CNRS, University of Bordeaux, 33600 Pessac, France;
| | - Zoi G. Lada
- Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas (FORTH/ICE-HT), Platani, P.O. Box 1414, 26504 Patras, Greece;
| | - Patroula Gkolfi
- Department of Chemistry, University of Patras, 26504 Patras, Greece; (C.S.); (P.G.); (V.R.)
| | - Vassiliki Riga
- Department of Chemistry, University of Patras, 26504 Patras, Greece; (C.S.); (P.G.); (V.R.)
| | - Catherine P. Raptopoulou
- Institute of Nanoscience and Nanotechnology, NCSR “Demokritos”, 15310 Aghia Paraskevi Attikis, Greece;
| | - Vassilis Psycharis
- Institute of Nanoscience and Nanotechnology, NCSR “Demokritos”, 15310 Aghia Paraskevi Attikis, Greece;
| | - Konstantis F. Konidaris
- Department of Chemistry, Materials Science and Chemical Engineering “Giulio Natta”, Via L. Mancinelli 7, 20131 Milan, Italy
| | - Christos T. Chasapis
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Spyros P. Perlepes
- Department of Chemistry, University of Patras, 26504 Patras, Greece; (C.S.); (P.G.); (V.R.)
- Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas (FORTH/ICE-HT), Platani, P.O. Box 1414, 26504 Patras, Greece;
| |
Collapse
|
2
|
Ntallis C, Tzoupis H, Tselios T, Chasapis CT, Vlamis-Gardikas A. Distinct or Overlapping Areas of Mitochondrial Thioredoxin 2 May Be Used for Its Covalent and Strong Non-Covalent Interactions with Protein Ligands. Antioxidants (Basel) 2023; 13:15. [PMID: 38275635 PMCID: PMC10812433 DOI: 10.3390/antiox13010015] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/09/2023] [Accepted: 12/16/2023] [Indexed: 01/27/2024] Open
Abstract
In silico approaches were employed to examine the characteristics of interactions between human mitochondrial thioredoxin 2 (HsTrx2) and its 38 previously identified mitochondrial protein ligands. All interactions appeared driven mainly by electrostatic forces. The statistically significant residues of HsTrx2 for interactions were characterized as "contact hot spots". Since these were identical/adjacent to putative thermodynamic hot spots, an energy network approach identified their neighbors to highlight possible contact interfaces. Three distinct areas for binding emerged: (i) one around the active site for covalent interactions, (ii) another antipodal to the active site for strong non-covalent interactions, and (iii) a third area involved in both kinds of interactions. The contact interfaces of HsTrx2 were projected as respective interfaces for Escherichia coli Trx1 (EcoTrx1), 2, and HsTrx1. Comparison of the interfaces and contact hot spots of HsTrx2 to the contact residues of EcoTx1 and HsTrx1 from existing crystal complexes with protein ligands supported the hypothesis, except for a part of the cleft/groove adjacent to Trp30 preceding the active site. The outcomes of this study raise the possibility for the rational design of selective inhibitors for the interactions of HsTrx2 with specific protein ligands without affecting the entirety of the functions of the Trx system.
Collapse
Affiliation(s)
- Charalampos Ntallis
- Department of Chemistry, University of Patras, 26504 Rion, Greece; (C.N.); (H.T.); (T.T.)
| | - Haralampos Tzoupis
- Department of Chemistry, University of Patras, 26504 Rion, Greece; (C.N.); (H.T.); (T.T.)
| | - Theodore Tselios
- Department of Chemistry, University of Patras, 26504 Rion, Greece; (C.N.); (H.T.); (T.T.)
| | - Christos T. Chasapis
- Institute of Chemical Biology, National Hellenic Research Foundation, Vas. Constantinou 48, 11635 Athens, Greece;
| | | |
Collapse
|
3
|
Ridgway H, Orbell JD, Matsoukas MT, Kelaidonis K, Moore GJ, Tsiodras S, Gorgoulis VG, Chasapis CT, Apostolopoulos V, Matsoukas JM. W254 in furin functions as a molecular gate promoting anti-viral drug binding: Elucidation of putative drug tunneling and docking by non-equilibrium molecular dynamics. Comput Struct Biotechnol J 2023; 21:4589-4612. [PMID: 37817778 PMCID: PMC10561063 DOI: 10.1016/j.csbj.2023.09.003] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2023] Open
Abstract
Furins are serine endoproteases that process precursor proteins into their biologically active forms, and they play essential roles in normal metabolism and disease presentation, including promoting expression of bacterial virulence factors and viral pathogenesis. Thus, furins represent vital targets for development of antimicrobial and antiviral therapeutics. Recent experimental evidence indicated that dichlorophenyl (DCP)-pyridine "BOS" drugs (e.g., BOS-318) competitively inhibit human furin by an induced-fit mechanism in which tryptophan W254 in the furin catalytic cleft (FCC) functions as a molecular gate, rotating nearly 180o through a steep energy barrier about its chi-1 dihedral to an "open" orientation, exposing a buried (i.e., cryptic) hydrophobic pocket 1. Once exposed, the non-polar DCP group of BOS-318, and similar halo-phenyl groups of analogs, enter the cryptic pocket, stabilizing drug binding. Here, we demonstrate flexible-receptor docking of BOS-318 (and various analogs) was unable to emulate the induced-fit motif, even when tryptophan was replaced with less bulky phenylalanine or glycine. While either substitution allowed access to the hydrophobic pocket for most ligands tested, optimal binding was observed only for W254, inferring a stabilizing effect of the indole sidechain. Furthermore, non-equilibrium steered molecular dynamics (sMD) in which the bound drugs (or their fragments) were extracted from the FCC did not cause closure of the open W254 gate, consistent with the thermodynamic stability of the open or closed W254 orientations. Finally, interactive molecular dynamics (iMD) revealed two putative conduits of drug entry and binding into the FCC, each coupled with W254 dihedral rotation and opening of the cryptic pocket. The iMD simulations further revealed ligand entry and binding in the FCC is likely driven in part by energy fluxes stemming from disruption and re-formation of ligand and protein solvation shells during drug migration from the solution phase into the FCC.
Collapse
Affiliation(s)
- Harry Ridgway
- Institute for Sustainable Industries and Liveable Cities, Victoria University, Melbourne, VIC 8001, Australia
- AquaMem Consultants, Rodeo, NM 88056, USA
| | - John D. Orbell
- Institute for Sustainable Industries and Liveable Cities, Victoria University, Melbourne, VIC 8001, Australia
- College of Sport, Health & Engineering, Victoria University, Melbourne, VIC 8001, Australia
| | | | | | - Graham J. Moore
- Pepmetics Inc., 772 Murphy Place, Victoria, BC V8Y 3H4, Canada
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Sotiris Tsiodras
- Department of Internal Medicine, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Vasilis G. Gorgoulis
- Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
- Department of Histology and Embryology, Faculty of Medicine, National Kapodistrian University of Athens, GR-11527 Athens, Greece
- Faculty Institute for Cancer Sciences, Manchester Academic Health Sciences Centre, University of Manchester, M20 4GJ Manchester, UK
- Biomedical Research Foundation, Academy of Athens, GR-11527 Athens, Greece
- Faculty of Health and Medical Sciences, University of Surrey, GU2 7XH Surrey, UK
| | - Christos T. Chasapis
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Vasso Apostolopoulos
- Institute for Health and Sport, Immunology and Translational Research, Victoria University, Melbourne 3030, VIC, Australia
- Immunology Program, Australian Institute for Musculoskeletal Science (AIMSS), Melbourne 3021, VIC, Australia
| | - John M. Matsoukas
- NewDrug/NeoFar PC, Patras Science Park, Patras 26504, Greece
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Institute for Health and Sport, Immunology and Translational Research, Victoria University, Melbourne 3030, VIC, Australia
- Department of Chemistry, University of Patras, 26504 Patras, Greece
| |
Collapse
|
4
|
Kiouri DP, Tsoupra E, Peana M, Perlepes SP, Stefanidou ME, Chasapis CT. Multifunctional role of zinc in human health: an update. EXCLI J 2023; 22:809-827. [PMID: 37780941 PMCID: PMC10539547 DOI: 10.17179/excli2023-6335] [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] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 07/26/2023] [Indexed: 10/03/2023]
Abstract
Zinc is a multipurpose trace element for the human body, as it plays a crucial part in various physiological processes, such as cell growth and development, metabolism, cognitive, reproductive, and immune system function. Its significance in human health is widely acknowledged, and this has led the scientific community towards more research that aims to uncover all of its beneficial properties, especially when compared to other essential metal ions. One notable area where zinc has shown beneficial effects is in the prevention and treatment of various diseases, including cancer. This review aims to explain the involvement of zinc in specific health conditions such as cancer, coronavirus disease 2019 (COVID-19) and neurological disorders like Alzheimer's disease, as well as its impact on the gut microbiome.
Collapse
Affiliation(s)
- Despoina P. Kiouri
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
- Department of Chemistry, Laboratory of Organic Chemistry, National Kapodistrian University of Athens, 15772 Athens, Greece
| | - Evi Tsoupra
- Department of Chemistry, University of Patras, 26504 Patras, Greece
| | - Massimiliano Peana
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, 07100 Sassari, Italy
| | | | - Maria E. Stefanidou
- Department of Forensic Medicine and Toxicology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Christos T. Chasapis
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| |
Collapse
|
5
|
Kiouri DP, Ntallis C, Kelaidonis K, Peana M, Tsiodras S, Mavromoustakos T, Giuliani A, Ridgway H, Moore GJ, Matsoukas JM, Chasapis CT. Network-Based Prediction of Side Effects of Repurposed Antihypertensive Sartans against COVID-19 via Proteome and Drug-Target Interactomes. Proteomes 2023; 11:21. [PMID: 37368467 DOI: 10.3390/proteomes11020021] [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] [Received: 04/10/2023] [Revised: 05/26/2023] [Accepted: 06/02/2023] [Indexed: 06/28/2023] Open
Abstract
The potential of targeting the Renin-Angiotensin-Aldosterone System (RAAS) as a treatment for the coronavirus disease 2019 (COVID-19) is currently under investigation. One way to combat this disease involves the repurposing of angiotensin receptor blockers (ARBs), which are antihypertensive drugs, because they bind to angiotensin-converting enzyme 2 (ACE2), which in turn interacts with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. However, there has been no in silico analysis of the potential toxicity risks associated with the use of these drugs for the treatment of COVID-19. To address this, a network-based bioinformatics methodology was used to investigate the potential side effects of known Food and Drug Administration (FDA)-approved antihypertensive drugs, Sartans. This involved identifying the human proteins targeted by these drugs, their first neighbors, and any drugs that bind to them using publicly available experimentally supported data, and subsequently constructing proteomes and protein-drug interactomes. This methodology was also applied to Pfizer's Paxlovid, an antiviral drug approved by the FDA for emergency use in mild-to-moderate COVID-19 treatment. The study compares the results for both drug categories and examines the potential for off-target effects, undesirable involvement in various biological processes and diseases, possible drug interactions, and the potential reduction in drug efficiency resulting from proteoform identification.
Collapse
Affiliation(s)
- Despoina P Kiouri
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
- Department of Chemistry, Laboratory of Organic Chemistry, National Kapodistrian University of Athens, 15772 Athens, Greece
| | - Charalampos Ntallis
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | | | - Massimiliano Peana
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, Via Vienna 2, 07100 Sassari, Italy
| | - Sotirios Tsiodras
- 4th Department of Internal Medicine, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Thomas Mavromoustakos
- Department of Chemistry, Laboratory of Organic Chemistry, National Kapodistrian University of Athens, 15772 Athens, Greece
| | - Alessandro Giuliani
- Environment and Health Department, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Harry Ridgway
- Institute for Sustainable Industries and Liveable Cities, Victoria University, Melbourne, VIC 8001, Australia
- AquaMem Consultants, Rodeo, NM 88056, USA
| | - Graham J Moore
- Pepmetics Inc., 772 Murphy Place, Victoria, BC V6Y 3H4, Canada
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - John M Matsoukas
- NewDrug PC, Patras Science Park, 26504 Patras, Greece
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia
- Department of Chemistry, University of Patras, 26504 Patras, Greece
| | - Christos T Chasapis
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| |
Collapse
|
6
|
Kelaidonis K, Ligielli I, Letsios S, Vidali VP, Mavromoustakos T, Vassilaki N, Moore GJ, Hoffmann W, Węgrzyn K, Ridgway H, Chasapis CT, Matsoukas JM. Computational and Enzymatic Studies of Sartans in SARS-CoV-2 Spike RBD-ACE2 Binding: The Role of Tetrazole and Perspectives as Antihypertensive and COVID-19 Therapeutics. Int J Mol Sci 2023; 24:ijms24098454. [PMID: 37176159 PMCID: PMC10179460 DOI: 10.3390/ijms24098454] [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] [Received: 03/24/2023] [Revised: 04/25/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
This study is an extension of current research into a novel class of synthetic antihypertensive drugs referred to as "bisartans", which are bis-alkylated imidazole derivatives bearing two symmetric anionic biphenyltetrazoles. Research to date indicates that bisartans are superior to commercially available hypertension drugs, since the former undergo stronger docking to angiotensin-converting enzyme 2 (ACE2). ACE2 is the key receptor involved in SARS-CoV-2 entry, thus initiating COVID-19 infection and in regulating levels of vasoactive peptides such as angiotensin II and beneficial heptapeptides A(1-7) and Alamandine in the renin-angiotensin system (RAS). In previous studies using in vivo rabbit-iliac arterial models, we showed that Na+ or K+ salts of selected Bisartans initiate a potent dose-response inhibition of vasoconstriction. Furthermore, computational studies revealed that bisartans undergo stable binding to the vital interfacial region between ACE2 and the SARS-CoV-2 "receptor binding domain" (i.e., the viral RBD). Thus, bisartan homologs are expected to interfere with SARS-CoV-2 infection and/or suppress disease expression in humans. The primary goal of this study was to investigate the role of tetrazole in binding and the network of amino acids of SARS-CoV-2 Spike RBD-ACE2 complex involved in interactions with sartans. This study would, furthermore, allow the expansion of the synthetic space to create a diverse suite of new bisartans in conjunction with detailed computational and in vitro antiviral studies. A critical role for tetrazole was uncovered in this study, shedding light on the vital importance of this group in the binding of sartans and bisartans to the ACE2/Spike complex. The in silico data predicting an interaction of tetrazole-containing sartans with ACE2 were experimentally validated by the results of surface plasmon resonance (SPR) analyses performed with a recombinant human ACE2 protein.
Collapse
Affiliation(s)
| | - Irene Ligielli
- Department of Chemistry, Laboratory of Organic Chemistry, National Kapodistrian University of Athens, 15772 Athens, Greece
| | | | - Veroniki P Vidali
- Natural Products and Bioorganic Chemistry Laboratory, Institute of Nanoscience & Nanotechnology, NCSR "Demokritos", 15341 Athens, Greece
| | - Thomas Mavromoustakos
- Department of Chemistry, Laboratory of Organic Chemistry, National Kapodistrian University of Athens, 15772 Athens, Greece
| | - Niki Vassilaki
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 11521 Athens, Greece
| | - Graham J Moore
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Weronika Hoffmann
- Laboratory of Virus Molecular Biology, Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Abrahama 58, 80-307 Gdansk, Poland
| | - Katarzyna Węgrzyn
- Laboratory of Molecular Biology, Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Abrahama 58, 80-307 Gdansk, Poland
| | - Harry Ridgway
- Institute for Sustainable Industries and Liveable Cities, Victoria University, Melbourne, VIC 8001, Australia
- AquaMem Consultants, Rodeo, NM 88056, USA
| | - Christos T Chasapis
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - John M Matsoukas
- NewDrug PC, Patras Science Park, 26504 Patras, Greece
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia
- Department of Chemistry, University of Patras, 26504 Patras, Greece
| |
Collapse
|
7
|
Triandafillidis DP, Karavassili F, Spiliopoulou M, Valmas A, Athanasiadou M, Nikolaras G, Fili S, Kontou P, Bowler MW, Chasapis CT, Von Dreele RB, Fitch AN, Margiolaki I. The T 2 structure of polycrystalline cubic human insulin. Acta Crystallogr D Struct Biol 2023; 79:374-386. [PMID: 37039669 PMCID: PMC10167666 DOI: 10.1107/s2059798323001328] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 02/13/2023] [Indexed: 04/12/2023] Open
Abstract
The polymorphism of human insulin upon pH variation was characterized via X-ray powder diffraction, employing a crystallization protocol previously established for co-crystallization with phenolic derivatives. Two distinct rhombohedral (R3) polymorphs and one cubic (I213) polymorph were identified with increasing pH, corresponding to the T6, T3R3f and T2 conformations of insulin, respectively. The structure of the cubic T2 polymorph was determined via multi-profile stereochemically restrained Rietveld refinement at 2.7 Å resolution. This constitutes the first cubic insulin structure to be determined from crystals grown in the presence of zinc ions, although no zinc binding was observed. The differences of the polycrystalline variant from other cubic insulin structures, as well as the nature of the pH-driven phase transitions, are discussed in detail.
Collapse
Affiliation(s)
- Dimitris P Triandafillidis
- Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
| | - Fotini Karavassili
- Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
| | - Maria Spiliopoulou
- Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
| | - Alexandros Valmas
- Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
| | - Maria Athanasiadou
- Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
| | - George Nikolaras
- Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
| | - Stavroula Fili
- Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
| | - Paraskevi Kontou
- Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
| | - Matthew W Bowler
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Christos T Chasapis
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Robert B Von Dreele
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Andrew N Fitch
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble CEDEX 9, France
| | - Irene Margiolaki
- Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
| |
Collapse
|
8
|
Ridgway H, Ntallis C, Chasapis CT, Kelaidonis K, Matsoukas MT, Plotas P, Apostolopoulos V, Moore G, Tsiodras S, Paraskevis D, Mavromoustakos T, Matsoukas JM. Molecular Epidemiology of SARS-CoV-2: The Dominant Role of Arginine in Mutations and Infectivity. Viruses 2023; 15:v15020309. [PMID: 36851526 PMCID: PMC9963001 DOI: 10.3390/v15020309] [Citation(s) in RCA: 5] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
Background, Aims, Methods, Results, Conclusions: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global challenge due to its ability to mutate into variants that spread more rapidly than the wild-type virus. The molecular biology of this virus has been extensively studied and computational methods applied are an example paradigm for novel antiviral drug therapies. The rapid evolution of SARS-CoV-2 in the human population is driven, in part, by mutations in the receptor-binding domain (RBD) of the spike (S-) protein, some of which enable tighter binding to angiotensin-converting enzyme (ACE2). More stable RBD-ACE2 association is coupled with accelerated hydrolysis by proteases, such as furin, trypsin, and the Transmembrane Serine Protease 2 (TMPRSS2) that augment infection rates, while inhibition of the 3-chymotrypsin-like protease (3CLpro) can prevent the viral replication. Additionally, non-RBD and non-interfacial mutations may assist the S-protein in adopting thermodynamically favorable conformations for stronger binding. This study aimed to report variant distribution of SARS-CoV-2 across European Union (EU)/European Economic Area (EEA) countries and relate mutations with the driving forces that trigger infections. Variants' distribution data for SARS-CoV-2 across EU/EEA countries were mined from the European Centre for Disease Prevention and Control (ECDC) based on the sequence or genotyping data that are deposited in the Global Science Initiative for providing genomic data (GISAID) and The European Surveillance System (TESSy) databases. Docking studies performed with AutoDock VINA revealed stabilizing interactions of putative antiviral drugs, e.g., selected anionic imidazole biphenyl tetrazoles, with the ACE2 receptor in the RBD-ACE2 complex. The driving forces of key mutations for Alpha, Beta, Gamma, Delta, Epsilon, Kappa, Lambda, and Omicron variants, which stabilize the RBD-ACE2 complex, were investigated by computational approaches. Arginine is the critical amino acid in the polybasic furin cleavage sites S1/S2 (681-PRRARS-686) S2' (814-KRS-816). Critical mutations into arginine residues that were found in the delta variant (L452R, P681R) and may be responsible for the increased transmissibility and morbidity are also present in two widely spreading omicron variants, named BA.4.6 and BQ.1, where mutation R346T in the S-protein potentially contributes to neutralization escape. Arginine binders, such as Angiotensin Receptor Blockers (ARBs), could be a class of novel drugs for treating COVID-19.
Collapse
Affiliation(s)
- Harry Ridgway
- Institute for Sustainable Industries and Liveable Cities, Victoria University, Melbourne 8001, VIC, Australia
- AquaMem Consultants, Rodeo, NM 88056, USA
| | - Charalampos Ntallis
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Christos T. Chasapis
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | | | | | - Panagiotis Plotas
- Laboratory of Primary Health Care, School of Health Rehabilitation Sciences, University of Patras, 26504 Patras, Greece
| | - Vasso Apostolopoulos
- Institute for Health and Sport, Victoria University, Melbourne 3030, VIC, Australia
- Immunology Program, Australian Institute for Musculoskeletal Science (AIMSS), Melbourne 3021, VIC, Australia
| | - Graham Moore
- Pepmetics Inc., 772 Murphy Place, Victoria, BC V6Y 3H4, Canada
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Sotirios Tsiodras
- 4th Department of Internal Medicine, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Thomas Mavromoustakos
- Department of Chemistry, National and Kapodistrian University of Athens, 11571 Athens, Greece
| | - John M. Matsoukas
- NewDrug PC, Patras Science Park, 26504 Patras, Greece
- Institute for Health and Sport, Victoria University, Melbourne 3030, VIC, Australia
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Department of Chemistry, University of Patras, 26504 Patras, Greece
- Correspondence:
| |
Collapse
|
9
|
Chasapis CT, Perlepes SP, Bjørklund G, Peana M. Structural modeling of protein ensembles between E3 RING ligases and SARS-CoV-2: The role of zinc binding domains. J Trace Elem Med Biol 2023; 75:127089. [PMID: 36209710 PMCID: PMC9531365 DOI: 10.1016/j.jtemb.2022.127089] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/13/2022] [Accepted: 09/28/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND The ubiquitin system is a modification process with many different cellular functions including immune signaling and antiviral functions. E3 ubiquitin ligases are enzymes that recruit an E2 ubiquitin-conjugating enzyme bound to ubiquitin in order to catalyze the transfer of ubiquitin from the E2 to a protein substrate. The RING E3s, the most abundant type of ubiquitin ligases, are characterized by a zinc (II)-binding domain called RING (Really Interesting New Gene). Viral replication requires modifying and hijacking key cellular pathways within host cells such as cellular ubiquitination. There are well-established examples where a viral proteins bind to RING E3s, redirecting them to degrade otherwise long-lived host proteins or inhibiting E3's ubiquitination activity. Recently, three binary interactions between SARS-CoV-2 proteins and innate human immune signaling Ε3 RING ligases: NSP15-RNF41, ORF3a-TRIM59 and NSP9-MIB1 have been experimentally established. METHODS In this work, we have investigated the mode of the previous experimentally supported NSP15-RNF41, ORF3a,-TRIM59 and NSP9-MIB1 binary interactions by in silico methodologies intending to provide structural insights of E3-virus interplay that can help identify potential inhibitors that could block SARS-CoV-2 infection of immune cells. CONCLUSION In silico methodologies have shown that the above human E3 ligases interact with viral partners through their Zn(II) binding domains. This RING mediated formation of stable SARS-CoV-2-E3 complexes indicates a critical structural role of RING domains in immune system disruption by SARS-CoV-2-infection. DATA AVAILABILITY The data used to support the findings of this research are included within the article and are labeled with references.
Collapse
Affiliation(s)
- Christos T Chasapis
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece.
| | | | - Geir Bjørklund
- Council for Nutritional and Environmental Medicine (CONEM), Mo i Rana, Norway
| | - Massimiliano Peana
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, Italy.
| |
Collapse
|
10
|
Peana M, Pelucelli A, Chasapis CT, Perlepes SP, Bekiari V, Medici S, Zoroddu MA. Biological Effects of Human Exposure to Environmental Cadmium. Biomolecules 2022; 13:biom13010036. [PMID: 36671421 PMCID: PMC9855641 DOI: 10.3390/biom13010036] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Cadmium (Cd) is a toxic metal for the human organism and for all ecosystems. Cd is naturally found at low levels; however, higher amounts of Cd in the environment result from human activities as it spreads into the air and water in the form of micropollutants as a consequence of industrial processes, pollution, waste incineration, and electronic waste recycling. The human body has a limited ability to respond to Cd exposure since the metal does not undergo metabolic degradation into less toxic species and is only poorly excreted. The extremely long biological half-life of Cd essentially makes it a cumulative toxin; chronic exposure causes harmful effects from the metal stored in the organs. The present paper considers exposure and potential health concerns due to environmental cadmium. Exposure to Cd compounds is primarily associated with an elevated risk of lung, kidney, prostate, and pancreatic cancer. Cd has also been linked to cancers of the breast, urinary system, and bladder. The multiple mechanisms of Cd-induced carcinogenesis include oxidative stress with the inhibition of antioxidant enzymes, the promotion of lipid peroxidation, and interference with DNA repair systems. Cd2+ can also replace essential metal ions, including redox-active ones. A total of 12 cancer types associated with specific genes coding for the Cd-metalloproteome were identified in this work. In addition, we summarize the proper treatments of Cd poisoning, based on the use of selected Cd detoxifying agents and chelators, and the potential for preventive approaches to counteract its chronic exposure.
Collapse
Affiliation(s)
- Massimiliano Peana
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, 07100 Sassari, Italy
- Correspondence: (M.P.); (A.P.)
| | - Alessio Pelucelli
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, 07100 Sassari, Italy
- Correspondence: (M.P.); (A.P.)
| | - Christos T. Chasapis
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | | | - Vlasoula Bekiari
- School of Agricultural Science, University of Patras, 30200 Messolonghi, Greece
| | - Serenella Medici
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, 07100 Sassari, Italy
| | - Maria Antonietta Zoroddu
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, 07100 Sassari, Italy
| |
Collapse
|
11
|
Podzimek S, Himmlova L, Janatova T, Bjørklund G, Vrbova R, Janovska M, Peana M, Chasapis CT, Vinsu A, Prochazkova J, Duskova J. Metal hypersensitivity and pro-inflammatory cytokine production in patients with failed orthopedic implants: A case-control study. Clin Immunol 2022; 245:109152. [DOI: 10.1016/j.clim.2022.109152] [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] [Received: 07/30/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/29/2022]
|
12
|
Bjørklund G, Zou L, Peana M, Chasapis CT, Hangan T, Lu J, Maes M. The Role of the Thioredoxin System in Brain Diseases. Antioxidants (Basel) 2022; 11:2161. [PMID: 36358532 PMCID: PMC9686621 DOI: 10.3390/antiox11112161] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 09/28/2022] [Revised: 10/23/2022] [Accepted: 10/28/2022] [Indexed: 08/08/2023] Open
Abstract
The thioredoxin system, consisting of thioredoxin (Trx), thioredoxin reductase (TrxR), and NADPH, plays a fundamental role in the control of antioxidant defenses, cell proliferation, redox states, and apoptosis. Aberrations in the Trx system may lead to increased oxidative stress toxicity and neurodegenerative processes. This study reviews the role of the Trx system in the pathophysiology and treatment of Alzheimer's, Parkinson's and Huntington's diseases, brain stroke, and multiple sclerosis. Trx system plays an important role in the pathophysiology of those disorders via multiple interactions through oxidative stress, apoptotic, neuro-immune, and pro-survival pathways. Multiple aberrations in Trx and TrxR systems related to other redox systems and their multiple reciprocal relationships with the neurodegenerative, neuro-inflammatory, and neuro-oxidative pathways are here analyzed. Genetic and environmental factors (nutrition, metals, and toxins) may impact the function of the Trx system, thereby contributing to neuropsychiatric disease. Aberrations in the Trx and TrxR systems could be a promising drug target to prevent and treat neurodegenerative, neuro-inflammatory, neuro-oxidative stress processes, and related brain disorders.
Collapse
Affiliation(s)
- Geir Bjørklund
- Council for Nutritional and Environmental Medicine, Toften 24, 8610 Mo i Rana, Norway
| | - Lili Zou
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang 443002, China
| | - Massimiliano Peana
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, Via Vienna 2, 07100 Sassari, Italy
| | - Christos T. Chasapis
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Tony Hangan
- Faculty of Medicine, Ovidius University of Constanta, 900470 Constanta, Romania
| | - Jun Lu
- School of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Michael Maes
- Department of Psychiatry, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| |
Collapse
|
13
|
Stamou C, Lada ZG, Chasapis CT, Papaioannou D, Dechambenoit P, Perlepes SP. Indium(III)/2-benzoylpyridine chemistry: interesting indium(III) bromide-assisted transformations of the ligand. Dalton Trans 2022; 51:15771-15782. [PMID: 36178466 DOI: 10.1039/d2dt02851d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reactions of 2-benzoylpyridine, (py)(ph)CO, with InX3 (X = Cl, Br) in EtOH at room temperature have been studied. The InCl3/(py)(ph)CO system has provided access to complex [InCl3{(py)(ph)CO}(EtOH)]·{(py)(ph)CO} (1) and the byproduct {(pyH)(ph)CO}Cl (2). The reaction of InBr3 with (py)(ph)CO has led to a mixture of (L)[InBr4{(py)(ph)CO}] (3) and [In2Br4{(py)(ph)CH(O)}2(EtOH)2] (4), where L+ is the 9-oxo-indolo[1,2-a]pyridinium cation and (py)(ph)CH(O)- is the anion of (pyridin-2-yl)methanol. Based on solubility and crystallisation time differences between the two components of the mixture, complex 4 was isolated in pure form, i.e. free from 3. The formations of the counterion L+ and the coordinated (py)(ph)CH(O)- anion represent clearly InBr3-promoted/assisted transformations. Reaction mechanisms have been proposed for the formation of 2, 3 and 4. Complex 4 could also be isolated by the reaction of InBr3 and pre-formed (py)(ph)CH(OH) in EtOH. The solid-state structures of 1, 3 and 4 were determined by single-crystal X-ray crystallography, while the identity of the salt 2 was confirmed by microanalyses and a variety of spectroscopic techniques, including ESI-MS spectra. In the indium(III) complexes, the metal ions are 6-coordinate with a distorted octahedral geometry. The halogeno groups (Cl-, Br-) in the three complexes are terminal. The (py)(ph)CO molecule behaves as a N,O-bidentate (1.11) ligand in 1 and 3. A terminal EtOH ligand completes the coordination sphere of InIII in 1. The alkoxo oxygen atoms of the two 2.21 (py)(ph)CH(O)- ligands doubly bridge the InIII centers in 4 creating a {InIII2(μ-OR)2}4+ core; a nitrogen atom of one reduced organic ligand, two bromo ions and one terminal EtOH molecule complete the 6-coordination at each metal centre. Complexes 1, 3 and 4 were characterised by IR and Raman spectroscopies, and the data were discussed in terms of their known solid-state structures. Molar conductivity data and 1H NMR spectra were used in an attempt to probe the behaviour of the complexes in DMSO. The to-date observed metal ion-assisted/promoted transformations of (py)(ph)CO are also discussed.
Collapse
Affiliation(s)
- Christina Stamou
- Department of Chemistry, University of Patras, 26504 Patras, Greece.
| | - Zoi G Lada
- Institute of Chemical Engineering Sciences (ICE-HT), Foundation for Research and Technology-Hellas (FORTH), P.O. Box 1414, Platani, 26504 Patras, Greece
| | - Christos T Chasapis
- NMR Facility, Instrumental Analysis Laboratory, School of Natural Sciences, University of Patras, 26504 Patras, Greece
| | | | - Pierre Dechambenoit
- Centre de Recherche Paul Pascal, UMR 5031, CNRS, University of Bordeaux, 33600 Pessac, France.
| | - Spyros P Perlepes
- Department of Chemistry, University of Patras, 26504 Patras, Greece. .,Institute of Chemical Engineering Sciences (ICE-HT), Foundation for Research and Technology-Hellas (FORTH), P.O. Box 1414, Platani, 26504 Patras, Greece
| |
Collapse
|
14
|
Polyzou CD, Gkolfi P, Chasapis CT, Bekiari V, Zianna A, Psomas G, Ondrej M, Tangoulis V. Stimuli-responsive spin crossover nanoparticles for drug delivery and DNA-binding studies. Dalton Trans 2022; 51:12427-12431. [PMID: 35920617 DOI: 10.1039/d2dt01509a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aminated silica hybrid, spin-crossover (SCO) nanoparticles (AmNPs) coupled with (S)-naproxen (NAP) were proposed for potential drug nanocarriers through drug release experiments at various pH values. DNA- and albumin-binding studies were also carried out using diverse techniques in order to investigate the interaction of the nanoparticles with calf-thymus DNA and serum albumins and to determine the corresponding binding constants.
Collapse
Affiliation(s)
- Christina D Polyzou
- Department of Chemistry, Laboratory of Inorganic Chemistry, University of Patras, 26504 Patras, Greece.
| | - Patroula Gkolfi
- Department of Chemistry, Laboratory of Inorganic Chemistry, University of Patras, 26504 Patras, Greece.
| | - Christos T Chasapis
- NMR Facility, Instrumental Analysis Laboratory, School of Natural Sciences, University of Patras, 26504 Patras, Greece
| | - Vlasoula Bekiari
- Department of Crop Science, University of Patras, 30200 Messolonghi, Greece
| | - Ariadni Zianna
- Laboratory of Inorganic Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, Thessaloniki GR-54124, Greece
| | - George Psomas
- Laboratory of Inorganic Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, Thessaloniki GR-54124, Greece
| | - Malina Ondrej
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Czech Republic
| | - Vassilis Tangoulis
- Department of Chemistry, Laboratory of Inorganic Chemistry, University of Patras, 26504 Patras, Greece.
| |
Collapse
|
15
|
Moore GJ, Ridgway H, Kelaidonis K, Chasapis CT, Ligielli I, Mavromoustakos T, Bojarska J, Matsoukas JM. Actions of Novel Angiotensin Receptor Blocking Drugs, Bisartans, Relevant for COVID-19 Therapy: Biased Agonism at Angiotensin Receptors and the Beneficial Effects of Neprilysin in the Renin Angiotensin System. Molecules 2022; 27:molecules27154854. [PMID: 35956801 PMCID: PMC9369639 DOI: 10.3390/molecules27154854] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/20/2022] [Accepted: 07/26/2022] [Indexed: 11/17/2022]
Abstract
Angiotensin receptor blockers (ARBs) used in the treatment of hypertension and potentially in SARS-CoV-2 infection exhibit inverse agonist effects at angiotensin AR1 receptors, suggesting the receptor may have evolved to accommodate naturally occurring angiotensin ‘antipeptides’. Screening of the human genome has identified a peptide (EGVYVHPV) encoded by mRNA, complementary to that encoding ANG II itself, which is an inverse agonist. Thus, opposite strands of DNA encode peptides with opposite effects at AR1 receptors. Agonism and inverse agonism at AR1 receptors can be explained by a receptor ‘switching’ between an activated state invoking receptor dimerization/G protein coupling and an inverse agonist state mediated by an alternative/second messenger that is slow to reverse. Both receptor states appear to be driven by the formation of the ANG II charge-relay system involving TyrOH-His/imidazole-Carboxylate (analogous to serine proteases). In this system, tyrosinate species formed are essential for activating AT1 and AT2 receptors. ANGII is also known to bind to the zinc-coordinated metalloprotease angiotensin converting enzyme 2 (ACE2) used by the COVID-19 virus to enter cells. Here we report in silico results demonstrating the binding of a new class of anionic biphenyl-tetrazole sartans (‘Bisartans’) to the active site zinc atom of the endopeptidase Neprilysin (NEP) involved in regulating hypertension, by modulating humoral levels of beneficial vasoactive peptides in the RAS such as vasodilator angiotensin (1–7). In vivo and modeling evidence further suggest Bisartans can inhibit ANG II-induced pulmonary edema and may be useful in combatting SARS-CoV-2 infection by inhibiting ACE2-mediated viral entry to cells.
Collapse
Affiliation(s)
- Graham J. Moore
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Pepmetics Inc., 772 Murphy Place, Victoria, BC V8Y 3H4, Canada
- Correspondence: (G.J.M.); (J.M.M.)
| | - Harry Ridgway
- Institute for Sustainable Industries and Liveable Cities, Victoria University, Melbourne, VIC 8001, Australia;
- AquaMem Consultants, Rodeo, New Mexico, NM 88056, USA
| | | | - Christos T. Chasapis
- NMR Facility, Instrumental Analysis Laboratory, School of Natural Sciences, University of Patras, 26504 Patras, Greece;
- Institute of Chemical Engineering Sciences, Foundation for Research and Technology, Hellas (FORTH/ICE-HT), 26504 Patras, Greece
| | - Irene Ligielli
- Department of Chemistry, National and Kapodistrian University of Athens, 15784 Athens, Greece; (I.L.); (T.M.)
| | - Thomas Mavromoustakos
- Department of Chemistry, National and Kapodistrian University of Athens, 15784 Athens, Greece; (I.L.); (T.M.)
| | - Joanna Bojarska
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland;
| | - John M. Matsoukas
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- NewDrug PC, Patras Science Park, 26504 Patras, Greece;
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia
- Correspondence: (G.J.M.); (J.M.M.)
| |
Collapse
|
16
|
Bjørklund G, Rahaman MS, Shanaida M, Lysiuk R, Oliynyk P, Lenchyk L, Chirumbolo S, Chasapis CT, Peana M. Natural Dietary Compounds in the Treatment of Arsenic Toxicity. Molecules 2022; 27:molecules27154871. [PMID: 35956821 PMCID: PMC9370003 DOI: 10.3390/molecules27154871] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/23/2022] [Accepted: 07/27/2022] [Indexed: 12/22/2022]
Abstract
Chronic exposure to arsenic (As) compounds leads to its accumulation in the body, with skin lesions and cancer being the most typical outcomes. Treating As-induced diseases continues to be challenging as there is no specific, safe, and efficacious therapeutic management. Therapeutic and preventive measures available to combat As toxicity refer to chelation therapy, antioxidant therapy, and the intake of natural dietary compounds. Although chelation therapy is the most commonly used method for detoxifying As, it has several side effects resulting in various toxicities such as hepatotoxicity, neurotoxicity, and other adverse consequences. Drugs of plant origin and natural dietary compounds show efficient and progressive relief from As-mediated toxicity without any particular side effects. These natural compounds have also been found to aid the elimination of As from the body and, therefore, can be more effective than conventional therapeutic agents in ameliorating As toxicity. This review provides an overview of the recently updated knowledge on treating As poisoning through natural dietary compounds. This updated information may serve as a basis for defining novel prophylactic and therapeutic formulations.
Collapse
Affiliation(s)
- Geir Bjørklund
- Council for Nutritional and Environmental Medicine, Toften 24, 8610 Mo i Rana, Norway
- Correspondence: (G.B.); (M.P.)
| | - Md. Shiblur Rahaman
- Department of Environmental and Preventive Medicine, Jichi Medical University School of Medicine, Shimotsuke 329-0498, Japan; or
- Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Mariia Shanaida
- Department of Pharmacognosy and Medical Botany, I. Horbachevsky Ternopil National Medical University, 46001 Ternopil, Ukraine;
| | - Roman Lysiuk
- Department of Pharmacognosy and Botany, Danylo Halytsky Lviv National Medical University, 79010 Lviv, Ukraine;
- CONEM Ukraine Life Science Research Group, Danylo Halytsky Lviv National Medical University, 79010 Lviv, Ukraine
| | - Petro Oliynyk
- Department of Disaster Medicine and Military Medicine, Danylo Halytsky Lviv National Medical University, 79010 Lviv, Ukraine;
| | - Larysa Lenchyk
- Department of Chemistry of Natural Compounds, National University of Pharmacy, 61002 Kharkiv, Ukraine;
- CONEM Ukraine Pharmacognosy and Natural Product Chemistry Research Group, National University of Pharmacy, 61002 Kharkiv, Ukraine
| | - Salvatore Chirumbolo
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy;
- CONEM Scientific Secretary, strada Le Grazie 9, 37134 Verona, Italy
| | - Christos T. Chasapis
- NMR Facility, Instrumental Analysis Laboratory, School of Natural Sciences, University of Patras, 265 04 Patras, Greece;
| | - Massimiliano Peana
- Department of Chemical, Physics, Mathematics and Natural Sciences, University of Sassari, Via Vienna 2, 07100 Sassari, Italy
- Correspondence: (G.B.); (M.P.)
| |
Collapse
|
17
|
Matsoukas JM, Gadanec LK, Zulli A, Apostolopoulos V, Kelaidonis K, Ligielli I, Moschovou K, Georgiou N, Plotas P, Chasapis CT, Moore G, Ridgway H, Mavromoustakos T. Diminazene Aceturate Reduces Angiotensin II Constriction and Interacts with the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus 2. Biomedicines 2022; 10:biomedicines10071731. [PMID: 35885036 PMCID: PMC9312513 DOI: 10.3390/biomedicines10071731] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/27/2022] [Accepted: 07/05/2022] [Indexed: 12/15/2022] Open
Abstract
Diminazene aceturate (DIZE) is a putative angiotensin-converting enzyme 2 (ACE2) activator and angiotensin type 1 receptor antagonist (AT1R). Its simple chemical structure possesses a negatively charged triazene segment that is homologous to the tetrazole of angiotensin receptor blockers (ARB), which explains its AT1R antagonistic activity. Additionally, the activation of ACE2 by DIZE converts the toxic octapeptide angiotensin II (AngII) to the heptapeptides angiotensin 1–7 and alamandine, which promote vasodilation and maintains homeostatic balance. Due to DIZE’s protective cardiovascular and pulmonary effects and its ability to target ACE2 (the predominant receptor utilized by severe acute respiratory syndrome coronavirus 2 to enter host cells), it is a promising treatment for coronavirus 2019 (COVID-19). To determine DIZE’s ability to inhibit AngII constriction, in vitro isometric tension analysis was conducted on rabbit iliac arteries incubated with DIZE or candesartan and constricted with cumulative doses of AngII. In silico docking and ligand interaction studies were performed to investigate potential interactions between DIZE and other ARBs with AT1R and the spike protein/ACE2 complex. DIZE, similar to the other ARBs investigated, was able to abolish vasoconstriction in response to AngII and exhibited a binding affinity for the spike protein/ACE2 complex (PDB 6LZ6). These results support the potential of DIZE as a treatment for COVID-19.
Collapse
Affiliation(s)
- John M. Matsoukas
- NewDrug PC, Patras Science Park, 26500 Patras, Greece;
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (L.K.G.); (A.Z.); (V.A.)
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Correspondence: (J.M.M.); (T.M.)
| | - Laura Kate Gadanec
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (L.K.G.); (A.Z.); (V.A.)
| | - Anthony Zulli
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (L.K.G.); (A.Z.); (V.A.)
| | - Vasso Apostolopoulos
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (L.K.G.); (A.Z.); (V.A.)
- Immunology Program, Australian Institute for Musculoskeletal Science, Melbourne, VIC 3021, Australia
| | | | - Irene Ligielli
- Department of Chemistry National and Kapodistrian, University of Athens, Zographou, 15784 Athens, Greece; (I.L.); (K.M.); (N.G.)
| | - Kalliopi Moschovou
- Department of Chemistry National and Kapodistrian, University of Athens, Zographou, 15784 Athens, Greece; (I.L.); (K.M.); (N.G.)
| | - Nikitas Georgiou
- Department of Chemistry National and Kapodistrian, University of Athens, Zographou, 15784 Athens, Greece; (I.L.); (K.M.); (N.G.)
| | - Panagiotis Plotas
- Laboratory of Primary Health Care, School of Health Rehabilitation Sciences, University of Patras, 26504 Patras, Greece;
| | - Christos T. Chasapis
- NMR Facility, Instrumental Analysis Laboratory, School of Natural Sciences, University of Patras, 26504 Patras, Greece;
- Institute of Chemical Engineering Sciences, Foundation for Research and Technology, Hellas (FORTH/ICE-HT), 26504 Patras, Greece
| | - Graham Moore
- Pepmetics Incorporated, 772 Murphy Pace, Victoria, BC V8Y 3H4, Canada;
| | - Harry Ridgway
- Institute for Sustainable Industries and Liveable Cities, Victoria University, Melbourne, VIC 8001, Australia;
- AquaMem Consultants, Rodeo, NM 88056, USA
| | - Thomas Mavromoustakos
- Department of Chemistry National and Kapodistrian, University of Athens, Zographou, 15784 Athens, Greece; (I.L.); (K.M.); (N.G.)
- Correspondence: (J.M.M.); (T.M.)
| |
Collapse
|
18
|
Ridgway H, Chasapis CT, Kelaidonis K, Ligielli I, Moore GJ, Gadanec LK, Zulli A, Apostolopoulos V, Mavromoustakos T, Matsoukas JM. Understanding the Driving Forces That Trigger Mutations in SARS-CoV-2: Mutational Energetics and the Role of Arginine Blockers in COVID-19 Therapy. Viruses 2022; 14:v14051029. [PMID: 35632769 PMCID: PMC9143829 DOI: 10.3390/v14051029] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/20/2022] [Accepted: 04/24/2022] [Indexed: 12/27/2022] Open
Abstract
SARS-CoV-2 is a global challenge due to its ability to mutate into variants that spread more rapidly than the wild-type virus. Because the molecular biology of this virus has been studied in such great detail, it represents an archetypal paradigm for research into new antiviral drug therapies. The rapid evolution of SARS-CoV-2 in the human population is driven, in part, by mutations in the receptor-binding domain (RBD) of the spike (S-) protein, some of which enable tighter binding to angiotensin-converting enzyme (ACE2). More stable RBD-ACE2 association is coupled with accelerated hydrolysis of furin and 3CLpro cleavage sites that augment infection. Non-RBD and non-interfacial mutations assist the S-protein in adopting thermodynamically favorable conformations for stronger binding. The driving forces of key mutations for Alpha, Beta, Gamma, Delta, Kappa, Lambda and Omicron variants, which stabilize the RBD-ACE2 complex, are investigated by free-energy computational approaches, as well as equilibrium and steered molecular dynamic simulations. Considered also are the structural hydropathy traits of the residues in the interface between SARS-CoV-2 RBD and ACE2 protein. Salt bridges and π-π interactions are critical forces that create stronger complexes between the RBD and ACE2. The trend of mutations is the replacement of non-polar hydrophobic interactions with polar hydrophilic interactions, which enhance binding of RBD with ACE2. However, this is not always the case, as conformational landscapes also contribute to a stronger binding. Arginine, the most polar and hydrophilic among the natural amino acids, is the most aggressive mutant amino acid for stronger binding. Arginine blockers, such as traditional sartans that bear anionic tetrazoles and carboxylates, may be ideal candidate drugs for retarding viral infection by weakening S-protein RBD binding to ACE2 and discouraging hydrolysis of cleavage sites. Based on our computational results it is suggested that a new generation of “supersartans”, called “bisartans”, bearing two anionic biphenyl-tetrazole pharmacophores, are superior to carboxylates in terms of their interactions with viral targets, suggesting their potential as drugs in the treatment of COVID-19. In Brief: This in silico study reviews our understanding of molecular driving forces that trigger mutations in the SARS-CoV-2 virus. It also reports further studies on a new class of “supersartans” referred to herein as “bisartans”, bearing two anionic biphenyltetrazole moieties that show potential in models for blocking critical amino acids of mutants, such as arginine, in the Delta variant. Bisartans may also act at other targets essential for viral infection and replication (i.e., ACE2, furin cleavage site and 3CLpro), rendering them potential new drugs for additional experimentation and translation to human clinical trials.
Collapse
Affiliation(s)
- Harry Ridgway
- AquaMem Consultants, Rodeo, New Mexico, NM 88056, USA
- Institute for Sustainable Industries and Liveable Cities, Victoria University, Melbourne, VIC 3030, Australia
- Correspondence: (H.R.); (J.M.M.)
| | - Christos T. Chasapis
- NMR Facility, Instrumental Analysis Laboratory, School of Natural Sciences, University of Patras, 26504 Patras, Greece;
- Institute of Chemical Engineering Sciences, Foundation for Research and Technology, Hellas (FORTH/ICE-HT), 26504 Patras, Greece
| | | | - Irene Ligielli
- Department of Chemistry, National and Kapodistrian University of Athens, 15784 Athens, Greece; (I.L.); (T.M.)
| | - Graham J. Moore
- Pepmetics Inc., 772 Murphy Place, Victoria, BC V6Y 3H4, Canada;
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Laura Kate Gadanec
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (L.K.G.); (A.Z.); (V.A.)
| | - Anthony Zulli
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (L.K.G.); (A.Z.); (V.A.)
| | - Vasso Apostolopoulos
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (L.K.G.); (A.Z.); (V.A.)
- Immunology Program, Australian Institute for Musculoskeletal Science (AIMSS), Melbourne, VIC 3021, Australia
| | - Thomas Mavromoustakos
- Department of Chemistry, National and Kapodistrian University of Athens, 15784 Athens, Greece; (I.L.); (T.M.)
| | - John M. Matsoukas
- NewDrug PC, Patras Science Park, 26504 Patras, Greece;
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (L.K.G.); (A.Z.); (V.A.)
- Correspondence: (H.R.); (J.M.M.)
| |
Collapse
|
19
|
Chasapis CT, Kelaidonis K, Ridgway H, Apostolopoulos V, Matsoukas JM. The Human Myelin Proteome and Sub-Metalloproteome Interaction Map: Relevance to Myelin-Related Neurological Diseases. Brain Sci 2022; 12:brainsci12040434. [PMID: 35447967 PMCID: PMC9029312 DOI: 10.3390/brainsci12040434] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Received: 03/11/2022] [Accepted: 03/22/2022] [Indexed: 02/01/2023] Open
Abstract
Myelin in humans is composed of about 80% lipids and 20% protein. Initially, myelin protein composition was considered low, but various recent proteome analyses have identified additional myelin proteins. Although, the myelin proteome is qualitatively and quantitatively identified through complementary proteomic approaches, the corresponding Protein–Protein Interaction (PPI) network of myelin is not yet available. In the present work, the PPI network was constructed based on available experimentally supported protein interactions of myelin in PPI databases. The network comprised 2017 PPIs between 567 myelin proteins. Interestingly, structure-based in silico analysis revealed that 20% of the myelin proteins that are interconnected in the proposed PPI network are metal-binding proteins/enzymes that construct the main sub-PPI network of myelin proteome. Finally, the PPI networks of the myelin proteome and sub-metalloproteome were analyzed ontologically to identify the biochemical processes of the myelin proteins and the interconnectivity of myelin-associated diseases in the interactomes. The presented PPI dataset could provide a useful resource to the scientific community to further our understanding of human myelin biology and serve as a basis for future studies of myelin-related neurological diseases and particular autoimmune diseases such as multiple sclerosis where myelin epitopes are implicated.
Collapse
Affiliation(s)
- Christos T. Chasapis
- NMR Facility, Instrumental Analysis Laboratory, School of Natural Sciences, University of Patras, 26504 Patras, Greece
- Institute of Chemical Engineering Sciences, Foundation for Research and Technology, Hellas (FORTH/ICE-HT), 26504 Patras, Greece
- Correspondence: (C.T.C.); (J.M.M.)
| | | | - Harry Ridgway
- Institute for Sustainable Industries and Liveable Cities, Victoria University, Melbourne, VIC 3030, Australia;
- AquaMem Scientific Consultants, Rodeo, NM 88056, USA
| | - Vasso Apostolopoulos
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia;
- Immunology Program, Australian Institute for Musculoskeletal Science (AIMSS), Melbourne, VIC 3021, Australia
| | - John M. Matsoukas
- NewDrug PC, Patras Science Park, 26504 Patras, Greece;
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia;
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Correspondence: (C.T.C.); (J.M.M.)
| |
Collapse
|
20
|
Routzomani A, Lada ZG, Angelidou V, P. Raptopoulou C, Psycharis V, Konidaris KF, Chasapis CT, Perlepes SP. Confirming the Molecular Basis of the Solvent Extraction of Cadmium(II) Using 2-Pyridyl Oximes through a Synthetic Inorganic Chemistry Approach and a Proposal for More Efficient Extractants. Molecules 2022; 27:molecules27051619. [PMID: 35268720 PMCID: PMC8911866 DOI: 10.3390/molecules27051619] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/10/2022] Open
Abstract
The present work describes the reactions of CdI2 with 2-pyridyl aldoxime (2paoH), 3-pyridyl aldoxime (3paoH), 4-pyridyl aldoxime (4paoH), 2-6-diacetylpyridine dioxime (dapdoH2) and 2,6-pyridyl diamidoxime (LH4). The primary goal was to contribute to understanding the molecular basis of the very good liquid extraction ability of 2-pyridyl ketoximes with long aliphatic chains towards toxic Cd(II) and the inability of their 4-pyridyl isomers for this extraction. Our systematic investigation provided access to coordination complexes [CdI2(2paoH)2] (1), {[CdI2(3paoH)2]}n (2), {[CdI2(4paoH)2]}n (3) and [CdI2(dapdoH2)] (4). The reaction of CdI2 and LH4 in EtOH resulted in a Cd(II)-involving reaction of the bis(amidoxime) and isolation of [CdI2(L'H2)] (5), where L'H2 is the new ligand 2,6-bis(ethoxy)pyridine diimine. A mechanism of this transformation has been proposed. The structures of 1, 2, 3, 4·2EtOH and 5 were determined by single-crystal X-ray crystallography. The complexes have been characterized by FT-IR and FT-Raman spectra in the solid state and the data are discussed in terms of structural features. The stability of the complexes in DMSO was investigated by 1H NMR spectroscopy. Our studies confirm that the excellent extraction ability of 2-pyridyl ketoximes is due to the chelating nature of the extractants leading to thermodynamically stable Cd(II) complexes. The monodentate coordination of 4-pyridyl ketoximes (as confirmed in our model complexes with 4paoH and 3paoH) seems to be responsible for their poor performance as extractants.
Collapse
Affiliation(s)
- Anastasia Routzomani
- Department of Chemistry, University of Patras, 265 04 Patras, Greece; (A.R.); (Z.G.L.); (V.A.)
| | - Zoi G. Lada
- Department of Chemistry, University of Patras, 265 04 Patras, Greece; (A.R.); (Z.G.L.); (V.A.)
- Institute of Chemical Engineering Sciences (ICE-HT), Foundation for Research and Technology-Hellas (FORTH), Platani, P.O. Box 1414, 265 04 Patras, Greece
| | - Varvara Angelidou
- Department of Chemistry, University of Patras, 265 04 Patras, Greece; (A.R.); (Z.G.L.); (V.A.)
| | - Catherine P. Raptopoulou
- Institute of Nanoscience and Nanotechnology, NCSR “Demokritos”, Aghia Paraskevi, Attikis, 153 10 Athens, Greece;
| | - Vassilis Psycharis
- Institute of Nanoscience and Nanotechnology, NCSR “Demokritos”, Aghia Paraskevi, Attikis, 153 10 Athens, Greece;
- Correspondence: (V.P.); (K.F.K.); (C.T.C.); (S.P.P.); Tel.: +30-210-650-3346 (V.P.); +39-031-238-6472 (K.F.K.); +30-261-0 99-6261 (C.T.C.); +30-261-099-6730 (S.P.P.)
| | - Konstantis F. Konidaris
- Department of Science and High Technology and INSTM, University of Insubria, 22 100 Como, Italy
- Correspondence: (V.P.); (K.F.K.); (C.T.C.); (S.P.P.); Tel.: +30-210-650-3346 (V.P.); +39-031-238-6472 (K.F.K.); +30-261-0 99-6261 (C.T.C.); +30-261-099-6730 (S.P.P.)
| | - Christos T. Chasapis
- Institute of Chemical Engineering Sciences (ICE-HT), Foundation for Research and Technology-Hellas (FORTH), Platani, P.O. Box 1414, 265 04 Patras, Greece
- NMR Facility, Instrumental Analysis Laboratory, School of Natural Sciences, University of Patras, 265 04 Patras, Greece
- Correspondence: (V.P.); (K.F.K.); (C.T.C.); (S.P.P.); Tel.: +30-210-650-3346 (V.P.); +39-031-238-6472 (K.F.K.); +30-261-0 99-6261 (C.T.C.); +30-261-099-6730 (S.P.P.)
| | - Spyros P. Perlepes
- Department of Chemistry, University of Patras, 265 04 Patras, Greece; (A.R.); (Z.G.L.); (V.A.)
- Institute of Chemical Engineering Sciences (ICE-HT), Foundation for Research and Technology-Hellas (FORTH), Platani, P.O. Box 1414, 265 04 Patras, Greece
- Correspondence: (V.P.); (K.F.K.); (C.T.C.); (S.P.P.); Tel.: +30-210-650-3346 (V.P.); +39-031-238-6472 (K.F.K.); +30-261-0 99-6261 (C.T.C.); +30-261-099-6730 (S.P.P.)
| |
Collapse
|
21
|
Kakoulidou C, Chasapis CT, Hatzidimitriou AG, Fylaktakidou KC, Psomas G. Transition metal( ii) complexes of halogenated derivatives of ( E)-4-(2-(pyridin-2-ylmethylene)hydrazinyl)quinazoline: structure, antioxidant activity, DNA-binding DNA photocleavage, interaction with albumin and in silico studies. Dalton Trans 2022; 51:16688-16705. [DOI: 10.1039/d2dt02622h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Six transition metal(ii) complexes with halogenated quinazoline derivatives as ligands were characterized and evaluated for interaction with calf-thymus DNA, photocleavage of plasmid-DNA, affinity for bovine serum albumin, and antioxidant activity.
Collapse
Affiliation(s)
- Chrisoula Kakoulidou
- Department of General and Inorganic Chemistry, Faculty of Chemistry, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
| | - Christos T. Chasapis
- NMR Facility, Instrumental Analysis Laboratory, School of Natural Sciences, University of Patras, Greece
| | - Antonios G. Hatzidimitriou
- Department of General and Inorganic Chemistry, Faculty of Chemistry, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
| | - Konstantina C. Fylaktakidou
- Laboratory of Organic Chemistry, Faculty of Chemistry, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
| | - George Psomas
- Department of General and Inorganic Chemistry, Faculty of Chemistry, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
| |
Collapse
|
22
|
Oulas A, Zachariou M, Chasapis CT, Tomazou M, Ijaz UZ, Schmartz GP, Spyrou GM, Vlamis-Gardikas A. Putative Antimicrobial Peptides Within Bacterial Proteomes Affect Bacterial Predominance: A Network Analysis Perspective. Front Microbiol 2021; 12:752674. [PMID: 34867874 PMCID: PMC8636115 DOI: 10.3389/fmicb.2021.752674] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/11/2021] [Indexed: 11/13/2022] Open
Abstract
The predominance of bacterial taxa in the gut, was examined in view of the putative antimicrobial peptide sequences (AMPs) within their proteomes. The working assumption was that compatible bacteria would share homology and thus immunity to their putative AMPs, while competing taxa would have dissimilarities in their proteome-hidden AMPs. A network-based method ("Bacterial Wars") was developed to handle sequence similarities of predicted AMPs among UniProt-derived protein sequences from different bacterial taxa, while a resulting parameter ("Die" score) suggested which taxa would prevail in a defined microbiome. T he working hypothesis was examined by correlating the calculated Die scores, to the abundance of bacterial taxa from gut microbiomes from different states of health and disease. Eleven publicly available 16S rRNA datasets and a dataset from a full shotgun metagenomics served for the analysis. The overall conclusion was that AMPs encrypted within bacterial proteomes affected the predominance of bacterial taxa in chemospheres.
Collapse
Affiliation(s)
- Anastasis Oulas
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,The Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Margarita Zachariou
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,The Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Christos T Chasapis
- NMR Center, Instrumental Analysis Laboratory, School of Natural Sciences, University of Patras, Patras, Greece
| | - Marios Tomazou
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,The Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Umer Z Ijaz
- School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | | | - George M Spyrou
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,The Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Alexios Vlamis-Gardikas
- Division of Organic Chemistry, Biochemistry and Natural Products, Department of Chemistry, University of Patras, Patras, Greece
| |
Collapse
|
23
|
Matsoukas JM, Ligielli I, Chasapis CT, Kelaidonis K, Apostolopoulos V, Mavromoustakos T. Novel Approaches in the Immunotherapy of Multiple Sclerosis: Cyclization of Myelin Epitope Peptides and Conjugation with Mannan. Brain Sci 2021; 11:1583. [PMID: 34942885 PMCID: PMC8699547 DOI: 10.3390/brainsci11121583] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 11/23/2021] [Accepted: 11/26/2021] [Indexed: 01/07/2023] Open
Abstract
Multiple Sclerosis (MS) is a serious autoimmune disease. The patient in an advanced state of the disease has restrained mobility and remains handicapped. It is therefore understandable that there is a great need for novel drugs and vaccines for the treatment of MS. Herein we summarise two major approaches applied for the treatment of the disease using peptide molecules alone or conjugated with mannan. The first approach focuses on selective myelin epitope peptide or peptide mimetic therapy alone or conjugated with mannan, and the second on immune-therapy by preventing or controlling disease through the release of appropriate cytokines. In both approaches the use of cyclic peptides offers the advantage of increased stability from proteolytic enzymes. In these approaches, the synthesis of myelin epitope peptides conjugated to mannan is of particular interest as this was found to protect mice against experimental autoimmune encephalomyelitis, an animal model of MS, in prophylactic and therapeutic protocols. Protection was peptide-specific and associated with reduced antigen-specific T cell proliferation. The aim of the studies of these peptide epitope analogs is to understand their molecular basis of interactions with human autoimmune T-cell receptor and a MS-associated human leucocyte antigen (HLA)-DR2b. This knowledge will lead the rational design to new beneficial non-peptide mimetic analogs for the treatment of MS. Some issues of the use of nanotechnology will also be addressed as a future trend to tackle the disease. We highlight novel immunomodulation and vaccine-based research against MS based on myelin epitope peptides and strategies developed in our laboratories.
Collapse
Affiliation(s)
- John M Matsoukas
- NewDrug PC, Patras Science Park, 265 04 Platani, Greece
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Irene Ligielli
- Department of Chemistry, University of Athens, 157 72 Athens, Greece
| | - Christos T Chasapis
- NMR Facility, Instrumental Analysis Laboratory, Institute of Chemical, School of Natural Sciences, University of Patras, 265 04 Patras, Greece
- Engineering Sciences, Foundation for Research and Technology, Hellas (FORTH/ICE-HT), 265 04 Patra, Greece
| | | | - Vasso Apostolopoulos
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia
- Australian Institute for Musculoskeletal Science (AIMSS), Immunology Program, Melbourne, VIC 3021, Australia
| | | |
Collapse
|
24
|
Gkolfi P, Tsivaka D, Tsougos I, Vassiou K, Malina O, Polaskova M, Polyzou CD, Chasapis CT, Tangoulis V. A facile approach to prepare silica hybrid, spin-crossover water-soluble nanoparticles as potential candidates for thermally responsive MRI agents. Dalton Trans 2021; 50:13227-13231. [PMID: 34546269 DOI: 10.1039/d1dt02479e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A reverse micelle method was used for the synthesis of water-soluble silica hybrid, spin-crossover (SCO) nanoparticles (NPs). MRI experiments provided temperature dependent T2 values, indicating their potential use as smart MRI agents, while lyophilization of NP dispersions in water yielded powders with a preserved but modified thermal hysteretic magnetic profile.
Collapse
Affiliation(s)
- Patroula Gkolfi
- Department of Chemistry, Laboratory of Inorganic Chemistry, University of Patras, 26504, Patras, Greece.
| | - Dimitra Tsivaka
- Department of Medical Physics, University Hospital of Larissa, University of Thessaly, Biopolis, GR-41110 Larissa, Greece.
| | - Ioannis Tsougos
- Department of Medical Physics, University Hospital of Larissa, University of Thessaly, Biopolis, GR-41110 Larissa, Greece.
| | - Katerina Vassiou
- Department of Radiology, University Hospital of Larissa, University of Thessaly, Biopolis, GR-41110 Larissa, Greece
| | - Ondřej Malina
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Czech Republic.
| | - Michaela Polaskova
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Czech Republic. .,Department of Experimental Physics, Faculty of Science, Palacký University Olomouc, 17. Listopadu 1192/12, 771 46 Olomouc, Czech Republic
| | - Christina D Polyzou
- Department of Chemistry, Laboratory of Inorganic Chemistry, University of Patras, 26504, Patras, Greece.
| | - Christos T Chasapis
- NMR Facility, Instrumental Analysis Laboratory, School of Natural Sciences, University of Patras, 26504, Patras, Greece
| | - Vassilis Tangoulis
- Department of Chemistry, Laboratory of Inorganic Chemistry, University of Patras, 26504, Patras, Greece.
| |
Collapse
|
25
|
Perontsis S, Chasapis CT, Hatzidimitriou AG, Psomas G. Synthesis, characterization and (in vitro and in silico) biological activity of a series of dioxouranium(VI) complexes with non-steroidal anti-inflammatory drugs. J Inorg Biochem 2021; 223:111534. [PMID: 34273715 DOI: 10.1016/j.jinorgbio.2021.111534] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/17/2021] [Accepted: 07/05/2021] [Indexed: 10/20/2022]
Abstract
The reaction of the dioxouranium(VI) ion with a series of non-steroidal anti-inflammatory drugs (NSAIDs), namely mefenamic acid, indomethacin, diclofenac, diflunisal and tolfenamic acid, as ligands in the absence or presence of diverse N,N'-donors (1,10-phenanthroline,2,2'-bipyridine or 2,2'-bipyridylamine) as co-ligands led to the formation of ten complexes bearing the formulas [UO2(NSAID-O,O')2(O-donor)2] or [UO2(NSAID-O,O')2(N,N'-donor)], respectively. The complexes were characterized with diverse spectroscopic techniques and the crystal structures of three complexes were determined by single-crystal X-ray crystallography. The biological profile of the resultant complexes was assessed in vitro and in silico. The in vitro studies include their antioxidant properties (ability to scavenge free radicals 1,1-diphenyl-picrylhydrazyl and 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) and to reduce H2O2), their interaction with DNA (linear calf-thymus DNA or supercoiled circular pBR322 plasmid DNA) and their affinity for serum albumins (bovine and human serum albumin). In silico molecular docking calculations were performed regarding the behavior of the complexes towards DNA and their binding to both albumins.
Collapse
Affiliation(s)
- Spyros Perontsis
- Department of General and Inorganic Chemistry, Faculty of Chemistry, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
| | - Christos T Chasapis
- NMR Facility, Instrumental Analysis Laboratory, School of Natural Sciences, University of Patras, Greece
| | - Antonios G Hatzidimitriou
- Department of General and Inorganic Chemistry, Faculty of Chemistry, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
| | - George Psomas
- Department of General and Inorganic Chemistry, Faculty of Chemistry, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece.
| |
Collapse
|
26
|
Butnariu M, Peana M, Sarac I, Chirumbolo S, Tzoupis H, Chasapis CT, Bjørklund G. Analytical and in silico study of the inclusion complexes between tropane alkaloids atropine and scopolamine with cyclodextrins. Chem Pap 2021. [DOI: 10.1007/s11696-021-01742-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
AbstractDatura stramonium L. (Solanaceae) possesses a rich tropane alkaloids (TAs) spectrum. The plant contains, in particular, the allelopathic compounds scopolamine and atropine, which are poorly soluble in water, thus limiting their use in agrochemical formulations as biocidal and deterrent agents against herbivore insects. The efficacy of the hydrophobic TAs extracts could be increased with the improvement of their dissolution/leaching properties. This is important for improving screening and test performance and for elucidating the activity of environmentally friendly agricultural approaches, with new perspectives for the production and use of those biodegradable insecticidal products. The present study explores the aspects of atropine and scopolamine complexation with cyclodextrin (CDs) through FT-IR and UV–Vis spectroscopies. In addition, the structures of the inclusion complex of atropine, scopolamine and β-CD have been investigated by molecular modeling techniques. The results obtained indicate that β-CDs are a promising carriers for improving the properties of TAs, therefore increasing their application potential in agrochemical formulations.
Graphic abstract
Collapse
|
27
|
Spiliopoulou M, Valmas A, Triandafillidis DP, Fili S, Christopoulou M, Filopoulou AJ, Piskopou A, Papadea P, Fitch AN, Beckers D, Degen T, Gozzo F, Morin M, Reinle-Schmitt ML, Karavassili F, Rosmaraki E, Chasapis CT, Margiolaki I. High-throughput macromolecular polymorph screening via an NMR and X-ray powder diffraction synergistic approach: the case of human insulin co-crystallized with resorcinol derivatives. J Appl Crystallogr 2021. [DOI: 10.1107/s160057672100426x] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Regular injections of insulin provide life-saving benefits to millions of diabetics. Apart from native insulin and insulin analogue formulations, microcrystalline insulin suspensions are also commercially available. The onset of action of the currently available basal insulins relies on the slow dissociation of insulin hexamers in the subcutaneous space due to the strong binding of small organic ligands. With the aim of identifying insulin–ligand complexes with enhanced pharmacokinetic and pharmacodynamic profiles, the binding affinity of two resorcinol-based molecules (4-chlororesorcinol and 4-bromoresorcinol) and the structural characteristics of insulin upon co-crystallization with them were investigated in the present study. `In solution' measurements were performed via saturation transfer difference (STD) NMR. Co-crystallization upon pH variation resulted in the production of polycrystalline precipitates, whose structural characteristics (i.e. unit-cell symmetry and dimension) were assessed. In both cases, different polymorphs (four and three, respectively) of monoclinic symmetry (P21 and C2 space groups) were identified via X-ray powder diffraction. The results demonstrate the efficiency of a new approach that combines spectroscopy and diffraction techniques and provides an innovative alternative for high-throughput examination of insulin and other therapeutic proteins.
Collapse
|
28
|
Lagoumintzis G, Chasapis CT, Alexandris N, Kouretas D, Tzartos S, Eliopoulos E, Farsalinos K, Poulas K. Nicotinic cholinergic system and COVID-19: In silico identification of interactions between α7 nicotinic acetylcholine receptor and the cryptic epitopes of SARS-Co-V and SARS-CoV-2 Spike glycoproteins. Food Chem Toxicol 2021; 149:112009. [PMID: 33503469 PMCID: PMC7830272 DOI: 10.1016/j.fct.2021.112009] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 10/30/2020] [Revised: 01/14/2021] [Accepted: 01/18/2021] [Indexed: 12/17/2022]
Abstract
SARS-CoV-2 is the coronavirus that originated in Wuhan in December 2019 and has spread globally. Studies have shown that smokers are less likely to be diagnosed with or be hospitalized for COVID-19 but, once hospitalized, have higher odds for an adverse outcome. We have previously presented the potential interaction between SARS-CoV-2 Spike glycoprotein and nicotinic acetylcholine receptors (nAChRs), due to a "toxin-like" epitope on the Spike glycoprotein, with homology to a sequence of a snake venom toxin. This epitope coincides with the well-described cryptic epitope for the human anti-SARS-CoV antibody CR3022. In this study, we present the molecular complexes of both SARS-CoV and SARS-CoV-2 Spike glycoproteins, at their open or closed conformations, with the model of the human α7 nAChR. We found that all studied protein complexes' interface involves a large part of the "toxin-like" sequences of SARS-CoV and SARS-CoV-2 Spike glycoproteins and toxin binding site of human α7 nAChR. Our findings provide further support to the hypothesis about the protective role of nicotine and other cholinergic agonists. The potential therapeutic role of CR3022 and other similar monoclonal antibodies with increased affinity for SARS-CoV-2 Spike glycoprotein against the clinical effects originating from the dysregulated cholinergic pathway should be further explored.
Collapse
Affiliation(s)
- George Lagoumintzis
- Laboratory of Molecular Biology and Immunology, Department of Pharmacy, University of Patras, Panepistimiopolis, 26500, Rio-Patras, Greece
| | - Christos T Chasapis
- Laboratory of Molecular Biology and Immunology, Department of Pharmacy, University of Patras, Panepistimiopolis, 26500, Rio-Patras, Greece
| | - Nikolaos Alexandris
- Laboratory of Molecular Biology and Immunology, Department of Pharmacy, University of Patras, Panepistimiopolis, 26500, Rio-Patras, Greece
| | - Dimitrios Kouretas
- Department of Biochemistry and Biotechnology, Faculty of Animal Physiology -Toxicology, University of Thessaly, Larissa, Greece
| | - Socrates Tzartos
- Laboratory of Molecular Biology and Immunology, Department of Pharmacy, University of Patras, Panepistimiopolis, 26500, Rio-Patras, Greece; Tzartos NeuroDiagnostics, 3, Eslin Street, Athens, 115 23, Greece
| | - Elias Eliopoulos
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece.
| | - Konstantinos Farsalinos
- Laboratory of Molecular Biology and Immunology, Department of Pharmacy, University of Patras, Panepistimiopolis, 26500, Rio-Patras, Greece.
| | - Konstantinos Poulas
- Laboratory of Molecular Biology and Immunology, Department of Pharmacy, University of Patras, Panepistimiopolis, 26500, Rio-Patras, Greece.
| |
Collapse
|
29
|
Alexandris N, Lagoumintzis G, Chasapis CT, Leonidas DD, Papadopoulos GE, Tzartos SJ, Tsatsakis A, Eliopoulos E, Poulas K, Farsalinos K. Nicotinic cholinergic system and COVID-19: In silico evaluation of nicotinic acetylcholine receptor agonists as potential therapeutic interventions. Toxicol Rep 2020; 8:73-83. [PMID: 33425684 PMCID: PMC7776751 DOI: 10.1016/j.toxrep.2020.12.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/01/2020] [Accepted: 12/14/2020] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 infection was announced as a pandemic in March 2020. Since then, several scientists have focused on the low prevalence of smokers among hospitalized COVID-19 patients. These findings led to our hypothesis that the Nicotinic Cholinergic System (NCS) plays a crucial role in the manifestation of COVID-19 and its severe symptoms. Molecular modeling revealed that the SARS-CoV-2 Spike glycoprotein might bind to nicotinic acetylcholine receptors (nAChRs) through a cryptic epitope homologous to snake toxins, substrates well documented and known for their affinity to the nAChRs. This binding model could provide logical explanations for the acute inflammatory disorder in patients with COVID-19, which may be linked to severe dysregulation of NCS. In this study, we present a series of complexes with cholinergic agonists that can potentially prevent SARS-CoV-2 Spike glycoprotein from binding to nAChRs, avoiding dysregulation of the NCS and moderating the symptoms and clinical manifestations of COVID-19. If our hypothesis is verified by in vitro and in vivo studies, repurposing agents currently approved for smoking cessation and neurological conditions could provide the scientific community with a therapeutic option in severe COVID-19.
Collapse
Key Words
- ACh, Acetylcholine
- AChBP, Acetylcholine-binding protein
- ARDS, acute respiratory distress syndrome
- BLAST, Basic Local Alignment Search Tool
- CHARMM, Chemistry at Harvard Macromolecular Mechanics
- CNS, Central Nervous System
- COVID-19
- Cholinergic agonists
- CoV, coronavirus
- DCD, single precision binary FORTRAN
- ECD, extracellular domain
- HADDOCK, High Ambiguity Driven protein-protein DOCKing
- HMGB1, High-mobility group protein 1
- IL, Interleukin
- Jak2, Janus kinases 2
- LBD, Ligand Binding Domain
- MD, Molecular Dynamics
- MDS, Molecular Dynamics Simulations
- MERS, Middle East Respiratory Syndrome
- NAMD, Nanoscale Molecular Dynamics
- NCBI, National Center for Biotechnology Information
- NCS, Nicotinic Cholinergic System
- NF-kB, nuclear factor kappa-light-chain-enhancer of activated B cells
- NPT, constant number, pressure, energy
- NVT, constant number, volume, energy
- Nicotinic acetylcholine receptors
- PDB, Protein Data Bank
- PME, Particle Mesh Ewald
- PRODIGY, PROtein binDIng enerGY prediction
- PyMOL, Python Molecule
- RBD, Receptor Binding Domain
- RMSD, Root-mean-square deviation
- SARS, Severe Acute Respiratory Syndrome
- SARS-CoV-2
- SARS-CoV-2 S1, SARS - 2 Spike Subunit 1 protein
- STAT3, signal transducer and activator of transcription 3
- STD NMR, Saturation Transfer Difference Nuclear Magnetic Resonance
- Spike glycoprotein
- TNF, Tumor Necrosis Factor
- VMD, Visual Molecular Dynamics
- lig, ligand
- nAChRs, nicotinic acetylcholine receptors
Collapse
Affiliation(s)
- Nikolaos Alexandris
- Laboratory of Molecular Biology and Immunology, Department of Pharmacy, University of Patras, 26500, Rio-Patras, Greece
| | - George Lagoumintzis
- Laboratory of Molecular Biology and Immunology, Department of Pharmacy, University of Patras, 26500, Rio-Patras, Greece
- Institute of Research and Innovation - IRIS, Patras Science Park SA, 26500 Patras, Greece
| | - Christos T. Chasapis
- Laboratory of Molecular Biology and Immunology, Department of Pharmacy, University of Patras, 26500, Rio-Patras, Greece
| | - Demetres D. Leonidas
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Georgios E. Papadopoulos
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | | | | | - Elias Eliopoulos
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Konstantinos Poulas
- Laboratory of Molecular Biology and Immunology, Department of Pharmacy, University of Patras, 26500, Rio-Patras, Greece
- Institute of Research and Innovation - IRIS, Patras Science Park SA, 26500 Patras, Greece
| | - Konstantinos Farsalinos
- Laboratory of Molecular Biology and Immunology, Department of Pharmacy, University of Patras, 26500, Rio-Patras, Greece
| |
Collapse
|
30
|
Mintis DG, Chasapi A, Poulas K, Lagoumintzis G, Chasapis CT. Assessing the Direct Binding of Ark-Like E3 RING Ligases to Ubiquitin and Its Implication on Their Protein Interaction Network. Molecules 2020; 25:molecules25204787. [PMID: 33086510 PMCID: PMC7594095 DOI: 10.3390/molecules25204787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 09/09/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 11/16/2022] Open
Abstract
The ubiquitin pathway required for most proteins’ targeted degradation involves three classes of enzymes: E1-activating enzyme, E2-conjugating enzyme, and E3-ligases. The human Ark2C is the single known E3 ligase that adopts an alternative, Ub-dependent mechanism for the activation of Ub transfer in the pathway. Its RING domain binds both E2-Ub and free Ub with high affinity, resulting in a catalytic active UbR-RING-E2-UbD complex formation. We examined potential changes in the conformational plasticity of the Ark2C RING domain and its ligands in their complexed form within the ubiquitin pathway through molecular dynamics (MD). Three molecular mechanics force fields compared to previous NMR relaxation studies of RING domain of Arkadia were used for effective and accurate assessment of MDs. Our results suggest the Ark2C Ub-RING docking site has a substantial impact on maintaining the conformational rigidity of E2-E3 assembly, necessary for the E3’s catalytic activity. In the UbR-RING-E2-UbD catalytic complex, the UbR molecule was found to have greater mobility than the other Ub, bound to E2. Furthermore, network-based bioinformatics helped us identify E3 RING ligase candidates which potentially exhibit similar structural modules as Ark2C, along with predicted substrates targeted by the Ub-binding RING Ark2C. Our findings could trigger a further exploration of related unrevealed functions of various other E3 RING ligases.
Collapse
Affiliation(s)
- Dimitris G. Mintis
- Laboratory of Statistical Thermodynamics and Macromolecules, Department of Chemical Engineering, University of Patras & FORTH/ICE-HT, 26504 Patras, Greece;
| | - Anastasia Chasapi
- Biological Computation & Process Lab, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, 57001 Thessaloniki, Greece;
| | - Konstantinos Poulas
- Laboratory of Molecular Biology and Immunology, Department of Pharmacy, University of Patras, 26504 Patras, Greece;
- Institute of Research and Innovation-IRIS, Patras Science Park SA, Stadiou, Platani, Rio, 26504 Patras, Greece
| | - George Lagoumintzis
- Laboratory of Molecular Biology and Immunology, Department of Pharmacy, University of Patras, 26504 Patras, Greece;
- Institute of Research and Innovation-IRIS, Patras Science Park SA, Stadiou, Platani, Rio, 26504 Patras, Greece
- Correspondence: (G.L.); (C.T.C.); Tel.: +30-2610-996-312 (G.L.); +30-2610-996-261 (C.T.C.)
| | - Christos T. Chasapis
- NMR Center, Instrumental Analysis Laboratory, School of Natural Sciences, University of Patras, 26504 Patras, Greece
- Institute of Chemical Engineering Sciences, Foundation for Research and Technology, Hellas (FORTH/ICE-HT), 26504 Patras, Greece
- Correspondence: (G.L.); (C.T.C.); Tel.: +30-2610-996-312 (G.L.); +30-2610-996-261 (C.T.C.)
| |
Collapse
|
31
|
Chasapis CT, Ntoupa PSA, Spiliopoulou CA, Stefanidou ME. Recent aspects of the effects of zinc on human health. Arch Toxicol 2020; 94:1443-1460. [PMID: 32394086 DOI: 10.1007/s00204-020-02702-9] [Citation(s) in RCA: 197] [Impact Index Per Article: 49.3] [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: 02/27/2020] [Accepted: 03/05/2020] [Indexed: 12/21/2022]
Abstract
Zinc (Zn) is one of the most important essential nutrients of great public health significance. It is involved in numerous biological functions and it is considered as a multipurpose trace element, due to its capacity to bind to more than 300 enzymes and more than 2000 transcriptional factors. Its role in biochemical pathways and cellular functions, such as the response to oxidative stress, homeostasis, immune responses, DNA replication, DNA damage repair, cell cycle progression, apoptosis and aging is significant. Zn is required for the synthesis of protein and collagen, thus contributing to wound healing and a healthy skin. Metallothioneins are metal-binding proteins and they are potent scavengers of heavy metals, including Zn, and protect the organism against stress. Zn deficiency is observed almost in 17% of the global population and affects many organ systems, leading to dysfunction of both humoral and cell-mediated immunity, thus increasing the susceptibility to infection. This review gives a thorough insight into the most recent evidence on the association between Zn biochemistry and human pathologies, epigenetic processes, gut microbial composition, drug targets and nanomedicine.
Collapse
Affiliation(s)
- Christos T Chasapis
- NMR Center, Instrumental Analysis Laboratory, School of Natural Sciences, University of Patras, Patras, Greece.,Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas (FORTH/ICE-HT), Patras, Greece
| | - Panagoula-Stamatina A Ntoupa
- Department of Forensic Medicine and Toxicology, School of Medicine, National and Kapodistrian University of Athens, 75, Mikras Asias Street, 11527, Goudi, Athens, Greece
| | - Chara A Spiliopoulou
- Department of Forensic Medicine and Toxicology, School of Medicine, National and Kapodistrian University of Athens, 75, Mikras Asias Street, 11527, Goudi, Athens, Greece
| | - Maria E Stefanidou
- Department of Forensic Medicine and Toxicology, School of Medicine, National and Kapodistrian University of Athens, 75, Mikras Asias Street, 11527, Goudi, Athens, Greece.
| |
Collapse
|
32
|
Chasapis CT, Konstantinoudis G. Protein isoelectric point distribution in the interactomes across the domains of life. Biophys Chem 2020; 256:106269. [PMID: 31733408 DOI: 10.1016/j.bpc.2019.106269] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 07/19/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 01/19/2023]
Abstract
The distribution of the protein isoelectric point (pI) in the protein-protein interaction (PPI) networks across the domains of life has not been investigated yet. This work attempts to correlate the pI with the number of direct interacting partners in the experimentally supported networks involving 226.085 PPIs from 14 various organisms including human, mouse, yeast, bacteria, viruses and 53.606 virus-host interactions. The results showed that the acidic proteins (pI<3) have the highest average number of interactions in eukaryotes, while in bacteria more neutral proteins. On the contrary, the basic proteins (pI>11) have the lowest average number of interactions in human, mouse, yeast, bacteria and human-viral interactomes and the highest average in intraviral interactomes. We examined the correlation of the pI of the interacting partners by calculating the assortativity index of various PPI networks. We found that the interactions between the acidic, neutral and basic proteins have a fairly random mix, implying weak if any association between the acidic and basic proteins. Furthermore, protein features such as biological function, structurally order and disorder, subcellular localization, and homodimerization were classified according to pI in prokaryote and eukaryote proteomes.
Collapse
Affiliation(s)
- Christos T Chasapis
- NMR Center, Instrumental Analysis Laboratory, School of Natural Sciences, University of Patras, Patras, Greece; Institute of Chemical Engineering Sciences, Foundation for Research and Technology, Hellas (FORTH/ICE-HT), Patras, Greece.
| | - Garyfallos Konstantinoudis
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, Imperial College, St. Mary's Campus, Norfolk Place, London W2 1PG, UK
| |
Collapse
|
33
|
Chasapis CT, Makridakis M, Damdimopoulos AE, Zoidakis J, Lygirou V, Mavroidis M, Vlahou A, Miranda-Vizuete A, Spyrou G, Vlamis-Gardikas A. Implications of the mitochondrial interactome of mammalian thioredoxin 2 for normal cellular function and disease. Free Radic Biol Med 2019; 137:59-73. [PMID: 31018154 DOI: 10.1016/j.freeradbiomed.2019.04.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 04/15/2019] [Indexed: 12/23/2022]
Abstract
Multiple thioredoxin isoforms exist in all living cells. To explore the possible functions of mammalian mitochondrial thioredoxin 2 (Trx2), an interactome of mouse Trx2 was initially created using (i) a monothiol mouse Trx2 species for capturing protein partners from different organs and (ii) yeast two hybrid screens on human liver and rat brain cDNA libraries. The resulting interactome consisted of 195 proteins (Trx2 included) plus the mitochondrial 16S RNA. 48 of these proteins were classified as mitochondrial (MitoCarta2.0 human inventory). In a second step, the mouse interactome was combined with the current four-membered mitochondrial sub-network of human Trx2 (BioGRID) to give a 53-membered human Trx2 mitochondrial interactome (52 interactor proteins plus the mitochondrial 16S RNA). Although thioredoxins are thiol-employing disulfide oxidoreductases, approximately half of the detected interactions were not due to covalent disulfide bonds. This finding reinstates the extended role of thioredoxins as moderators of protein function by specific non-covalent, protein-protein interactions. Analysis of the mitochondrial interactome suggested that human Trx2 was involved potentially in mitochondrial integrity, formation of iron sulfur clusters, detoxification of aldehydes, mitoribosome assembly and protein synthesis, protein folding, ADP ribosylation, amino acid and lipid metabolism, glycolysis, the TCA cycle and the electron transport chain. The oxidoreductase functions of Trx2 were verified by its detected interactions with mitochondrial peroxiredoxins and methionine sulfoxide reductase. Parkinson's disease, triosephosphate isomerase deficiency, combined oxidative phosphorylation deficiency, and lactate dehydrogenase b deficiency are some of the diseases where the proposed mitochondrial network of Trx2 may be implicated.
Collapse
Affiliation(s)
- Christos T Chasapis
- Institute of Chemical Engineering Sciences (ICE-HT), Foundation for Research and Technology, Hellas (FORTH), Platani 26504, Greece
| | | | - Anastassios E Damdimopoulos
- Department of Biosciences and Nutrition, Center for Innovative Medicine (CIMED), Karolinska Institutet, Huddinge, Sweden
| | - Jerome Zoidakis
- Biomedical Research Foundation, Academy of Athens (BRFAA), Athens, Greece
| | - Vasiliki Lygirou
- Biomedical Research Foundation, Academy of Athens (BRFAA), Athens, Greece
| | - Manolis Mavroidis
- Biomedical Research Foundation, Academy of Athens (BRFAA), Athens, Greece
| | - Antonia Vlahou
- Biomedical Research Foundation, Academy of Athens (BRFAA), Athens, Greece
| | - Antonio Miranda-Vizuete
- Redox Homeostasis Group, Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Sevilla, Spain
| | - Giannis Spyrou
- Department of Clinical and Experimental Medicine, Division of Clinical Chemistry, Linköping University, S-581 85 Linköping, Sweden
| | | |
Collapse
|
34
|
|
35
|
Peana M, Chasapis CT, Simula G, Medici S, Zoroddu MA. A Model for Manganese interaction with Deinococcus radiodurans proteome network involved in ROS response and defense. J Trace Elem Med Biol 2018; 50:465-473. [PMID: 29449107 DOI: 10.1016/j.jtemb.2018.02.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/17/2018] [Accepted: 02/01/2018] [Indexed: 01/28/2023]
Abstract
A complex network of regulatory proteins takes part in the mechanism underlying the radioresistance of Deinoccocus radiodurans bacterium (DR). The interaction of Mn(II) ions with DR-proteins and peptides seems to be responsible for proteins protection from oxidative damage induced by Reactive Oxygen Species during irradiation. In the present work we describe a combined approach of bioinformatic strategies based on structural data and annotation to predict the Mn(II)-binding proteins encoded by the genome of DR and, in parallel, the same predictions for other bacteria were performed; the comparison revealed that, in most of the cases, the content of Mn(II)-binding proteins is significantly higher in radioresistant than in radiosensitive bacteria. Moreover, we report the in silico protein-protein interaction network of the putative Mn(II)-proteins, remodeled in order to enhance the knowledge about the impact of Mn-binding proteins in DR ability to protect also DNA from various damaging agents such as ionizing radiation, UV radiation and oxidative stress.
Collapse
Affiliation(s)
- M Peana
- Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy.
| | - C T Chasapis
- Institute of Chemical Engineering Sciences (ICE-HT), Foundation for Research and Technology, Hellas (FORTH), 26504, Patras, Greece.
| | - G Simula
- Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy
| | - S Medici
- Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy
| | - M A Zoroddu
- Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy
| |
Collapse
|
36
|
Chasapis CT. Preliminary results from structural systems biology approach in Tetrahymena thermophila reveal novel perspectives for this toxicological model. Arch Microbiol 2018; 201:51-59. [PMID: 30194464 DOI: 10.1007/s00203-018-1571-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 07/16/2018] [Revised: 08/28/2018] [Accepted: 09/05/2018] [Indexed: 11/29/2022]
Abstract
Tetrahymena is a unicellular microbial eukaryotic organism that has been used extensively in toxicology and environmental research. This work attempts to model for the first time the wiring of proteins involved in cellular mechanisms of Cd toxicity in Tetrahymena thermophila. 1975 high-confidence PPIs between 68 Cd-binding proteins and 422 partners were inferred through a novel structural systems biology approach that utilizes comparative analysis between Tetrahymena and other eukaryotes for which experimentally supported protein interactomes exist. The PPIs of the potential network were confirmed by known domain interactions in the Protein Data Bank and its topological characteristics were compared with publicly available experimental information for T. thermophila. To experimentally validate the robustness of the proposed PPI network, the interaction between the two most interconnected hub proteins was detected through GST pull-down assay. Potential effects on Tetrahymena's cellular and metabolic processes by PPIs involving Cd-binding proteins were uncovered. Furthermore, 244 PPIs in which Cd-binding proteins or/and their partners are encoded by orthologs of human disease genes in T. thermophila, but not in yeast, were identified and analyzed. The findings suggest that Tetrahymena could be possibly a useful model for an improved understanding of molecular mechanisms of Cd toxicity in human diseases.
Collapse
Affiliation(s)
- Christos T Chasapis
- Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas (FORTH/ICE-HT), 26504, Patras, Greece.
| |
Collapse
|
37
|
Chasapis CT. Interactions between metal binding viral proteins and human targets as revealed by network-based bioinformatics. J Inorg Biochem 2018; 186:157-161. [DOI: 10.1016/j.jinorgbio.2018.06.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/24/2018] [Accepted: 06/14/2018] [Indexed: 12/13/2022]
|
38
|
Chasapis CT. Hierarchical core decomposition of RING structure as a method to capture novel functional residues within RING-type E3 ligases: a structural systems biology approach. Comput Biol Med 2018; 100:86-91. [DOI: 10.1016/j.compbiomed.2018.06.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 06/26/2018] [Accepted: 06/27/2018] [Indexed: 11/15/2022]
|
39
|
Abstract
In this work, for the first time, the human heavy metal proteome was predicted.
Collapse
Affiliation(s)
- Christos T. Chasapis
- Institute of Chemical Engineering Sciences
- Foundation for Research & Technology – Hellas (FORTH/ICE-HT)
- Patras
- Greece
| |
Collapse
|
40
|
Birkou M, Chasapis CT, Marousis KD, Loutsidou AK, Bentrop D, Lelli M, Herrmann T, Carthy JM, Episkopou V, Spyroulias GA. A Residue Specific Insight into the Arkadia E3 Ubiquitin Ligase Activity and Conformational Plasticity. J Mol Biol 2017; 429:2373-2386. [PMID: 28647409 DOI: 10.1016/j.jmb.2017.06.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [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: 03/21/2017] [Revised: 06/15/2017] [Accepted: 06/15/2017] [Indexed: 12/17/2022]
Abstract
Arkadia (Rnf111) is an E3 ubiquitin ligase that plays a central role in the amplification of transforming growth factor beta (TGF-β) signaling responses by targeting for degradation the negative regulators of the pathway, Smad6 and Smad7, and the nuclear co-repressors Ski and Skil (SnoN). Arkadia's function in vivo depends on the really interesting new gene (RING)-H2 interaction with the E2 enzyme UbcH5b in order to ligate ubiquitin chains on its substrates. A conserved tryptophan (W972) in the C-terminal α-helix is widely accepted as essential for E2 recruitment and interaction and thus also for E3 enzymatic activity. The present NMR-driven study provides an atomic-level investigation of the structural and dynamical properties of two W972 Arkadia RING mutants, attempting to illuminate for the first time the differences between a functional and a nonfunctional mutant W972A and W972R, respectively. A TGF-β-responsive promoter driving luciferase was used to assay for Arkadia function in vivo. These experiments showed that the Arkadia W972A mutant has the same activity as wild-type (WT) Arkadia in enhancing TGF-β signaling responses, while W972R does not. Only minor structural differences exist between the W972A RING domain and WT-RING. In contrast, the W972R mutant hardly interacts with E2. The loss of function correlates with structural changes in the C-terminal α-helix and an increase in the distance between the Zn(II) ions. Our data show that the position occupied by W972 within WT Arkadia is critical for the function of RING and that it depends on the nature of the residue at this position.
Collapse
Affiliation(s)
- Maria Birkou
- Department of Pharmacy, University of Patras, GR-26504 Patras, Greece
| | | | | | | | - Detlef Bentrop
- Institute of Physiology II, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Moreno Lelli
- Institut des Sciences Analytiques, Centre de RMN à Très Hauts Champs, UMR 5280 CNRS, ENS Lyon, UCB Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Torsten Herrmann
- Institut des Sciences Analytiques, Centre de RMN à Très Hauts Champs, UMR 5280 CNRS, ENS Lyon, UCB Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Jonathon M Carthy
- Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Burlington Danes, London W12 0NN, UK
| | - Vasso Episkopou
- Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Burlington Danes, London W12 0NN, UK.
| | | |
Collapse
|
41
|
Chasapis CT, Andreini C, Georgiopolou AK, Stefanidou ME, Vlamis-Gardikas A. Identification of the zinc, copper and cadmium metalloproteome of the protozoon Tetrahymena thermophila by systematic bioinformatics. Arch Microbiol 2017; 199:1141-1149. [DOI: 10.1007/s00203-017-1385-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/24/2017] [Accepted: 05/02/2017] [Indexed: 11/30/2022]
|
42
|
Chasapis CT, Argyriou AI, Apostolidi M, Konstantinidou P, Bentrop D, Stathopoulos C, Spyroulias GA. (1)H, (13)C and (15)N backbone and side-chain resonance assignment of the LAM-RRM1 N-terminal module of La protein from Dictyostelium discoideum. Biomol NMR Assign 2015; 9:303-307. [PMID: 25687647 DOI: 10.1007/s12104-015-9597-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 02/09/2015] [Indexed: 06/04/2023]
Abstract
The N-terminal half of La protein consists of two concatenated motifs: La motif (LAM) and the N-terminal RNA recognition motif (RRM1) both of which are responsible for poly(U) RNA binding. Here, we present the backbone and side-chain assignments of the (1)H, (13)C and (15)N resonances of the 191-residue LAM-RRM1 region of the La protein from the lower eukaryote Dictyostelium discoideum and its secondary structure prediction.
Collapse
Affiliation(s)
| | | | - Maria Apostolidi
- Department of Biochemistry, School of Medicine, University of Patras, 26504, Patras, Greece
| | | | - Detlef Bentrop
- Institute of Physiology II, University of Freiburg, 79104, Freiburg, Germany
| | | | | |
Collapse
|
43
|
Melekis E, Tsika AC, Lichière J, Chasapis CT, Margiolaki I, Papageorgiou N, Coutard B, Bentrop D, Spyroulias GA. NMR study of non-structural proteins--part I: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Mayaro virus (MAYV). Biomol NMR Assign 2015; 9:191-195. [PMID: 25217003 DOI: 10.1007/s12104-014-9572-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 09/02/2014] [Indexed: 06/03/2023]
Abstract
Macro domains are ADP-ribose-binding modules present in all eukaryotic organisms, bacteria and archaea. They are also found in non-structural proteins of several positive strand RNA viruses such as alphaviruses. Here, we report the high yield expression and preliminary structural analysis through solution NMR spectroscopy of the macro domain from New World Mayaro Alphavirus. The recombinant protein was well-folded and in a monomeric state. An almost complete sequence-specific assignment of its (1)H, (15)N and (13)C resonances was obtained and its secondary structure determined by TALOS+.
Collapse
|
44
|
Argyriou AI, Chasapis CT, Apostolidi M, Konstantinidou P, Stathopoulos C, Bentrop D, Spyroulias GA. Backbone and side chain NMR assignment, along with the secondary structure prediction of RRM2 domain of La protein from a lower eukaryote exhibiting identical structural organization with its human homolog. Biomol NMR Assign 2015; 9:219-222. [PMID: 25281001 DOI: 10.1007/s12104-014-9578-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 09/26/2014] [Indexed: 06/03/2023]
Abstract
The La protein (Lupus antigen), a key mediator during biogenesis of RNA polymerase III transcripts, contains a characteristic La motif and one or two RNA recognition motif (RRM) domains, depending on the organism of origin. The RRM1 domain is conserved in higher eukaryotes and located in the N-terminal region, whereas the C-terminal RRM2 domain is absent in most lower eukaryotes and its specific role remains, so far, uncharacterized. Here, we present the backbone and side-chain assignment of the (1)H, (13)C and (15)N resonances of RRM2 of La protein from Dictyostelium discoideum. Interestingly, the La protein in this lower eukaryote, exhibits high homology to its human counterpart. Moreover, it contains two RRM domains, instead of one, raising questions on its evolutionary origin and the putative role of RRM2 in vivo. We also provide its secondary structure as predicted by the TALOS+ online tool.
Collapse
|
45
|
Asimakopoulou A, Panopoulos P, Chasapis CT, Coletta C, Zhou Z, Cirino G, Giannis A, Szabo C, Spyroulias GA, Papapetropoulos A. Selectivity of commonly used pharmacological inhibitors for cystathionine β synthase (CBS) and cystathionine γ lyase (CSE). Br J Pharmacol 2014; 169:922-32. [PMID: 23488457 PMCID: PMC3687671 DOI: 10.1111/bph.12171] [Citation(s) in RCA: 304] [Impact Index Per Article: 30.4] [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: 11/25/2012] [Revised: 02/01/2013] [Accepted: 02/17/2013] [Indexed: 12/01/2022] Open
Abstract
Background and Purpose Hydrogen sulfide (H2S) is a signalling molecule that belongs to the gasotransmitter family. Two major sources for endogenous enzymatic production of H2S are cystathionine β synthase (CBS) and cystathionine γ lyase (CSE). In the present study, we examined the selectivity of commonly used pharmacological inhibitors of H2S biosynthesis towards CSE and CBS. Experimental Approach To address this question, human CSE or CBS enzymes were expressed and purified from Escherichia coli as fusion proteins with GSH-S-transferase. After purification, the activity of the recombinant enzymes was tested using the methylene blue method. Key Results β-cyanoalanine (BCA) was more potent in inhibiting CSE than propargylglycine (PAG) (IC50 14 ± 0.2 μM vs. 40 ± 8 μM respectively). Similar to PAG, L-aminoethoxyvinylglycine (AVG) only inhibited CSE, but did so at much lower concentrations. On the other hand, aminooxyacetic acid (AOAA), a frequently used CBS inhibitor, was more potent in inhibiting CSE compared with BCA and PAG (IC50 1.1 ± 0.1 μM); the IC50 for AOAA for inhibiting CBS was 8.5 ± 0.7 μM. In line with our biochemical observations, relaxation to L-cysteine was blocked by AOAA in aortic rings that lacked CBS expression. Trifluoroalanine and hydroxylamine, two compounds that have also been used to block H2S biosynthesis, blocked the activity of CBS and CSE. Trifluoroalanine had a fourfold lower IC50 for CBS versus CSE, while hydroxylamine was 60-fold more selective against CSE. Conclusions and Implications In conclusion, although PAG, AVG and BCA exhibit selectivity in inhibiting CSE versus CBS, no selective pharmacological CBS inhibitor is currently available.
Collapse
Affiliation(s)
- Antonia Asimakopoulou
- Department of Pharmacy, Laboratory of Molecular Pharmacology, University of Patras, Patras, Greece
| | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Vourtsis DJ, Chasapis CT, Pairas G, Bentrop D, Spyroulias GA. NMR conformational properties of an Anthrax Lethal Factor domain studied by multiple amino acid-selective labeling. Biochem Biophys Res Commun 2014; 450:335-40. [PMID: 24944022 DOI: 10.1016/j.bbrc.2014.05.123] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [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: 05/22/2014] [Accepted: 05/25/2014] [Indexed: 11/28/2022]
Abstract
NMR-based structural biology urgently needs cost- and time-effective methods to assist both in the process of acquiring high-resolution NMR spectra and their subsequent analysis. Especially for bigger proteins (>20 kDa) selective labeling is a frequently used means of sequence-specific assignment. In this work we present the successful overexpression of a polypeptide of 233 residues, corresponding to the structured part of the N-terminal domain of Anthrax Lethal Factor, using Escherichia coli expression system. The polypeptide was subsequently isolated in pure, soluble form and analyzed structurally by solution NMR spectroscopy. Due to the non-satisfying quality and resolution of the spectra of this 27 kDa protein, an almost complete backbone assignment became feasible only by the combination of uniform and novel amino acid-selective labeling schemes. Moreover, amino acid-type selective triple-resonance NMR experiments proved to be very helpful.
Collapse
Affiliation(s)
| | | | - George Pairas
- Department of Pharmacy, University of Patras, GR-26504 Patras, Greece
| | - Detlef Bentrop
- Institute of Physiology II, University of Freiburg, D-79104 Freiburg, Germany
| | | |
Collapse
|
47
|
Apostolidi M, Vourtsis DJ, Chasapis CT, Stathopoulos C, Bentrop D, Spyroulias GA. ¹H, ¹⁵N, ¹³C assignment and secondary structure determination of two domains of La protein from D. discoideum. Biomol NMR Assign 2014; 8:47-51. [PMID: 23239108 DOI: 10.1007/s12104-012-9450-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 12/04/2012] [Indexed: 06/01/2023]
Abstract
Biosynthesis of RNA polymerase III transcripts requires binding of the La protein at their 3' end. La is an abundant nuclear RNA-binding protein which protects the nascent transcripts from 3' exonuclease degradation. Here, we report the high yield expression and preliminary structural analysis through NMR spectroscopy of two recombinant RNA binding domains (La motif and NRRM) from the La protein of Dictyostelium discoideum. Both recombinant protein constructs were well-folded and allowed for an almost complete sequence-specific assignment of the (15)N and (13)C labeled domains and their secondary structure prediction using PECAN online tool.
Collapse
Affiliation(s)
- Maria Apostolidi
- Department of Biochemistry, School of Medicine, University of Patras, 26504, Patras, Greece
| | | | | | | | | | | |
Collapse
|
48
|
Loutsidou AC, Hatzi VI, Chasapis CT, Terzoudi GI, Spiliopoulou CA, Stefanidou ME. DNA content alterations in Tetrahymena pyriformis macronucleus after exposure to food preservatives sodium nitrate and sodium benzoate. Acta Biol Hung 2012; 63:483-9. [PMID: 23134605 DOI: 10.1556/abiol.63.2012.4.7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The toxicity, in terms of changes in the DNA content, of two food preservatives, sodium nitrate and sodium benzoate was studied on the protozoan Tetrahymena pyriformis using DNA image analysis technology. For this purpose, selected doses of both food additives were administered for 2 h to protozoa cultures and DNA image analysis of T. pyriformis nuclei was performed. The analysis was based on the measurement of the Mean Optical Density which represents the cellular DNA content. The results have shown that after exposure of the protozoan cultures to doses equivalent to ADI, a statistically significant increase in the macronuclear DNA content compared to the unexposed control samples was observed. The observed increase in the macronuclear DNA content is indicative of the stimulation of the mitotic process and the observed increase in MOD, accompanied by a stimulation of the protozoan proliferation activity is in consistence with this assumption. Since alterations at the DNA level such as DNA content and uncontrolled mitogenic stimulation have been linked with chemical carcinogenesis, the results of the present study add information on the toxicogenomic profile of the selected chemicals and may potentially lead to reconsideration of the excessive use of nitrates aiming to protect public health.
Collapse
|
49
|
Chasapis CT, Kandias NG, Episkopou V, Bentrop D, Spyroulias GA. NMR-based insights into the conformational and interaction properties of Arkadia RING-H2 E3 Ub ligase. Proteins 2012; 80:1484-9. [PMID: 22411132 DOI: 10.1002/prot.24048] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 01/03/2012] [Accepted: 01/11/2012] [Indexed: 11/11/2022]
Abstract
Arkadia (Rnf111), an E3 Ubiquitin (Ub) ligase, amplifies TGF-β signaling responses by targeting for degradation of the negative regulators Smad6/7 and the SnoN/Ski transcriptional repressors when they block the TGF-β effectors Smad2/3. The E3 ligase activity of Arkadia depends on its C-terminal RING-H2 domain that constitutes the docking site for the E2 Ub-conjugating enzyme carrying the activated Ub. We determined the nuclear magnetic resonance solution structure of Arkadia's RING-H2 domain and revealed a (β)ββα fold, fully consistent with the expected "cross-brace" mode of Zn(II)-ligation. In addition, the interaction of the Arkadia RING-H2 domain with its E2 partner enzyme (UbcH5b) was examined through chemical shift perturbation. Proteins 2012. © 2012 Wiley Periodicals, Inc.
Collapse
|
50
|
Abstract
The importance of micronutrients in health and nutrition is undisputable, and among them, zinc is an essential element whose significance to health is increasingly appreciated and whose deficiency may play an important role in the appearance of diseases. Zinc is one of the most important trace elements in the organism, with three major biological roles, as catalyst, structural, and regulatory ion. Zinc-binding motifs are found in many proteins encoded by the human genome physiologically, and free zinc is mainly regulated at the single-cell level. Zinc has critical effect in homeostasis, in immune function, in oxidative stress, in apoptosis, and in aging, and significant disorders of great public health interest are associated with zinc deficiency. In many chronic diseases, including atherosclerosis, several malignancies, neurological disorders, autoimmune diseases, aging, age-related degenerative diseases, and Wilson's disease, the concurrent zinc deficiency may complicate the clinical features, affect adversely immunological status, increase oxidative stress, and lead to the generation of inflammatory cytokines. In these diseases, oxidative stress and chronic inflammation may play important causative roles. It is therefore important that status of zinc is assessed in any case and zinc deficiency is corrected, since the unique properties of zinc may have significant therapeutic benefits in these diseases. In the present paper, we review the zinc as a multipurpose trace element, its biological role in homeostasis, proliferation and apoptosis and its role in immunity and in chronic diseases, such as cancer, diabetes, depression, Wilson's disease, Alzheimer's disease, and other age-related diseases.
Collapse
Affiliation(s)
- Christos T Chasapis
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | | | | | | |
Collapse
|