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Novikova D, Al Mustafa A, Grigoreva T, Vorona S, Selivanov S, Tribulovich V. NMR-Verified Dearomatization of 5,7-Substituted Pyrazolo[1,5-a]pyrimidines. Molecules 2023; 28:6584. [PMID: 37764360 PMCID: PMC10535613 DOI: 10.3390/molecules28186584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/03/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Tetrahydropyrazolo[1,5-a]pyrimidine (THPP) is an attractive scaffold for designing biologically active compounds. The most obvious way to obtain such compounds is to reduce pyrazolopyrimidines with complex hydrides, because the pyrimidine ring is reduced in the preference over the pyrazole ring. The presence of substituents at positions five and seven of pyrazolo[1,5-a]pyrimidines complicates the set of reaction products but makes it more attractive for medicinal chemistry because four possible stereoisomers can be formed during reduction. However, the formation of only syn-isomers has been described in the literature. This article is the first report on the formation of anti-configured isomers along with syn-isomers in the reduction of model 5,7-dimethylpyrazolo[1,5-a]pyrimidine, which was confirmed by NMR. The bicyclic core in the syn-configuration was shown to be conformationally stable, which was used to estimate the long-range interproton distances using NOESY data. At the same time, long-range dipole-dipole interactions corresponding to a distance between protons of more than 6 Å were first registered and quantified. In turn, the bicyclic core in the trans-configuration represents a conformationally labile system. For these structures, an analysis of conformations observed in solutions was carried out. Our results indicate the significant potential of trans-configured tetrahydropyrazolo[1,5-a]pyrimidines for the development of active small molecules. While possessing structural lability due to the low energy of the conformational transition, they have the ability to adjust to the active site of the desired target.
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Affiliation(s)
- Daria Novikova
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology, St. Petersburg 190013, Russia; (A.A.M.); (T.G.); (S.V.)
| | - Ammar Al Mustafa
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology, St. Petersburg 190013, Russia; (A.A.M.); (T.G.); (S.V.)
| | - Tatyana Grigoreva
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology, St. Petersburg 190013, Russia; (A.A.M.); (T.G.); (S.V.)
| | - Svetlana Vorona
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology, St. Petersburg 190013, Russia; (A.A.M.); (T.G.); (S.V.)
| | - Stanislav Selivanov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg 199034, Russia;
- Department of Organic Chemistry, St. Petersburg State Institute of Technology, St. Petersburg 190013, Russia
| | - Vyacheslav Tribulovich
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology, St. Petersburg 190013, Russia; (A.A.M.); (T.G.); (S.V.)
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Novikova D, Grigoreva T, Gurzhiy V, Tribulovich V. Is It Possible to Obtain a Product of the Desired Configuration from a Single Knoevenagel Condensation? Isomerization vs. Stereodefined Synthesis. Int J Mol Sci 2023; 24:11339. [PMID: 37511099 PMCID: PMC10379276 DOI: 10.3390/ijms241411339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
The biological activity of compounds directly depends on the three-dimensional arrangement of affinity fragments since a high degree of pharmacophore compliance with the binding site is required. 3-Benzylidene oxindoles are privileged structures due to their wide spectrum of biological activity, synthetic availability, and ease of modification. In particular, both kinase inhibitors and kinase activators can be found among 3-benzylidene oxindoles. In this work, we studied model compounds obtained via oxindole condensation with aldehydes and alkylphenones. These condensation products can exist in the form of E- and Z-isomers and also undergo isomerization in solutions. The factors causing isomeric transformation of these compounds were established. Comparative kinetic studies to obtain quantitative characteristics of UV-driven isomerization were first performed. The results obtained indicate dramatic differences in two subclasses, which should be considered when developing biologically active molecules.
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Affiliation(s)
- Daria Novikova
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology (Technical University), St. Petersburg 190013, Russia
| | - Tatyana Grigoreva
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology (Technical University), St. Petersburg 190013, Russia
| | - Vladislav Gurzhiy
- Crystallography Department, Institute of Earth Sciences, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Vyacheslav Tribulovich
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology (Technical University), St. Petersburg 190013, Russia
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Grigoreva TA, Vorona SV, Novikova DS, Tribulovich VG. Analysis of P-Glycoprotein Transport Cycle Reveals a New Way to Identify Efflux Inhibitors. ACS OMEGA 2022; 7:42835-42844. [PMID: 36467933 PMCID: PMC9713869 DOI: 10.1021/acsomega.2c04768] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/28/2022] [Indexed: 06/17/2023]
Abstract
P-glycoprotein (P-gp) is found to be of considerable interest for the design of drugs capable of treating chemoresistant tumors. This transporter is an interesting target for which an efficient approach has not yet been developed in terms of computer simulation. In this work, we use a combination of docking, molecular dynamics, and metadynamics to fully explore the states that occur during the capture of a ligand and subsequent efflux by P-gp. The proposed approach allowed us to substantiate a number of experimentally established facts, as well as to develop a new criterion for identifying potential P-gp inhibitors.
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Grigoreva TA, Sagaidak AV, Vorona SV, Novikova DS, Tribulovich VG. ATP Mimetic Attack on the Nucleotide-Binding Domain to Overcome ABC Transporter Mediated Chemoresistance. ACS Med Chem Lett 2022; 13:1848-1855. [DOI: 10.1021/acsmedchemlett.2c00196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 11/10/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- Tatyana A. Grigoreva
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology (Technical University), Moskovskii pr., 26, St. Petersburg, 190013 Russia
| | - Aleksandra V. Sagaidak
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology (Technical University), Moskovskii pr., 26, St. Petersburg, 190013 Russia
| | - Svetlana V. Vorona
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology (Technical University), Moskovskii pr., 26, St. Petersburg, 190013 Russia
| | - Daria S. Novikova
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology (Technical University), Moskovskii pr., 26, St. Petersburg, 190013 Russia
| | - Vyacheslav G. Tribulovich
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology (Technical University), Moskovskii pr., 26, St. Petersburg, 190013 Russia
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Serusi L, Massa A, Tedesco C, Capobianco A, Palombi L. The First Highly Enantioselective Synthesis of 3-Sulfinyl-Substituted Isoindolinones Having Adjacent Carbon and Sulfur Stereocenters. J Org Chem 2021; 86:10630-10639. [PMID: 34255964 DOI: 10.1021/acs.joc.1c01300] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A highly stereoselective access to 3-sulfinyl-substituted isoindolinones has been achieved by a tandem organocatalytic addition/cyclization reaction of 2-carbobenzyloxy-N-tosylbenzylidenimine with thiols and succeeding diastereoselective oxidation with MCPBA. First, enantioenriched isoindolinone N,S-acetals have been obtained through a dynamic kinetic asymmetric transformation induced by a bifunctional chiral thiourea organocatalyst. In turn, the newly created carbon stereocenter enabled a high diastereocontrol in the subsequent sulfoxidation. Based on DFT calculations, a theoretical rationale for the stereoselectivity of the oxidation reaction is also provided.
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Affiliation(s)
- Lorenzo Serusi
- Dipartimento di Chimica e Biologia "A. Zambelli″, Università di Salerno, Via Giovanni Paolo II, Fisciano, Salerno 132-84084, Italy
| | - Antonio Massa
- Dipartimento di Chimica e Biologia "A. Zambelli″, Università di Salerno, Via Giovanni Paolo II, Fisciano, Salerno 132-84084, Italy
| | - Consiglia Tedesco
- Dipartimento di Chimica e Biologia "A. Zambelli″, Università di Salerno, Via Giovanni Paolo II, Fisciano, Salerno 132-84084, Italy
| | - Amedeo Capobianco
- Dipartimento di Chimica e Biologia "A. Zambelli″, Università di Salerno, Via Giovanni Paolo II, Fisciano, Salerno 132-84084, Italy
| | - Laura Palombi
- Dipartimento di Scienze Fisiche e Chimiche, Università dell'Aquila, Via Vetoio, L'Aquila 10-67100, Italy
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Grigoreva T, Sagaidak A, Romanova A, Novikova D, Garabadzhiu A, Tribulovich V. Establishment of drug-resistant cell lines under the treatment with chemicals acting through different mechanisms. Chem Biol Interact 2021; 344:109510. [PMID: 33974899 DOI: 10.1016/j.cbi.2021.109510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 04/28/2021] [Accepted: 05/05/2021] [Indexed: 02/07/2023]
Abstract
The problem of chemoresistance development is an inescapable flipside of modern oncotherapy, in particular for сolorectal cancer patients. The search for or development of drugs effective against resistant tumors involves the use of model resistant cell lines in vitro. To obtain such lines, we reproduced the development of chemoresistance of human colon adenocarcinoma cells under the treatment with drugs of different mechanisms, a cytostatic (paclitaxel) and a targeted agent (Nutlin-3a, an inhibitor of p53-Mdm2 protein-protein interaction). In each case, we gradually increased the content of the substance in the medium, starting from effective concentrations that do not cause total cell death. When studying the lines resistant to the corresponding drug, we noted a reduced sensitivity to the drug of another mechanism of action. Analysis of the original and resistant lines showed that the cells use the universal efflux defense mechanism. The observed effect can be partially neutralized using inhibitors of the ABC transport proteins, including P-glycoprotein, known for its oncoprotective function. The role of the latter was confirmed by real-time RT-PCR and Western blotting.
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Affiliation(s)
- Tatyana Grigoreva
- St. Petersburg State Institute of Technology (Technical University), Moskovskii Prospect, 26, St. Petersburg, 190013, Russia.
| | - Aleksandra Sagaidak
- St. Petersburg State Institute of Technology (Technical University), Moskovskii Prospect, 26, St. Petersburg, 190013, Russia
| | - Angelina Romanova
- St. Petersburg State Institute of Technology (Technical University), Moskovskii Prospect, 26, St. Petersburg, 190013, Russia
| | - Daria Novikova
- St. Petersburg State Institute of Technology (Technical University), Moskovskii Prospect, 26, St. Petersburg, 190013, Russia
| | - Aleksander Garabadzhiu
- St. Petersburg State Institute of Technology (Technical University), Moskovskii Prospect, 26, St. Petersburg, 190013, Russia
| | - Viacheslav Tribulovich
- St. Petersburg State Institute of Technology (Technical University), Moskovskii Prospect, 26, St. Petersburg, 190013, Russia
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Novikova DS, Grigoreva TA, Ivanov GS, Melino G, Barlev NA, Tribulovich VG. Activating Effect of 3‐Benzylidene Oxindoles on AMPK: From Computer Simulation to High‐Content Screening. ChemMedChem 2020; 15:2521-2529. [DOI: 10.1002/cmdc.202000579] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Daria S. Novikova
- Laboratory of Molecular Pharmacology Saint Petersburg State Institute of Technology (Technical University) Moskovskii pr. 26 190013 Saint Petersburg Russia
| | - Tatyana A. Grigoreva
- Laboratory of Molecular Pharmacology Saint Petersburg State Institute of Technology (Technical University) Moskovskii pr. 26 190013 Saint Petersburg Russia
| | - Gleb S. Ivanov
- Laboratory of Molecular Pharmacology Saint Petersburg State Institute of Technology (Technical University) Moskovskii pr. 26 190013 Saint Petersburg Russia
- Laboratory of Regulation of Gene Expression Institute of Cytology RAS Tikhoretskii pr. 4 194064 Saint Petersburg Russia
| | - Gerry Melino
- Department of Experimental Medicine and Surgery University of Rome Tor Vergata Via Montpellier 1 00133 Rome Italy
| | - Nickolai A. Barlev
- Laboratory of Regulation of Gene Expression Institute of Cytology RAS Tikhoretskii pr. 4 194064 Saint Petersburg Russia
| | - Vyacheslav G. Tribulovich
- Laboratory of Molecular Pharmacology Saint Petersburg State Institute of Technology (Technical University) Moskovskii pr. 26 190013 Saint Petersburg Russia
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Grigoreva T, Romanova A, Sagaidak A, Vorona S, Novikova D, Tribulovich V. Mdm2 inhibitors as a platform for the design of P-glycoprotein inhibitors. Bioorg Med Chem Lett 2020; 30:127424. [DOI: 10.1016/j.bmcl.2020.127424] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/06/2020] [Accepted: 07/16/2020] [Indexed: 01/21/2023]
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Simulation of MDM2 N-terminal domain conformational lability in the presence of imidazoline based inhibitors of MDM2-p53 protein–protein interaction. J Comput Aided Mol Des 2019; 34:55-70. [DOI: 10.1007/s10822-019-00260-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 11/21/2019] [Indexed: 12/18/2022]
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Novikova DS, Grigoreva TA, Zolotarev AA, Garabadzhiu AV, Tribulovich VG. Advanced palladium free approach to the synthesis of substituted alkene oxindoles via aluminum-promoted Knoevenagel reaction. RSC Adv 2018; 8:34543-34551. [PMID: 35548634 PMCID: PMC9086994 DOI: 10.1039/c8ra07576j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 10/02/2018] [Indexed: 11/22/2022] Open
Abstract
A synthetic route for the synthesis of C24, as well as for the design of focused libraries of direct AMPK activators was developed based on a convergent strategy. The proposed scheme corresponds to the current trends in C-H bond functionalization. The use of aluminum isopropoxide for the Knoevenagel condensation of oxindole with benzophenones is a noticeable point of this work.
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Affiliation(s)
- Daria S Novikova
- Laboratory of Molecular Pharmacology, Saint Petersburg State Institute of Technology (Technical University) Moskovskii pr. 26 Saint Petersburg 190013 Russia
| | - Tatyana A Grigoreva
- Laboratory of Molecular Pharmacology, Saint Petersburg State Institute of Technology (Technical University) Moskovskii pr. 26 Saint Petersburg 190013 Russia
| | - Andrey A Zolotarev
- Department of Crystallography, Saint Petersburg State University per. Dekabristov 16 Saint Petersburg 199155 Russia
| | - Alexander V Garabadzhiu
- Laboratory of Molecular Pharmacology, Saint Petersburg State Institute of Technology (Technical University) Moskovskii pr. 26 Saint Petersburg 190013 Russia
| | - Vyacheslav G Tribulovich
- Laboratory of Molecular Pharmacology, Saint Petersburg State Institute of Technology (Technical University) Moskovskii pr. 26 Saint Petersburg 190013 Russia
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