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Morak-Młodawska B, Jeleń M, Martula E, Korlacki R. Study of Lipophilicity and ADME Properties of 1,9-Diazaphenothiazines with Anticancer Action. Int J Mol Sci 2023; 24:ijms24086970. [PMID: 37108135 PMCID: PMC10138389 DOI: 10.3390/ijms24086970] [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: 04/03/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Lipophilicity is one of the key properties of a potential drug that determines the solubility, the ability to penetrate through cell barriers, and transport to the molecular target. It affects pharmacokinetic processes such as adsorption, distribution, metabolism, excretion (ADME). The 10-substituted 1,9-diazaphenothiazines show promising if not impressive in vitro anticancer potential, which is associated with the activation of the mitochondrial apoptosis pathway connected with to induction BAX, forming a channel in MOMP and releasing cytochrome c for the activation of caspases 9 and 3. In this publication, the lipophilicity of previously obtained 1,9-diazaphenothiazines was determined theoretically using various computer programs and experimentally using reverse-phase thin-layer chromatography (RP-TLC) and a standard curve. The study presents other physicochemical, pharmacokinetic, and toxicological properties affecting the bioavailability of the test compounds. ADME analysis was determined in silico using the SwissADME server. Molecular targets studies were identified in silico using the SwissTargetPrediction server. Lipinski's rule of five, Ghose's, and Veber's rules were checked for the tested compounds, confirming their bioavailability.
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Affiliation(s)
- Beata Morak-Młodawska
- Department of Organic Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, The Medical University of SilesiaJagiellońska 4, 41-200 Sosnowiec, Poland
| | - Małgorzata Jeleń
- Department of Organic Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, The Medical University of SilesiaJagiellońska 4, 41-200 Sosnowiec, Poland
| | - Emilia Martula
- Doctoral School, The Medical University of Silesia, 40-055 Katowice, Poland
| | - Rafał Korlacki
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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Fontes JV, Santos IA, Rosa LB, Lima RLA, Jardim ACG, Miguel DC, Abbehausen C. Antileishmanial and Anti‐Chikungunya Activity of Cu(I)‐N‐Heterocyclic Carbenes. ChemistrySelect 2022. [DOI: 10.1002/slct.202201560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Josielle V. Fontes
- Institute of Chemistry University of Campinas - UNICAMP PO Box 6154 13083-970 Campinas SP Brazil
| | - Igor A. Santos
- Institute of Biomedical Sciences Federal University of Uberlândia Uberlandia MG Brazil
| | - Letícia B. Rosa
- Institute of Biology University of Campinas - UNICAMP 13083-862 Campinas SP Brazil
| | - Rochanna L. A. Lima
- Institute of Chemistry University of Campinas - UNICAMP PO Box 6154 13083-970 Campinas SP Brazil
| | - Ana C. G. Jardim
- Institute of Biomedical Sciences Federal University of Uberlândia Uberlandia MG Brazil
| | - Danilo C. Miguel
- Institute of Biology University of Campinas - UNICAMP 13083-862 Campinas SP Brazil
| | - Camilla Abbehausen
- Institute of Chemistry University of Campinas - UNICAMP PO Box 6154 13083-970 Campinas SP Brazil
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Schlagintweit JF, Jakob CHG, Meighen-Berger K, Gronauer TF, Weigert Muñoz A, Weiß V, Feige MJ, Sieber SA, Correia JDG, Kühn FE. Fluorescent palladium(II) and platinum(II) NHC/1,2,3-triazole complexes: antiproliferative activity and selectivity against cancer cells. Dalton Trans 2021; 50:2158-2166. [PMID: 33496310 DOI: 10.1039/d0dt04114a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Fluorescent Pd(ii) and Pt(ii) complexes bearing 4-methylene-7-methoxycoumarin (MMC) and 2,6-diispropylphenyl (Dipp) substituted NHC/1,2,3-triazole hybrid ligands are described. Depending on the reaction conditions two different ligand coordination modes are observed, i.e., bidentate solely coordinating via NHCs or tetradentate coordinating via NHCs and 1,2,3-triazoles. All Dipp substituted complexes show antiproliferative activity against cervix (HeLa) and breast (MCF-7) human carcinoma cells. The activity significantly depends on the coordination mode, with the tetradentate motif being notably more effective (HeLa: IC50 = 3.9 μM to 4.7 μM; MCF-7: IC50 = 2.07 μM to 2.35 μM). Amongst the MMC series, only the Pd(ii) complex featuring the bidentate coordination mode is active against HeLa (IC50 = 6.1 μM). In contrast to its structurally related Dipp derivative (SI = 0.6), it shows a high selectivity for HeLa (SI > 16) compared to healthy skin cells (HaCaT). According to fluorescence microscopy, this compound is presumably located in late endosomes or lysosomes.
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Affiliation(s)
- Jonas F Schlagintweit
- Molecular Catalysis, Catalysis Research Center and Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, D-85748 Garching bei München, Germany.
| | - Christian H G Jakob
- Molecular Catalysis, Catalysis Research Center and Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, D-85748 Garching bei München, Germany.
| | - Kevin Meighen-Berger
- Cellular Protein Biochemistry, Department of Chemistry and Institute for Advanced Study, Technische Universität München, Lichtenbergstraße 4, D-85748 Garching bei München, Germany
| | - Thomas F Gronauer
- Chair of Organic Chemistry II, Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, D-85748 Garching bei München, Germany
| | - Angela Weigert Muñoz
- Chair of Organic Chemistry II, Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, D-85748 Garching bei München, Germany
| | - Vanessa Weiß
- Molecular Catalysis, Catalysis Research Center and Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, D-85748 Garching bei München, Germany. and Ausbildungszentrum der Technischen Universität München, Lichtenbergstraße 4, D-85748 Garching bei München, Germany
| | - Matthias J Feige
- Cellular Protein Biochemistry, Department of Chemistry and Institute for Advanced Study, Technische Universität München, Lichtenbergstraße 4, D-85748 Garching bei München, Germany
| | - Stephan A Sieber
- Chair of Organic Chemistry II, Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, D-85748 Garching bei München, Germany
| | - João D G Correia
- Centro de Ciências e Tecnologias Nucleares and Departamento de Engenharia e Ciências Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Campus Tecnológico e Nuclear, Estrada Nacional N°10 (km 139, 7), 2695-066 Bobadela LRS, Portugal
| | - Fritz E Kühn
- Molecular Catalysis, Catalysis Research Center and Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, D-85748 Garching bei München, Germany.
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Cabrera-Andrade A, López-Cortés A, Munteanu CR, Pazos A, Pérez-Castillo Y, Tejera E, Arrasate S, González-Díaz H. Perturbation-Theory Machine Learning (PTML) Multilabel Model of the ChEMBL Dataset of Preclinical Assays for Antisarcoma Compounds. ACS OMEGA 2020; 5:27211-27220. [PMID: 33134682 PMCID: PMC7594149 DOI: 10.1021/acsomega.0c03356] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
Sarcomas are a group of malignant neoplasms of connective tissue with a different etiology than carcinomas. The efforts to discover new drugs with antisarcoma activity have generated large datasets of multiple preclinical assays with different experimental conditions. For instance, the ChEMBL database contains outcomes of 37,919 different antisarcoma assays with 34,955 different chemical compounds. Furthermore, the experimental conditions reported in this dataset include 157 types of biological activity parameters, 36 drug targets, 43 cell lines, and 17 assay organisms. Considering this information, we propose combining perturbation theory (PT) principles with machine learning (ML) to develop a PTML model to predict antisarcoma compounds. PTML models use one function of reference that measures the probability of a drug being active under certain conditions (protein, cell line, organism, etc.). In this paper, we used a linear discriminant analysis and neural network to train and compare PT and non-PT models. All the explored models have an accuracy of 89.19-95.25% for training and 89.22-95.46% in validation sets. PTML-based strategies have similar accuracy but generate simplest models. Therefore, they may become a versatile tool for predicting antisarcoma compounds.
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Affiliation(s)
- Alejandro Cabrera-Andrade
- Grupo
de Bio-Quimioinformática, Universidad
de Las Américas, de los Granados Avenue, Quito 170125, Ecuador
- Carrera
de Enfermería, Facultad de Ciencias de la Salud, Universidad de Las Américas, de los Granados Avenue, Quito 170125, Ecuador
- RNASA-IMEDIR,
Computer Sciences Faculty, University of
A Coruña, A Coruña 15071, Spain
| | - Andrés López-Cortés
- RNASA-IMEDIR,
Computer Sciences Faculty, University of
A Coruña, A Coruña 15071, Spain
- Centro
de Investigación Genética y Genómica, Facultad
de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Mariscal Sucre Avenue, Quito 170129, Ecuador
| | - Cristian R. Munteanu
- RNASA-IMEDIR,
Computer Sciences Faculty, University of
A Coruña, A Coruña 15071, Spain
- Biomedical
Research Institute of A Coruña (INIBIC), University Hospital Complex of A Coruña (CHUAC), A Coruña 15006, Spain
- Centro de
Investigación en Tecnologías de la Información
y las Comunicaciones (CITIC), Campus de
Elviña s/n, A Coruña 15071, Spain
| | - Alejandro Pazos
- RNASA-IMEDIR,
Computer Sciences Faculty, University of
A Coruña, A Coruña 15071, Spain
- Biomedical
Research Institute of A Coruña (INIBIC), University Hospital Complex of A Coruña (CHUAC), A Coruña 15006, Spain
| | - Yunierkis Pérez-Castillo
- Grupo
de Bio-Quimioinformática, Universidad
de Las Américas, de los Granados Avenue, Quito 170125, Ecuador
- Escuela
de Ciencias Físicas y Matemáticas, Universidad de Las Américas, de los Granados Avenue, Quito 170125, Ecuador
| | - Eduardo Tejera
- Grupo
de Bio-Quimioinformática, Universidad
de Las Américas, de los Granados Avenue, Quito 170125, Ecuador
- Facultad
de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, de los Granados Avenue, Quito 170125, Ecuador
| | - Sonia Arrasate
- Department
of Organic Chemistry II and Basque Center for Biophysics, University of Basque Country UPV/EHU, Leioa 48940, Biscay, Spain
| | - Humbert González-Díaz
- Department
of Organic Chemistry II and Basque Center for Biophysics, University of Basque Country UPV/EHU, Leioa 48940, Biscay, Spain
- Ikerbasque,
Basque Foundation for Science, Bilbao 48011, Biscay, Spain
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Poole CF, Atapattu SN. Determination of physicochemical properties of small molecules by reversed-phase liquid chromatography. J Chromatogr A 2020; 1626:461427. [DOI: 10.1016/j.chroma.2020.461427] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/19/2020] [Accepted: 07/22/2020] [Indexed: 02/07/2023]
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6
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Ciura K, Fedorowicz J, Andrić F, Žuvela P, Greber KE, Baranowski P, Kawczak P, Nowakowska J, Bączek T, Sączewski J. Lipophilicity Determination of Antifungal Isoxazolo[3,4- b]pyridin-3(1 H)-ones and Their N1-Substituted Derivatives with Chromatographic and Computational Methods. Molecules 2019; 24:E4311. [PMID: 31779124 PMCID: PMC6930598 DOI: 10.3390/molecules24234311] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/14/2019] [Accepted: 11/21/2019] [Indexed: 11/16/2022] Open
Abstract
The lipophilicity of a molecule is a well-recognized as a crucial physicochemical factor that conditions the biological activity of a drug candidate. This study was aimed to evaluate the lipophilicity of isoxazolo[3,4-b]pyridine-3(1H)-ones and their N1-substituted derivatives, which demonstrated pronounced antifungal activities. Several methods, including reversed-phase thin layer chromatography (RP-TLC), reversed phase high-performance liquid chromatography (RP-HPLC), and micellar electrokinetic chromatography (MEKC), were employed. Furthermore, the calculated logP values were estimated using various freely and commercially available software packages and online platforms, as well as density functional theory computations (DFT). Similarities and dissimilarities between the determined lipophilicity indices were assessed using several chemometric approaches. Principal component analysis (PCA) indicated that other features beside lipophilicity affect antifungal activities of the investigated derivatives. Quantitative-structure-retention-relationship (QSRR) analysis by means of genetic algorithm-partial least squares (GA-PLS)-was implemented to rationalize the link between the physicochemical descriptors and lipophilicity. Among the studied compounds, structure 16 should be considered as the best starting structure for further studies, since it demonstrated the lowest lipophilic character within the series while retaining biological activity. Sum of ranking differences (SRD) analysis indicated that the chromatographic approach, regardless of the technique employed, should be considered as the best approach for lipophilicity assessment of isoxazolones.
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Affiliation(s)
- Krzesimir Ciura
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland; (K.E.G.); (P.B.); (J.N.)
| | - Joanna Fedorowicz
- Department of Chemical Technology of Drugs, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland;
| | - Filip Andrić
- Department of Analytical Chemistry, University of Belgrade—Faculty of Chemistry, Studentski trg 12–16, 11000 Belgrade, Serbia;
| | - Petar Žuvela
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland; (P.Ž.); (P.K.); (T.B.)
| | - Katarzyna Ewa Greber
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland; (K.E.G.); (P.B.); (J.N.)
| | - Paweł Baranowski
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland; (K.E.G.); (P.B.); (J.N.)
| | - Piotr Kawczak
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland; (P.Ž.); (P.K.); (T.B.)
| | - Joanna Nowakowska
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland; (K.E.G.); (P.B.); (J.N.)
| | - Tomasz Bączek
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland; (P.Ž.); (P.K.); (T.B.)
| | - Jarosław Sączewski
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland;
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Affiliation(s)
- Sonia Lobo
- Department of Medical Education, Geisinger Commonwealth School of Medicine, Scranton, PA, USA
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