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Tentellino C, Tipping WJ, McGee LMC, Bain LM, Wetherill C, Laing S, Tyson-Hirst I, Suckling CJ, Beveridge R, Scott FJ, Faulds K, Graham D. Ratiometric imaging of minor groove binders in mammalian cells using Raman microscopy. RSC Chem Biol 2022; 3:1403-1415. [PMID: 36544571 PMCID: PMC9709774 DOI: 10.1039/d2cb00159d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/23/2022] [Indexed: 02/02/2023] Open
Abstract
Quantitative drug imaging in live cells is a major challenge in drug discovery and development. Many drug screening techniques are performed in solution, and therefore do not consider the impact of the complex cellular environment in their result. As such, important features of drug-cell interactions may be overlooked. In this study, Raman microscopy is used as a powerful technique for semi-quantitative imaging of Strathclyde-minor groove binders (S-MGBs) in mammalian cells under biocompatible imaging conditions. Raman imaging determined the influence of the tail group of two novel minor groove binders (S-MGB-528 and S-MGB-529) in mammalian cell models. These novel S-MGBs contained alkyne moieties which enabled analysis in the cell-silent region of the Raman spectrum. The intracellular uptake concentration, distribution and mechanism were evaluated as a function of the pK a of the tail group, morpholine and amidine, for S-MGB-528 and S-MGB-529, respectively. Although S-MGB-529 had a higher binding affinity to the minor groove of DNA in solution-phase measurements, the Raman imaging data indicated that S-MGB-528 showed a greater degree of intracellular accumulation. Furthermore, using high resolution stimulated Raman scattering (SRS) microscopy, the initial localisation of S-MGB-528 was shown to be in the nucleus before accumulation in the lysosome, which was demonstrated using a multimodal imaging approach. This study highlights the potential of Raman spectroscopy for semi-quantitative drug imaging studies and highlights the importance of imaging techniques to investigate drug-cell interactions, to better inform the drug design process.
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Affiliation(s)
- Christian Tentellino
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde Glasgow G1 1RD UK
| | - William J. Tipping
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of StrathclydeGlasgow G1 1RDUK
| | - Leah M. C. McGee
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of StrathclydeGlasgowG1 1XLUK
| | - Laura M. Bain
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of StrathclydeGlasgowG1 1XLUK
| | - Corinna Wetherill
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde Glasgow G1 1RD UK
| | - Stacey Laing
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde Glasgow G1 1RD UK
| | - Izaak Tyson-Hirst
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde Glasgow G1 1XL UK
| | - Colin J. Suckling
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of StrathclydeGlasgowG1 1XLUK
| | - Rebecca Beveridge
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde Glasgow G1 1XL UK
| | - Fraser J. Scott
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of StrathclydeGlasgowG1 1XLUK
| | - Karen Faulds
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde Glasgow G1 1RD UK
| | - Duncan Graham
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde Glasgow G1 1RD UK
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Shahabadi N, Farhadi R. Multispectroscopic and molecular docking studies on DNA binding of guaifenesin drug. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2021; 40:317-335. [PMID: 33463400 DOI: 10.1080/15257770.2021.1872793] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The interaction mechanism of guaifenesin drug; (RS)-3-(2-methoxyphenoxy)propane-1,2-diol; and calf thymus DNA was characterized by multiple spectroscopic and molecular docking approaches. The changes in drug electronic absorption with increasing DNA concentration and also the observed significant quenching of guaifenesin emission in the presence of DNA proved the complex formation between guaifenesin and DNA during the interactions. Both the binding constant and thermodynamic parameters for the interaction have been calculated in 283, 298, and 310 K at pH 7.4. The results Δ H 0 = 17.87 kJ/mol and Δ S 0 = 143.31 J/mol.K confirmed the role of hydrophobic force in the guaifenesin-DNA interaction. Circular dichroism study showed that guaifenesin causes decrease in the negative band of CT-DNA and at the same time the positive band increases which indicated the transition of DNA conformation from B to A. KI quenching experiment specifies that guaifenesin binds to DNA via nonintercalative mode. The competitive studies based on known Hoechst 33258 and methylene blue probes proved the groove binding mode in guaifenesin-DNA adduct. Further, full agreement of molecular docking simulation with the experimental results of binding constant and interaction mode, support high accuracy of the results.
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Affiliation(s)
- Nahid Shahabadi
- Faculty of Chemistry, Department of Inorganic Chemistry, Razi University, Kermanshah, Iran.,Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Reza Farhadi
- Faculty of Chemistry, Department of Inorganic Chemistry, Razi University, Kermanshah, Iran
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Khajeh MA, Dehghan G, Dastmalchi S, Shaghaghi M, Iranshahi M. Spectroscopic profiling and computational study of the binding of tschimgine: A natural monoterpene derivative, with calf thymus DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 192:384-392. [PMID: 29195192 DOI: 10.1016/j.saa.2017.11.042] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 10/23/2017] [Accepted: 11/19/2017] [Indexed: 06/07/2023]
Abstract
DNA is a major target for a number of anticancer substances. Interaction studies between small molecules and DNA are essential for rational drug designing to influence main biological processes and also introducing new probes for the assay of DNA. Tschimgine (TMG) is a monoterpene derivative with anticancer properties. In the present study we tried to elucidate the interaction of TMG with calf thymus DNA (CT-DNA) using different spectroscopic methods. UV-visible absorption spectrophotometry, fluorescence and circular dichroism (CD) spectroscopies as well as molecular docking study revealed formation of complex between TMG and CT-DNA. Binding constant (Kb) between TMG and DNA was 2.27×104M-1, that is comparable to groove binding agents. The fluorescence spectroscopic data revealed that the quenching mechanism of fluorescence of TMG by CT-DNA is static quenching. Thermodynamic parameters (ΔH<0 and ΔS<0) at different temperatures indicated that van der Waals forces and hydrogen bonds were involved in the binding process of TMG with CT-DNA. Competitive binding assay with methylene blue (MB) and Hoechst 33258 using fluorescence spectroscopy displayed that TMG possibly binds to the minor groove of CT-DNA. These observations were further confirmed by CD spectral analysis, viscosity measurements and molecular docking.
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Affiliation(s)
| | - Gholamreza Dehghan
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran.
| | - Siavoush Dastmalchi
- Biotechnology Research Center, School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Masoomeh Shaghaghi
- Department of Chemistry, Payame Noor University, P. O. Box 19395-3697, Tehran, Iran
| | - Mehrdad Iranshahi
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
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Chattopadhyay SK, Kundu I, Maitra R. The coumarin–pterocarpan conjugate – a natural product inspired hybrid molecular probe for DNA recognition. Org Biomol Chem 2014; 12:8087-93. [DOI: 10.1039/c4ob01360c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thermally induced cascade sigmatropic rearrangement of a butynyloxycoumarin derivative has led to a quick access to the coumarin–pterocarpan hybrid molecule. Biophysical studies together with molecular modeling show that this nature-inspired hybrid molecule is capable of binding to the minor groove of DNA as a non-conventional entity.
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Affiliation(s)
| | - Indranil Kundu
- Department of Chemistry
- University of Kalyani
- Nadia-742135, India
| | - Ratnava Maitra
- Department of Chemistry
- University of Kalyani
- Nadia-742135, India
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5
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Chattopadhyay SK, Maitra R, Kundu I, Jana M, Mandal SK, Khuda-Bukhsh AR. Acridone-Pterocarpan Conjugate: A Hybrid Molecular Probe for Recognition of Nucleic Acids. European J Org Chem 2013. [DOI: 10.1002/ejoc.201301007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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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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7
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From multiply active natural product to candidate drug? Antibacterial (and other) minor groove binders for DNA. Future Med Chem 2012; 4:971-89. [DOI: 10.4155/fmc.12.52] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Natural products that bind to DNA in the minor groove are valuable templates for drug design. Examples include distamycin, netropsin, duocarmycin and anthramycin. Anticancer and anti-infective drugs feature strongly amongst their derivatives. The structures and activities of chemotypes with various therapeutic actions are discussed in the context of the broader field of therapeutically active minor groove binders. The evolution of a series of exceptionally potent and nontoxic antibacterial compounds is discussed using the general design principle of introducing additional hydrophobicity into the distamycin template to increase the strength of binding to DNA. As well as potent antibacterial compounds, antifungal and antiparasitic compounds with exceptional cellular activity against trypanosomes have been identified. Possible mechanisms of action including gene regulation and topoisomerase inhibition are discussed with the need in mind to understand selective toxicity in the series to support future drug discovery.
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Fuchs JE, Spitzer GM, Javed A, Biela A, Kreutz C, Wellenzohn B, Liedl KR. Minor groove binders and drugs targeting proteins cover complementary regions in chemical shape space. J Chem Inf Model 2011; 51:2223-32. [PMID: 21819135 DOI: 10.1021/ci200237c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA minor groove binders (MGBs) are known to influence gene expression and are therefore widely studied to explore their therapeutic potential. We identified shape-based virtual screening with ROCS as a highly effective computational approach to enrich known MGBs in top-ranked molecules. Discovery of ten previously unknown MGBs by shape-based screening further confirmed the relevance of ligand shape for minor groove affinity. Based on experimental testing we propose three simple rules (at least two positive charges, four nitrogen atoms, and one aromatic ring) as filters to reach even better enrichment of true positives in ROCS hit lists. Interestingly, shape-based ranking of MGBs versus FDA-approved drugs again leads to high enrichment rates, indicating complementary coverage of chemical shape space and indicating minor groove affinity to be unfavorable for approval of drugs targeting proteins.
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Affiliation(s)
- Julian E Fuchs
- Faculty of Chemistry and Pharmacy, University of Innsbruck, Innsbruck, Austria
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9
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Stolić I, Mišković K, Piantanida I, Lončar MB, Glavaš-Obrovac L, Bajić M. Synthesis, DNA/RNA affinity and antitumour activity of new aromatic diamidines linked by 3,4-ethylenedioxythiophene. Eur J Med Chem 2011; 46:743-55. [PMID: 21227551 DOI: 10.1016/j.ejmech.2010.12.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Revised: 12/04/2010] [Accepted: 12/14/2010] [Indexed: 10/18/2022]
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10
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Synthesis and evaluation of a netropsin–proximicin-hybrid library for DNA binding and cytotoxicity. Bioorg Med Chem Lett 2009; 19:3811-5. [DOI: 10.1016/j.bmcl.2009.04.042] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2009] [Revised: 04/07/2009] [Accepted: 04/08/2009] [Indexed: 11/21/2022]
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11
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Effect of 3,4-ethylenedioxy-extension of thiophene core on the DNA/RNA binding properties and biological activity of bisbenzimidazole amidines. Bioorg Med Chem 2009; 17:2544-54. [PMID: 19231203 DOI: 10.1016/j.bmc.2009.01.071] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Revised: 01/20/2009] [Accepted: 01/22/2009] [Indexed: 11/22/2022]
Abstract
Novel bisbenzimidazoles (4-6), characterized by 3,4-ethylenedioxy-extension of thiophene core, revealed pronounced affinity and strong thermal stabilization effect toward ds-DNA. They interact within ds-DNA grooves as dimmers or even oligomers and agglomerate along ds-RNA. Compounds 4-6 have shown moderate to strong antiproliferative effect toward panel of eight carcinoma cell lines. Compound 5 displayed the best inhibitory potential and in equitoxic concentration (IC(50)=1 x 10(-6)M) induced accumulation of cells in G2/M phase after 48 h of incubation. Fluorescence microscopy showed that 5 entered into live HeLa cells within 30 min, but did not accumulate in nuclei even after 2.5h. Compound 5 inhibited the growth of Trypanosome cruzi epimastigotes (IC(50)=4.3 x 10(-6)M).
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12
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Breen D, Kennedy AR, Suckling CJ. A divergent synthesis of minor groove binders with tail group variation. Org Biomol Chem 2009; 7:178-86. [PMID: 19081961 DOI: 10.1039/b814452d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new synthesis of polyamide minor groove binders in which diversity is introduced by the nucleophilic substitution of a 2-sulfido-1,3,2-diazaphospholidinyloxy substituent by volatile secondary amine nucleophiles is described. Such a method has potential value for economically investigating structure-activity relationships in this important class of compounds through library synthesis. As an example using this method are prepared two new minor groove binders with pyrrolidinyl or piperidinyl tail groups that are close relatives of highly active antibacterial minor groove binders with morpholinyl tail groups. The antibacterial activity found against Staphylococcus aureus and Mycobacterium spp. indicates that the pK(a) of this set of compounds is not the dominant factor in determining the antibacterial activity.
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Affiliation(s)
- David Breen
- WestCHEM, Department of Pure & Applied Chemistry, University of Strathclyde, 296 Cathedral Street, Glasgow, G1 1XL, Scotland
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13
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Schneider K, Keller S, Wolter F, Röglin L, Beil W, Seitz O, Nicholson G, Bruntner C, Riedlinger J, Fiedler HP, Süssmuth R. Proximicin A, B und C – antitumoraktive Furananaloga des Netropsins aus dem marinen ActinomycetenVerrucosispora induzieren die Hochregulation von p53 und des Cyclinkinase-Inhibitors p21. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200705295] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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14
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Schneider K, Keller S, Wolter F, Röglin L, Beil W, Seitz O, Nicholson G, Bruntner C, Riedlinger J, Fiedler HP, Süssmuth R. Proximicins A, B, and C—Antitumor Furan Analogues of Netropsin from the Marine ActinomyceteVerrucosispora Induce Upregulation of p53 and the Cyclin Kinase Inhibitor p21. Angew Chem Int Ed Engl 2008; 47:3258-61. [DOI: 10.1002/anie.200705295] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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15
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Anthony NG, Breen D, Clarke J, Donoghue G, Drummond AJ, Ellis EM, Gemmell CG, Helesbeux JJ, Hunter IS, Khalaf AI, Mackay SP, Parkinson JA, Suckling CJ, Waigh RD. Antimicrobial Lexitropsins Containing Amide, Amidine, and Alkene Linking Groups. J Med Chem 2007; 50:6116-25. [DOI: 10.1021/jm070831g] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Spitzer GM, Wellenzohn B, Laggner C, Langer T, Liedl KR. DNA minor groove pharmacophores describing sequence specific properties. J Chem Inf Model 2007; 47:1580-9. [PMID: 17518460 DOI: 10.1021/ci600500v] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The more that is known about human and other genome sequences and the correlation between gene expression and the course of a disease, the more evident it seems to be that DNA is chosen as a drug target instead of proteins which are built with the information encoded by DNA. According to this approach, small minor groove binding molecules have been designed to bind the DNA sequence specifically and thereby downregulate genes. Because of their lack of druglikeness, we plan to use them as templates for forthcoming virtual screening experiments to discover molecules with the same bioactivity and a different scaffold. In this proof of principle study, carried out with the software tool Catalyst, we present a model work for description of a ligand-DNA complex with the aid of pharmacophore modeling methods. The successful reproduction of sequence specificity of a polyamidic minor groove binding ligand is the precondition for later model application to virtual screening.
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Affiliation(s)
- Gudrun M Spitzer
- Theoretical Chemistry, Faculty of Chemistry and Pharmacy, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria.
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17
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Baraldi PG, Preti D, Fruttarolo F, Tabrizi MA, Romagnoli R. Hybrid molecules between distamycin A and active moieties of antitumor agents. Bioorg Med Chem 2007; 15:17-35. [PMID: 17081759 DOI: 10.1016/j.bmc.2006.07.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2006] [Revised: 06/29/2006] [Accepted: 07/01/2006] [Indexed: 10/24/2022]
Abstract
The DNA minor groove is an attractive target for the design and development of molecules able to specifically recognize predetermined DNA sequences. The pyrrole-amide skeleton of distamycin A has been also used as DNA sequence selective vehicle for the delivery of alkylating functions to DNA targets. Selectivity for specific sequences may be of particular importance in affecting the activity of regulatory genes (oncogenes and tumor suppressor genes). Recent work on a number of hybrid compounds, in which known antitumor compounds or simple active moieties of known antitumor agents have been tethered to distamycin frame or hairpin polyamides derived from distamycin, is reviewed. The DNA alkylating and growth inhibition activities against several tumor cell lines are reported and discussed in terms of their structural differences in relation to both the number of N-methyl pyrrolic rings and the type of the alkylating unit tethered to the oligopyrrolic frame.
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Affiliation(s)
- Pier Giovanni Baraldi
- University of Ferrara, Dipartimento di Scienze Farmaceutiche, Via Fossato di Mortara 17/19, 44100 Ferrara, Italy.
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18
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Cimino P, Bifulco G, Riccio R, Gomez-Paloma L, Barone V. On the role of stereo-electronic effects in tuning the selectivity and rate of DNA alkylation by duocarmycins. Org Biomol Chem 2006; 4:1242-51. [PMID: 16557312 DOI: 10.1039/b514890a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The role of local geometric and stereo-electronic effects in tuning the alkylation of DNA by duocarmycins has been analyzed by an integrated computational tool rooted in the density functional theory and the polarizable continuum model. Our study points out that together with steric accessibility, different electronic delocalisations also contribute to determine the higher reactivity of adenine with respect to guanine. Also the effect of the methyl ester group on the alkylating agent has an electronic origin. Furthermore, deviations from the planarity in the drug structure (conformational catalysis) could be less important than currently accepted since, according to our computations, compounds with strongly different reactivity have nearly constant and very similar out of plane distortions before and after the reaction. Model computations suggest, instead, that specific non covalent interactions could discriminate between different drugs selectively reducing some activation energies with respect to the corresponding processes in solution.
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Affiliation(s)
- Paola Cimino
- Dipartimento di Chimica, Università Federico II, Complesso Universitario Monte S. Angelo, via Cintia, I-80126, Napoli, Italy
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