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Herlah B, Janežič M, Ogris I, Grdadolnik SG, Kološa K, Žabkar S, Žegura B, Perdih A. Nature-inspired substituted 3-(imidazol-2-yl) morpholines targeting human topoisomerase IIα: Dynophore-derived discovery. Biomed Pharmacother 2024; 175:116676. [PMID: 38772152 DOI: 10.1016/j.biopha.2024.116676] [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: 03/12/2024] [Revised: 04/22/2024] [Accepted: 04/29/2024] [Indexed: 05/23/2024] Open
Abstract
The molecular nanomachine, human DNA topoisomerase IIα, plays a crucial role in replication, transcription, and recombination by catalyzing topological changes in the DNA, rendering it an optimal target for cancer chemotherapy. Current clinical topoisomerase II poisons often cause secondary tumors as side effects due to the accumulation of double-strand breaks in the DNA, spurring the development of catalytic inhibitors. Here, we used a dynamic pharmacophore approach to develop catalytic inhibitors targeting the ATP binding site of human DNA topoisomerase IIα. Our screening of a library of nature-inspired compounds led to the discovery of a class of 3-(imidazol-2-yl) morpholines as potent catalytic inhibitors that bind to the ATPase domain. Further experimental and computational studies identified hit compound 17, which exhibited selectivity against the human DNA topoisomerase IIα versus human protein kinases, cytotoxicity against several human cancer cells, and did not induce DNA double-strand breaks, making it distinct from clinical topoisomerase II poisons. This study integrates an innovative natural product-inspired chemistry and successful implementation of a molecular design strategy that incorporates a dynamic component of ligand-target molecular recognition, with comprehensive experimental characterization leading to hit compounds with potential impact on the development of more efficient chemotherapies.
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Affiliation(s)
- Barbara Herlah
- National Institute of Chemistry, Hajdrihova 19, Ljubljana SI 1000, Slovenia; University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, Ljubljana SI 1000, Slovenia
| | - Matej Janežič
- National Institute of Chemistry, Hajdrihova 19, Ljubljana SI 1000, Slovenia
| | - Iza Ogris
- National Institute of Chemistry, Hajdrihova 19, Ljubljana SI 1000, Slovenia; University of Ljubljana, Faculty of Medicine, Vrazov trg 2, Ljubljana SI 1000, Slovenia
| | | | - Katja Kološa
- National institute of Biology, Department of Genetic Toxicology and Cancer Biology, Večna pot 121, Ljubljana SI 1000, Slovenia
| | - Sonja Žabkar
- National institute of Biology, Department of Genetic Toxicology and Cancer Biology, Večna pot 121, Ljubljana SI 1000, Slovenia
| | - Bojana Žegura
- National institute of Biology, Department of Genetic Toxicology and Cancer Biology, Večna pot 121, Ljubljana SI 1000, Slovenia
| | - Andrej Perdih
- National Institute of Chemistry, Hajdrihova 19, Ljubljana SI 1000, Slovenia; University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, Ljubljana SI 1000, Slovenia.
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2
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Herlah B, Pavlin M, Perdih A. Molecular choreography: Unveiling the dynamic landscape of type IIA DNA topoisomerases before T-segment passage through all-atom simulations. Int J Biol Macromol 2024; 269:131991. [PMID: 38714283 DOI: 10.1016/j.ijbiomac.2024.131991] [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: 01/09/2024] [Revised: 04/09/2024] [Accepted: 04/28/2024] [Indexed: 05/09/2024]
Abstract
Type IIA DNA topoisomerases are molecular nanomachines responsible for controlling topological states of DNA molecules. Here, we explore the dynamic landscape of yeast topoisomerase IIA during key stages of its catalytic cycle, focusing in particular on the events preceding the passage of the T-segment. To this end, we generated six configurations of fully catalytic yeast topo IIA, strategically inserted a T-segment into the N-gate in relevant configurations, and performed all-atom simulations. The essential motion of topo IIA protein dimer was characterized by rotational gyrating-like movement together with sliding motion within the DNA-gate. Both appear to be inherent properties of the enzyme and an inbuilt feature that allows passage of the T-segment through the cleaved G-segment. Coupled dynamics of the N-gate and DNA-gate residues may be particularly important for controlled and smooth passage of the T-segment and consequently the prevention of DNA double-strand breaks. QTK loop residue Lys367, which interacts with ATP and ADP molecules, is involved in regulating the size and stability of the N-gate. The unveiled features of the simulated configurations provide insights into the catalytic cycle of type IIA topoisomerases and elucidate the molecular choreography governing their ability to modulate the topological states of DNA topology.
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Affiliation(s)
- Barbara Herlah
- Theory Department, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia; University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Matic Pavlin
- Department of Catalysis and Chemical Reaction Engineering, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Andrej Perdih
- Theory Department, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia; University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia.
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Dai Q, Sun Q, Ouyang X, Liu J, Jin L, Liu A, He B, Fan T, Jiang Y. Antitumor Activity of s-Triazine Derivatives: A Systematic Review. Molecules 2023; 28:molecules28114278. [PMID: 37298753 DOI: 10.3390/molecules28114278] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
1,3,5-triazine derivatives, also called s-triazines, are a series of containing-nitrogen heterocyclic compounds that play an important role in anticancer drug design and development. To date, three s-triazine derivatives, including altretamine, gedatolisib, and enasidenib, have already been approved for refractory ovarian cancer, metastatic breast cancer, and leukemia therapy, respectively, demonstrating that the s-triazine core is a useful scaffold for the discovery of novel anticancer drugs. In this review, we mainly focus on s-triazines targeting topoisomerases, tyrosine kinases, phosphoinositide 3-kinases, NADP+-dependent isocitrate dehydrogenases, and cyclin-dependent kinases in diverse signaling pathways, which have been extensively studied. The medicinal chemistry of s-triazine derivatives as anticancer agents was summarized, including discovery, structure optimization, and biological applications. This review will provide a reference to inspire new and original discoveries.
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Affiliation(s)
- Qiuzi Dai
- The Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha 410219, China
| | - Qinsheng Sun
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Xiaorong Ouyang
- The Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha 410219, China
| | - Jinyang Liu
- The Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha 410219, China
| | - Liye Jin
- The Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha 410219, China
| | - Ahao Liu
- The Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha 410219, China
| | - Binsheng He
- The Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha 410219, China
| | - Tingting Fan
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yuyang Jiang
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, China
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
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4
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Design, Synthesis and Evaluation of Fused Bicyclo[2.2.2]octene as a Potential Core Scaffold for the Non-Covalent Inhibitors of SARS-CoV-2 3CLpro Main Protease. Pharmaceuticals (Basel) 2022; 15:ph15050539. [PMID: 35631364 PMCID: PMC9145702 DOI: 10.3390/ph15050539] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 04/22/2022] [Accepted: 04/24/2022] [Indexed: 12/22/2022] Open
Abstract
The emergence of SARS-CoV-2, responsible for the global COVID-19 pandemic, requires the rapid development of novel antiviral drugs that would contribute to an effective treatment alongside vaccines. Drug repurposing and development of new molecules targeting numerous viral targets have already led to promising drug candidates. To this end, versatile molecular scaffolds with high functionalization capabilities play a key role. Starting with the clinically used conformationally flexible HIV-1 protease inhibitors that inhibit replication of SARS-CoV-2 and bind major protease 3CLpro, we designed and synthesized a series of rigid bicyclo[2.2.2]octenes fused to N-substituted succinimides to test whether this core scaffold could support the development of non-covalent 3CLpro inhibitors. Inhibition assays confirmed that some compounds can inhibit the SARS-CoV-2 main protease; the most promising compound 11a inhibited 3CLpro in micromolar range (IC50 = 102.2 μM). Molecular simulations of the target-ligand complex in conjunction with dynophore analyses and endpoint free energy calculations provide additional insight and first recommendations for future optimization. The fused bicyclo[2.2.2]octenes can be used as a new potential starting point in the development of non-covalent SARS-CoV-2 3CLpro protease inhibitors and the study also substantiates the potential of this versatile scaffold for the development of biologically active molecules.
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Synthesis and biological evaluation of xanthone derivatives as anti-cancer agents targeting topoisomerase II and DNA. Med Chem Res 2022. [DOI: 10.1007/s00044-022-02862-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Maliszewski D, Drozdowska D. Recent Advances in the Biological Activity of s-Triazine Core Compounds. Pharmaceuticals (Basel) 2022; 15:ph15020221. [PMID: 35215333 PMCID: PMC8875733 DOI: 10.3390/ph15020221] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/05/2022] [Accepted: 02/10/2022] [Indexed: 12/18/2022] Open
Abstract
An effective strategy for successful chemotherapy relies on creating compounds with high selectivity against cancer cells compared to normal cells and relatively low cytotoxicity. One such approach is the discovery of critical points in cancer cells, i.e., where specific enzymes that are potential therapeutic targets are generated. Triazine is a six-membered heterocyclic ring compound with three nitrogen replacing carbon-hydrogen units in the benzene ring structure. The subject of this review is the symmetrical 1,3,5-triazine, known as s-triazine. 1,3,5-triazine is one of the oldest heterocyclic compounds available. Because of its low cost and high availability, it has attracted researcher attention for novel synthesis. s-Triazine has a weak base, it has much weaker resonance energy than benzene, therefore, nucleophilic substitution is preferred to electrophilic substitution. Heterocyclic bearing a symmetrical s-triazine core represents an interesting class of compounds possessing a wide spectrum of biological properties such as anti-cancer, antiviral, fungicidal, insecticidal, bactericidal, herbicidal and antimicrobial, antimalarial agents. They also have applications as dyes, lubricants, and analytical reagents. Hence, the group of 1,3,5-triazine derivatives has developed over the years. Triazine is not only the core amongst them, but is also a factor increasing the kinetic potential of the entire derivatives. Modifying the structure and introducing new substituents makes it possible to obtain compounds with broad inhibitory activity on processes such as proliferation. In some cases, s-triazine derivatives induce cell apoptosis. In this review we will present currently investigated 1,3,5-triazine derivatives with anti-cancer activities, with particular emphasis on their inhibition of enzymes involved in the process of tumorigenesis.
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Ravikumar C, Selvan ST, Saminathan M, Safin DA. Crystal structure, quantum computational, molecular docking and in vitro anti-proliferative investigations of 1H‐imidazole‐2‐thione analogues derivative. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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8
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Janežič M, Valjavec K, Loboda KB, Herlah B, Ogris I, Kozorog M, Podobnik M, Grdadolnik SG, Wolber G, Perdih A. Dynophore-Based Approach in Virtual Screening: A Case of Human DNA Topoisomerase IIα. Int J Mol Sci 2021; 22:ijms222413474. [PMID: 34948269 PMCID: PMC8703789 DOI: 10.3390/ijms222413474] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/23/2021] [Accepted: 12/10/2021] [Indexed: 12/04/2022] Open
Abstract
In this study, we utilized human DNA topoisomerase IIα as a model target to outline a dynophore-based approach to catalytic inhibitor design. Based on MD simulations of a known catalytic inhibitor and the native ATP ligand analog, AMP-PNP, we derived a joint dynophore model that supplements the static structure-based-pharmacophore information with a dynamic component. Subsequently, derived pharmacophore models were employed in a virtual screening campaign of a library of natural compounds. Experimental evaluation identified flavonoid compounds with promising topoisomerase IIα catalytic inhibition and binding studies confirmed interaction with the ATPase domain. We constructed a binding model through docking and extensively investigated it with molecular dynamics MD simulations, essential dynamics, and MM-GBSA free energy calculations, thus reconnecting the new results to the initial dynophore-based screening model. We not only demonstrate a new design strategy that incorporates a dynamic component of molecular recognition, but also highlight new derivates in the established flavonoid class of topoisomerase II inhibitors.
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Affiliation(s)
- Matej Janežič
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.J.); (K.V.); (K.B.L.); (B.H.); (I.O.); (M.K.); (M.P.); (S.G.G.)
- Laboratory for Structural Bioinformatics, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Katja Valjavec
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.J.); (K.V.); (K.B.L.); (B.H.); (I.O.); (M.K.); (M.P.); (S.G.G.)
| | - Kaja Bergant Loboda
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.J.); (K.V.); (K.B.L.); (B.H.); (I.O.); (M.K.); (M.P.); (S.G.G.)
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Barbara Herlah
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.J.); (K.V.); (K.B.L.); (B.H.); (I.O.); (M.K.); (M.P.); (S.G.G.)
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Iza Ogris
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.J.); (K.V.); (K.B.L.); (B.H.); (I.O.); (M.K.); (M.P.); (S.G.G.)
- Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia
| | - Mirijam Kozorog
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.J.); (K.V.); (K.B.L.); (B.H.); (I.O.); (M.K.); (M.P.); (S.G.G.)
| | - Marjetka Podobnik
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.J.); (K.V.); (K.B.L.); (B.H.); (I.O.); (M.K.); (M.P.); (S.G.G.)
| | - Simona Golič Grdadolnik
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.J.); (K.V.); (K.B.L.); (B.H.); (I.O.); (M.K.); (M.P.); (S.G.G.)
| | - Gerhard Wolber
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2-4, 14195 Berlin, Germany;
| | - Andrej Perdih
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.J.); (K.V.); (K.B.L.); (B.H.); (I.O.); (M.K.); (M.P.); (S.G.G.)
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
- Correspondence: ; Tel.: +386-1-4760-376
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Radaeva M, Dong X, Cherkasov A. The Use of Methods of Computer-Aided Drug Discovery in the Development of Topoisomerase II Inhibitors: Applications and Future Directions. J Chem Inf Model 2020; 60:3703-3721. [DOI: 10.1021/acs.jcim.0c00325] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Mariia Radaeva
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia V6H 3Z6, Canada
| | - Xuesen Dong
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia V6H 3Z6, Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia V6H 3Z6, Canada
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Bergant Loboda K, Janežič M, Štampar M, Žegura B, Filipič M, Perdih A. Substituted 4,5'-Bithiazoles as Catalytic Inhibitors of Human DNA Topoisomerase IIα. J Chem Inf Model 2020; 60:3662-3678. [PMID: 32484690 PMCID: PMC7469689 DOI: 10.1021/acs.jcim.0c00202] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human type II topoisomerases, molecular motors that alter the DNA topology, are a major target of modern chemotherapy. Groups of catalytic inhibitors represent a new approach to overcome the known limitations of topoisomerase II poisons such as cardiotoxicity and induction of secondary tumors. Here, we present a class of substituted 4,5'-bithiazoles as catalytic inhibitors targeting the human DNA topoisomerase IIα. Based on a structural comparison of the ATPase domains of human and bacterial type II topoisomerase, a focused chemical library of 4,5'-bithiazoles was assembled and screened to identify compounds that better fit the topology of the human topo IIα adenosine 5'-triphosphate (ATP) binding site. Selected compounds showed inhibition of human topo IIα comparable to that of the etoposide topo II drug, revealing a new class of inhibitors targeting this molecular motor. Further investigations showed that compounds act as catalytic inhibitors via competitive ATP inhibition. We also confirmed binding to the truncated ATPase domain of topo IIα and modeled the inhibitor molecular recognition with molecular simulations and dynophore models. The compounds also displayed promising cytotoxicity against HepG2 and MCF-7 cell lines comparable to that of etoposide. In a more detailed study with the HepG2 cell line, there was no induction of DNA double-strand breaks (DSBs), and the compounds were able to reduce cell proliferation and stop the cell cycle mainly in the G1 phase. This confirms the mechanism of action of these compounds, which differs from topo II poisons also at the cellular level. Substituted 4,5'-bithiazoles appear to be a promising class for further development toward efficient and potentially safer cancer therapies exploiting the alternative topo II inhibition paradigm.
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Affiliation(s)
- Kaja Bergant Loboda
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.,Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Matej Janežič
- Laboratory for Structural Bioinformatics, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Martina Štampar
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia
| | - Bojana Žegura
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia
| | - Metka Filipič
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia
| | - Andrej Perdih
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
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Design and synthesis of 3,5-substituted 1,2,4-oxadiazoles as catalytic inhibitors of human DNA topoisomerase IIα. Bioorg Chem 2020; 99:103828. [DOI: 10.1016/j.bioorg.2020.103828] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/20/2020] [Accepted: 04/05/2020] [Indexed: 01/05/2023]
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12
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Bergant K, Janežič M, Valjavec K, Sosič I, Pajk S, Štampar M, Žegura B, Gobec S, Filipič M, Perdih A. Structure-guided optimization of 4,6-substituted-1,3,5-triazin-2(1H)-ones as catalytic inhibitors of human DNA topoisomerase IIα. Eur J Med Chem 2019; 175:330-348. [PMID: 31096154 DOI: 10.1016/j.ejmech.2019.04.055] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 04/19/2019] [Indexed: 01/03/2023]
Abstract
Human DNA topoisomerases represent one of the key targets of modern chemotherapy. An emerging group of catalytic inhibitors of human DNA topoisomerase IIα comprises a new paradigm directed to circumvent the known limitations of topoisomerase II poisons such as cardiotoxicity and induction of secondary tumors. In our previous studies, 4,6-substituted-1,3,5-triazin-2(1H)-ones were discovered as catalytic inhibitors of topo IIα. Here, we report the results of our efforts to optimize several properties of the initial chemical series that did not exhibit cytotoxicity on cancer cell lines. Using an optimized synthetic route, a focused chemical library was designed aimed at further functionalizing substituents at the position 4 of the 1,3,5-triazin-2(1H)-one scaffold to enable additional interactions with the topo IIα ATP binding site. After virtual screening, selected 36 analogues were synthesized and experimentally evaluated for human topo IIα inhibition. The optimized series displayed improved inhibition of topo IIα over the initial series and the catalytic mode of inhibition was confirmed for the selected active compounds. The optimized series also showed cytotoxicity against HepG2 and MCF-7 cell lines and did not induce double-strand breaks, thus displaying a mechanism of action that differs from the topo II poisons on the cellular level. The new series represents a new step in the development of the 4,6-substituted-1,3,5-triazin-2(1H)-one class towards novel efficient anticancer therapies utilizing the catalytic topo IIα inhibition paradigm.
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Affiliation(s)
- Kaja Bergant
- National Institute of Chemistry, Hajdrihova 19, SI 1001, Ljubljana, Slovenia; University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, SI 1000, Ljubljana, Slovenia
| | - Matej Janežič
- Laboratory for Structural Bioinformatics, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Katja Valjavec
- National Institute of Chemistry, Hajdrihova 19, SI 1001, Ljubljana, Slovenia
| | - Izidor Sosič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, SI 1000, Ljubljana, Slovenia
| | - Stane Pajk
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, SI 1000, Ljubljana, Slovenia
| | - Martina Štampar
- National Institute of Biology, Department of Genetic Toxicology and Cancer Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Bojana Žegura
- National Institute of Biology, Department of Genetic Toxicology and Cancer Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Stanislav Gobec
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, SI 1000, Ljubljana, Slovenia
| | - Metka Filipič
- National Institute of Biology, Department of Genetic Toxicology and Cancer Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Andrej Perdih
- National Institute of Chemistry, Hajdrihova 19, SI 1001, Ljubljana, Slovenia.
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Murugavel S, Ravikumar C, Jaabil G, Alagusundaram P. Synthesis, computational quantum chemical study, in silico ADMET and molecular docking analysis, in vitro biological evaluation of a novel sulfur heterocyclic thiophene derivative containing 1,2,3-triazole and pyridine moieties as a potential human topoisomerase IIα inhibiting anticancer agent. Comput Biol Chem 2019; 79:73-82. [PMID: 30731361 DOI: 10.1016/j.compbiolchem.2019.01.013] [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] [Received: 04/24/2018] [Revised: 01/17/2019] [Accepted: 01/25/2019] [Indexed: 02/07/2023]
Abstract
Computational quantum chemical study and biological evaluation of a synthesized novel sulfur heterocyclic thiophene derivative containing 1,2,3-triazole and pyridine moieties namely BTPT [2-(1-benzyl-5-methyl-1H-1,2,3-triazol-4-yl)-6-methoxy-4-(thiophen-2-yl) pyridine] was presented in this study. The crystal structure was determined by SCXRD method. For the title compound BTPT, spectroscopic characterization like 1H NMR, 13C NMR, FTIR, UV-vis were carried out theoretically by computational DFT method and compared with experimental data. Druglikeness parameters of BTPT were found through in silico pharmacological ADMET properties estimation. The molecular docking investigation was performed with human topoisomerase IIα (PDB ID:1ZXM) targeting ATP binding site. In vitro cytotoxicity activity of BTPT/doxorubicin were examined by MTT assay procedure against three human cancer cell lines A549, PC-3, MDAMB-231 with IC50 values of 0.68/0.70, 1.03/0.77 and 0.88/0.98 μM, respectively. Our title compound BTPT reveals notable cytotoxicity against breast cancer cell (MDAMB-231), moderate activity with human lung cancer cell (A-549) and less inhibition with human prostate cancer cell (PC-3) compared to familiar cancer medicine doxorubicin. From the results, BTPT could be observed as a potential candidate for novel anticancer drug development process.
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Affiliation(s)
- S Murugavel
- Department of Physics, Thanthai Periyar Government Institute of Technology, Vellore, 632002, Tamil Nadu, India.
| | - C Ravikumar
- Department of Physics, Thanthai Periyar EVR Government Polytechnic College, Vellore, 632002, Tamil Nadu, India
| | - G Jaabil
- Department of Organic Chemistry, School of Chemistry, Madurai Kamaraj University, Madurai, 625021, Tamil Nadu, India
| | - Ponnuswamy Alagusundaram
- Department of Organic Chemistry, School of Chemistry, Madurai Kamaraj University, Madurai, 625021, Tamil Nadu, India
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Zhao HW, Guo JM, Wang LR, Ding WQ, Tang Z, Song XQ, Wu HH, Fan XZ, Bi XF. Diastereoselective formal [3 + 3] cycloaddition of isatin-based α-(trifluoromethyl)imines with N,N′-dialkyloxyureas. Org Chem Front 2019. [DOI: 10.1039/c9qo01181a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The diastereoselective formal [3 + 3] cycloaddition of isatin-based α-(trifluoromethyl)imines with N,N′-dialkyloxyureas furnished trans-configured novel spiro-1,3,5-triazinan-2-ones in reasonable chemical yields.
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Affiliation(s)
- Hong-Wu Zhao
- Beijing Key Laboratory of Environmental and Viral Oncology
- College of Life Science and Bio-engineering
- Beijing University of Technology
- Beijing 100124
- P. R. China
| | - Jia-Ming Guo
- Beijing Key Laboratory of Environmental and Viral Oncology
- College of Life Science and Bio-engineering
- Beijing University of Technology
- Beijing 100124
- P. R. China
| | - Li-Ru Wang
- Beijing Key Laboratory of Environmental and Viral Oncology
- College of Life Science and Bio-engineering
- Beijing University of Technology
- Beijing 100124
- P. R. China
| | - Wan-Qiu Ding
- Beijing Key Laboratory of Environmental and Viral Oncology
- College of Life Science and Bio-engineering
- Beijing University of Technology
- Beijing 100124
- P. R. China
| | - Zhe Tang
- Beijing Key Laboratory of Environmental and Viral Oncology
- College of Life Science and Bio-engineering
- Beijing University of Technology
- Beijing 100124
- P. R. China
| | - Xiu-Qing Song
- Beijing Key Laboratory of Environmental and Viral Oncology
- College of Life Science and Bio-engineering
- Beijing University of Technology
- Beijing 100124
- P. R. China
| | - Hui-Hui Wu
- Beijing Key Laboratory of Environmental and Viral Oncology
- College of Life Science and Bio-engineering
- Beijing University of Technology
- Beijing 100124
- P. R. China
| | - Xiao-Zu Fan
- Beijing Key Laboratory of Environmental and Viral Oncology
- College of Life Science and Bio-engineering
- Beijing University of Technology
- Beijing 100124
- P. R. China
| | - Xiao-Fan Bi
- Beijing Key Laboratory of Environmental and Viral Oncology
- College of Life Science and Bio-engineering
- Beijing University of Technology
- Beijing 100124
- P. R. China
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15
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Towards Intelligent Drug Design System: Application of Artificial Dipeptide Receptor Library in QSAR-Oriented Studies. Molecules 2018; 23:molecules23081964. [PMID: 30082652 PMCID: PMC6222794 DOI: 10.3390/molecules23081964] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 07/29/2018] [Accepted: 08/05/2018] [Indexed: 12/23/2022] Open
Abstract
The pharmacophore properties of a new series of potential purinoreceptor (P2X) inhibitors determined using a coupled neural network and the partial least squares method with iterative variable elimination (IVE-PLS) are presented in a ligand-based comparative study of the molecular surface by comparative molecular surface analysis (CoMSA). Moreover, we focused on the interpretation of noticeable variations in the potential selectiveness of interactions of individual inhibitor-receptors due to their physicochemical properties; therefore, the library of artificial dipeptide receptors (ADP) was designed and examined. The resulting library response to individual inhibitors was arranged in the array, preprocessed and transformed by the principal component analysis (PCA) and PLS procedures. A dominant absolute contribution to PC1 of the Glu attached to heptanoic gating acid and Phe bonded to the linker m-phenylenediamine/triazine scaffold was revealed by the PCA. The IVE-PLS procedure indicated the receptor systems with predominant Pro bonded to the linker and Glu, Gln, Cys and Val directly attached to the gating acid. The proposed comprehensive ligand-based and simplified structure-based methodology allows the in-depth study of the performance of peptide receptors against the tested set of compounds.
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16
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Zaki I, Abdelhameid MK, El-Deen IM, Abdel Wahab AHA, Ashmawy AM, Mohamed KO. Design, synthesis and screening of 1, 2, 4-triazinone derivatives as potential antitumor agents with apoptosis inducing activity on MCF-7 breast cancer cell line. Eur J Med Chem 2018; 156:563-579. [PMID: 30025350 DOI: 10.1016/j.ejmech.2018.07.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 06/28/2018] [Accepted: 07/02/2018] [Indexed: 10/28/2022]
Abstract
Some triazinone derivatives are designed and synthesized as potential antitumor agents. Triazinone derivatives 4c, 5e and 7c show potent anticancer activity over MCF-7 breast cancer cells higher than podophyllotoxin (podo) by approximate 6-fold. DNA flow cytometry analysis for the compounds 3c, 4c, 5e, 6c and 7c show a potent inhibitory activity of cell proliferation and cell cycle arrest at G2/M phase. Compounds 4c, 5e and 7c exhibit low to moderate β-tubulin polymerization inhibition percentage. Meanwhile, compound 6c displayed excellent β-tubulin percentage of polymerization inhibition equivalent to that exhibited by podo. In addition, compounds 4c, 5e and 7c show strong topoisomerase (topo) II inhibitory activity in nano-molar concentration, compared to known topo inhibitor as etoposide. Finally, apoptotic inducing activity over MCF-7 of compounds 4c, 5e, 6c and 7c is due to up-regulation of p53, increased Bax/Bcl-2 ratio and caspase3/7 levels 2-fold higher than podo.
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Affiliation(s)
- Islam Zaki
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Port Said University, Port Said, Egypt
| | - Mohammed K Abdelhameid
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt.
| | - Ibrahim M El-Deen
- Chemistry Department, Faculty of Science, Port Said University, Port Said, Egypt
| | | | - Abeer M Ashmawy
- Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Khaled O Mohamed
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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17
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Łączkowski KZ, Anusiak J, Świtalska M, Dzitko K, Cytarska J, Baranowska-Łączkowska A, Plech T, Paneth A, Wietrzyk J, Białczyk J. Synthesis, molecular docking, ctDNA interaction, DFT calculation and evaluation of antiproliferative and anti- Toxoplasma gondii activities of 2,4-diaminotriazine-thiazole derivatives. Med Chem Res 2018; 27:1131-1148. [PMID: 29576720 PMCID: PMC5854716 DOI: 10.1007/s00044-018-2136-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 01/13/2018] [Indexed: 01/23/2023]
Abstract
Synthesis, characterization, and investigation of antiproliferative activities against human cancer cell lines (MV4-11, MCF-7, and A549) and Toxoplasma gondii parasite of twelve novel 2,4-diaminotriazine-thiazoles are presented. The toxicity of the compounds was studied at three different cell types, normal mouse fibroblast (Balb/3T3), mouse fibroblast (L929), and human VERO cells. The structures of novel compounds were determined using 1H and 13C NMR, FAB(+)-MS, and elemental analyses. Among the derivatives, 4a–k showed very high activity against MV4-11 cell line with IC50 values between 1.13 and 3.21 µg/ml. Additionally, the cytotoxic activity of compounds 4a–k against normal mouse fibroblast Balb/3T3 cells is about 20–100 times lower than against cancer cell lines. According to our results, compounds 4a, 4b, 4d, and 4i have very strong activity against human breast carcinoma MCF-7, with IC50 values from 3.18 to 4.28 µg/ml. Moreover, diaminotriazines 4a–l showed significant anti-Toxoplasma gondii activity, with IC50 values 9–68 times lower than those observed for sulfadiazine. Molecular docking studies indicated DNA-binding site of hTopoI and hTopoII as possible anticancer targets and purine nucleoside phosphorylase as possible anti-toxoplasmosis target. Our UV–Vis spectroscopic results indicate also that diaminotriazine-thiazoles tends to interact with DNA by intercalation. Additionally, the structure and the interaction and binding energies of a model complex formed by compound 4a and two thymine molecules are investigated using quantum mechanical methods.
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Affiliation(s)
- Krzysztof Z Łączkowski
- 1Department of Chemical Technology and Pharmaceuticals, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Jurasza 2, 85-089 Bydgoszcz, Poland
| | - Joanna Anusiak
- 1Department of Chemical Technology and Pharmaceuticals, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Jurasza 2, 85-089 Bydgoszcz, Poland
| | - Marta Świtalska
- 2Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla 12, 53-114 Wrocław, Poland
| | - Katarzyna Dzitko
- 3Department of Immunoparasitology, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland
| | - Joanna Cytarska
- 1Department of Chemical Technology and Pharmaceuticals, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Jurasza 2, 85-089 Bydgoszcz, Poland
| | | | - Tomasz Plech
- 5Department of Pharmacology, Faculty of Health Sciences, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland
| | - Agata Paneth
- 6Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland
| | - Joanna Wietrzyk
- 1Department of Chemical Technology and Pharmaceuticals, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Jurasza 2, 85-089 Bydgoszcz, Poland.,2Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla 12, 53-114 Wrocław, Poland.,3Department of Immunoparasitology, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland.,4Institute of Physics, Kazimierz Wielki University, Plac Weyssenhoffa 11, 85-072 Bydgoszcz, Poland.,5Department of Pharmacology, Faculty of Health Sciences, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland.,6Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland
| | - Joanna Białczyk
- 1Department of Chemical Technology and Pharmaceuticals, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Jurasza 2, 85-089 Bydgoszcz, Poland.,2Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla 12, 53-114 Wrocław, Poland.,3Department of Immunoparasitology, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland.,4Institute of Physics, Kazimierz Wielki University, Plac Weyssenhoffa 11, 85-072 Bydgoszcz, Poland.,5Department of Pharmacology, Faculty of Health Sciences, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland.,6Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland
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18
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Ahmadi F, Mirzaei P, Bazgir A. Cobalt-catalyzed isocyanide insertion cyclization to dihydrobenzoimidazotriazins. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.09.088] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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19
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Han X, Zhong Y, Zhou G, Qi H, Li S, Ding Q, Liu Z, Song Y, Qiao X. Synthesis and biological evaluation of N-(carbobenzyloxy)-l-phenylalanine and N-(carbobenzyloxy)-l-aspartic acid-β-benzyl ester derivatives as potent topoisomerase IIα inhibitors. Bioorg Med Chem 2017; 25:3116-3126. [PMID: 28462840 DOI: 10.1016/j.bmc.2017.03.065] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/28/2017] [Indexed: 12/20/2022]
Abstract
A new series of thirteen N-(carbobenzyloxy)-l-phenylalanine and N-(carbobenzyloxy)-l-aspartic acid-β-benzyl ester compounds were synthesized and evaluated for antiproliferative activity against four different human cancer cell lines: cervical cancer (HeLa), lung cancer (A549), gastric cancer (MGC-803) and breast cancer (MCF-7) as well as topoisomerase I and IIα inhibitory activity. Compounds (5a, 5b, 5e, 8a, 8b) showed significant antiproliferative activity with low IC50 values against the four cancer cell lines. Equally, compounds 5a, 5b, 5e, 5f, 8a, 8d, 8e and 8f showed topoisomerase IIα inhibitory activity at 100μM with 5b, 5e, 8f exhibiting potential topoisomerase IIα inhibitory activity compared to positive control at 100μM and 20μM, respectively. Conversely compounds 5e, 5f, 5g and 8a showed weaker topoisomerase I inhibitory activity compared to positive control at 100μM. Compound 5b exhibited the most potent topoisomerase IIα inhibitory activity at low concentration and better antiproliferative activity against the four human cancer cell lines. The molecular interactions between compounds 5a-5g, 8a-8f and the topoisomerase IIα (PDB ID: 1ZXM) were further investigated through molecular docking. The results indicated that these compounds could serve as promising leads for further optimization as novel antitumor agents.
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Affiliation(s)
- Xiaoyan Han
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, College of Pharmaceutical Sciences, Hebei University, Baoding 071002, China
| | - Yifan Zhong
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, College of Pharmaceutical Sciences, Hebei University, Baoding 071002, China
| | - Guan Zhou
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, College of Pharmaceutical Sciences, Hebei University, Baoding 071002, China
| | - Hui Qi
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, College of Pharmaceutical Sciences, Hebei University, Baoding 071002, China
| | - Shengbin Li
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, College of Pharmaceutical Sciences, Hebei University, Baoding 071002, China
| | - Qiang Ding
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, College of Pharmaceutical Sciences, Hebei University, Baoding 071002, China
| | - Zhenming Liu
- Drug Design Center, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yali Song
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, College of Pharmaceutical Sciences, Hebei University, Baoding 071002, China.
| | - Xiaoqiang Qiao
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, College of Pharmaceutical Sciences, Hebei University, Baoding 071002, China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, China.
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20
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Yenice I, Basceken S, Balci M. Nucleophilic and electrophilic cyclization of N-alkyne-substituted pyrrole derivatives: Synthesis of pyrrolopyrazinone, pyrrolotriazinone, and pyrrolooxazinone moieties. Beilstein J Org Chem 2017; 13:825-834. [PMID: 28546840 PMCID: PMC5433174 DOI: 10.3762/bjoc.13.83] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/07/2017] [Indexed: 11/29/2022] Open
Abstract
Intramolecular nucleophilic and electrophilic cyclization of N-alkyne-substituted pyrrole esters is described. Efficient routes towards the synthesis of pyrrolopyrazinone, pyrrolotriazinone and pyrrolooxazinone have been developed. First, N-alkyne-substituted pyrrole ester derivatives were synthesized. Introduction of various substituents into the alkyne functionality was accomplished by a copper-catalyzed cross-coupling reaction. Nucleophilic cyclization of N-alkyne-substituted methyl 1H-pyrrole-2-carboxylates with hydrazine afforded the 6-exo-dig/6-endo-dig cyclization products depending on the electronic nature of the substituents attached to the alkyne. On the other hand, cyclization of N-alkyne-substituted methyl 1H-pyrrole-2-carboxylates with iodine only resulted in the formation of the 6-endo-dig cyclization product regardless of the substitution of the alkyne functionality.
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Affiliation(s)
- Işıl Yenice
- Department of Chemistry, Middle East Technical University, 06800 Ankara, Turkey
| | - Sinan Basceken
- Department of Chemistry, Middle East Technical University, 06800 Ankara, Turkey
- Department of Chemistry, Hitit University, 19030 Corum, Turkey
| | - Metin Balci
- Department of Chemistry, Middle East Technical University, 06800 Ankara, Turkey
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21
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Kumar M, Kaur T, Sharma A. Role of computational efficiency indices and pose clustering in effective decision making: An example of annulated furanones in Pf-DHFR space. Comput Biol Chem 2017; 67:48-61. [PMID: 28049061 DOI: 10.1016/j.compbiolchem.2016.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 11/04/2016] [Accepted: 12/22/2016] [Indexed: 10/20/2022]
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22
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Janežič M, Pogorelčnik B, Brvar M, Solmajer T, Perdih A. 3-substituted-1H-indazoles as Catalytic Inhibitors of the Human DNA Topoisomerase IIα. ChemistrySelect 2017. [DOI: 10.1002/slct.201601554] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Matej Janežič
- National Institute of Chemistry; Hajdrihova 19, SI- 1001 Ljubljana Slovenia
| | | | - Matjaž Brvar
- National Institute of Chemistry; Hajdrihova 19, SI- 1001 Ljubljana Slovenia
| | - Tom Solmajer
- National Institute of Chemistry; Hajdrihova 19, SI- 1001 Ljubljana Slovenia
| | - Andrej Perdih
- National Institute of Chemistry; Hajdrihova 19, SI- 1001 Ljubljana Slovenia
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23
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Entzian C, Schubert T. Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis. J Vis Exp 2017. [PMID: 28117825 DOI: 10.3791/55070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Characterization of molecular interactions in terms of basic binding parameters such as binding affinity, stoichiometry, and thermodynamics is an essential step in basic and applied science. MicroScale Thermophoresis (MST) is a sensitive biophysical method to obtain this important information. Relying on a physical effect called thermophoresis, which describes the movement of molecules through temperature gradients, this technology allows for the fast and precise determination of binding parameters in solution and allows the free choice of buffer conditions (from buffer to lysates/sera). MST uses the fact that an unbound molecule displays a different thermophoretic movement than a molecule that is in complex with a binding partner. The thermophoretic movement is altered in the moment of molecular interaction due to changes in size, charge, and hydration shell. By comparing the movement profiles of different molecular ratios of the two binding partners, quantitative information such as binding affinity (pM to mM) can be determined. Even challenging interactions between molecules of small sizes, such as aptamers and small compounds, can be studied by MST. Using the well-studied model interaction between the DH25.42 DNA aptamer and ATP, this manuscript provides a protocol to characterize aptamer-small molecule interactions. This study demonstrates that MST is highly sensitive and permits the mapping of the binding site of the 7.9 kDa DNA aptamer to the adenine of ATP.
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25
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Viira B, Selyutina A, García-Sosa AT, Karonen M, Sinkkonen J, Merits A, Maran U. Design, discovery, modelling, synthesis, and biological evaluation of novel and small, low toxicity s-triazine derivatives as HIV-1 non-nucleoside reverse transcriptase inhibitors. Bioorg Med Chem 2016; 24:2519-2529. [PMID: 27108399 DOI: 10.1016/j.bmc.2016.04.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 03/10/2016] [Accepted: 04/08/2016] [Indexed: 11/15/2022]
Abstract
A set of top-ranked compounds from a multi-objective in silico screen was experimentally tested for toxicity and the ability to inhibit the activity of HIV-1 reverse transcriptase (RT) in cell-free assay and in cell-based assay using HIV-1 based virus-like particles. Detailed analysis of a commercial sample that indicated specific inhibition of HIV-1 reverse transcription revealed that a minor component that was structurally similar to that of the main compound was responsible for the strongest inhibition. As a result, novel s-triazine derivatives were proposed, modelled, discovered, and synthesised, and their antiviral activity and cellular toxicity were tested. Compounds 18a and 18b were found to be efficient HIV-1 RT inhibitors, with an IC50 of 5.6±1.1μM and 0.16±0.05μM in a cell-based assay using infectious HIV-1, respectively. Compound 18b also had no detectable toxicity for different human cell lines. Their binding mode and interactions with the RT suggest that there was strong and adaptable binding in a tight (NNRTI) hydrophobic pocket. In summary, this iterative study produced structural clues and led to a group of non-toxic, novel compounds to inhibit HIV-RT with up to nanomolar potency.
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Affiliation(s)
- Birgit Viira
- Institute of Chemistry, University of Tartu, Tartu 50411, Estonia
| | | | | | - Maarit Karonen
- Department of Chemistry, University of Turku, FI-20014 Turku, Finland
| | - Jari Sinkkonen
- Department of Chemistry, University of Turku, FI-20014 Turku, Finland
| | - Andres Merits
- Institute of Technology, University of Tartu, Tartu 50411, Estonia.
| | - Uko Maran
- Institute of Chemistry, University of Tartu, Tartu 50411, Estonia.
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26
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Mao ZW, Li QL, Wang P, Sun YL, Liu Y. Design and Development of Novel 4-(4-(1H-Tetrazol-5-yl)-1H-pyrazol-1-yl)-6-morpholino-N-(4-nitrophenyl)-1,3,5-triazin-2-amine as Cardiotonic Agent via Inhibition of PDE3. Arch Pharm (Weinheim) 2016; 349:268-76. [PMID: 26934198 DOI: 10.1002/ardp.201500388] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 01/20/2016] [Accepted: 01/26/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Zhi-Wei Mao
- Department of Cardiovasology; Zhengzhou Central Hospital Affiliated to Zhengzhou University; Zhengzhou Henan P. R. China
| | - Qiao-Ling Li
- Department of Kidney Rheumatology; The Fifth Affiliated Hospital of Zhengzhou University; Zhengzhou Henan P. R. China
| | - Ping Wang
- Department of Cardiovasology; Zhengzhou Central Hospital Affiliated to Zhengzhou University; Zhengzhou Henan P. R. China
| | - Yang-Li Sun
- Department of Cardiovasology; Zhengzhou Central Hospital Affiliated to Zhengzhou University; Zhengzhou Henan P. R. China
| | - Yu Liu
- Department of Cardiovasology; Zhengzhou Central Hospital Affiliated to Zhengzhou University; Zhengzhou Henan P. R. China
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