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Shafiq M, Sherwani ZA, Mushtaq M, Nur-E-Alam M, Ahmad A, Ul-Haq Z. A deep learning-based theoretical protocol to identify potentially isoform-selective PI3Kα inhibitors. Mol Divers 2024:10.1007/s11030-023-10799-0. [PMID: 38305819 DOI: 10.1007/s11030-023-10799-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/22/2023] [Indexed: 02/03/2024]
Abstract
Phosphoinositide 3-kinase alpha (PI3Kα) is one of the most frequently dysregulated kinases known for their pivotal role in many oncogenic diseases. While the side effects linked to existing drugs against PI3Kα-induced cancers provide an avenue for further research, the significant structural conservation among PI3Ks makes it extremely difficult to develop new isoform-selective PI3Kα inhibitors. Embracing this challenge, we herein designed a hybrid protocol by integrating machine learning (ML) with in silico drug-designing strategies. A deep learning classification model was developed and trained on the physicochemical descriptors data of known PI3Kα inhibitors and used as a screening filter for a database of small molecules. This approach led us to the prediction of 662 compounds showcasing appropriate features to be considered as PI3Kα inhibitors. Subsequently, a multiphase molecular docking was applied to further characterize the predicted hits in terms of their binding affinities and binding modes in the targeted cavity of the PI3Kα. As a result, a total of 12 compounds were identified whereas the best poses highlighted the efficiency of these ligands in maintaining interactions with the crucial residues of the protein to be targeted for the inhibition of associated activity. Notably, potential activity of compound 12 in counteracting PI3Kα function was found in a previous in vitro study. Following the drug-likeness and pharmacokinetic characterizations, six compounds (compounds 1, 2, 3, 6, 7, and 11) with suitable ADME-T profiles and promising bioavailability were selected. The mechanistic studies in dynamic mode further endorsed the potential of identified hits in blocking the ATP-binding site of the receptor with higher binding affinities than the native inhibitor, alpelisib (BYL-719), particularly the compounds 1, 2, and 11. These outcomes support the reliability of the developed classification model and the devised computational strategy for identifying new isoform-selective drug candidates for PI3Kα inhibition.
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Affiliation(s)
- Muhammad Shafiq
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Zaid Anis Sherwani
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Mamona Mushtaq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Mohammad Nur-E-Alam
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box. 2457, Riyadh, 11451, Kingdom of Saudi Arabia
| | - Aftab Ahmad
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, 92618, USA
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
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Zhang K, Liu Y, Jia H, Wang H, Deng M, Liu Y, Zhao X, Xiu X, Li Z, Yang H, Cheng M. Design, synthesis, and evaluation of N-methyl-propargylamine derivates as isoform-selective monoamine oxidases inhibitors for the treatment of nervous system diseases. Bioorg Chem 2023; 134:106441. [PMID: 36854233 DOI: 10.1016/j.bioorg.2023.106441] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/16/2023] [Accepted: 02/19/2023] [Indexed: 02/25/2023]
Abstract
A novel series of N-methyl-propargylamine derivates were designed, synthesized, and evaluated as isoform-selective monoamine oxidases (MAO) inhibitors for the treatment of nervous system diseases. The in vitro studies showed some of the compounds exhibited considerable MAO-A selective inhibitory activity (IC50 of 14.86-17.16 nM), while some of the others exhibited great MAO-B selective inhibitory activity (IC50 of 4.37-17.00 nM). Further studies revealed that compounds A2 (IC50 against MAO-A: 17.16 ± 1.17 nM) and A5 (IC50 against MAO-B: 17.00 ± 1.10 nM) had significant abilities to protect PC12 cells from H2O2-induced apoptosis and reactive oxygen species (ROS) production. The parallel artificial membrane permeability assay showed A2 and A5 would be potent to cross the blood-brain barrier. The results indicated that A2 showed potential use in the therapy of MAO-A related diseases, such as depression and anxiety; while A5 exhibited promising ability in the treatment of MAO-B related diseases, such as Alzheimer's disease and Parkinson's disease.
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Affiliation(s)
- Kaicheng Zhang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning, Shenyang 110016, China
| | - Yang Liu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning, Shenyang 110016, China
| | - Hongwei Jia
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning, Shenyang 110016, China
| | - Hanxun Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning, Shenyang 110016, China
| | - Minghui Deng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning, Shenyang 110016, China
| | - Yaoyang Liu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning, Shenyang 110016, China
| | - Xueqi Zhao
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning, Shenyang 110016, China
| | - Xiaomeng Xiu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning, Shenyang 110016, China
| | - Zhenli Li
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning, Shenyang 110016, China
| | - Huali Yang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning, Shenyang 110016, China.
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning, Shenyang 110016, China.
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Zaraei SO, El-Gamal MI, Shafique Z, Amjad ST, Afridi S, Zaib S, Anbar HS, El-Gamal R, Iqbal J. Sulfonate and sulfamate derivatives possessing benzofuran or benzothiophene nucleus as potent carbonic anhydrase II/IX/XII inhibitors. Bioorg Med Chem 2019; 27:3889-3901. [PMID: 31345748 DOI: 10.1016/j.bmc.2019.07.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/10/2019] [Accepted: 07/12/2019] [Indexed: 12/30/2022]
Abstract
In the current work, we report the discovery of new sulfonate and sulfamate derivatives of benzofuran- and benzothiophene as potent inhibitors of human carbonic anhydrases (hCAs) II, IX and XII. A set of derivatives, 1a-t, having different substituents on the fused benzofuran and benzothiophene rings (R = alkyl, cyclohexyl, aryl, NH2, NHMe, or NMe2) was designed and synthesized. Most of the derivatives exhibited higher potency than acetazolamide as inhibitors of the purified hCAII, IX and XII isoforms. The most potent inhibitors for hCAII, hCAIX and hCAXII were 1g, 1b and 1d with an IC50 ± SEM values of 0.14 ± 0.03, 0.13 ± 0.03 and 0.17 ± 0.06 µM, respectively. In addition, compounds 1d and 1n exerted preferential inhibitory effect against hCAXII isozyme with good potencies. Some selected compounds were docked within the active pocket of these isozymes and binding of the molecules revealed that sulfonate and sulfamate rings were located towards the active cavity and compounds coordinated to zinc ions.
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Affiliation(s)
- Seyed-Omar Zaraei
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Mohammed I El-Gamal
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, United Arab Emirates; Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates; Faculty of Pharmacy, University of Mansoura, Mansoura 35516, Egypt.
| | - Zainab Shafique
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Sayyeda Tayyeba Amjad
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Saifullah Afridi
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan; Department of Biological Sciences (DBS), National University of Medical Sciences (NUMS), Secretariat c/o Military Hospital, Adjacent to Armed Force Institute of Cardiology, The Mall Rawalpindi 46000, Pakistan
| | - Sumera Zaib
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Hanan S Anbar
- Faculty of Pharmacy, University of Mansoura, Mansoura 35516, Egypt
| | - Randa El-Gamal
- Department of Medical Biochemistry, Faculty of Medicine, University of Mansoura, Mansoura 35516, Egypt
| | - Jamshed Iqbal
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan.
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Costa G, Carta F, Ambrosio FA, Artese A, Ortuso F, Moraca F, Rocca R, Romeo I, Lupia A, Maruca A, Bagetta D, Catalano R, Vullo D, Alcaro S, Supuran CT. A computer-assisted discovery of novel potential anti-obesity compounds as selective carbonic anhydrase VA inhibitors. Eur J Med Chem 2019; 181:111565. [PMID: 31387062 DOI: 10.1016/j.ejmech.2019.111565] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/25/2019] [Accepted: 07/26/2019] [Indexed: 11/25/2022]
Abstract
The human Carbonic anhydrases (hCA) VA and VB play a key role in ureagenesis, gluconeogenesis, lipogenesis and in the metabolism regulation, thus representing highly popular drug targets. Albeit several hCA inhibitors have been designed and are currently in clinical use, serious drug interactions have been reported due to their poor selectivity. In this perspective, the drug repurposing approach could be a useful tool in order to investigate the drug promiscuity/polypharmacology profile. In this study, virtual screening techniques and in vitro assays were combined to identify novel selective hCA VA inhibitors from among around 94000 compounds. The docking analysis highlighted 12 promising best hits, biologically characterized in terms of their hCA VA inhibitory activity. Interestingly, among them, the anticancer agents fludarabine and lenvatinib and the antiepileptic rufinamide were able to selectively inhibit the enzyme activity in the micromolar range, while a pyrido-indole derivative, the homovanillic acid sulfate and the desacetyl metabolite of the antibacterial cephapirin in the nanomolar range.
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Affiliation(s)
- Giosuè Costa
- Dipartimento di Scienze della Salute, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy; Net4Science Academic Spin-Off, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Fabrizio Carta
- Dipartimento NEUROFARBA, Sezione di Scienze Farmaceutiche, Università; degli Studi di Firenze, Sesto Fiorentino, Florence, Italy
| | - Francesca Alessandra Ambrosio
- Dipartimento di Scienze della Salute, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Anna Artese
- Dipartimento di Scienze della Salute, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy; Net4Science Academic Spin-Off, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy.
| | - Francesco Ortuso
- Dipartimento di Scienze della Salute, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy; Net4Science Academic Spin-Off, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Federica Moraca
- Department of Pharmacy, University "Federico II" of Naples, Via D. Montesano, 49 I-80131, Naples, Italy; Net4Science Academic Spin-Off, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy; Dipartimento di Scienze della Salute, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Roberta Rocca
- Dipartimento di Scienze della Salute, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy; Department of Experimental and Clinical Medicine, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy; Net4Science Academic Spin-Off, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Isabella Romeo
- Dipartimento di Chimica e Tecnologie chimiche, Università della Calabria, Via Pietro Bucci, 87036, Arcavacata di Rende, Cosenza, Italy; Net4Science Academic Spin-Off, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Antonio Lupia
- Dipartimento di Scienze della Salute, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy; Net4Science Academic Spin-Off, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Annalisa Maruca
- Dipartimento di Scienze della Salute, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy; Net4Science Academic Spin-Off, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Donatella Bagetta
- Dipartimento di Scienze della Salute, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy; Net4Science Academic Spin-Off, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Raffaella Catalano
- Dipartimento di Scienze della Salute, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy; Net4Science Academic Spin-Off, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Daniela Vullo
- Dipartimento NEUROFARBA, Sezione di Scienze Farmaceutiche, Università; degli Studi di Firenze, Sesto Fiorentino, Florence, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy; Net4Science Academic Spin-Off, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Claudiu T Supuran
- Dipartimento NEUROFARBA, Sezione di Scienze Farmaceutiche, Università; degli Studi di Firenze, Sesto Fiorentino, Florence, Italy
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Krasavin M, Shetnev A, Baykov S, Kalinin S, Nocentini A, Sharoyko V, Poli G, Tuccinardi T, Korsakov M, Tennikova TB, Supuran CT. Pyridazinone-substituted benzenesulfonamides display potent inhibition of membrane-bound human carbonic anhydrase IX and promising antiproliferative activity against cancer cell lines. Eur J Med Chem 2019; 168:301-314. [PMID: 30826507 DOI: 10.1016/j.ejmech.2019.02.044] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/10/2019] [Accepted: 02/12/2019] [Indexed: 01/09/2023]
Abstract
An expanded set of pyridazine-containing benzene sulfonamides was investigated for inhibition of four human carbonic anhydrase isoforms, which revealed a pronounced inhibition trend toward hCA IX, a cancer-related, membrane-bound isoform of the enzyme. Comparison of antiproliferative effects of these compounds against cancer (PANC-1) and normal (ARPE-19) cells at 50 μM concentration narrowed the selection of compounds to the eight which displayed selective growth inhibition toward the cancer cells. More detailed investigation in concentration-dependent mode against normal (ARPE-19) and two cancer cell lines (PANC-1 and SK-MEL-2) identified two lead compounds one of which displayed a notable cytotoxicity toward pancreatic cancer cells while the other targeted the melanoma cells. These findings significantly expand the knowledge base concerning the hCA IX inhibitors whose inhibitory potency against a recombinant enzyme translates into selective anticancer activity under hypoxic conditions which are aimed to model the environment of a growing tumor.
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Affiliation(s)
- Mikhail Krasavin
- Saint Petersburg State University, Saint Petersburg, 199034, Russian Federation.
| | - Anton Shetnev
- The Ushinsky Yaroslavl State Pedagogical University, Yaroslavl, 150000, Russian Federation
| | - Sergey Baykov
- Saint Petersburg State University, Saint Petersburg, 199034, Russian Federation
| | - Stanislav Kalinin
- Saint Petersburg State University, Saint Petersburg, 199034, Russian Federation
| | - Alessio Nocentini
- Neurofarba Department, Universita degli Studi di Firenze, Florence, Italy
| | - Vladimir Sharoyko
- Saint Petersburg State University, Saint Petersburg, 199034, Russian Federation
| | - Giulio Poli
- Department of Pharmacy, University of Pisa, 56126, Pisa, Italy
| | | | - Mikhail Korsakov
- The Ushinsky Yaroslavl State Pedagogical University, Yaroslavl, 150000, Russian Federation
| | - Tatiana B Tennikova
- Saint Petersburg State University, Saint Petersburg, 199034, Russian Federation
| | - Claudiu T Supuran
- Neurofarba Department, Universita degli Studi di Firenze, Florence, Italy.
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Krasavin M, Shetnev A, Sharonova T, Baykov S, Kalinin S, Nocentini A, Sharoyko V, Poli G, Tuccinardi T, Presnukhina S, Tennikova TB, Supuran CT. Continued exploration of 1,2,4-oxadiazole periphery for carbonic anhydrase-targeting primary arene sulfonamides: Discovery of subnanomolar inhibitors of membrane-bound hCA IX isoform that selectively kill cancer cells in hypoxic environment. Eur J Med Chem 2018; 164:92-105. [PMID: 30594030 DOI: 10.1016/j.ejmech.2018.12.049] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/20/2018] [Accepted: 12/20/2018] [Indexed: 01/01/2023]
Abstract
An expanded set of diversely substituted 1,2,4-oxadiazole-containing primary aromatic sulfonamides was synthesized and tested for inhibition of human carbonic anhydrase I, II, IX and XII isoforms. The initial biochemical profiling revealed a significantly more potent inhibition of cancer-related, membrane-bound isoform hCA IX (reaching into submicromolar range), on top of potent inhibition of hCA XII that is another cancer target. The observed structure-activity relationships have been rationalized by molecular modeling. Comparative single-concentration profiling of the carbonic anhydrase inhibitors synthesized for antiproliferative effects against normal (ARPE-19) and cancer (PANC-1) cell lines under chemically induced hypoxia conditions revealed several candidate compounds selectively targeting cancer cells. More in-depth characterization of these leads revealed two structurally related compounds that showed promising selective cytotoxicity against pancreatic cancer (PANC-1) and melanoma (SK-MEL-2) cell lines.
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Affiliation(s)
- Mikhail Krasavin
- Saint Petersburg State University, Saint Petersburg, 199034, Russian Federation.
| | - Anton Shetnev
- The Ushinsky Yaroslavl State Pedagogical University, Yaroslavl, 150000, Russian Federation
| | - Tatyana Sharonova
- Saint Petersburg State University, Saint Petersburg, 199034, Russian Federation
| | - Sergey Baykov
- Saint Petersburg State University, Saint Petersburg, 199034, Russian Federation
| | - Stanislav Kalinin
- Saint Petersburg State University, Saint Petersburg, 199034, Russian Federation
| | - Alessio Nocentini
- Neurofarba Department, Universita degli Studi di Firenze, Florence, Italy
| | - Vladimir Sharoyko
- Saint Petersburg State University, Saint Petersburg, 199034, Russian Federation
| | - Giulio Poli
- Department of Pharmacy, University of Pisa, 56126, Pisa, Italy
| | | | - Sofia Presnukhina
- The Ushinsky Yaroslavl State Pedagogical University, Yaroslavl, 150000, Russian Federation
| | - Tatiana B Tennikova
- Saint Petersburg State University, Saint Petersburg, 199034, Russian Federation
| | - Claudiu T Supuran
- Neurofarba Department, Universita degli Studi di Firenze, Florence, Italy.
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