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Alniss HY, Kemp BM, Holmes E, Hoffmann J, Ploch RM, Ramadan WS, Msallam YA, Al-Jubeh HM, Madkour MM, Celikkaya BC, Scott FJ, El-Awady R, Parkinson JA. Spectroscopic, biochemical and computational studies of bioactive DNA minor groove binders targeting 5'-WGWWCW-3' motif. Bioorg Chem 2024; 148:107414. [PMID: 38733748 DOI: 10.1016/j.bioorg.2024.107414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/18/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024]
Abstract
Spectroscopic, biochemical, and computational modelling studies have been used to assess the binding capability of a set of minor groove binding (MGB) ligands against the self-complementary DNA sequences 5'-d(CGCACTAGTGCG)-3' and 5'-d(CGCAGTACTGCG)-3'. The ligands were carefully designed to target the DNA response element, 5'-WGWWCW-3', the binding site for several nuclear receptors. Basic 1D 1H NMR spectra of the DNA samples prepared with three MGB ligands show subtle variations suggestive of how each ligand associates with the double helical structure of both DNA sequences. The variations among the investigated ligands were reflected in the line shape and intensity of 1D 1H and 31P-{1H} NMR spectra. Rapid visual inspection of these 1D NMR spectra proves to be beneficial in providing valuable insights on MGB binding molecules. The NMR results were consistent with the findings from both UV DNA denaturation and molecular modelling studies. Both the NMR spectroscopic and computational analyses indicate that the investigated ligands bind to the minor grooves as antiparallel side-by-side dimers in a head-to-tail fashion. Moreover, comparisons with results from biochemical studies offered valuable insights into the mechanism of action, and antitumor activity of MGBs in relation to their structures, essential pre-requisites for future optimization of MGBs as therapeutic agents.
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Affiliation(s)
- Hasan Y Alniss
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, Sharjah 27272, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates.
| | - Bryony M Kemp
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, UK
| | - Elizabeth Holmes
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, UK
| | - Joanna Hoffmann
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, UK
| | - Rafal M Ploch
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, UK
| | - Wafaa S Ramadan
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Yousef A Msallam
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, Sharjah 27272, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Hadeel M Al-Jubeh
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Moustafa M Madkour
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, Sharjah 27272, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Bekir C Celikkaya
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, UK
| | - Fraser J Scott
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, UK
| | - Raafat El-Awady
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, Sharjah 27272, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - John A Parkinson
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, UK.
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Alniss HY, Al-Jubeh HM, Msallam YA, Siddiqui R, Makhlouf Z, Ravi A, Hamdy R, Soliman SSM, Khan NA. Structure-based drug design of DNA minor groove binders and evaluation of their antibacterial and anticancer properties. Eur J Med Chem 2024; 271:116440. [PMID: 38678825 DOI: 10.1016/j.ejmech.2024.116440] [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: 12/07/2023] [Revised: 04/09/2024] [Accepted: 04/18/2024] [Indexed: 05/01/2024]
Abstract
Antimicrobial and chemotherapy resistance are escalating medical problem of paramount importance. Yet, research for novel antimicrobial and anticancer agents remains lagging behind. With their reported medical applications, DNA minor groove binders (MGBs) are worthy of exploration. In this study, the approach of structure-based drug design was implemented to generate 11 MGB compounds including a novel class of bioactive alkyne-linked MGBs. The NCI screening protocol was utilized to evaluate the antitumor activity of the target MGBs. Furthermore, a variety of bactericidal, cytopathogenicity, MIC90, and cytotoxicity assays were carried out using these MGBs against 6 medically relevant bacteria: Salmonella enterica, Escherichia coli, Serratia marcescens, Bacillus cereus, Streptococcus pneumoniae and Streptococcus pyogenes. Moreover, molecular docking, molecular dynamic simulations, DNA melting, and isothermal titration calorimetry (ITC) analyses were utilized to explore the binding mode and interactions between the most potent MGBs and the DNA duplex d(CGACTAGTCG)2. NCI results showed that alkyne-linked MGBs (26 & 28) displayed the most significant growth inhibition among the NCI-60 panel. In addition, compounds MGB3, MGB4, MGB28, and MGB32 showed significant bactericidal effects, inhibited B. cereus and S. enterica-mediated cytopathogenicity, and exhibited low cytotoxicity. MGB28 and MGB32 demonstrated significant inhibition of S. pyogenes, whereas MGB28 notably inhibited S. marcescens and all four minor groove binders significantly inhibited B. cereus. The ability of these compounds to bind with DNA and distort its groove dimensions provides the molecular basis for the allosteric perturbation of proteins-DNA interactions by MGBs. This study shed light on the mechanism of action of MGBs and revealed the important structural features for their antitumor and antibacterial activities, which are important to guide future development of MGB derivatives as novel antibacterial and anticancer agents.
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Affiliation(s)
- Hasan Y Alniss
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, 27272, Sharjah, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates.
| | - Hadeel M Al-Jubeh
- Research Institute for Medical and Health Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Yousef A Msallam
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, 27272, Sharjah, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Ruqaiyyah Siddiqui
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University Edinburgh, EH14 4AS, United Kingdom; Department of Medical Biology, Faculty of Medicine, Istinye University, Istanbul, 34010, Turkey
| | - Zinb Makhlouf
- College of Medicine, Department of Clinical Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Anil Ravi
- Research Institute for Medical and Health Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Rania Hamdy
- Research Institute for Medical and Health Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Sameh S M Soliman
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, 27272, Sharjah, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Naveed A Khan
- Department of Medical Biology, Faculty of Medicine, Istinye University, Istanbul, 34010, Turkey.
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Abdullah S, Ganguly S. An overview of imidazole and its analogues as potent anticancer agents. Future Med Chem 2023; 15:1621-1646. [PMID: 37727960 DOI: 10.4155/fmc-2023-0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023] Open
Abstract
The quest for novel, physiologically active imidazoles remains an exciting topic of research among medicinal chemists. The imidazole ring is a five-membered aromatic heterocycle that is found in both natural and synthesized compounds. Multiple anticancer drug classes are currently available on the market, but concerns including toxicity, limited efficacy and solubility have lowered the overall therapeutic index. Therefore, the hunt for new potential chemotherapeutic agents persists. The development of imidazole as a reliable and safer alternative to anticancer treatment is generating much attention among experts. Tubulin or microtubule polymerization inhibition and changes in the structure and function of DNA, VEGF, topoisomerase, kinases, histone deacetylases and certain other proteins that affect gene expression are among the putative targets.
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Affiliation(s)
- Salik Abdullah
- Department of Pharmaceutical Sciences, Birla Institute of Technology, Mesra, Jharkhand, 835215, India
| | - Swastika Ganguly
- Department of Pharmaceutical Sciences, Birla Institute of Technology, Mesra, Jharkhand, 835215, India
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Alniss HY, Chu C, Ramadan WS, Msallam YA, Srinivasulu V, El-Awady R, Macgregor RB, Al-Tel TH. Interaction of an anticancer benzopyrane derivative with DNA: Biophysical, biochemical, and molecular modeling studies. Biochim Biophys Acta Gen Subj 2023; 1867:130347. [PMID: 36958685 DOI: 10.1016/j.bbagen.2023.130347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/09/2023] [Accepted: 03/20/2023] [Indexed: 03/25/2023]
Abstract
BACKGROUND SIMR1281 is a potent anticancer lead candidate with multi- target activity against several proteins; however, its mechanism of action at the molecular level is not fully understood. Revealing the mechanism and the origin of multitarget activity is important for the rational identification and optimization of multitarget drugs. METHODS We have used a variety of biophysical (circular dichroism, isothermal titration calorimetry, viscosity, and UV DNA melting), biochemical (topoisomerase I & II assays) and computational (molecular docking and MD simulations) methods to study the interaction of SIMR1281 with duplex DNA structures. RESULTS The biophysical results revealed that SIMR1281 binds to dsDNA via an intercalation-binding mode with an average binding constant of 3.1 × 106 M-1. This binding mode was confirmed by the topoisomerases' inhibition assays and molecular modeling simulations, which showed the intercalation of the benzopyrane moiety between DNA base pairs, while the remaining moieties (thiazole and phenyl rings) sit in the minor groove and interact with the flanking base pairs adjacent to the intercalation site. CONCLUSIONS The DNA binding characteristics of SIMR1281, which can disrupt/inhibit DNA function as confirmed by the topoisomerases' inhibition assays, indicate that the observed multi-target activity might originate from ligand intervention at nucleic acids level rather than due to direct interactions with multiple biological targets at the protein level. GENERAL SIGNIFICANCE The findings of this study could be helpful to guide future optimization of benzopyrane-based ligands for therapeutic purposes.
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Affiliation(s)
- Hasan Y Alniss
- College of Pharmacy, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
| | - Chen Chu
- Graduate Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Wafaa S Ramadan
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
| | - Yousef A Msallam
- College of Pharmacy, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
| | - Vunnam Srinivasulu
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
| | - Raafat El-Awady
- College of Pharmacy, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
| | - Robert B Macgregor
- Graduate Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Taleb H Al-Tel
- College of Pharmacy, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
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Phan N, Shear TA, Zakharov LN, Johnson DW. An Efficient Route to Symmetrical and Unsymmetrical Disulfide, Thioether, and Hydrocarbon Cyclophanes. European J Org Chem 2020. [DOI: 10.1002/ejoc.202001242] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Ngoc‐Minh Phan
- Department of Chemistry & Biochemistry and Materials Science Institute University of Oregon 97403‐1253 Eugene Oregon USA
| | - Trevor A. Shear
- Department of Chemistry & Biochemistry and Materials Science Institute University of Oregon 97403‐1253 Eugene Oregon USA
| | - Lev N. Zakharov
- CAMCOR Center for Advanced Materials Characterization in Oregon University of Oregon 97403‐1443 Eugene OR USA
| | - Darren W. Johnson
- Department of Chemistry & Biochemistry and Materials Science Institute University of Oregon 97403‐1253 Eugene Oregon USA
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Pithan PM, Kuhlmann C, Engelhard C, Ihmels H. Synthesis of 5-Alkyl- and 5-Phenylamino-Substituted Azothiazole Dyes with Solvatochromic and DNA-Binding Properties. Chemistry 2019; 25:16088-16098. [PMID: 31523866 PMCID: PMC6973281 DOI: 10.1002/chem.201903657] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 09/09/2019] [Indexed: 01/24/2023]
Abstract
A series of new 5-mono- and 5,5'-bisamino-substituted azothiazole derivatives was synthesized from the readily available diethyl azothiazole-4,4'-dicarboxylate. This reaction most likely comprises an initial Michael-type addition by the respective primary alkyl and aromatic amines at the carbon atom C5 of the substrate. Subsequently, the resulting intermediates are readily oxidized by molecular oxygen to afford the amino-substituted azothiazole derivatives. The latter exhibit remarkably red-shifted absorption bands (λabs =507-661 nm) with high molar extinction coefficients and show a strong positive solvatochromism. As revealed by spectrometric titrations and circular and linear dichroism studies, the water-soluble, bis-(dimethylaminopropylamino)-substituted azo dye associates with duplex DNA by formation of aggregates along the phosphate backbone at high ligand-DNA ratios (LDR) and by intercalation at low LDR, which also leads to a significant increase of the otherwise low emission intensity at 671 nm.
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Affiliation(s)
- Phil M. Pithan
- Department of Chemistry and Biology, and Center of Micro- and Nanochemistry and EngineeringUniversity of SiegenAdolf-Reichwein-Str. 257068SiegenGermany
| | - Christopher Kuhlmann
- Department of Chemistry and Biology, and Center of Micro- and Nanochemistry and EngineeringUniversity of SiegenAdolf-Reichwein-Str. 257068SiegenGermany
| | - Carsten Engelhard
- Department of Chemistry and Biology, and Center of Micro- and Nanochemistry and EngineeringUniversity of SiegenAdolf-Reichwein-Str. 257068SiegenGermany
| | - Heiko Ihmels
- Department of Chemistry and Biology, and Center of Micro- and Nanochemistry and EngineeringUniversity of SiegenAdolf-Reichwein-Str. 257068SiegenGermany
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Alniss HY, Witzel II, Semreen MH, Panda PK, Mishra YK, Ahuja R, Parkinson JA. Investigation of the Factors That Dictate the Preferred Orientation of Lexitropsins in the Minor Groove of DNA. J Med Chem 2019; 62:10423-10440. [DOI: 10.1021/acs.jmedchem.9b01534] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Hasan Y. Alniss
- College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
- Sharjah Institute for Medical Research, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Ini-Isabée Witzel
- Core Technology Platform, New York University of Abu Dhabi, P.O. Box 129188, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Mohammad H. Semreen
- College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
- Sharjah Institute for Medical Research, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Pritam Kumar Panda
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-75120, Uppsala Sweden
| | - Yogendra Kumar Mishra
- Functional Nanomaterials, Institute for Materials Science, Kiel University, Kaiserstraße 2, D-24143 Kiel, Germany
| | - Rajeev Ahuja
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-75120, Uppsala Sweden
- Department of Materials and Engineering, Royal Institute of Technology (KTH), SE-10044 Stockholm Sweden
| | - John A. Parkinson
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
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Padroni G, Parkinson JA, Fox KR, Burley GA. Structural basis of DNA duplex distortion induced by thiazole-containing hairpin polyamides. Nucleic Acids Res 2019; 46:42-53. [PMID: 29194552 PMCID: PMC5758887 DOI: 10.1093/nar/gkx1211] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 11/28/2017] [Indexed: 01/05/2023] Open
Abstract
This manuscript reports the molecular basis for double-stranded DNA (dsDNA) binding of hairpin polyamides incorporating a 5-alkyl thiazole (Nt) unit. Hairpin polyamides containing an N-terminal Nt unit induce higher melting stabilisation of target dsDNA sequences relative to an archetypical hairpin polyamide incorporating an N-terminal imidazole (Im) unit. However, modification of the N-terminus from Im to Nt-building blocks results in an increase in dsDNA binding affinity but lower G-selectivity. A general G-selectivity trend is observed for Nt-containing polyamide analogues. G-selectivity increases as the steric bulk in the Nt 5-position increases. Solution-based NMR structural studies reveal differences in the modulation of the target DNA duplex of Nt-containing hairpin polyamides relative to the Im-containing archetype. A structural hallmark of an Nt polyamide•dsDNA complex is a more significant degree of major groove compression of the target dsDNA sequence relative to the Im-containing hairpin polyamide.
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Affiliation(s)
- Giacomo Padroni
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, UK
| | - John A Parkinson
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, UK
| | - Keith R Fox
- Centre for Biological Sciences, University of Southampton, Life Sciences Building 85, Southampton SO17 1BJ, UK
| | - Glenn A Burley
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, UK
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9
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Affiliation(s)
- Hasan Y. Alniss
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
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10
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Ali I, Lone MN, Aboul-Enein HY. Imidazoles as potential anticancer agents. MEDCHEMCOMM 2017; 8:1742-1773. [PMID: 30108886 PMCID: PMC6084102 DOI: 10.1039/c7md00067g] [Citation(s) in RCA: 196] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/21/2017] [Indexed: 12/19/2022]
Abstract
Cancer is a black spot on the face of humanity in this era of science and technology. Presently, several classes of anticancer drugs are available in the market, but issues such as toxicity, low efficacy and solubility have decreased the overall therapeutic indices. Thus, the search for new promising anticancer agents continues, and the battle against cancer is far from over. Imidazole is an aromatic diazole and alkaloid with anticancer properties. There is considerable interest among scientists in developing imidazoles as safe alternatives to anticancer chemotherapy. The present article describes the structural, chemical, and biological features of imidazoles. Several classes of imidazoles as anticancer agents based on their mode of action have been critically discussed. A careful observation has been made into pharmacologically active imidazoles with better or equal therapeutic effects compared to well-known imidazole-based anticancer drugs, which are available on the market. A brief discussion of the toxicities of imidazoles has been made. Finally, the current challenges and future perspectives of imidazole based anticancer drug development are conferred.
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Affiliation(s)
- Imran Ali
- Department of Chemistry , Jamia Millia Islamia (Central University) , New Delhi-110025 , India . ;
| | - Mohammad Nadeem Lone
- Department of Chemistry , Jamia Millia Islamia (Central University) , New Delhi-110025 , India . ;
| | - Haasan Y Aboul-Enein
- Pharmaceutical and Medicinal Chemistry Department , Pharmaceutical and Drug Industries Research Division , National Research Centre , Dokki , Giza 12622 , Egypt
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11
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Dacarbazine as a minor groove binder of DNA: Spectroscopic, biophysical and molecular docking studies. Int J Biol Macromol 2015; 79:193-200. [DOI: 10.1016/j.ijbiomac.2015.04.055] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Revised: 04/23/2015] [Accepted: 04/25/2015] [Indexed: 11/19/2022]
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McKenna JM, Parkinson JA. HOBS methods for enhancing resolution and sensitivity in small DNA oligonucleotide NMR studies. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:249-255. [PMID: 25353689 DOI: 10.1002/mrc.4182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/30/2014] [Accepted: 10/13/2014] [Indexed: 06/04/2023]
Abstract
(1) H NMR spectra from biopolymers give chemical shifts classified according to proton type and often suffer from signal degeneracy. Data from nucleic acids are particularly prone to this failing. Recent developments in proton broadband decoupling techniques with the promise of enhanced resolution at full sensitivity have allowed us to investigate the application of homonuclear band-selective (HOBS) decoupling to the study of small synthetic DNA molecules and to compare these with results from classical and pure shift techniques. Improved signal resolution at full sensitivity in both HOBS-1D (1) H and HOBS-2D [(1) H, (1) H] NOESY NMR data is reported for three example small DNA molecules. Comparisons of (1) H T1 and integrals of signals from HOBS-1D (1) H and HOBS-2D [(1) H, (1) H] NOESY NMR data with those of standard data collection methods are also reported. The results show that homonuclear HOBS-NOESY data are useful for data assignment purposes and have some merit for quantification purposes. In general, we show that resolution and sensitivity enhancement of (1) H NMR data for small DNA samples may be achieved without recourse to higher magnetic field strength at full sensitivity in a band-selected manner.
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Affiliation(s)
- Josiah M McKenna
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK
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Rubinson M, Parkinson J, Evstigneev M. Entropic binding mode preference in cooperative homo-dimeric drug–DNA recognition. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Choi M, Won SW, Jo H, Viji M, Seo SY, Lee YJ, Lee HS, Lee H, Hong JT, Kwak YS, Jung JK. A novel and efficient amidation of 2-aminothiazole. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.10.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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15
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Alniss HY, Salvia MV, Sadikov M, Golovchenko I, Anthony NG, Khalaf AI, MacKay SP, Suckling CJ, Parkinson JA. Recognition of the DNA minor groove by thiazotropsin analogues. Chembiochem 2014; 15:1978-90. [PMID: 25045155 DOI: 10.1002/cbic.201402202] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Indexed: 01/14/2023]
Abstract
Solution-phase self-association characteristics and DNA molecular-recognition properties are reported for three close analogues of minor-groove-binding ligands from the thiazotropsin class of lexitropsin molecules; they incorporate isopropyl thiazole as a lipophilic building block. Thiazotropsin B (AcImPy(iPr) ThDp) shows similar self-assembly characteristics to thiazotropsin A (FoPyPy(iPr) ThDp), although it is engineered, by incorporation of imidazole in place of N-methyl pyrrole, to swap its DNA recognition target from 5'-ACTAGT-3' to 5'-ACGCGT-3'. Replacement of the formamide head group in thiazotropsin A by nicotinamide in AIK-18/51 results in a measureable difference in solution-phase self-assembly character and substantially enhanced DNA association characteristics. The structures and associated thermodynamic parameters of self-assembled ligand aggregates and their complexes with their respective DNA targets are considered in the context of cluster targeting of DNA by minor-groove complexes.
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Affiliation(s)
- Hasan Y Alniss
- Department of Pharmacy, An-Najah National University, University Street, Nablus (Palestine); Present address: Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 2J7 (Canada)
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Mati SS, Roy SS, Chall S, Bhattacharya S, Bhattacharya SC. Unveiling the groove binding mechanism of a biocompatible naphthalimide-based organoselenocyanate with calf thymus DNA: an "ex vivo" fluorescence imaging application appended by biophysical experiments and molecular docking simulations. J Phys Chem B 2013; 117:14655-65. [PMID: 24205834 DOI: 10.1021/jp4090553] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The present study embodies a detailed investigation of the binding modes of a potential anticancer and neuroprotective fluorescent drug, 2-(5-selenocyanato-pentyl)-6-chloro benzo[de]isoquinoline-1,3-dione (NPOS) with calf thymus DNA (ctDNA). Experimental results based on spectroscopy, isothermal calorimetry, electrochemistry aided with DNA-melting, and circular dichroism studies unambiguously established the formation of a groove binding network between the NPOS and ctDNA. Molecular docking analysis ascertained a hydrogen bonding mediated 'A-T rich region of B-DNA' as the preferential docking site for NPOS. The cellular uptake and binding of NPOS with DNA from "Ehrlich Ascites Carcinoma" cells confirmed its biocompatibility within tumor cells. Experimental and ex vivo cell imaging studies vividly signify the importance of NPOS as a potential prerequisite for its use in therapeutic purposes.
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Salvia MV, Addison F, Alniss HY, Buurma NJ, Khalaf AI, Mackay SP, Anthony NG, Suckling CJ, Evstigneev MP, Santiago AH, Waigh RD, Parkinson JA. Thiazotropsin aggregation and its relationship to molecular recognition in the DNA minor groove. Biophys Chem 2013; 179:1-11. [PMID: 23714424 DOI: 10.1016/j.bpc.2013.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 04/19/2013] [Accepted: 04/19/2013] [Indexed: 11/29/2022]
Abstract
Aggregated states have been alluded to for many DNA minor groove binders but details of the molecule-on-molecule relationship have either been under-reported or ignored. Here we report our findings from ITC and NMR measurements carried out with AIK-18/51, a compound representative of the thiazotropsin class of DNA minor groove binders. The free aqueous form of AIK-18/51 is compared with that found in its complex with cognate DNA duplex d(CGACTAGTCG)2. Molecular self-association of AIK-18/51 is consistent with anti-parallel, face-to-face dimer formation, the building block on which the molecule aggregates. This underlying structure is closely allied to the form found in the ligand's DNA complex. NMR chemical shift and diffusion measurements yield a self-association constant Kass=(61±19)×10(3)M(-1) for AIK-18/51 that fits with a stepwise self-assembly model and is consistent with ITC data. The deconstructed energetics of this assembly process are reported with respect to a design strategy for ligand/DNA recognition.
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Affiliation(s)
- Marie-Virginie Salvia
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
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Parkinson JA, Scott FJ, Suckling CJ, Wilson G. Exceptionally strong intermolecular association in hydrophobic DNA minor groove binders and their potential therapeutic consequences. MEDCHEMCOMM 2013. [DOI: 10.1039/c3md00071k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Brucoli F, Natoli A, Marimuthu P, Borrello MT, Stapleton P, Gibbons S, Schätzlein A. Efficient synthesis and biological evaluation of proximicins A, B and C. Bioorg Med Chem 2012; 20:2019-24. [PMID: 22364744 DOI: 10.1016/j.bmc.2012.01.043] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2011] [Accepted: 01/26/2012] [Indexed: 10/14/2022]
Abstract
A quick and efficient synthesis and the biological evaluation of promising antitumor-antibiotics proximicins A, B and C are reported. The characteristic repetitive unit of these molecules, the methyl 4-Boc-aminofuran-2-carboxylate 15, was prepared in three synthetic steps in good yield using an optimised copper-catalysed amidation method. The proximicins were evaluated for their antitumor activity using cellular methods. Proximicin B induced apoptosis in both Hodgkin's lymphoma and T-cell leukemia cell lines and proximicin C exhibited significantly high cytotoxicity against glioblastoma and breast carcinoma cells. The proximicins were also screened against Escherichia coli, Enterococcus faecalis and several strains of methicillin-and multidrug-resistant Staphylococcus aureus. Proximicin B showed noteworthy activity against antibiotic-resistant Gram-positive cocci.
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Affiliation(s)
- Federico Brucoli
- UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, UK.
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