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Latosińska JN, Latosińska M, Orzeszko A, Maurin JK. Synthesis and Crystal Structure of Adamantylated 4,5,6,7-Tetrahalogeno-1 H-benzimidazoles Novel Multi-Target Ligands (Potential CK2, M2 and SARS-CoV-2 Inhibitors); X-ray/DFT/QTAIM/Hirshfeld Surfaces/Molecular Docking Study. Molecules 2022; 28:molecules28010147. [PMID: 36615341 PMCID: PMC9822452 DOI: 10.3390/molecules28010147] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
A series of new congeners, 1-[2-(1-adamantyl)ethyl]-1H-benzimidazole (AB) and 1-[2-(1-adamantyl)ethyl]-4,5,6,7-tetrahalogeno-1H-benzimidazole (Hal=Cl, Br, I; tClAB, tBrAB, tIAB), have been synthesized and studied. These novel multi-target ligands combine a benzimidazole ring known to show antitumor activity and an adamantyl moiety showing anti-influenza activity. Their crystal structures were determined by X-ray, while intermolecular interactions were studied using topological Bader's Quantum Theory of Atoms in Molecules, Hirshfeld Surfaces, CLP and PIXEL approaches. The newly synthesized compounds crystallize within two different space groups, P-1 (AB and tIAB) and P21/c (tClAB and tBrAB). A number of intramolecular hydrogen bonds, C-H⋯Hal (Hal=Cl, Br, I), were found in all halogen-containing congeners studied, but the intermolecular C-H⋯N hydrogen bond was detected only in AB and tIAB, while C-Hal⋯π only in tClAB and tBrAB. The interplay between C-H⋯N and C-H⋯Hal hydrogen bonds and a shift from the strong (C-H⋯Cl) to the very weak (C-H⋯I) attractive interactions upon Hal exchange, supplemented with Hal⋯Hal overlapping, determines the differences in the symmetry of crystalline packing and is crucial from the biological point of view. The hypothesis about the potential dual inhibitor role of the newly synthesized congeners was verified using molecular docking and the congeners were found to be pharmaceutically attractive as Human Casein Kinase 2, CK2, inhibitors, Membrane Matrix 2 Protein, M2, blockers and Severe Acute Respiratory Syndrome Coronavirus 2, SARS-CoV-2, inhibitors. The addition of adamantyl moiety seems to broaden and modify the therapeutic indices of the 4,5,6,7-tetrahalogeno-1H-benzimidazoles.
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Affiliation(s)
- Jolanta Natalia Latosińska
- Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, 61-614 Poznań, Poland
- Correspondence: ; Tel.: +48-61-8295277
| | - Magdalena Latosińska
- Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, 61-614 Poznań, Poland
| | - Andrzej Orzeszko
- Institute of Chemistry, Warsaw University of Life Sciences, 159C Nowoursynowska St., 02-787 Warsaw, Poland
| | - Jan Krzysztof Maurin
- National Medicines Institute, Chełmska 30/34, 00-750 Warsaw, Poland
- National Centre for Nuclear Research, Andrzeja Sołtana 7, 05-400 Otwock-Świerk, Poland
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Baglini E, Salerno S, Barresi E, Robello M, Da Settimo F, Taliani S, Marini AM. Multiple Topoisomerase I (TopoI), Topoisomerase II (TopoII) and Tyrosyl-DNA Phosphodiesterase (TDP) inhibitors in the development of anticancer drugs. Eur J Pharm Sci 2021; 156:105594. [DOI: 10.1016/j.ejps.2020.105594] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 02/08/2023]
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Sun Y, Saha LK, Saha S, Jo U, Pommier Y. Debulking of topoisomerase DNA-protein crosslinks (TOP-DPC) by the proteasome, non-proteasomal and non-proteolytic pathways. DNA Repair (Amst) 2020; 94:102926. [DOI: 10.1016/j.dnarep.2020.102926] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 01/24/2023]
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Ibrahim HA, Refaat HM. Versatile mechanisms of 2-substituted benzimidazoles in targeted cancer therapy. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2020. [DOI: 10.1186/s43094-020-00048-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Abstract
Background
The aim of this review is to provide an overview on diverse anticancer activities of 2-substituted benzimidazole derivatives.
Main body
This review provides a correlation between the various mechanisms of action of benzimidazoles as anticancer and the substitution pattern around the nucleus.
Conclusion
The linker group and substitution at N-1, C-2, C-5, and C-6 positions have been found to be the most contributory factors for anticancer activity. This will help in the further design to afford more selective, potent, and multi-target anticancer of 2-substituted benzimidazole-based compounds.
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Dubey S, Prabitha P, Bhardwaj S, Singh E. A study of pyrazolo-benzimidazole derivatives as spleen tyrosine kinase inhibitors: an in-silico approach. Struct Chem 2019. [DOI: 10.1007/s11224-018-1189-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Combined pharmacophore-guided 3D-QSAR, molecular docking, and virtual screening on bis-benzimidazoles and ter-benzimidazoles as DNA–topoisomerase I poisons. Struct Chem 2019. [DOI: 10.1007/s11224-018-1257-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Bansal S, Bajaj P, Pandey S, Tandon V. Topoisomerases: Resistance versus Sensitivity, How Far We Can Go? Med Res Rev 2016; 37:404-438. [PMID: 27687257 DOI: 10.1002/med.21417] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/04/2016] [Accepted: 08/29/2016] [Indexed: 12/15/2022]
Abstract
DNA topoisomerases are ubiquitously present remarkable molecular machines that help in altering topology of DNA in living cells. The crucial role played by these nucleases during DNA replication, transcription, and recombination vis-à-vis less sequence similarity among different species makes topoisomerases unique and attractive targets for different anticancer and antibacterial drugs. However, druggability of topoisomerases by the existing class of molecules is increasingly becoming questationable due to resistance development predominated by mutations in the corresponding genes. The current scenario facing a decline in the development of new molecules further comprises an important factor that may challenge topoisomerase-targeting therapy. Thus, it is imperative to wisely use the existing inhibitors lest with this rapid rate of losing grip over the target we may not go too far. Furthermore, it is important not only to design new molecules but also to develop new approaches that may avoid obstacles in therapies due to multiple resistance mechanisms. This review provides a succinct account of different classes of topoisomerase inhibitors, focuses on resistance acquired by mutations in topoisomerases, and discusses the various approaches to increase the efficacy of topoisomerase inhibitors. In a later section, we also suggest the possibility of using bisbenzimidazoles along with efflux pump inhibitors for synergistic bactericidal effects.
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Affiliation(s)
- Sandhya Bansal
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, New Delhi, India
| | - Priyanka Bajaj
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Stuti Pandey
- Department of Chemistry, University of Delhi, New Delhi, India
| | - Vibha Tandon
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India.,Department of Chemistry, University of Delhi, New Delhi, India
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Błaszczak-Świątkiewicz K, Sikora J, Szymański J, Danilewicz M, Mikiciuk-Olasik E. Biological evaluation of the toxicity and the cell cycle interruption by some benzimidazole derivatives. Tumour Biol 2016; 37:11135-45. [PMID: 26932526 PMCID: PMC4999476 DOI: 10.1007/s13277-016-4828-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 01/08/2016] [Indexed: 11/07/2022] Open
Abstract
In this work, the in vitro tests of biological activity of benzimidazoles were conducted. This group of benzimidazole derivatives was evaluated as potential bioreductive agents and their characteristic pro-apoptosis activity and cell cycle interruption on the human lung adenocarcinoma A549 cells were discussed. Their toxicity on the healthy human erythrocytes and their influence on the healthy human erythrocytes acetylcholinesterase enzyme (AChE) were established. Their apoptosis activity on A549 cells line was determined by Annexin V-APC test, and it was visualized by Hoechst test. In the next stage, their influence on the cell cycle interruption was determined by using the ribonuclease reagent. The AChE inhibition test was defined by the Ellman method, and the red blood cell lysis was defined by erythrotoxicity test. The results proved the pro-apoptosis properties of all tested compounds in normoxia and hypoxia. The DNA content assay showed that the benzimidazoles possess the ability to interrupt S phase of tumor cell cycle. The best activity in this action was presented by compound 1, especially in hypoxia, and it proves that the N-oxide analogs are predispositioned to the hypoxic target. In this study, the benzimidazoles were found as potentially biocompatible and their inhibition of acetylcholinesterase was lower than tirapazamine and much lower than tacrine which constitutes their desired effect of potential biological activity.
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Affiliation(s)
| | - Joanna Sikora
- Laboratory of Bioanalysis, Department of Pharmaceutical Chemistry, Drug Analysis and Radiopharmacy, Medical University, Muszynskiego 1, 90-151, Lodz, Poland
| | - Jacek Szymański
- Central Scientific Laboratory, Medical University, Mazowiecka 6/8, 92-215, Lodz, Poland
| | - Marian Danilewicz
- Educational Center of the Medical University of Lodz, Pomorska 251, 92-213, Lodz, Poland
| | - Elżbieta Mikiciuk-Olasik
- Department of Pharmaceutical Chemistry, Drug Analysis and Radiopharmacy, Medical University, Muszynskiego 1, 90-151, Lodz, Poland
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Błaszczak-Świątkiewicz K, Mikiciuk-Olasik E. Some characteristics of activity of potential chemotherapeutics--benzimidazole derivatives. Adv Med Sci 2015; 60:125-32. [PMID: 25725479 DOI: 10.1016/j.advms.2015.01.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Revised: 12/21/2014] [Accepted: 01/08/2015] [Indexed: 01/26/2023]
Abstract
In this work, the biological activity of some benzimidazoles and benzimidazole-4,7-diones was compared. These two groups of compounds were evaluated as potential chemotherapeutics and their characteristic relationship structure to biological activity was discussed. The authors compared their effect into the cytotoxic, apoptosis and DNA destruction approach. Their cytotoxic effect on the human lung adenocarcinoma A549 cells line was determined by WST-1 test. Next the cytotoxic way of tumor cells death was determined by caspase 3/7 test. The last point referred to the DNA destruction of A549 cells and test in situ DNA Assay Kit was applied. Two of the examined compounds (B2 and D2) show a very good correlation of the cytotoxic effect normoxia to hypoxia and they have been found as the potential agents of the DNA damage. The most cytotoxic feature possesses N-oxide benzimidazole derivatives (D and B groups). The screening test of the DNA damage established that N-oxide benzimidazole derivatives (D and B groups) can be more potent as the hypoxia-selective agents for tumor cells than benzimidazole derivatives (A and C groups). Additionally, the test of the caspase-dependent apoptosis proved that the exposure of benzimidazole-4,7-diones against A549 cells, especially in hypoxia, promotes apoptotic cell death.
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Affiliation(s)
| | - Elżbieta Mikiciuk-Olasik
- Department of Pharmaceutical Chemistry, Drug Analysis and Radiopharmacy, Medical University of Lodz, Lodz, Poland
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Biological evaluation of the activity of some benzimidazole-4,7-dione derivatives. Molecules 2014; 19:15361-73. [PMID: 25264827 PMCID: PMC6271954 DOI: 10.3390/molecules191015361] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 09/09/2014] [Accepted: 09/11/2014] [Indexed: 11/17/2022] Open
Abstract
The study presented here is a follow up of the authors’ interest in the approach to selective and cytotoxic bioreductive anticancer prodrugs. The current work is devoted to explore both the biological activity of some previously obtained compounds and the search for an explanation of their target(s) in hypoxic pathways. In this work the biological activity of some benzimidazole-4,7-diones was evaluated. These compounds were examined as potential bioreductive agents specific for the hypoxic environment found in tumor cells. The main aim was concerned with establishing their cytotoxic properties by using proliferation, apoptosis and DNA destruction tests on selected tumor cells. Their cytotoxic effects on two tumor cell lines (human lung adenocarcinoma A549 cells line and human malignant melanoma WM115) was compared by means of a WST-1 test. Next, the mode of cytotoxicity behind the selected tumor cells’ death was determined by the caspase 3/7 test. The last point referred to the DNA destruction of A549 and WM115 cells and the in situ DNA Assay Kit test was applied. The cytotoxic tests confirmed their activity against the tumor cells and target hypoxia (compounds 2b, 2a, 2d). The screening test of the caspase-dependent apoptosis proved that the exposure of the tested tumor cells in hypoxia to these benzimidazole-4,7-diones promoted the apoptotic cell death. Additionally, the DNA damage test established that benzimidazole-4,7-diones can be potential hypoxia-selective agents for tumor cells, especially compound 2b. All results classify the tested benzimidazole-4,7-diones as promising, lead molecules and provide a rationale for further molecular studies to explain their usefulness as potential inhibitors of the hypoxia-inducible factor 1 (HIF1).
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Rational approaches, design strategies, structure activity relationship and mechanistic insights for anticancer hybrids. Eur J Med Chem 2014; 77:422-87. [PMID: 24685980 DOI: 10.1016/j.ejmech.2014.03.018] [Citation(s) in RCA: 306] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Revised: 03/02/2014] [Accepted: 03/06/2014] [Indexed: 12/16/2022]
Abstract
A Hybrid drug which comprises the incorporation of two drug pharmacophores in one single molecule are basically designed to interact with multiple targets or to amplify its effect through action on another bio target as one single molecule or to counterbalance the known side effects associated with the other hybrid part(.) The present review article offers a detailed account of the design strategies employed for the synthesis of anticancer agents via molecular hybridization techniques. Over the years, the researchers have employed this technique to discover some promising chemical architectures displaying significant anticancer profiles. Molecular hybridization as a tool has been particularly utilized for targeting tubulin protein as exemplified through the number of research papers. The microtubule inhibitors such as taxol, colchicine, chalcones, combretasatin, phenstatins and vinca alkaloids have been utilized as one of the functionality of the hybrids and promising results have been obtained in most of the cases with some of the tubulin based hybrids exhibiting anticancer activity at nanomolar level. Linkage with steroids as biological carrier vector for anticancer drugs and the inclusion of pyrrolo [2,1-c] [1,4]benzodiazepines (PBDs), a family of DNA interactive antitumor antibiotics derived from Streptomyces species in hybrid structure based drug design has also emerged as a potential strategy. Various heteroaryl based hybrids in particular isatin and coumarins have also been designed and reported to posses' remarkable inhibitory potential. Apart from presenting the design strategies, the article also highlights the structure activity relationship along with mechanistic insights revealed during the biological evaluation of the hybrids.
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12
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Synthesis, anticancer activity and UPLC analysis of the stability of some new benzimidazole-4,7-dione derivatives. Molecules 2013; 19:400-13. [PMID: 24384922 PMCID: PMC6271476 DOI: 10.3390/molecules19010400] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 12/09/2013] [Accepted: 12/16/2013] [Indexed: 12/18/2022] Open
Abstract
In this work, a sensitive analytical method to study the stability of two new series of synthesized heterocyclic compounds, the benzimidazole-4,7-diones 5 and N-oxide benzimidazole-4,7-dione derivatives 6 was established and validated. These derivatives were developed as potential anticancer substances to be activated under hypoxic conditions. At this point we were concerned with establishing their stability in some specific environments for further biological studies. For that, we developed and validated an RP-UPLC method. Next, selected compounds were tested in vitro for possible anticancer activity. Their effect on A549 tumour cell lines under normoxia and hypoxia conditions was determined by a WST-1 test. Four of the examined compounds (compounds 5a–c and 6c) showed very good antiproliferative effects and three of them (compounds 6a, 6b and 6d) were specific for hypoxia conditions. The hypoxia/normoxia cytotoxic coefficient of compound 6b is close to that of tirapazamine—a reference compound in our experiments—and this parameter locates it between mitomycin C and 2-nitroimidazole (misonidazole).
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Al-Mudaris ZA, Majid ASA, Ji D, Al-Mudarris BA, Chen SH, Liang PH, Osman H, Jamal Din SKK, Abdul Majid AMS. Conjugation of benzylvanillin and benzimidazole structure improves DNA binding with enhanced antileukemic properties. PLoS One 2013; 8:e80983. [PMID: 24260527 PMCID: PMC3829952 DOI: 10.1371/journal.pone.0080983] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 10/18/2013] [Indexed: 11/19/2022] Open
Abstract
Benzyl-o-vanillin and benzimidazole nucleus serve as important pharmacophore in drug discovery. The benzyl vanillin (2-(benzyloxy)-3-methoxybenzaldehyde) compound shows anti-proliferative activity in HL60 leukemia cancer cells and can effect cell cycle progression at G2/M phase. Its apoptosis activity was due to disruption of mitochondrial functioning. In this study, we have studied a series of compounds consisting of benzyl vanillin and benzimidazole structures. We hypothesize that by fusing these two structures we can produce compounds that have better anticancer activity with improved specificity particularly towards the leukemia cell line. Here we explored the anticancer activity of three compounds namely 2-(2-benzyloxy-3-methoxyphenyl)-1H-benzimidazole, 2MP, N-1-(2-benzyloxy-3-methoxybenzyl)-2-(2-benzyloxy-3-methoxyphenyl)-1H-benzimidazole, 2XP, and (R) and (S)-1-(2-benzyloxy-3-methoxyphenyl)-2, 2, 2-trichloroethyl benzenesulfonate, 3BS and compared their activity to 2-benzyloxy-3-methoxybenzaldehyde, (Bn1), the parent compound. 2XP and 3BS induces cell death of U937 leukemic cell line through DNA fragmentation that lead to the intrinsic caspase 9 activation. DNA binding study primarily by the equilibrium binding titration assay followed by the Viscosity study reveal the DNA binding through groove region with intrinsic binding constant 7.39 µM/bp and 6.86 µM/bp for 3BS and 2XP respectively. 2XP and 3BS showed strong DNA binding activity by the UV titration method with the computational drug modeling showed that both 2XP and 3BS failed to form any electrostatic linkages except via hydrophobic interaction through the minor groove region of the nucleic acid. The benzylvanillin alone (Bn1) has weak anticancer activity even after it was combined with the benzimidazole (2MP), but after addition of another benzylvanillin structure (2XP), stronger activity was observed. Also, the combination of benzylvanillin with benzenesulfonate (3BS) significantly improved the anticancer activity of Bn1. The present study provides a new insight of benzyl vanillin derivatives as potential anti-leukemic agent.
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Affiliation(s)
- Zena A. Al-Mudaris
- School of Pharmaceutical Sciences, University Sains Malaysia, Minden, Penang, Malaysia
| | - Aman S. A. Majid
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bandar Putra Bertam, Penang, Malaysia
| | - Dan Ji
- Key Laboratory of Visual Damage and Regeneration & Restoration of Chongqing, Southwest Eye Hospital, Southwest Hospital, The Third Military Medical University, Chongqing, P.R.China
| | - Ban A. Al-Mudarris
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bandar Putra Bertam, Penang, Malaysia
- College of Dentistry, Ajman University, Ajman, UAE
| | - Shih-Hsun Chen
- Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan
| | - Po-Huang Liang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Hasnah Osman
- School of Chemical Sciences, University Sains Malaysia, Minden, Penang, Malaysia
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Kim SO, Sakchaisri K, N. R. T, Soung NK, Jang JH, Kim YS, Lee KS, Kwon YT, Asami Y, Ahn JS, Erikson RL, Kim BY. STK295900, a dual inhibitor of topoisomerase 1 and 2, induces G(2) arrest in the absence of DNA damage. PLoS One 2013; 8:e53908. [PMID: 23349762 PMCID: PMC3551932 DOI: 10.1371/journal.pone.0053908] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 12/04/2012] [Indexed: 11/18/2022] Open
Abstract
STK295900, a small synthetic molecule belonging to a class of symmetric bibenzimidazoles, exhibits antiproliferative activity against various human cancer cell lines from different origins. Examining the effect of STK295900 in HeLa cells indicates that it induces G(2) phase arrest without invoking DNA damage. Further analysis shows that STK295900 inhibits DNA relaxation that is mediated by topoisomerase 1 (Top 1) and topoisomerase 2 (Top 2) in vitro. In addition, STK295900 also exhibits protective effect against DNA damage induced by camptothecin. However, STK295900 does not affect etoposide-induced DNA damage. Moreover, STK295900 preferentially exerts cytotoxic effect on cancer cell lines while camptothecin, etoposide, and Hoechst 33342 affected both cancer and normal cells. Therefore, STK295900 has a potential to be developed as an anticancer chemotherapeutic agent.
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Affiliation(s)
- Sun-Ok Kim
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang, Cheongwon, Korea
- Department of Biochemistry, College of Natural Sciences, ChungNam National University, Yuseonggu, Daejeon, Korea
| | - Krisada Sakchaisri
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang, Cheongwon, Korea
| | - Thimmegowda N. R.
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang, Cheongwon, Korea
| | - Nak Kyun Soung
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang, Cheongwon, Korea
| | - Jae-Hyuk Jang
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang, Cheongwon, Korea
| | - Young Sang Kim
- Department of Biochemistry, College of Natural Sciences, ChungNam National University, Yuseonggu, Daejeon, Korea
| | - Kyung Sang Lee
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Yong Tae Kwon
- World Class University (WCU), Graduate School of Convergence Science and Technology and College of Medicine, Seoul National University, Seoul, Korea
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, School of Pharmacy, Universigy of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Yukihiro Asami
- Chemical Biology Department, RIKEN Advanced Science Institute, Wako-shi, Saitama, Japan
| | - Jong Seog Ahn
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang, Cheongwon, Korea
| | - Raymond Leo Erikson
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Bo Yeon Kim
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang, Cheongwon, Korea
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Mamedov VA, Zhukova NA, Syakaev VV, Gubaidullin AT, Beschastnova TN, Adgamova DI, Samigullina AI, Latypov SK. A new facile, efficient synthesis and structure peculiarity of quinoxaline derivatives with two benzimidazole fragments. Tetrahedron 2013. [DOI: 10.1016/j.tet.2012.10.045] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Chen CH, Kuo J, Yellol GS, Sun CM. Regioselective, Unconventional Pictet-Spengler Cyclization Strategy Toward the Synthesis of Benzimidazole-Linked Imidazoquinoxalines on a Soluble Polymer Support. Chem Asian J 2011; 6:1557-65. [DOI: 10.1002/asia.201000913] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Indexed: 11/10/2022]
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17
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Modelling topoisomerase I inhibition by minor groove binders. Bioorg Med Chem 2011; 19:1450-7. [PMID: 21273082 DOI: 10.1016/j.bmc.2011.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2010] [Revised: 01/03/2011] [Accepted: 01/04/2011] [Indexed: 10/18/2022]
Abstract
Topoisomerase inhibition is an extremely useful target for anticancer and antimicrobial drugs, and an undesirable side effect of some drugs targeting other proteins. Published modelling studies are sparse, and have used small data sets with relatively low molecular diversity. Given the important role of minor groove binding in the mechanism of topoisomerase I inhibition, we have conducted the first 3D QSAR study of topoisomerase I inhibition of a large, diverse set of minor groove binders using the minor groove binding conformation as the alignment template. The highly significant QSAR models resulting from this alignment identify the roles played by molecular features, most importantly the hydrogen bond donor properties.
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Alpan AS, Zencir S, Zupkó I, Coban G, Réthy B, Gunes HS, Topcu Z. Biological activity of bis-benzimidazole derivatives on DNA topoisomerase I and HeLa, MCF7 and A431 cells. J Enzyme Inhib Med Chem 2009; 24:844-9. [DOI: 10.1080/14756360802420831] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- A. Selcen Alpan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ege University, Izmir, 35100, Turkey
| | - Sevil Zencir
- Department of Medical Biology, Faculty of Medicine, Pamukkale University, Denizli, Turkey
| | - István Zupkó
- Department of Pharmacodynamics and Biopharmacy, University of Szeged, Szeged, H-6720, Hungary
| | - Gunes Coban
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ege University, Izmir, 35100, Turkey
| | - Borbála Réthy
- Department of Pharmacodynamics and Biopharmacy, University of Szeged, Szeged, H-6720, Hungary
| | - H. Semih Gunes
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ege University, Izmir, 35100, Turkey
| | - Zeki Topcu
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Ege University, Izmir, 35100, Turkey
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Liu YQ, Liu YQ, Tian X, Yang L. Synthesis of novel derivatives of bispodophyllotoxin as potential antineoplastic agents--part XVI. Nat Prod Res 2008; 22:285-91. [PMID: 18322843 DOI: 10.1080/14786410701757298] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Podophyllotoxin and related analogs present numerous challenges associated with optimal antitumor activity and severe unpredictable toxicity. In an attempt to find biorational podophyllotoxin-related drug, two moieties of podophyllotoxin have been linked at C4-position by a simple modification of the carbodiimide procedure to provide novel bispodophyllotoxin analogs (4a-4e) and their structural information was extensively characterized by using 1H-NMR, IR, and HRMS.
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Affiliation(s)
- Ying-Qian Liu
- School of Pharmacy, Lanzhou University, Lanzhou, PR China.
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22
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Chang CM, Kulkarni MV, Chen CH, Wang CH, Sun CM. Parallel Synthesis of 2-Sulphanylated Bis-benzimidazoles on Soluble Polymer Support. ACTA ACUST UNITED AC 2008; 10:466-74. [PMID: 18407696 DOI: 10.1021/cc7002045] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Chia-Mao Chang
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu 300-10, Taiwan, ROC, and Department of Applied Science, National Taitung University, Taitung 950, Taiwan, ROC
| | - Manohar V. Kulkarni
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu 300-10, Taiwan, ROC, and Department of Applied Science, National Taitung University, Taitung 950, Taiwan, ROC
| | - Chih-Hau Chen
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu 300-10, Taiwan, ROC, and Department of Applied Science, National Taitung University, Taitung 950, Taiwan, ROC
| | - Chi-Hsiang Wang
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu 300-10, Taiwan, ROC, and Department of Applied Science, National Taitung University, Taitung 950, Taiwan, ROC
| | - Chung-Ming Sun
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu 300-10, Taiwan, ROC, and Department of Applied Science, National Taitung University, Taitung 950, Taiwan, ROC
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23
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Khan QA, Pilch DS. Topoisomerase I-mediated DNA cleavage induced by the minor groove-directed binding of bibenzimidazoles to a distal site. J Mol Biol 2007; 365:561-9. [PMID: 17095016 PMCID: PMC1849979 DOI: 10.1016/j.jmb.2006.10.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Revised: 09/13/2006] [Accepted: 10/09/2006] [Indexed: 10/23/2022]
Abstract
Many agents (e.g. camptothecins, indolocarbazoles, indenoisoquinolines, and dibenzonaphthyridines) stimulate topoisomerase I (TOP1)-mediated DNA cleavage (a behavior termed topoisomerase I poisoning) by interacting with both the DNA and the enzyme at the site of cleavage (typically by intercalation between the -1 and +1 base-pairs). The bibenzimidazoles, which include Hoechst 33258 and 33342, are a family of DNA minor groove-directed agents that also stimulate topoisomerase I-mediated DNA cleavage. However, the molecular mechanism by which these ligands poison TOP1 is poorly understood. Toward this goal, we have used a combination of mutational, footprinting, and DNA binding affinity analyses to define the DNA binding site for Hoechst 33258 and a related derivative that results in optimal induction of TOP1-mediated DNA cleavage. We show that this DNA binding site is located downstream from the site of DNA cleavage, encompassing the base-pairs from position +4 to +8. The distal nature of this binding site relative to the site of DNA cleavage suggests that minor groove-directed agents like the bibenzimidazoles poison TOP1 via a mechanism distinct from compounds like the camptothecins, which interact at the site of cleavage.
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Affiliation(s)
- Qasim A. Khan
- Department of Pharmacology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, NJ 08854-5635
| | - Daniel S. Pilch
- Department of Pharmacology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, NJ 08854-5635
- The Cancer Institute of New Jersey, New Brunswick, NJ 08901
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Bond A, Reichert Z, Stivers JT. Novel and specific inhibitors of a poxvirus type I topoisomerase. Mol Pharmacol 2005; 69:547-57. [PMID: 16267207 DOI: 10.1124/mol.105.019067] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Vaccinia DNA topoisomerase (vTopo) is a prototypic pox virus family topoisomerase that shares extensive structural and mechanistic properties with the human type IB enzyme (hTopo) and is important for viral replication. Despite their far-reaching similarities, vTopo and hTopo have surprisingly distinct pharmacological properties. To further exploit these differences, we have developed recently the first high-throughput screen for vTopo, which has allowed rapid screening of a 1990-member small-molecule library for inhibitors. Using this approach, 21 compounds were identified with IC(90) values less than 10 muM, and 19 of these were also found to inhibit DNA supercoil relaxation by vTopo. Four of the most potent compounds were completely characterized and are structurally novel topo I inhibitors with efficacies at nanomolar concentrations. These inhibitors were highly specific for vTopo, showing no inhibition of the human enzyme even at 500- to 2000-fold greater concentrations. We describe a battery of efficient experiments to characterize the unique mechanisms of these vTopo inhibitors and discuss the surprising promiscuity of this enzyme to inhibition by structurally diverse small molecules.
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Affiliation(s)
- Alexis Bond
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University, School of Medicine, Baltimore, MD 21205-2185, USA
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26
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Raouafi N, Freytag M, Jones PG, Boujlel K, BenKhoud ML. Synthesis, Spectral and Structural Study of N-[1-(N,N,N?,N?-Tetramethylphosphoramidoyl)- 1H-Benzimidazol-2-yl]-Propionimidic Ethyl Ether. Struct Chem 2005. [DOI: 10.1007/s11224-005-2848-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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27
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Ruchelman AL, Kerrigan JE, Li TK, Zhou N, Liu A, Liu LF, LaVoie EJ. Nitro and amino substitution within the A-ring of 5H-8,9-dimethoxy-5-(2-N,N-dimethylaminoethyl)dibenzo[c,h][1,6]naphthyridin-6-ones: influence on topoisomerase I-targeting activity and cytotoxicity. Bioorg Med Chem 2004; 12:3731-42. [PMID: 15186859 DOI: 10.1016/j.bmc.2004.03.076] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2003] [Accepted: 03/11/2004] [Indexed: 10/26/2022]
Abstract
Recently, 5H-8,9-dimethoxy-5-(2-N,N-dimethylaminoethyl)-2,3-methylenedioxydibenzo[c,h][1,6]naphthyridin-6-one, 1, was identified as a TOP1-targeting agent with pronounced antitumor activity. In the present study, the effect on activity of substituting a single nitro or amino group in the A-ring in lieu of the methylenedioxy moiety of 1 was evaluated. The presence of either a nitro or amino substituent at the 4-position had a pronounced adverse affect on both TOP1-targeting activity and cytotoxicity. To a lesser extent, derivatives with a nitro or amino substituent at the 1-position were also less active than 1. Replacement of the methylenedioxy moiety of 1 with either a nitro or amino substituent at either the 2- and 3-position did result in analogues with potent TOP1-targeting activity and cytotoxicity.
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Affiliation(s)
- Alexander L Ruchelman
- Department of Pharmaceutical Chemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854-8020, USA
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Alper S, Temiz Arpaci O, Sener Aki E, Yalçin I. Some new bi- and ter-benzimidazole derivatives as topoisomerase I inhibitors. FARMACO (SOCIETA CHIMICA ITALIANA : 1989) 2003; 58:497-507. [PMID: 12818688 DOI: 10.1016/s0014-827x(03)00042-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The discovery of DNA topoisomerases has added a new dimension to the study of anticancer drugs. In the last years detailed investigation of bi- and ter-benzimidazole derivatives revealed that these compounds are a new class of topoisomerase I inhibitors that poisons mammalian topoisomerase I. In this context a survey about topoisomerase I poisoning activity and cytotoxicity of bi- and ter-benzimidazoles is given. Moreover some recent results about new derivatives, some structure-activity relationships and comparison of activity of various functional groups are discussed.
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Affiliation(s)
- Sabiha Alper
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University 06100 Tandogan, Ankara, Turkey
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Abstract
Liquid-phase synthesis of 2-arylaminobenzimidazoles using soluble polymer support strategy is first described. The key step to benzimidazole skeleton is achieved in the presence of diisopropylcarbodimide (DICDI) and isothiocyanates. A mechanism study for one-pot cyclodesulfurization is also investigated on the support. A wide range of benzimidazole derivatives is synthesized in excellent yield and purity just by simple wash and precipitation.
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Affiliation(s)
- Kuo-Ting Huang
- Department of Chemistry, National Dong Hwa University, Shou-Feng, Hualien 974, Taiwan
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