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Kairytė K, Vaickelionienė R, Grybaitė B, Anusevičius K, Mickevičius V, Petrikaitė V. The Effect of 4-(Dimethylamino)phenyl-5-oxopyrrolidines on Breast and Pancreatic Cancer Cell Colony Formation, Migration, and Growth of Tumor Spheroids. Int J Mol Sci 2024; 25:1834. [PMID: 38339112 PMCID: PMC10855844 DOI: 10.3390/ijms25031834] [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: 01/04/2024] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
A series of hydrazones, azoles, and azines bearing a 4-dimethylaminophenyl-5-oxopyrrolidine scaffold was synthesized. Their cytotoxic effect against human pancreatic carcinoma Panc-1 and triple-negative breast cancer MDA-MB-231 cell lines was established by MTT assay. Pyrrolidinone derivatives 3c and 3d, with incorporated 5-chloro and 5-methylbenzimidazole fragments; hydrazone 5k bearing a 5-nitrothien-2-yl substitution; and hydrazone 5l with a naphth-1-yl fragment in the structure significantly decreased the viability of both cancer cell lines. Compounds 3c and 5k showed the highest selectivity, especially against the MDA-MB-231 cancer cell line. The EC50 values of the most active compound 5k against the MDA-MB231 cell line was 7.3 ± 0.4 μM, which were slightly higher against the Panc-1 cell line (10.2 ± 2.6 μM). Four selected pyrrolidone derivatives showed relatively high activity in a clonogenic assay. Compound 5k was the most active in both cell cultures, and it completely disturbed MDA-MB-231 cell colony growth at 1 and 2 μM and showed a strong effect on Panc-1 cell colony formation, especially at 2 μM. The compounds did not show an inhibitory effect on cell line migration by the 'wound-healing' assay. Compound 3d most efficiently inhibited the growth of Panc-1 spheroids and reduced cell viability in MDA-MB-231 spheroids. Considering these different activities in biological assays, the selected pyrrolidinone derivatives could be further tested to better understand the structure-activity relationship and their mechanism of action.
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Affiliation(s)
- Karolina Kairytė
- Department of Organic Chemistry, Kaunas University of Technology, Radvilėnų Rd. 19, LT-50254 Kaunas, Lithuania; (K.K.); (R.V.); (B.G.); (K.A.); (V.M.)
| | - Rita Vaickelionienė
- Department of Organic Chemistry, Kaunas University of Technology, Radvilėnų Rd. 19, LT-50254 Kaunas, Lithuania; (K.K.); (R.V.); (B.G.); (K.A.); (V.M.)
| | - Birutė Grybaitė
- Department of Organic Chemistry, Kaunas University of Technology, Radvilėnų Rd. 19, LT-50254 Kaunas, Lithuania; (K.K.); (R.V.); (B.G.); (K.A.); (V.M.)
| | - Kazimieras Anusevičius
- Department of Organic Chemistry, Kaunas University of Technology, Radvilėnų Rd. 19, LT-50254 Kaunas, Lithuania; (K.K.); (R.V.); (B.G.); (K.A.); (V.M.)
| | - Vytautas Mickevičius
- Department of Organic Chemistry, Kaunas University of Technology, Radvilėnų Rd. 19, LT-50254 Kaunas, Lithuania; (K.K.); (R.V.); (B.G.); (K.A.); (V.M.)
| | - Vilma Petrikaitė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio Al. 7, LT-10257 Vilnius, Lithuania
- Faculty of Medicine, Lithuanian University of Health Sciences, A. Mickevičiaus 9, LT-44307 Kaunas, Lithuania
- Laboratory of Drug Targets Histopathology, Institute of Cardiology, Lithuanian University of Health Sciences, Sukilėlių Pr. 13, LT-50162 Kaunas, Lithuania
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Beta and Gamma Amino Acid-Substituted Benzenesulfonamides as Inhibitors of Human Carbonic Anhydrases. Pharmaceuticals (Basel) 2022; 15:ph15040477. [PMID: 35455474 PMCID: PMC9033141 DOI: 10.3390/ph15040477] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/24/2022] [Accepted: 04/07/2022] [Indexed: 02/06/2023] Open
Abstract
A series of novel benzenesulfonamide derivatives were synthesized bearing para-N β,γ-amino acid or para-N β-amino acid and thiazole moieties and their binding to the human carbonic anhydrase (CA) isozymes determined. These enzymes are involved in various illnesses, such as glaucoma, altitude sickness, epilepsy, obesity, and even cancer. There are numerous compounds that are inhibitors of CA and used as pharmaceuticals. However, most of them bind to most CA isozymes with little selectivity. The design of high affinity and selectivity towards one CA isozyme remains a significant challenge. The beta and gamma amino acid-substituted compound affinities were determined by the fluorescent thermal shift assay and isothermal titration calorimetry for all 12 catalytically active human carbonic anhydrase isozymes, showing the full affinity and selectivity profile. The structures of several compounds were determined by X-ray crystallography, and the binding mode in the active site of CA enzyme was shown.
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Smirnovienė J, Smirnov A, Zakšauskas A, Zubrienė A, Petrauskas V, Mickevičiūtė A, Michailovienė V, Čapkauskaitė E, Manakova E, Gražulis S, Baranauskienė L, Chen W, Ladbury JE, Matulis D. Switching the Inhibitor-Enzyme Recognition Profile via Chimeric Carbonic Anhydrase XII. ChemistryOpen 2021; 10:567-580. [PMID: 33945229 PMCID: PMC8095314 DOI: 10.1002/open.202100042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/08/2021] [Indexed: 01/02/2023] Open
Abstract
A key part of the optimization of small molecules in pharmaceutical inhibitor development is to vary the molecular design to enhance complementarity of chemical features of the compound with the positioning of amino acids in the active site of a target enzyme. Typically this involves iterations of synthesis, to modify the compound, and biophysical assay, to assess the outcomes. Selective targeting of the anti-cancer carbonic anhydrase isoform XII (CA XII), this process is challenging because the overall fold is very similar across the twelve CA isoforms. To enhance drug development for CA XII we used a reverse engineering approach where mutation of the key six amino acids in the active site of human CA XII into the CA II isoform was performed to provide a protein chimera (chCA XII) which is amenable to structure-based compound optimization. Through determination of structural detail and affinity measurement of the interaction with over 60 compounds we observed that the compounds that bound CA XII more strongly than CA II, switched their preference and bound more strongly to the engineered chimera, chCA XII, based on CA II, but containing the 6 key amino acids from CA XII, behaved as CA XII in its compound recognition profile. The structures of the compounds in the chimeric active site also resembled those determined for complexes with CA XII, hence validating this protein engineering approach in the development of new inhibitors.
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Affiliation(s)
- Joana Smirnovienė
- Department of Biothermodynamics and Drug DesignInstitute of BiotechnologyLife Sciences CenterVilnius UniversitySaulėtekio 7Vilnius10257Lithuania
| | - Alexey Smirnov
- Department of Biothermodynamics and Drug DesignInstitute of BiotechnologyLife Sciences CenterVilnius UniversitySaulėtekio 7Vilnius10257Lithuania
| | - Audrius Zakšauskas
- Department of Biothermodynamics and Drug DesignInstitute of BiotechnologyLife Sciences CenterVilnius UniversitySaulėtekio 7Vilnius10257Lithuania
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug DesignInstitute of BiotechnologyLife Sciences CenterVilnius UniversitySaulėtekio 7Vilnius10257Lithuania
| | - Vytautas Petrauskas
- Department of Biothermodynamics and Drug DesignInstitute of BiotechnologyLife Sciences CenterVilnius UniversitySaulėtekio 7Vilnius10257Lithuania
| | - Aurelija Mickevičiūtė
- Department of Biothermodynamics and Drug DesignInstitute of BiotechnologyLife Sciences CenterVilnius UniversitySaulėtekio 7Vilnius10257Lithuania
| | - Vilma Michailovienė
- Department of Biothermodynamics and Drug DesignInstitute of BiotechnologyLife Sciences CenterVilnius UniversitySaulėtekio 7Vilnius10257Lithuania
| | - Edita Čapkauskaitė
- Department of Biothermodynamics and Drug DesignInstitute of BiotechnologyLife Sciences CenterVilnius UniversitySaulėtekio 7Vilnius10257Lithuania
| | - Elena Manakova
- Department of Protein-DNA InteractionsInstitute of BiotechnologyLife Sciences CenterVilnius UniversitySaulėtekio 7Vilnius10257Lithuania
| | - Saulius Gražulis
- Department of Protein-DNA InteractionsInstitute of BiotechnologyLife Sciences CenterVilnius UniversitySaulėtekio 7Vilnius10257Lithuania
| | - Lina Baranauskienė
- Department of Biothermodynamics and Drug DesignInstitute of BiotechnologyLife Sciences CenterVilnius UniversitySaulėtekio 7Vilnius10257Lithuania
| | - Wen‐Yih Chen
- Department of Chemical and Materials EngineeringInstitute of Systems Biology and BioinformaticsNational Central UniversityTaiwan
| | - John E. Ladbury
- School of Molecular and Cellular BiologyUniversity of LeedsLC Miall BuildingLeedsLS2 9JTUK
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug DesignInstitute of BiotechnologyLife Sciences CenterVilnius UniversitySaulėtekio 7Vilnius10257Lithuania
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Balandis B, Ivanauskaitė G, Smirnovienė J, Kantminienė K, Matulis D, Mickevičius V, Zubrienė A. Synthesis and structure-affinity relationship of chlorinated pyrrolidinone-bearing benzenesulfonamides as human carbonic anhydrase inhibitors. Bioorg Chem 2020; 97:103658. [PMID: 32088419 DOI: 10.1016/j.bioorg.2020.103658] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/05/2020] [Accepted: 02/10/2020] [Indexed: 11/26/2022]
Abstract
A novel set of pyrrolidinone-based chlorinated benzenesulfonamide derivatives were synthesized and investigated for their binding affinity and selectivity against recombinant human carbonic anhydrases I-XIV using fluorescent thermal shift, p-nitrophenyl acetate hydrolysis and stopped-flow enzymatic inhibition assays. The hydrazones 10-22 prepared from 1-(2-chloro-4-sulfamoylphenyl)-5-oxopyrrolidine-3-carboxylic acid exhibited low nanomolar affinity against cancer-related CA IX (Kd in the range of 5.0-37 nM). Compounds with triazole or oxadiazole groups attached directly to pyrrolidinone moiety bound all CAs weaker than compounds with more flexible tail groups. Chloro group at the meta position of benzenesulfonamide derivatives increased affinity to all CAs as compared with binding data for nonchlorinated compounds. The compounds have a potential for further development of CA inhibitors with higher selectivity for a particular CA isozyme.
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Affiliation(s)
- Benas Balandis
- Department of Organic Chemistry, Kaunas University of Technology, Radvilėnų pl. 19, Kaunas LT-50254, Lithuania
| | - Guostė Ivanauskaitė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Joana Smirnovienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Kristina Kantminienė
- Department of Physical and Inorganic Chemistry, Kaunas University of Technology, Radvilėnų pl. 19, Kaunas LT-50254, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Vytautas Mickevičius
- Department of Organic Chemistry, Kaunas University of Technology, Radvilėnų pl. 19, Kaunas LT-50254, Lithuania
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania.
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Thermodynamic, kinetic, and structural parameterization of human carbonic anhydrase interactions toward enhanced inhibitor design. Q Rev Biophys 2019; 51:e10. [PMID: 30912486 DOI: 10.1017/s0033583518000082] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The aim of rational drug design is to develop small molecules using a quantitative approach to optimize affinity. This should enhance the development of chemical compounds that would specifically, selectively, reversibly, and with high affinity interact with a target protein. It is not yet possible to develop such compounds using computational (i.e., in silico) approach and instead the lead molecules are discovered in high-throughput screening searches of large compound libraries. The main reason why in silico methods are not capable to deliver is our poor understanding of the compound structure-thermodynamics and structure-kinetics correlations. There is a need for databases of intrinsic binding parameters (e.g., the change upon binding in standard Gibbs energy (ΔGint), enthalpy (ΔHint), entropy (ΔSint), volume (ΔVintr), heat capacity (ΔCp,int), association rate (ka,int), and dissociation rate (kd,int)) between a series of closely related proteins and a chemically diverse, but pharmacophoric group-guided library of compounds together with the co-crystal structures that could help explain the structure-energetics correlations and rationally design novel compounds. Assembly of these data will facilitate attempts to provide correlations and train data for modeling of compound binding. Here, we report large datasets of the intrinsic thermodynamic and kinetic data including over 400 primary sulfonamide compound binding to a family of 12 catalytically active human carbonic anhydrases (CA). Thermodynamic parameters have been determined by the fluorescent thermal shift assay, isothermal titration calorimetry, and by the stopped-flow assay of the inhibition of enzymatic activity. Kinetic measurements were performed using surface plasmon resonance. Intrinsic thermodynamic and kinetic parameters of binding were determined by dissecting the binding-linked protonation reactions of the protein and sulfonamide. The compound structure-thermodynamics and kinetics correlations reported here helped to discover compounds that exhibited picomolar affinities, hour-long residence times, and million-fold selectivities over non-target CA isoforms. Drug-lead compounds are suggested for anticancer target CA IX and CA XII, antiglaucoma CA IV, antiobesity CA VA and CA VB, and other isoforms. Together with 85 X-ray crystallographic structures of 60 compounds bound to six CA isoforms, the database should be of help to continue developing the principles of rational target-based drug design.
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Synthesis of 1-(5-Chloro-2-hydroxyphenyl)-5-oxopyrrolidine-3-carboxylic Acid Derivatives and Their Antioxidant Activity. Molecules 2019; 24:molecules24050971. [PMID: 30857336 PMCID: PMC6429199 DOI: 10.3390/molecules24050971] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 11/17/2022] Open
Abstract
A series of novel 1-(5-chloro-2-hydroxyphenyl)-5-oxopyrrolidine-3-carboxylic acid derivatives containing chloro, hydroxyl, isopropyl, nitro, nitroso, and amino substituents at benzene ring and 1-(5-chloro-2-hydroxyphenyl)-5-oxopyrrolidine-3-carbohydrazide derivatives bearing heterocyclic moieties were synthesized. Antioxidant activity of the synthesized compounds was screened by DPPH radical scavenging method and reducing power assay. A number of compounds were identified as potent antioxidants. Antioxidant activity of 1-(5-chloro-2-hydroxyphenyl)-4-(5-thioxo-4,5-dihydro-1,3,4-oxadiazol-2-yl)pyrrolidin-2-one has been tested to be 1.5 times higher than that of a well-known antioxidant ascorbic acid. 1-(5-Chloro-2-hydroxyphenyl)-4-(4-methyl-5-thioxo-4,5-dihydro-1H-1,2,4-triazol-3-yl)pyrrolidin-2-one has shown 1.35 times higher antioxidant activity than that of vitamin C by DPPH radical scavenging method and optical density value of 1.149 in reducing power assay. The structure of 1-(5-chloro-2-hydroxyphenyl)-N-(1,3-dioxoisoindolin-2-yl)-5-oxopyrrolidine-3-carboxamide was unambiguously assigned by means of X-ray diffraction analysis data.
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Vaškevičienė I, Paketurytė V, Pajanok N, Žukauskas Š, Sapijanskaitė B, Kantminienė K, Mickevičius V, Zubrienė A, Matulis D. Pyrrolidinone-bearing methylated and halogenated benzenesulfonamides as inhibitors of carbonic anhydrases. Bioorg Med Chem 2018; 27:322-337. [PMID: 30553625 DOI: 10.1016/j.bmc.2018.12.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/29/2018] [Accepted: 12/05/2018] [Indexed: 12/19/2022]
Abstract
Two series of benzenesulfonamides bearing methyl groups at ortho/ortho or meta/ortho positions and a pyrrolidinone moiety at para position were synthesized and tested as inhibitors of the twelve catalytically active human carbonic anhydrase (CA) isoforms. Observed binding affinities were determined by fluorescent thermal shift assay and intrinsic binding affinities representing the binding of benzenesulfonamide anion to the Zn(II)-bound water form of CA were calculated. Introduction of dimethyl groups into benzenesulfonamide ring decreased the binding affinity to almost all CA isoforms, but gained in selectivity towards one CA isoform. A chloro group at the meta position of 2,6-dimethylbenzenesulfonamide derivatives did not influence the binding to CA I, but it increased the affinity to all other CAs, especially, CA VII and CA XIII (up to 500 fold). The compounds may be used for further development of CA inhibitors with higher selectivity to particular CA isoforms.
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Affiliation(s)
- Irena Vaškevičienė
- Department of Organic Chemistry, Kaunas University of Technology, LT-50254, Radvilėnų pl. 19, Kaunas, Lithuania
| | - Vaida Paketurytė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Nikita Pajanok
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Šarūnas Žukauskas
- Department of Organic Chemistry, Kaunas University of Technology, LT-50254, Radvilėnų pl. 19, Kaunas, Lithuania
| | - Birutė Sapijanskaitė
- Department of Organic Chemistry, Kaunas University of Technology, LT-50254, Radvilėnų pl. 19, Kaunas, Lithuania
| | - Kristina Kantminienė
- Department of Physical and Inorganic Chemistry, Kaunas University of Technology, LT-50254, Radvilėnų pl. 19, Kaunas, Lithuania
| | - Vytautas Mickevičius
- Department of Organic Chemistry, Kaunas University of Technology, LT-50254, Radvilėnų pl. 19, Kaunas, Lithuania
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania.
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
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