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Vettorazzi M, Díaz I, Angelina E, Salido S, Gutierrez L, Alvarez SE, Cobo J, Enriz RD. Second generation of pyrimidin-quinolone hybrids obtained from virtual screening acting as sphingosine kinase 1 inhibitors and potential anticancer agents. Bioorg Chem 2024; 144:107112. [PMID: 38237390 DOI: 10.1016/j.bioorg.2024.107112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/22/2023] [Accepted: 01/08/2024] [Indexed: 02/17/2024]
Abstract
We report here the virtual screening design, synthesis and activity of eight new inhibitors of SphK1. For this study we used a pre-trained Graph Convolutional Network (GCN) combined with docking calculations. This exploratory analysis proposed nine compounds from which eight displayed significant inhibitory effect against sphingosine kinase 1 (SphK1) demonstrating a high level of efficacy for this approach. Four of these compounds also displayed anticancer activity against different tumor cell lines, and three of them (5), (6) and (7) have shown a wide inhibitory action against many of the cancer cell line tested, with GI50 below 5 µM, being (5) the most promising with TGI below 10 µM for the half of cell lines. Our results suggest that the three most promising compounds reported here are the pyrimidine-quinolone hybrids (1) and (6) linked by p-aminophenylsulfanyl and o-aminophenol fragments respectively, and (8) without such aryl linker. We also performed an exhaustive study about the molecular interactions that stabilize the different ligands at the binding site of SphK1. This molecular modeling analysis was carried out by using combined techniques: docking calculations, MD simulations and QTAIM analysis. In this study we also included PF543, as reference compound, in order to better understand the molecular behavior of these ligands at the binding site of SphK1.These results provide useful information for the design of new inhibitors of SphK1 possessing these structural scaffolds.
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Affiliation(s)
- Marcela Vettorazzi
- Universidad Nacional de San Luis, Facultad de Química, Bioquímica y Farmacia, Ejercito de los Andes 950, (5700) San Luis, Argentina; Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Ejercito de los Andes 950, (5700) San Luis, Argentina
| | - Iván Díaz
- Universidad de Jaén, Departamento de Química Inorgánica y Orgánica, Campus Las Lagunillas s/n, 23071 Jaén, Spain
| | - Emilio Angelina
- Universidad Nacional del Nordeste, Facultad de Ciencias Exactas y Naturales y Agrimensura, Departamento de Química, Área de Química Física, Laboratorio de Estructura Molecular y Propiedades, Avda. Libertad 5460, 3400 Corrientes, Argentina
| | - Sofía Salido
- Universidad de Jaén, Departamento de Química Inorgánica y Orgánica, Campus Las Lagunillas s/n, 23071 Jaén, Spain
| | - Lucas Gutierrez
- Universidad Nacional de San Luis, Facultad de Química, Bioquímica y Farmacia, Ejercito de los Andes 950, (5700) San Luis, Argentina; Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Ejercito de los Andes 950, (5700) San Luis, Argentina
| | - Sergio E Alvarez
- Universidad Nacional de San Luis, Facultad de Química, Bioquímica y Farmacia, Ejercito de los Andes 950, (5700) San Luis, Argentina; Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Ejercito de los Andes 950, (5700) San Luis, Argentina
| | - Justo Cobo
- Universidad de Jaén, Departamento de Química Inorgánica y Orgánica, Campus Las Lagunillas s/n, 23071 Jaén, Spain.
| | - Ricardo D Enriz
- Universidad Nacional de San Luis, Facultad de Química, Bioquímica y Farmacia, Ejercito de los Andes 950, (5700) San Luis, Argentina; Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Ejercito de los Andes 950, (5700) San Luis, Argentina.
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Isert C, Atz K, Riniker S, Schneider G. Exploring protein-ligand binding affinity prediction with electron density-based geometric deep learning. RSC Adv 2024; 14:4492-4502. [PMID: 38312732 PMCID: PMC10835705 DOI: 10.1039/d3ra08650j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/19/2024] [Indexed: 02/06/2024] Open
Abstract
Rational structure-based drug design relies on accurate predictions of protein-ligand binding affinity from structural molecular information. Although deep learning-based methods for predicting binding affinity have shown promise in computational drug design, certain approaches have faced criticism for their potential to inadequately capture the fundamental physical interactions between ligands and their macromolecular targets or for being susceptible to dataset biases. Herein, we propose to include bond-critical points based on the electron density of a protein-ligand complex as a fundamental physical representation of protein-ligand interactions. Employing a geometric deep learning model, we explore the usefulness of these bond-critical points to predict absolute binding affinities of protein-ligand complexes, benchmark model performance against existing methods, and provide a critical analysis of this new approach. The models achieved root-mean-squared errors of 1.4-1.8 log units on the PDBbind dataset, and 1.0-1.7 log units on the PDE10A dataset, not indicating significant advantages over benchmark methods, and thus rendering the utility of electron density for deep learning models context-dependent. The relationship between intermolecular electron density and corresponding binding affinity was analyzed, and Pearson correlation coefficients r > 0.7 were obtained for several macromolecular targets.
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Affiliation(s)
- Clemens Isert
- ETH Zurich, Department of Chemistry and Applied Biosciences Vladimir-Prelog-Weg 4 8093 Zurich Switzerland +41 44 633 73 27
| | - Kenneth Atz
- ETH Zurich, Department of Chemistry and Applied Biosciences Vladimir-Prelog-Weg 4 8093 Zurich Switzerland +41 44 633 73 27
| | - Sereina Riniker
- ETH Zurich, Department of Chemistry and Applied Biosciences Vladimir-Prelog-Weg 4 8093 Zurich Switzerland +41 44 633 73 27
| | - Gisbert Schneider
- ETH Zurich, Department of Chemistry and Applied Biosciences Vladimir-Prelog-Weg 4 8093 Zurich Switzerland +41 44 633 73 27
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Hsieh CJ, Giannakoulias S, Petersson EJ, Mach RH. Computational Chemistry for the Identification of Lead Compounds for Radiotracer Development. Pharmaceuticals (Basel) 2023; 16:317. [PMID: 37259459 PMCID: PMC9964981 DOI: 10.3390/ph16020317] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 11/19/2023] Open
Abstract
The use of computer-aided drug design (CADD) for the identification of lead compounds in radiotracer development is steadily increasing. Traditional CADD methods, such as structure-based and ligand-based virtual screening and optimization, have been successfully utilized in many drug discovery programs and are highlighted throughout this review. First, we discuss the use of virtual screening for hit identification at the beginning of drug discovery programs. This is followed by an analysis of how the hits derived from virtual screening can be filtered and culled to highly probable candidates to test in in vitro assays. We then illustrate how CADD can be used to optimize the potency of experimentally validated hit compounds from virtual screening for use in positron emission tomography (PET). Finally, we conclude with a survey of the newest techniques in CADD employing machine learning (ML).
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Affiliation(s)
- Chia-Ju Hsieh
- Division of Nuclear Medicine and Clinical Molecular Imaging, Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sam Giannakoulias
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - E. James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert H. Mach
- Division of Nuclear Medicine and Clinical Molecular Imaging, Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Jonathan FVM, Darling D, Cecilia RHM, Alan EP, Lubriel MFH, Ivonne OC, Elena MWJ, Augusto RLC, Sayuri VQJ, Angel GRL, José CB. UHPLC-MS/MS Studies and Antiproliferative Effects in Breast Cancer Cells of Mexican Sargassum. Anticancer Agents Med Chem 2023; 23:76-86. [PMID: 35418289 DOI: 10.2174/1871520622666220412125740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 02/08/2023]
Abstract
BACKGROUND Sargassum is a marine organism that, under specific conditions, drastically increases its population damaging the environment and risking other organisms. However, sargassum could represent a source of bioactive compounds to treat different diseases such as cancer. Thus, aqueous, ethanolic, and ethyl acetate extracts of sargassum from Playa del Carmen, Mexico, were subjected to metabolomic and antiproliferative assays in breast cancer cells. OBJECTIVE To evaluate the biological effect of different extracts of sargassum, its toxicity over Artemia salina and its antiproliferative effect tested in MCF-7, MDA-MB-231, and NIH3T3 cell lines. Finally, using UHPLC-MS/MS to identify the metabolites in each extract to correlate them with its antiproliferative effect. METHODS The sargassum sample collection was carried out in September at three different points in Playa del Carmen, Quintana Roo, Mexico. The aqueous, ethanolic, and ethyl acetate extracts of Mexican sargassum were obtained by evaporation of solvent and lyophilization. Then, these extracts were evaluated in the cytotoxicity bioassay of Artemia salina. Next, its antiproliferative effect was assessed in MCF-7, MDA-MB-231, and NIH3T3 cell lines. Using UHPLC-MS/MS, the metabolites present in each extract were identified. Finally, docking studies on sphingosine kinase 1 (PDB ID: 3VZB) of sphingosine were carried out. RESULTS The extracts from sargassum showed a greater effect in the antiproliferative assays in cells than in cytotoxic assays in Artemia salina. The ethanolic extract obtained from sargassum showed the best antiproliferative activity in MCF7 and MDA-MB-231 cells. Despite its antiproliferative effect on NIH3T3 cells, an additional extract is required indicating that this extract has compounds that could have a better effect on cancer cells in fibroblast (NIH3T3). The UHPLC-MS/MS of ethanolic and the ethyl acetate extract showed that these extracts have compounds such as sphinganine C16, N, N-Dimethylsphingosine compound, and that it could be possible that the effect observed is due to their metabolites which could be ligands for the sphingosine kinase 1 as demonstrated by docking studies. CONCLUSION The ethanolic extract obtained from sargassum has better antiproliferative activity, despite not having a cytotoxic effect in Artemia salina. The antiproliferative effect could be related to the sphinganine C16, N,NDimethylphingosine identified with more abundance by UHPLC-MS/MS. In addition, these metabolites could be targets of sphingosine kinase 1.
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Affiliation(s)
- Fragoso-Vázquez Manuel Jonathan
- Departamento de Quimica Organica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala, Col. Casco de Santo Tomas, Mexico City, CP 11340, Mexico
| | - Duclosel Darling
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Casco de Santo Tomás, 11340, Mexico City, Mexico
| | - Rosales-Hernández Martha Cecilia
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Casco de Santo Tomás, 11340, Mexico City, Mexico
| | - Estrada-Pérez Alan
- Laboratorio de Diseno y Desarrollo de Nuevos Farmacos e Innovacion Biotecnológica de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico. Plan de San Luis Y Diaz Mirón S/N, Col. Casco de Santo Tomás, México City, CP 11340, Mexico
| | - Mendoza-Figueroa Humberto Lubriel
- Laboratorio de Diseno y Desarrollo de Nuevos Farmacos e Innovacion Biotecnológica de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico. Plan de San Luis Y Diaz Mirón S/N, Col. Casco de Santo Tomás, México City, CP 11340, Mexico
| | - Olivares-Corichi Ivonne
- Laboratory of Oxidative Stress in Research and Graduate Studies Section, Instituto Politécnico Nacional, Escuela Superior de Medicina, Mexico City, México
| | - Mendieta-Wejebe Jessica Elena
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Casco de Santo Tomás, 11340, Mexico City, Mexico
| | - Reyes-López Cesar Augusto
- Instituto Politécnico Nacional, Escuela Nacional de Medicina y Homeopatía, Laboratorio de Bioquímica Estructural. Ciudad de México, México
| | - Velasco-Quijano Jessica Sayuri
- Laboratorio de Diseno y Desarrollo de Nuevos Farmacos e Innovacion Biotecnológica de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico. Plan de San Luis Y Diaz Mirón S/N, Col. Casco de Santo Tomás, México City, CP 11340, Mexico
| | - Gil-Ruiz Luis Angel
- Laboratorio de Diseno y Desarrollo de Nuevos Farmacos e Innovacion Biotecnológica de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico. Plan de San Luis Y Diaz Mirón S/N, Col. Casco de Santo Tomás, México City, CP 11340, Mexico
| | - Correa-Basurto José
- Laboratorio de Diseno y Desarrollo de Nuevos Farmacos e Innovacion Biotecnologica de la Escuela Superior de Medicina, Instituto Politecnico Nacional, Mexico. Plan de San Luis Y Diaz Miron S/N, Col. Casco de Santo Tomas, Mexico City, CP 11340, Mexico
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Tosso RD, Zarycz MNC, Schiel A, Goicoechea Moro L, Baldoni HA, Angelina E, Enriz RD. Evaluating the conformational space of the active site of D 2 dopamine receptor. Scope and limitations of the standard docking methods. J Comput Chem 2022; 43:1298-1312. [PMID: 35638694 DOI: 10.1002/jcc.26938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/11/2022] [Accepted: 05/08/2022] [Indexed: 11/05/2022]
Abstract
We report here for the first time the potential energy surfaces (PES) of phenyletilamine (PEA) and meta-tyramine (m-OH-PEA) at the D2 dopamine receptor (D2DR) binding site. PESs not only allow us to observe all the critical points of the surface (minimums, maximums, and transition states), but also to note the ease or difficulty that each local minima have for their conformational inter-conversions and therefore know the conformational flexibility that these ligands have in their active sites. Taking advantage of possessing this valuable information, we analyze how accurate a standard docking study is in these cases. Our results indicate that although we have to be careful in how to carry out this type of study and to consider performing some extra-simulations, docking calculations can be satisfactory. In order to analyze in detail the different molecular interactions that are stabilizing the different ligand-receptor (L-R) complexes, we carried out quantum theory of atoms in molecules (QTAIM) computations and NMR shielding calculations. Although some of these techniques are a bit tedious and require more computational time, our results demonstrate the importance of performing computational simulations using different types of combined techniques (docking/MD/hybrid QM-MM/QTAIM and NMR shielding calculations) in order to obtain more accurate results. Our results allow us to understand in details the molecular interactions stabilizing and destabilizing the different L-R complexes reported here. Thus, the different activities observed for dopamine (DA), m-OH-PEA, and PEA can be clearly explained at molecular level.
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Affiliation(s)
- Rodrigo D Tosso
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas, San Luis, Argentina
| | - M Natalia C Zarycz
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas, San Luis, Argentina
| | - Ayelén Schiel
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas, San Luis, Argentina
| | - Luisa Goicoechea Moro
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas, San Luis, Argentina
| | - Héctor A Baldoni
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis; Instituto de Matemáticas, San Luis, Argentina
| | - Emilio Angelina
- Laboratorio de Estructura Molecular y Propiedades, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Instituto de Química Básica y Aplicada, Corrientes, Argentina
| | - Ricardo D Enriz
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas, San Luis, Argentina
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Emam AM, Dahal A, Singh SS, Tosso RD, Ibrahim SM, El-Sadek M, Jois SD, Enriz RD, Kothayer H. Quinazoline-tethered hydrazone: A versatile scaffold toward dual anti-TB and EGFR inhibition activities in NSCLC. Arch Pharm (Weinheim) 2021; 354:e2100281. [PMID: 34585758 DOI: 10.1002/ardp.202100281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 11/07/2022]
Abstract
Globally, lung cancer and tuberculosis are considered to be very serious and complex diseases. Evidence suggests that chronic infection with tuberculosis (TB) can often lead to lung tumors; therefore, developing drugs that target both diseases is of great clinical significance. In our study, we designed and synthesized a suite of 14 new quinazolinones (5a-n) and performed biological investigations of these compounds in Mycobacterium tuberculosis (MTB) and cancer cell lines. In addition, we conducted a molecular modeling study to determine the mechanism of action of these compounds at the molecular level. Compounds that showed anticancer activity in the preliminary screening were further evaluated in three cancer cell lines (A549, Calu-3, and BT-474 cells) and characterized in an epidermal growth factor receptor (EGFR) binding assay. Cytotoxicity in noncancerous lung fibroblast cells was also evaluated to obtain safety data. Our theoretical and experimental studies indicated that our compounds showed a mechanism of action similar to that of erlotinib by inhibiting the EGFR tyrosine kinase. In turn, the antituberculosis activity of these compounds would be produced by the inhibition of enoyl-ACP-reductase. From our findings, we were able to identify two potential lead compounds (5i and 5l) with dual activity and elevated safety toward noncancerous lung fibroblast cells. In addition, our data identified three compounds with excellent anti-TB activities (compounds 5i, 5l, and 5n).
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Affiliation(s)
- Aya M Emam
- Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Achyut Dahal
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana Monroe, Monroe, Louisiana, USA
| | - Sitanshu S Singh
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana Monroe, Monroe, Louisiana, USA
| | - Rodrigo D Tosso
- Pharmacy Department, Facultad de Química, Bioquímica y Farmacia, IMIBIO-CONICET, Universidad Nacional de San Luis, San Luis, Argentina
| | - Samy M Ibrahim
- Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Mohamed El-Sadek
- Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Seetharama D Jois
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana Monroe, Monroe, Louisiana, USA
| | - Ricardo D Enriz
- Pharmacy Department, Facultad de Química, Bioquímica y Farmacia, IMIBIO-CONICET, Universidad Nacional de San Luis, San Luis, Argentina
| | - Hend Kothayer
- Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
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Magar P, Parravicini O, Štěpánková Š, Svrčková K, Garro AD, Jendrzejewska I, Pauk K, Hošek J, Jampílek J, Enriz RD, Imramovský A. Novel Sulfonamide-Based Carbamates as Selective Inhibitors of BChE. Int J Mol Sci 2021; 22:9447. [PMID: 34502357 PMCID: PMC8430704 DOI: 10.3390/ijms22179447] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/28/2021] [Indexed: 11/16/2022] Open
Abstract
A series of 14 target benzyl [2-(arylsulfamoyl)-1-substituted-ethyl]carbamates was prepared by multi-step synthesis and characterized. All the final compounds were tested for their ability to inhibit acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) in vitro, and the selectivity index (SI) was determined. Except for three compounds, all compounds showed strong preferential inhibition of BChE, and nine compounds were even more active than the clinically used rivastigmine. Benzyl {(2S)-1-[(2-methoxybenzyl)sulfamoyl]-4-methylpentan-2-yl}carbamate (5k), benzyl {(2S)-1-[(4-chlorobenzyl)sulfamoyl]-4-methylpentan-2-yl}carbamate (5j), and benzyl [(2S)-1-(benzylsulfamoyl)-4-methylpentan-2-yl]carbamate (5c) showed the highest BChE inhibition (IC50 = 4.33, 6.57, and 8.52 µM, respectively), indicating that derivatives 5c and 5j had approximately 5-fold higher inhibitory activity against BChE than rivastigmine, and 5k was even 9-fold more effective than rivastigmine. In addition, the selectivity index of 5c and 5j was approx. 10 and that of 5k was even 34. The process of carbamylation and reactivation of BChE was studied for the most active derivatives 5k, 5j. The detailed information about the mode of binding of these compounds to the active site of both BChE and AChE was obtained in a molecular modeling study. In this study, combined techniques (docking, molecular dynamic simulations, and QTAIM (quantum theory of atoms in molecules) calculations) were employed.
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Affiliation(s)
- Pratibha Magar
- Institute of Organic Chemistry and Technology, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532 10 Pardubice, Czech Republic; (P.M.); (K.P.)
| | - Oscar Parravicini
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Chacabuco 915, 5700 San Luis, Argentina; (O.P.); (A.D.G.)
| | - Šárka Štěpánková
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532 10 Pardubice, Czech Republic; (Š.Š.); (K.S.)
| | - Katarina Svrčková
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532 10 Pardubice, Czech Republic; (Š.Š.); (K.S.)
| | - Adriana D. Garro
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Chacabuco 915, 5700 San Luis, Argentina; (O.P.); (A.D.G.)
| | | | - Karel Pauk
- Institute of Organic Chemistry and Technology, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532 10 Pardubice, Czech Republic; (P.M.); (K.P.)
| | - Jan Hošek
- Department of Pharmacology and Toxicology, Veterinary Research Institute, Hudcova 296/70, 621 00 Brno, Czech Republic;
| | - Josef Jampílek
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15 Bratislava, Slovakia;
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska Cesta 9, 845 10 Bratislava, Slovakia
| | - Ricardo D. Enriz
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Chacabuco 915, 5700 San Luis, Argentina; (O.P.); (A.D.G.)
| | - Aleš Imramovský
- Institute of Organic Chemistry and Technology, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532 10 Pardubice, Czech Republic; (P.M.); (K.P.)
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Structure activity relationships and the binding mode of quinolinone-pyrimidine hybrids as reversal agents of multidrug resistance mediated by P-gp. Sci Rep 2021; 11:16856. [PMID: 34413359 PMCID: PMC8376931 DOI: 10.1038/s41598-021-96226-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/06/2021] [Indexed: 02/07/2023] Open
Abstract
P-gp-associated multidrug resistance is a major impediment to the success of chemotherapy. With the aim of finding non-toxic and effective P-gp inhibitors, we investigated a panel of quinolin-2-one-pyrimidine hybrids. Among the active compounds, two of them significantly increased intracellular doxorubicin and rhodamine 123 accumulation by inhibiting the efflux mediated by P-gp and restored doxorubicin toxicity at nanomolar range. Structure-activity relationships showed that the number of methoxy groups, an optimal length of the molecule in its extended conformation, and at least one flexible methylene group bridging the quinolinone to the moiety bearing the pyrimidine favored the inhibitory potency of P-gp. The best compounds showed a similar binding pattern and interactions to those of doxorubicin and tariquidar, as revealed by MD and hybrid QM/MM simulations performed with the recent experimental structure of P-gp co-crystallized with paclitaxel. Analysis of the molecular interactions stabilizing the different molecular complexes determined by MD and QTAIM showed that binding to key residues from TMH 4-7 and 12 is required for inhibition.
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Jiang X, Zhang Z, Zuo J, Wu C, Zha L, Xu Y, Wang S, Shi J, Liu XH, Zhang J, Tang W. Novel cannabidiol-carbamate hybrids as selective BuChE inhibitors: Docking-based fragment reassembly for the development of potential therapeutic agents against Alzheimer's disease. Eur J Med Chem 2021; 223:113735. [PMID: 34371367 DOI: 10.1016/j.ejmech.2021.113735] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/08/2021] [Accepted: 07/28/2021] [Indexed: 01/04/2023]
Abstract
Cannabidiol (CBD) and rivastigmine have been launched as drugs for treating dementia and cholinesterases (ChEs) are ideal drug targets. This study focused on developing novel ChE inhibitors as drug leads against dementia through molecular modeling and fragment reassembly approaches. A potent carbamate fragment binding to active site gorge of BuChE was found via a docking-based structural splicing approach, thus, 17 novel compounds were designed by structural reassembly. Compound C16 was identified as a highly selective potent BuChE inhibitor (IC50 = 5.3 nM, SI > 4000), superior to CBD (IC50 = 0.67 μM). C16 possessed BBB penetrating ability, benign safety, neuroprotection, antioxidant and pseudo-irreversible BuChE inhibition (Kd = 13 nM, k2 = 0.26 min-1), showing good drug-like properties. In vivo studies confirmed that C16 significantly ameliorated the scopolamine-induced cognition impairment, almost entirely recovered the Aβ1-42 (icv)-impaired cognitive function to the normal level, showed better behavioral performance than donepezil and good anti-amyloidogenic effect. Hence, the potential BuChE inhibitor C16 can be developed as a promising disease-modifying treatment of AD.
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Affiliation(s)
- Xia Jiang
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, 230032, China
| | - Ziwen Zhang
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, 230032, China
| | - Jiawei Zuo
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, 230032, China
| | - Chengyao Wu
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, 230032, China
| | - Liang Zha
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, 230032, China
| | - Yingying Xu
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, 230032, China
| | - Sheng Wang
- Center for Scientific Research, Anhui Medical University, Hefei, 230032, China
| | - Jingbo Shi
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, 230032, China
| | - Xin-Hua Liu
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, 230032, China
| | - Jing Zhang
- Anhui Prevention and Treatment Center for Occupational Disease, Anhui No. 2 Provincial People's Hospital, Hefei, 230041, China.
| | - Wenjian Tang
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, 230032, China.
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10
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Chen H, Yang X, Sun P, Zhi Y, Yao Q, Liu B. L-ascorbyl 6-palmitate as lead compound targeting SphK1: an in silico and in vitro investigation. JOURNAL OF CHEMICAL RESEARCH 2021. [DOI: 10.1177/17475198211001819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Sphingosine kinases (SphKs) are a class of lipid kinases, that have received extensive attention as important rate-limiting enzyme in tumor. Inhibition of the activity of SphK1 can lead to an anticancer effect. Herein, we describe the discovery process and biological characteristics of a new SphK1 inhibitor, ascorbyl palmitate, discovered through computer-aided drug design. Biochemical experiments show that ascorbyl palmitate has a strong inhibitory effect on SphK1, with an IC50 value of 6.4 μM. The MTT experiment showed that ascorbyl palmitate had anti-cancer effects toward the U87, A549, 22RV1, and A375 cell lines. Among them, ascorbyl palmitate has prominent inhibitory activity against the 22RV1 cell line, with an IC50 value of 41.57 μM. To explore the structure–activity relationship, four ascorbyl palmitate derivatives were synthesized and tested for kinase activity. The outstanding effect of ascorbyl palmitate toward SphK1 and its known non-toxicity suggest that ascorbyl palmitate may be a lead compound for the development of effective SphK1 anti-cancer inhibitors.
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Affiliation(s)
- HaiJiao Chen
- Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, P.R. China
| | - Xinmei Yang
- Department of Clinical Pharmacy, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, P.R. China
| | - Peng Sun
- Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, P.R. China
| | - Ying Zhi
- Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, P.R. China
| | - Qingqiang Yao
- Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, P.R. China
| | - Bo Liu
- Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, P.R. China
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11
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Ding T, Zhi Y, Xie W, Yao Q, Liu B. Rational design of SphK inhibitors using crystal structures aided by computer. Eur J Med Chem 2021; 213:113164. [PMID: 33454547 DOI: 10.1016/j.ejmech.2021.113164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/09/2020] [Accepted: 01/04/2021] [Indexed: 10/22/2022]
Abstract
Sphingosine kinases (SphKs) are lipid kinases that catalyze the phosphorylation of sphingosine (Sph) to sphingosine-1-phosphate (S1P). As a bioactive lipid, S1P plays a role outside and inside the cell to regulate biological processes. The overexpression of SphKs is related to a variety of pathophysiological conditions. Targeting the S1P signaling pathway is a potential treatment strategy for many diseases. SphKs are key kinases of the S1P signaling pathway. The SphK family includes two isoforms: SphK1 and SphK2. Determination of the co-crystal structure of SphK1 with various inhibitors has laid a solid foundation for the development of small molecule inhibitors targeting SphKs. This paper reviews the differences and connections between the two isoforms and the structure of SphK1 crystals, especially the structure of its Sph "J-shaped" channel binding site. This review also summarizes the recent development of SphK1 and SphK2 selective inhibitors and the exploration of the unresolved SphK2 structure.
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Affiliation(s)
- Tiandi Ding
- Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, PR China
| | - Ying Zhi
- Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, PR China
| | - Weilin Xie
- Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, PR China
| | - Qingqiang Yao
- Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, PR China.
| | - Bo Liu
- Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, PR China.
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12
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Rojas S, Parravicini O, Vettorazzi M, Tosso R, Garro A, Gutiérrez L, Andújar S, Enriz R. Combined MD/QTAIM techniques to evaluate ligand-receptor interactions. Scope and limitations. Eur J Med Chem 2020; 208:112792. [PMID: 32949964 DOI: 10.1016/j.ejmech.2020.112792] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 12/29/2022]
Abstract
In medicinal chemistry, it is extremely important to evaluate, as accurately as possible, the molecular interactions involved in the formation of different ligand-receptor (L-R) complexes. Evaluating the different molecular interactions by quantum mechanics calculations is not a simple task, since formation of an L-R complex is a dynamic process. In this case, the use of combined techniques of molecular dynamics (MD) and quantum calculations is one the best possible approaches. In this work we report a comparative study using combined MD and QTAIM (Quantum Theory of Atoms In Molecules) calculations for five biological systems with different levels of structural complexity. We have studied Acetylcholinesterase (AChE), D2 Dopamine Receptor (D2DR), beta Secretase (BACE1), Dihydrofolate Reductase (DHFR) and Sphingosine Kinase 1 (SphK1). In these molecular targets, we have analyzed different ligands with diverse structural characteristics. The inhibitory activities of most of them have been previously measured in our laboratory. Our results indicate that QTAIM calculations can be extremely useful for in silico studies. It is possible to obtain very accurate information about the strength of the molecular interactions that stabilize the formation of the different L-R complexes. Better correlations can be obtained between theoretical and experimental data by using QTAIM calculations, allowing us to discriminate among ligands with similar affinities. QTAIM analysis gives fairly accurate information for weak interactions which are not well described by MD simulations. QTAIM study also allowed us to evaluate and determine which parts of the ligand need to be modified in order to increase its interactions with the molecular target. In this study we have discussed the importance of combined MD/QTAIM calculations for this type of simulations, showing their scopes and limitations.
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Affiliation(s)
- Sebastián Rojas
- IMIBIO-SL CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de Los Andes 950, 5700, San Luis, Argentina
| | - Oscar Parravicini
- IMIBIO-SL CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de Los Andes 950, 5700, San Luis, Argentina
| | - Marcela Vettorazzi
- IMIBIO-SL CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de Los Andes 950, 5700, San Luis, Argentina
| | - Rodrigo Tosso
- IMIBIO-SL CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de Los Andes 950, 5700, San Luis, Argentina
| | - Adriana Garro
- IMIBIO-SL CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de Los Andes 950, 5700, San Luis, Argentina
| | - Lucas Gutiérrez
- IMIBIO-SL CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de Los Andes 950, 5700, San Luis, Argentina
| | - Sebastián Andújar
- IMIBIO-SL CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de Los Andes 950, 5700, San Luis, Argentina
| | - Ricardo Enriz
- IMIBIO-SL CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de Los Andes 950, 5700, San Luis, Argentina.
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13
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Campos LE, Garibotto F, Angelina E, Kos J, Gonec T, Marvanova P, Vettorazzi M, Oravec M, Jendrzejewska I, Jampilek J, Alvarez SE, Enriz RD. Hydroxynaphthalenecarboxamides and substituted piperazinylpropandiols, two new series of BRAF inhibitors. A theoretical and experimental study. Bioorg Chem 2020; 103:104145. [PMID: 32801082 DOI: 10.1016/j.bioorg.2020.104145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/17/2020] [Accepted: 07/24/2020] [Indexed: 12/19/2022]
Abstract
The oncogenic mutated kinase BRAFV600E is an attractive molecular target because it is expressed in several human cancers, including melanoma. To present, only three BRAF small inhibitors are approved by the FDA for the treatment of patients with metastatic melanoma: Vemurafenib, Dabrafenib and Encorafenib. Although many protocol treatments have been probed in clinical trials, BRAF inhibition has a limited effectiveness because patients invariably develop resistance and secondary toxic effects associated with the therapy. These limitations highlight the importance of designing new and better inhibitors with different structures that could establish different interactions in the active site of the enzyme and therefore decrease resistance progress. Considering the data from our previous report, here we studied two series of derivatives of structural scaffolds as potential BRAF inhibitors: hydroxynaphthalenecarboxamides and substituted piperazinylpropandiols. Our results indicate that structural analogues of substituted piperazinylpropandiols do not show significantly better activities to that previously reported. In contrast, the hydroxynaphthalenecarboxamides derivatives significantly inhibited cell viability and ERK phosphorylation, a measure of BRAF activity, in Lu1205 BRAFV600E melanoma cells. In order to better understand these experimental results, we carried out a molecular modeling study using different combined techniques: docking, MD simulations and quantum theory of atoms in molecules (QTAIM) calculations. Thus, by using this approach we determined that the molecular interactions that stabilize the different molecular complexes are closely related to Vemurafenib, a well-documented BRAF inhibitor. Furthermore, we found that bi-substituted compounds may interact more strongly respect to the mono-substituted analogues, by establishing additional interactions with the DFG-loop at the BRAF-active site. On the bases of these results we synthesized and tested a new series of hydroxynaphthalenecarboxamides bi-substituted. Remarkably, all these compounds displayed significant inhibitory effects on the bioassays performed. Thus, the structural information reported here is important for the design of new BRAFV600E inhibitors possessing this type of structural scaffold.
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Affiliation(s)
- Ludmila E Campos
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Ejército de los Andes 950, 5700 San Luis, Argentina
| | - Francisco Garibotto
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Ejército de los Andes 950, 5700 San Luis, Argentina
| | - Emilio Angelina
- Laboratorio de Estructura Molecular y Propiedades, Área de Química Física, Departamento de Química, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Avda. Libertad 5460, (3400) Corrientes, Argentina
| | - Jiri Kos
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Slechtitelu 27, 78371 Olomouc, Czech Republic
| | - Tomas Gonec
- Department of Chemical Drugs, Faculty of Pharmacy, Masaryk University, Palackeho 1, 612 00 Brno, Czech Republic
| | - Pavlina Marvanova
- Department of Chemical Drugs, Faculty of Pharmacy, Masaryk University, Palackeho 1, 612 00 Brno, Czech Republic
| | - Marcela Vettorazzi
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Ejército de los Andes 950, 5700 San Luis, Argentina
| | - Michal Oravec
- Global Change Research Institute CAS, Belidla 986/4a, 603 00 Brno, Czech Republic
| | | | - Josef Jampilek
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Slechtitelu 27, 78371 Olomouc, Czech Republic
| | - Sergio E Alvarez
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Ejército de los Andes 950, 5700 San Luis, Argentina.
| | - Ricardo D Enriz
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Ejército de los Andes 950, 5700 San Luis, Argentina.
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14
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Newton J, Palladino END, Weigel C, Maceyka M, Gräler MH, Senkal CE, Enriz RD, Marvanova P, Jampilek J, Lima S, Milstien S, Spiegel S. Targeting defective sphingosine kinase 1 in Niemann-Pick type C disease with an activator mitigates cholesterol accumulation. J Biol Chem 2020; 295:9121-9133. [PMID: 32385114 PMCID: PMC7335787 DOI: 10.1074/jbc.ra120.012659] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 04/29/2020] [Indexed: 12/12/2022] Open
Abstract
Niemann-Pick type C (NPC) disease is a lysosomal storage disorder arising from mutations in the cholesterol-trafficking protein NPC1 (95%) or NPC2 (5%). These mutations result in accumulation of low-density lipoprotein-derived cholesterol in late endosomes/lysosomes, disruption of endocytic trafficking, and stalled autophagic flux. Additionally, NPC disease results in sphingolipid accumulation, yet it is unique among the sphingolipidoses because of the absence of mutations in the enzymes responsible for sphingolipid degradation. In this work, we examined the cause for sphingosine and sphingolipid accumulation in multiple cellular models of NPC disease and observed that the activity of sphingosine kinase 1 (SphK1), one of the two isoenzymes that phosphorylate sphingoid bases, was markedly reduced in both NPC1 mutant and NPC1 knockout cells. Conversely, SphK1 inhibition with the isotype-specific inhibitor SK1-I in WT cells induced accumulation of cholesterol and reduced cholesterol esterification. Of note, a novel SphK1 activator (SK1-A) that we have characterized decreased sphingoid base and complex sphingolipid accumulation and ameliorated autophagic defects in both NPC1 mutant and NPC1 knockout cells. Remarkably, in these cells, SK1-A also reduced cholesterol accumulation and increased cholesterol ester formation. Our results indicate that a SphK1 activator rescues aberrant cholesterol and sphingolipid storage and trafficking in NPC1 mutant cells. These observations highlight a previously unknown link between SphK1 activity, NPC1, and cholesterol trafficking and metabolism.
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Affiliation(s)
- Jason Newton
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA.
| | - Elisa N D Palladino
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Cynthia Weigel
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Michael Maceyka
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Markus H Gräler
- Department of Anesthesiology and Intensive Care Medicine, Center for Sepsis Control and Care (CSCC), and Center for Molecular Biomedicine (CMB), University Hospital Jena, Jena, Germany
| | - Can E Senkal
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Ricardo D Enriz
- Facultad de Quimica, Bioquimica, y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-CONICET), San Luis, Argentina
| | - Pavlina Marvanova
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
| | - Josef Jampilek
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Santiago Lima
- Department of Biology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Sheldon Milstien
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Sarah Spiegel
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA.
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15
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Pospisilova S, Malik I, Curillova J, Michnova H, Cerna L, Padrtova T, Hosek J, Pecher D, Cizek A, Jampilek J. Insight into antimicrobial activity of substituted phenylcarbamoyloxypiperazinylpropanols. Bioorg Chem 2020; 102:104060. [PMID: 32663668 DOI: 10.1016/j.bioorg.2020.104060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/20/2020] [Accepted: 06/26/2020] [Indexed: 12/23/2022]
Abstract
3-[4-(Substituted)phenyl-/4-(diphenylmethyl)phenylpiperazin-1-yl]-2-hydroxypropyl-1-[(substituted)phenyl]carbamates and their salts with hydrochloric acid were synthesized, characterized, and tested in vitro against Staphylococcus aureus ATCC 29213 and Enterococcus faecalis ATCC 29212 as reference and quality control strains, against three methicillin-resistant isolates of S. aureus, and three isolates of vancomycin-resistant E. faecalis. All the compounds were evaluated against Mycobacterium tuberculosis H37Ra/ATCC 25177, M. kansasii DSM 44162, and M. smegmatis ATCC 700084. All of the tested compounds demonstrated very good activity against all the tested strains/isolates comparable with or better than that of clinically used drugs (ampicillin, ciprofloxacin, vancomycin, isoniazid). 1-[{(3-Trifluoromethyl)phenyl}carbamoyloxy-2-hydroxypropyl]-4-(3,4-dichlorophenyl)piperazin-1-ium chloride demonstrated the highest potency against all the tested strains/isolates (MICs ranged from 3.78 to 30.2 µM), and 1-[{(3-trifluoromethyl)phenyl}carbamoyloxy-2-hydroxypropyl]-4-(diphenylmethyl)piperazin-1-ium chloride was the most effective against all the screened mycobacterial strains (MICs ranged from 3.64 to 14.5 µM). All the investigated derivatives had strong antibiofilm activity against S. aureus ATCC 29123 and a synergistic or additive effect with gentamicin against isolates of E. faecalis with both intrinsic and acquired resistance to gentamicin. The screening of the cytotoxicity of the compounds was performed using human monocytic leukemia THP-1 cells. The IC50 values of the most effective compounds ranged from ca. 2.8 to 7.3 µM; thus, it can be stated that the antimicrobial effect is closely connected with their cytotoxicity. These observations disqualify these compounds from further development as antimicrobial agents, but they can be considered potential multi-target drugs with a preferred anticancer effect with good water solubility and additional anti-infectious activity.
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Affiliation(s)
- Sarka Pospisilova
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Slechtitelu 27, 783 71 Olomouc, Czech Republic
| | - Ivan Malik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University in Bratislava, Odbojarov 10, 832 32 Bratislava, Slovak Republic.
| | - Jana Curillova
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University in Bratislava, Odbojarov 10, 832 32 Bratislava, Slovak Republic
| | - Hana Michnova
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Slechtitelu 27, 783 71 Olomouc, Czech Republic
| | - Lucie Cerna
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Slechtitelu 27, 783 71 Olomouc, Czech Republic
| | - Tereza Padrtova
- Department of Chemical Drugs, Faculty of Pharmacy, Masaryk University, Palackeho 1946/1, 612 00 Brno, Czech Republic
| | - Jan Hosek
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Slechtitelu 27, 783 71 Olomouc, Czech Republic
| | - Daniel Pecher
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Odbojarov 10, 832 32 Bratislava, Slovak Republic
| | - Alois Cizek
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences, Palackeho 1946/1, 612 42 Brno, Czech Republic
| | - Josef Jampilek
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Slechtitelu 27, 783 71 Olomouc, Czech Republic.
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16
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Roy S, Mahapatra AD, Mohammad T, Gupta P, Alajmi MF, Hussain A, Rehman MT, Datta B, Hassan MI. Design and Development of Novel Urea, Sulfonyltriurea, and Sulfonamide Derivatives as Potential Inhibitors of Sphingosine Kinase 1. Pharmaceuticals (Basel) 2020; 13:E118. [PMID: 32526899 PMCID: PMC7346089 DOI: 10.3390/ph13060118] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 05/30/2020] [Accepted: 06/01/2020] [Indexed: 12/17/2022] Open
Abstract
Sphingosine kinase 1 (SphK1) is one of the well-studied drug targets for cancer and inflammatory diseases. Recently discovered small-molecule inhibitors of SphK1 have been recommended in cancer therapeutics; however, selectivity and potency of first-generation inhibitors are great challenge. In search of effective SphK1 inhibitors, a set of small molecules have been designed and synthesized bearing urea, sulfonylurea, sulfonamide, and sulfonyltriurea groups. The binding affinity of these inhibitors was measured by fluorescence-binding assay and isothermal titration calorimetry. Compounds 1, 5, 6, and 7 showed an admirable binding affinity to the SphK1 in the sub-micromolar range and significantly inhibited SphK1 activity with admirable IC50 values. Molecular docking studies revealed that these compounds fit well into the sphingosine binding pocket of SphK1 and formed significant number of hydrogen bonds and van der Waals interactions. These molecules may be exploited as potent and selective inhibitors of SphK1 that could be implicated in cancer therapeutics after the required in vivo validation.
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Affiliation(s)
- Sonam Roy
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (S.R.); (T.M.); (P.G.)
| | - Amarjyoti Das Mahapatra
- Department of Chemistry, Indian Institute of Technology, Palaj, Gandhinagar, Gujarat 382355, India;
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (S.R.); (T.M.); (P.G.)
| | - Preeti Gupta
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (S.R.); (T.M.); (P.G.)
| | - Mohamed F. Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (M.F.A.); (A.H.); (M.T.R.)
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (M.F.A.); (A.H.); (M.T.R.)
| | - Md. Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (M.F.A.); (A.H.); (M.T.R.)
| | - Bhaskar Datta
- Department of Chemistry, Indian Institute of Technology, Palaj, Gandhinagar, Gujarat 382355, India;
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (S.R.); (T.M.); (P.G.)
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17
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Papakyriakou A, Cencetti F, Puliti E, Morelli L, Tricomi J, Bruni P, Compostella F, Richichi B. Glycans Meet Sphingolipids: Structure-Based Design of Glycan Containing Analogues of a Sphingosine Kinase Inhibitor. ACS Med Chem Lett 2020; 11:913-920. [PMID: 32435405 PMCID: PMC7236250 DOI: 10.1021/acsmedchemlett.9b00665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 03/30/2020] [Indexed: 01/23/2023] Open
Abstract
Sphingosine 1-phosphate (S1P) is a bioactive lipid mediator associated with diverse homeostatic and signaling roles. Enhanced biosynthesis of S1P, mediated by the sphingosine kinase isozymes (SK1 and SK2), is implicated in several pathophysiological conditions and diseases, including skeletal muscle fibrosis, inflammation, multiple sclerosis, and cancer. Therefore, therapeutic approaches that control S1P production have focused on the development of SK1/2 inhibitors. In this framework, we designed a series of natural monosaccharide-based compounds to enhance anchoring of the known SK1 inhibitor PF-543 at the polar head of the J-shaped substrate-binding channel. Herein, we describe the structure-based design and synthesis of new glycan-containing PF-543 analogues and we demonstrate their efficiency in a TGFβ1-induced pro-fibrotic assay.
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Affiliation(s)
- Athanasios Papakyriakou
- Institute
of Biosciences & Applications, National
Centre for Scientific Research “Demokritos”, GR-15341 Agia Paraskevi, Athens, Greece
| | - Francesca Cencetti
- Department
of Experimental and Clinical Biomedical Sciences, University of Florence, Viale GB Morgagni 50, 50134 Firenze, Italy
| | - Elisa Puliti
- Department
of Experimental and Clinical Biomedical Sciences, University of Florence, Viale GB Morgagni 50, 50134 Firenze, Italy
| | - Laura Morelli
- Department
of Medical Biotechnology and Translational Medicine, University of Milan, Via Saldini 50, 20133 Milano, Italy
| | - Jacopo Tricomi
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, FI, Italy)
| | - Paola Bruni
- Department
of Experimental and Clinical Biomedical Sciences, University of Florence, Viale GB Morgagni 50, 50134 Firenze, Italy
| | - Federica Compostella
- Department
of Medical Biotechnology and Translational Medicine, University of Milan, Via Saldini 50, 20133 Milano, Italy
- Federica Compostella,
| | - Barbara Richichi
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, FI, Italy)
- Barbara Richichi,
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18
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Pospisilova S, Marvanova P, Treml J, Moricz AM, Ott PG, Mokry P, Odehnalova K, Sedo O, Cizek A, Jampilek J. Activity of N-Phenylpiperazine Derivatives Against Bacterial and Fungal Pathogens. Curr Protein Pept Sci 2020; 20:1119-1129. [PMID: 31518219 DOI: 10.2174/1389203720666190913114041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/01/2019] [Accepted: 04/04/2019] [Indexed: 01/21/2023]
Abstract
BACKGROUND As the bacterial resistance to antibacterial chemotherapeutics is one of the greatest problems in modern medicine, efforts are made to develop new antimicrobial drugs. Compounds with a piperazine ring have proved to be promising agents against various pathogens. OBJECTIVE The aim of the study was to prepare a series of new N-phenylpiperazines and determine their activity against various pathogens. METHOD Target compounds were prepared by multi-step synthesis starting from an appropriate substituted acid to an oxirane intermediate reacting with 1-(4-nitrophenyl)piperazine. Lipophilicity and pKa values were experimentally determined. Other molecular parameters were calculated. The inhibitory activity of the target compounds against Staphylococcus aureus, four mycobacteria strains, Bipolaris sorokiniana, and Fusarium avenaceum was tested. In vitro antiproliferative activity was determined on a THP-1 cell line, and toxicity against plant was determined using Nicotiana tabacum. RESULTS In general, most compounds demonstrated only moderate effects. 1-(2-Hydroxy-3-{[4-(propan- 2-yloxy)benzoyl]oxy}propyl)-4-(4-nitrophenyl)piperazinediium dichloride and 1-{3-[(4-butoxybenzoyl)- oxy]-2-hydroxypropyl}-4-(4-nitrophenyl)piperazinediium dichloride showed the highest inhibition activity against M. kansasii (MIC = 15.4 and 15.0 µM, respectively) and the latter also against M. marinum (MIC = 15.0 µM). 1-(2-Hydroxy-3-{[4-(2-propoxyethoxy)benzoyl]oxy}propyl)-4-(4-nitrophenyl)piperazinediium dichloride had the highest activity against F. avenaceum (MIC = 14.2 µM). All the compounds showed only insignificant toxic effects on human and plant cells. CONCLUSION Ten new 1-(4-nitrophenyl)piperazine derivatives were prepared and analyzed, and their antistaphylococcal, antimycobacterial, and antifungal activities were determined. The activity against M. kansasii was positively influenced by higher lipophilicity, the electron-donor properties of substituent R and a lower dissociation constant. The exact mechanism of action will be investigated in follow-up studies.
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Affiliation(s)
- Sarka Pospisilova
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Pavlina Marvanova
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
| | - Jakub Treml
- Department of Molecular Biology and Pharmaceutical Biotechnology, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
| | - Agnes M Moricz
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Peter G Ott
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Petr Mokry
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
| | - Klara Odehnalova
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
| | - Ondrej Sedo
- Research Group of Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Alois Cizek
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
| | - Josef Jampilek
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Olomouc, Czech Republic
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19
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Magli E, Corvino A, Fiorino F, Frecentese F, Perissutti E, Saccone I, Santagada V, Caliendo G, Severino B. Design of Sphingosine Kinases Inhibitors: Challenges and Recent Developments. Curr Pharm Des 2020; 25:956-968. [PMID: 30947653 DOI: 10.2174/1381612825666190404115424] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 03/27/2019] [Indexed: 12/28/2022]
Abstract
BACKGROUND Sphingosine kinases (SphKs) catalyze the phosphorylation of sphingosine to form the bioactive sphingolipid metabolite sphingosine-1-phosphate (S1P). S1P is an important lipid mediator with a wide range of biological functions; it is also involved in a variety of diseases such as inflammatory diseases, Alzheimer's disease and cancer. METHODS This review reports the recent advancement in the research of SphKs inhibitors. Our purpose is also to provide a complete overview useful for underlining the features needed to select a specific pharmacological profile. DISCUSSION Two distinct mammalian SphK isoforms have been identified, SphK1 and SphK2. These isoforms are encoded by different genes and exhibit distinct subcellular localizations, biochemical properties and functions. SphK1 and SphK2 inhibition can be useful in different pathological conditions. CONCLUSION SphK1 and SphK2 have many common features but different and even opposite biological functions. For this reason, several research groups are interested in understanding the therapeutic usefulness of a selective or non-selective inhibitor of SphKs. Moreover, a compensatory mechanism for the two isoforms has been demonstrated, thus leading to the development of dual inhibitors.
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Affiliation(s)
- Elisa Magli
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Angela Corvino
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Ferdinando Fiorino
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Francesco Frecentese
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Elisa Perissutti
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Irene Saccone
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Vincenzo Santagada
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Giuseppe Caliendo
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Beatrice Severino
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Naples, Italy
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20
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Luchi A, Villafañe RN, Gómez Chávez JL, Bogado ML, Angelina EL, Peruchena NM. Combining Charge Density Analysis with Machine Learning Tools To Investigate the Cruzain Inhibition Mechanism. ACS OMEGA 2019; 4:19582-19594. [PMID: 31788588 PMCID: PMC6881835 DOI: 10.1021/acsomega.9b01934] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 10/18/2019] [Indexed: 05/28/2023]
Abstract
Trypanosoma cruzi, a flagellate protozoan parasite, is responsible for Chagas disease. The parasite major cysteine protease, cruzain (Cz), plays a vital role at every stage of its life cycle and the active-site region of the enzyme, similar to those of other members of the papain superfamily, is well characterized. Taking advantage of structural information available in public databases about Cz bound to known covalent inhibitors, along with their corresponding activity annotations, in this work, we performed a deep analysis of the molecular interactions at the Cz binding cleft, in order to investigate the enzyme inhibition mechanism. Our toolbox for performing this study consisted of the charge density topological analysis of the complexes to extract the molecular interactions and machine learning classification models to relate the interactions with biological activity. More precisely, such a combination was useful for the classification of molecular interactions as "active-like" or "inactive-like" according to whether they are prevalent in the most active or less active complexes, respectively. Further analysis of interactions with the help of unsupervised learning tools also allowed the understanding of how these interactions come into play together to trigger the enzyme into a particular conformational state. Most active inhibitors induce some conformational changes within the enzyme that lead to an overall better fit of the inhibitor into the binding cleft. Curiously, some of these conformational changes can be considered as a hallmark of the substrate recognition event, which means that most active inhibitors are likely recognized by the enzyme as if they were its own substrate so that the catalytic machinery is arranged as if it is about to break the substrate scissile bond. Overall, these results contribute to a better understanding of the enzyme inhibition mechanism. Moreover, the information about main interactions extracted through this work is already being used in our lab to guide docking solutions in ongoing prospective virtual screening campaigns to search for novel noncovalent cruzain inhibitors.
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21
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Vettorazzi M, Insuasty D, Lima S, Gutiérrez L, Nogueras M, Marchal A, Abonia R, Andújar S, Spiegel S, Cobo J, Enriz RD. Design of new quinolin-2-one-pyrimidine hybrids as sphingosine kinases inhibitors. Bioorg Chem 2019; 94:103414. [PMID: 31757412 DOI: 10.1016/j.bioorg.2019.103414] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 12/27/2022]
Abstract
Sphingosine-1-phosphate is now emerging as an important player in cancer, inflammation, autoimmune, neurological and cardiovascular disorders. Abundance evidence in animal and humans cancer models has shown that SphK1 is linked to cancer. Thus, there is a great interest in the development new SphK1 inhibitors as a potential new treatment for cancer. In a search for new SphK1 inhibitors we selected the well-known SKI-II inhibitor as the starting structure and we synthesized a new inhibitor structurally related to SKI-II with a significant but moderate inhibitory effect. In a second approach, based on our molecular modeling results, we designed new structures based on the structure of PF-543, the most potent known SphK1 inhibitor. Using this approach, we report the design, synthesis and biological evaluation of a new series of compounds with inhibitory activity against both SphK1 and SphK2. These new inhibitors were obtained incorporating new connecting chains between their polar heads and hydrophobic tails. On the other hand, the combined techniques of molecular dynamics simulations and QTAIM calculations provided complete and detailed information about the molecular interactions that stabilize the different complexes of these new inhibitors with the active sites of the SphK1. This information will be useful in the design of new SphK inhibitors.
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Affiliation(s)
- Marcela Vettorazzi
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL). Ejercito de los Andes 950, 5700 San Luis, Argentina
| | - Daniel Insuasty
- Departamento de Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia; Inorganic and Organic Department, University of Jaén, Campus Las Lagunillas s/n, 23071 Jaén, Spain
| | - Santiago Lima
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298 USA
| | - Lucas Gutiérrez
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL). Ejercito de los Andes 950, 5700 San Luis, Argentina
| | - Manuel Nogueras
- Inorganic and Organic Department, University of Jaén, Campus Las Lagunillas s/n, 23071 Jaén, Spain
| | - Antonio Marchal
- Inorganic and Organic Department, University of Jaén, Campus Las Lagunillas s/n, 23071 Jaén, Spain
| | - Rodrigo Abonia
- Research Group of Heterocyclic Compounds, Department of Chemistry, Universidad del Valle, A. A. 25360 Cali, Colombia
| | - Sebastián Andújar
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL). Ejercito de los Andes 950, 5700 San Luis, Argentina
| | - Sarah Spiegel
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298 USA
| | - Justo Cobo
- Inorganic and Organic Department, University of Jaén, Campus Las Lagunillas s/n, 23071 Jaén, Spain.
| | - Ricardo D Enriz
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL). Ejercito de los Andes 950, 5700 San Luis, Argentina.
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22
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Campos LE, Garibotto FM, Angelina E, Kos J, Tomašič T, Zidar N, Kikelj D, Gonec T, Marvanova P, Mokry P, Jampilek J, Alvarez SE, Enriz RD. Searching new structural scaffolds for BRAF inhibitors. An integrative study using theoretical and experimental techniques. Bioorg Chem 2019; 91:103125. [PMID: 31401373 DOI: 10.1016/j.bioorg.2019.103125] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/04/2019] [Accepted: 07/11/2019] [Indexed: 01/12/2023]
Abstract
The identification of the V600E activating mutation in the protein kinase BRAF in around 50% of melanoma patients has driven the development of highly potent small inhibitors (BRAFi) of the mutated protein. To date, Dabrafenib and Vemurafenib, two specific BRAFi, have been clinically approved for the treatment of metastatic melanoma. Unfortunately, after the initial response, tumors become resistant and patients develop a progressive and lethal disease, making imperative the development of new therapeutic options. The main objective of this work was to find new BRAF inhibitors with different structural scaffolds than those of the known inhibitors. Our study was carried out in different stages; in the first step we performed a virtual screening that allowed us to identify potential new inhibitors. In the second step, we synthesized and tested the inhibitory activity of the novel compounds founded. Finally, we conducted a molecular modelling study that allowed us to understand interactions at the molecular level that stabilize the formation of the different molecular complexes. Our theoretical and experimental study allowed the identification of four new structural scaffolds, which could be used as starting structures for the design and development of new inhibitors of BRAF. Our experimental data indicate that the most active compounds reduced significantly ERK½ phosphorylation, a measure of BRAF inhibition, and cell viability. Thus, from our theoretical and experimental results, we propose new substituted hydroxynaphthalenecarboxamides, N-(hetero)aryl-piperazinylhydroxyalkylphenylcarbamates, substituted piperazinylethanols and substituted piperazinylpropandiols as initial structures for the development of new inhibitors for BRAF. Moreover, by performing QTAIM analysis, we are able to describe in detail the molecular interactions that stabilize the different Ligand-Receptor complexes. Such analysis indicates which portion of the different molecules must be changed in order to obtain an increase in the binding affinity of these new ligands.
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Affiliation(s)
- Ludmila E Campos
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de los Andes 950, 5700 San Luis, Argentina; Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Ejército de los Andes 950, 5700 San Luis, Argentina
| | - Francisco M Garibotto
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de los Andes 950, 5700 San Luis, Argentina; Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Ejército de los Andes 950, 5700 San Luis, Argentina
| | - Emilio Angelina
- Laboratorio de Estructura Molecular y Propiedades, Área de Química Física, Departamento de Química, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Avda. Libertad 5460, 3400 Corrientes, Argentina
| | - Jiri Kos
- Division of Biologically Active Complexes and Molecular Magnets, Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University Olomouc, Slechtitelu 27, 78371 Olomouc, Czech Republic
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Nace Zidar
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Danijel Kikelj
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Tomas Gonec
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho 1, 61242 Brno, Czech Republic
| | - Pavlina Marvanova
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho 1, 61242 Brno, Czech Republic
| | - Petr Mokry
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho 1, 61242 Brno, Czech Republic
| | - Josef Jampilek
- Division of Biologically Active Complexes and Molecular Magnets, Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University Olomouc, Slechtitelu 27, 78371 Olomouc, Czech Republic; Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 84215 Bratislava, Slovakia
| | - Sergio E Alvarez
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de los Andes 950, 5700 San Luis, Argentina; Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Ejército de los Andes 950, 5700 San Luis, Argentina.
| | - Ricardo D Enriz
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de los Andes 950, 5700 San Luis, Argentina; Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Ejército de los Andes 950, 5700 San Luis, Argentina.
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Novel Benzene-Based Carbamates for AChE/BChE Inhibition: Synthesis and Ligand/Structure-Oriented SAR Study. Int J Mol Sci 2019; 20:ijms20071524. [PMID: 30934674 PMCID: PMC6479915 DOI: 10.3390/ijms20071524] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 03/19/2019] [Accepted: 03/23/2019] [Indexed: 12/26/2022] Open
Abstract
A series of new benzene-based derivatives was designed, synthesized and comprehensively characterized. All of the tested compounds were evaluated for their in vitro ability to potentially inhibit the acetyl- and butyrylcholinesterase enzymes. The selectivity index of individual molecules to cholinesterases was also determined. Generally, the inhibitory potency was stronger against butyryl- compared to acetylcholinesterase; however, some of the compounds showed a promising inhibition of both enzymes. In fact, two compounds (23, benzyl ethyl(1-oxo-1-phenylpropan-2-yl)carbamate and 28, benzyl (1-(3-chlorophenyl)-1-oxopropan-2-yl) (methyl)carbamate) had a very high selectivity index, while the second one (28) reached the lowest inhibitory concentration IC50 value, which corresponds quite well with galanthamine. Moreover, comparative receptor-independent and receptor-dependent structure–activity studies were conducted to explain the observed variations in inhibiting the potential of the investigated carbamate series. The principal objective of the ligand-based study was to comparatively analyze the molecular surface to gain insight into the electronic and/or steric factors that govern the ability to inhibit enzyme activities. The spatial distribution of potentially important steric and electrostatic factors was determined using the probability-guided pharmacophore mapping procedure, which is based on the iterative variable elimination method. Additionally, planar and spatial maps of the host–target interactions were created for all of the active compounds and compared with the drug molecules using the docking methodology.
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24
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Vettorazzi M, Vila L, Lima S, Acosta L, Yépes F, Palma A, Cobo J, Tengler J, Malik I, Alvarez S, Marqués P, Cabedo N, Sanz MJ, Jampilek J, Spiegel S, Enriz RD. Synthesis and biological evaluation of sphingosine kinase 2 inhibitors with anti-inflammatory activity. Arch Pharm (Weinheim) 2019; 352:e1800298. [DOI: 10.1002/ardp.201800298] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/28/2018] [Accepted: 12/05/2018] [Indexed: 01/19/2023]
Affiliation(s)
- Marcela Vettorazzi
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis; Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL); San Luis Argentina
| | - Laura Vila
- Department of Pharmacology; University of Valencia; Valencia Spain
- Institute of Health Research INCLIVA University Clinic Hospital of Valencia; Valencia Spain
| | - Santiago Lima
- Department of Biology and Department of Biochemistry and Molecular Biology; Virginia Commonwealth University School of Medicine; Richmond Virginia
| | - Lina Acosta
- Laboratorio de Síntesis Orgánica, Escuela de Química; Universidad Industrial de Santander; Bucaramanga Colombia
| | - Felipe Yépes
- Laboratorio de Síntesis Orgánica, Escuela de Química; Universidad Industrial de Santander; Bucaramanga Colombia
| | - Alirio Palma
- Laboratorio de Síntesis Orgánica, Escuela de Química; Universidad Industrial de Santander; Bucaramanga Colombia
| | - Justo Cobo
- Inorganic and Organic Department; University of Jaén; Jaén Spain
| | - Jan Tengler
- Medis International a.s.; Bolatice Czech Republic
| | - Ivan Malik
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry; Comenius University; Bratislava Slovakia
| | - Sergio Alvarez
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis; Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL); San Luis Argentina
| | - Patrice Marqués
- Department of Pharmacology; University of Valencia; Valencia Spain
- Institute of Health Research INCLIVA University Clinic Hospital of Valencia; Valencia Spain
| | - Nuria Cabedo
- Department of Pharmacology; University of Valencia; Valencia Spain
- Institute of Health Research INCLIVA University Clinic Hospital of Valencia; Valencia Spain
| | - María J. Sanz
- Department of Pharmacology; University of Valencia; Valencia Spain
- Institute of Health Research INCLIVA University Clinic Hospital of Valencia; Valencia Spain
| | - Josef Jampilek
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry; Comenius University; Bratislava Slovakia
| | - Sarah Spiegel
- Department of Biology and Department of Biochemistry and Molecular Biology; Virginia Commonwealth University School of Medicine; Richmond Virginia
| | - Ricardo D. Enriz
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis; Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL); San Luis Argentina
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25
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Theoretical models to predict the inhibitory effect of ligands of sphingosine kinase 1 using QTAIM calculations and hydrogen bond dynamic propensity analysis. J Comput Aided Mol Des 2018; 32:781-791. [DOI: 10.1007/s10822-018-0129-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/02/2018] [Indexed: 11/27/2022]
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Synthesis and In Vitro Antimycobacterial Activity of Novel N-Arylpiperazines Containing an Ethane-1,2-diyl Connecting Chain. Molecules 2017; 22:molecules22122100. [PMID: 29189762 PMCID: PMC6149664 DOI: 10.3390/molecules22122100] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 11/20/2017] [Accepted: 11/27/2017] [Indexed: 11/17/2022] Open
Abstract
Novel 1-(2-{3-/4-[(alkoxycarbonyl)amino]phenyl}-2-hydroxyethyl)-4-(2-fluorophenyl)-piperazin-1-ium chlorides (alkoxy = methoxy to butoxy; 8a-h) have been designed and synthesized through multistep reactions as a part of on-going research programme focused on finding new antimycobacterials. Lipophilic properties of these compounds were estimated by RP-HPLC using methanol/water mobile phases with a various volume fraction of the organic modifier. The log kw values, which were extrapolated from intercepts of a linear relationship between the logarithm of a retention factor k (log k) and volume fraction of a mobile phase modifier (ϕM), varied from 2.113 (compound 8e) to 2.930 (compound 8h) and indicated relatively high lipophilicity of these salts. Electronic properties of the molecules 8a-h were investigated by evaluation of their UV/Vis spectra. In a next phase of the research, the compounds 8a-h were in vitro screened against M. tuberculosis CNCTC My 331/88 (identical with H37Rv and ATCC 2794), M. kansasii CNCTC My 235/80 (identical with ATCC 12478), a M. kansasii 6 509/96 clinical isolate, M. avium CNCTC My 330/80 (identical with ATCC 25291) and M. avium intracellulare ATCC 13950, respectively, as well as against M. kansasii CIT11/06, M. avium subsp. paratuberculosis CIT03 and M. avium hominissuis CIT10/08 clinical isolates using isoniazid, ethambutol, ofloxacin, ciprofloxacin or pyrazinamide as reference drugs. The tested compounds 8a-h were found to be the most promising against M. tuberculosis; a MIC = 8 μM was observed for the most effective 1-(2-{4-[(butoxycarbonyl)amino]phen-ylphenyl}-2-hydroxyethyl)-4-(2-fluorophenyl)piperazin-1-ium chloride (8h). In addition, all of them showed low (insignificant) in vitro toxicity against a human monocytic leukemia THP-1 cell line, as observed LD50 values > 30 μM indicated. The structure-antimycobacterial activity relationships of the analyzed 8a-h series are also discussed.
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27
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Proline-Based Carbamates as Cholinesterase Inhibitors. Molecules 2017; 22:molecules22111969. [PMID: 29135926 PMCID: PMC6150311 DOI: 10.3390/molecules22111969] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 10/28/2017] [Accepted: 11/10/2017] [Indexed: 12/25/2022] Open
Abstract
Series of twenty-five benzyl (2S)-2-(arylcarbamoyl)pyrrolidine-1-carboxylates was prepared and completely characterized. All the compounds were tested for their in vitro ability to inhibit acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), and the selectivity of compounds to individual cholinesterases was determined. Screening of the cytotoxicity of all the compounds was performed using a human monocytic leukaemia THP-1 cell line, and the compounds demonstrated insignificant toxicity. All the compounds showed rather moderate inhibitory effect against AChE; benzyl (2S)-2-[(2-chlorophenyl)carbamoyl]pyrrolidine-1-carboxylate (IC50 = 46.35 μM) was the most potent agent. On the other hand, benzyl (2S)-2-[(4-bromophenyl)-] and benzyl (2S)-2-[(2-bromophenyl)carbamoyl]pyrrolidine-1-carboxylates expressed anti-BChE activity (IC50 = 28.21 and 27.38 μM, respectively) comparable with that of rivastigmine. The ortho-brominated compound as well as benzyl (2S)-2-[(2-hydroxyphenyl)carbamoyl]pyrrolidine-1-carboxylate demonstrated greater selectivity to BChE. The in silico characterization of the structure–inhibitory potency for the set of proline-based carbamates considering electronic, steric and lipophilic properties was provided using comparative molecular surface analysis (CoMSA) and principal component analysis (PCA). Moreover, the systematic space inspection with splitting data into the training/test subset was performed to monitor the statistical estimators performance in the effort to map the probability-guided pharmacophore pattern. The comprehensive screening of the AChE/BChE profile revealed potentially relevant structural and physicochemical features that might be essential for mapping of the carbamates inhibition efficiency indicating qualitative variations exerted on the reaction site by the substituent in the 3′-/4′-position of the phenyl ring. In addition, the investigation was completed by a molecular docking study of recombinant human AChE.
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Gonec T, Kos J, Pesko M, Dohanosova J, Oravec M, Liptaj T, Kralova K, Jampilek J. Halogenated 1-Hydroxynaphthalene-2-Carboxanilides Affecting Photosynthetic Electron Transport in Photosystem II. Molecules 2017; 22:molecules22101709. [PMID: 29023407 PMCID: PMC6151762 DOI: 10.3390/molecules22101709] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 10/09/2017] [Indexed: 12/29/2022] Open
Abstract
Series of seventeen new multihalogenated 1-hydroxynaphthalene-2-carboxanilides was prepared and characterized. All the compounds were tested for their activity related to the inhibition of photosynthetic electron transport (PET) in spinach (Spinacia oleracea L.) chloroplasts. 1-Hydroxy-N-phenylnaphthalene-2-carboxamides substituted in the anilide part by 3,5-dichloro-, 4-bromo-3-chloro-, 2,5-dibromo- and 3,4,5-trichloro atoms were the most potent PET inhibitors (IC50 = 5.2, 6.7, 7.6 and 8.0 µM, respectively). The inhibitory activity of these compounds depends on the position and the type of halogen substituents, i.e., on lipophilicity and electronic properties of individual substituents of the anilide part of the molecule. Interactions of the studied compounds with chlorophyll a and aromatic amino acids present in pigment-protein complexes mainly in PS II were documented by fluorescence spectroscopy. The section between P680 and plastoquinone QB in the PET chain occurring on the acceptor side of PS II can be suggested as the site of action of the compounds. The structure-activity relationships are discussed.
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Affiliation(s)
- Tomas Gonec
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Palackeho 1, Brno 61242, Czech Republic.
| | - Jiri Kos
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Palackeho 1, Brno 61242, Czech Republic.
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University, Odbojarov 10, Bratislava 83232, Slovakia.
| | - Matus Pesko
- Department of Environmental Ecology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, Bratislava 84215, Slovakia.
| | - Jana Dohanosova
- Central Laboratories, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinskeho 9, Bratislava 81237, Slovakia.
| | - Michal Oravec
- Global Change Research Institute CAS, Belidla 986/4a, 60300 Brno, Czech Republic.
| | - Tibor Liptaj
- Central Laboratories, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinskeho 9, Bratislava 81237, Slovakia.
| | - Katarina Kralova
- Institute of Chemistry, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, Bratislava 84215, Slovakia.
| | - Josef Jampilek
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University, Odbojarov 10, Bratislava 83232, Slovakia.
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