1
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Cytotoxic and genotoxic evaluation of dipyridamole and its alternative therapeutic potential in cancer therapy: an in vitro and in vivo approach. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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2
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Purohit P, Mittal RK, Khatana K. Quinoline-3-Carboxylic Acids "DNA Minor Groove-Binding Agent. Anticancer Agents Med Chem 2021; 22:344-348. [PMID: 33992065 DOI: 10.2174/1871520621666210513160714] [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: 11/13/2020] [Revised: 02/16/2021] [Accepted: 03/08/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND The lead compounds from the series of 2, 4-disubstituted quinoline-3-carboxylic acid derivatives were selected for the in-silico mechanistic study. The compounds were found selective and potent for the cancer cell. Moreover, the relevant ADME in-silico data also support the safety of lead. Objective- The objective of the study is to correlate the interaction of DNA and quinoline derivative, which was reported with the fluorescence microscopy images of cells in-vitro data in the recently published data. METHODS The detailed interaction study with the DNA dodecanucleotide sequenced d(CGCGAATTCGCG) shows the present lead bounds with the A/T minor groove region of a B-DNA duplex through important major and minor hydrogen-bonds. RESULT The present in-silico study supports the interactions of the drug with DNA with sufficient binding interactions and energy. The present study also gives vital information related to the mechanism of drug action, which was initially declared as a DNA targeting molecule through a fluorescence based target study. CONCLUSION The substitution at 2nd position (the carbonyl group) of the lead was revealed as a hydrogen bond donor/acceptor for the adenine and guanine nucleic acid-base pair. The in-silico prediction also confirmed the interaction pattern of the lead with the DNA, which will be further utilized for drug development.
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Affiliation(s)
- Priyank Purohit
- Department of Pharmacy, HIMT, Gautam Budh Nagar, Greater Noida, Uttar Pradesh, 201308, India
| | - Ravi K Mittal
- Department of Natural Product, National Institute of Pharmaceutical Education and Research (NIPER), Sector-67, SAS Nagar, Punjab-160062, India
| | - Kavita Khatana
- Department of chemistry, School of basic and applied sciences, SBAS, Galgotias University, Greater Noida. U.P, India
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Adımcılar V, Çeşme M, Şenel P, Danış İ, Ünal D, Gölcü A. Comparative study of cytotoxic activities, DNA binding and molecular docking interactions of anticancer agent epirubicin and its novel copper complex. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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4
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A spectroscopic deciphering of the differential interaction behavior of alkaloid drugs with native B-DNA and protonated DNA. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113426] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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5
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Çeşme M, Gölcü A. Metal-Based Molecular Compounds: Structure, Analytical Properties, dsDNA Binding Studies and In Vitro Antiproliferative Activity on Selected Cancer Cell Lines. Pharm Chem J 2019. [DOI: 10.1007/s11094-019-02011-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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6
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Khalid S, Rodger P. Molecular Dynamics Simulations of Dna and Its Complexes. PROGRESS IN REACTION KINETICS AND MECHANISM 2019. [DOI: 10.3184/007967404777726232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This article describes how classical molecular simulation methods are being used to gain a molecular-level understanding of the interaction mechanisms responsible for DNA–ligand recognition, and that govern the response of DNA to ligand binding. Case studies using a variety of different ligands—including small pharmaceutical drugs, proteins and lipids—are used to illustrate the power of modern molecular dynamics simulation methods for understanding how we may control the function and structure of DNA.
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Affiliation(s)
- Syma Khalid
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
- Current address: Laboratory of Molecular Biophysics, University of Oxford, South Parks Rd, Oxford, OX1 3QU, UK
| | - P.Mark Rodger
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
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Basu A, Kumar GS. Nucleic acids binding strategies of small molecules: Lessons from alkaloids. Biochim Biophys Acta Gen Subj 2018; 1862:1995-2016. [DOI: 10.1016/j.bbagen.2018.06.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/11/2018] [Accepted: 06/11/2018] [Indexed: 01/14/2023]
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8
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Jolley EA, Hardebeck LKE, Ren Y, Adams MS, Lewis M, Znosko BM. The effects of varying the substituent and DNA sequence on the stability of 4-substituted DNA-naphthalimide complexes. Biophys Chem 2018; 239:29-37. [PMID: 29804029 DOI: 10.1016/j.bpc.2018.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/22/2018] [Accepted: 04/26/2018] [Indexed: 11/30/2022]
Abstract
DNA duplexes are stabilized by many interactions, one of which is stacking interactions between the nucleic acid bases. These interactions are useful for designing small molecules that bind to DNA. Naphthalimide intercalators have been shown to be valuable anti-cancer agents that stack between the DNA bases and exhibit stabilizing effects. There is a continued need to design intercalators that will exhibit these stabilizing effects while being more selective toward DNA binding. This work investigates 4-substituted naphthalimides with varying functional groups and their interactions with nucleic acid duplexes. Mode of binding was determined via wavelength scans, circular dichroism, and viscosity measurements. Optical melting experiments were used to measure the absorbance of the sample as a function of temperature. The Tm values derived from the DNA duplexes were subtracted from the Tm values derived from the DNA-intercalator complexes, resulting in ΔTm values. The ΔTm values demonstrated that the substituents on the intercalator affect the stability of the DNA-intercalator complex. From the results of this study and comparison to results from previous work, we conclude that the substituent type and position on the core intercalator molecule affect the stability of the complex it forms with DNA.
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Affiliation(s)
- Elizabeth A Jolley
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave., St. Louis, MO 63103, United States
| | - Laura K E Hardebeck
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave., St. Louis, MO 63103, United States
| | - Yi Ren
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave., St. Louis, MO 63103, United States
| | - Miranda S Adams
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave., St. Louis, MO 63103, United States
| | - Michael Lewis
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave., St. Louis, MO 63103, United States
| | - Brent M Znosko
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave., St. Louis, MO 63103, United States.
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Parveen M, Aslam A, Nami SAA, Malla AM, Alam M, Lee DU, Rehman S, Silva PSP, Silva MR. Potent acetylcholinesterase inhibitors: Synthesis, biological assay and docking study of nitro acridone derivatives. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 161:304-11. [PMID: 27295412 DOI: 10.1016/j.jphotobiol.2016.05.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 05/15/2016] [Accepted: 05/30/2016] [Indexed: 01/02/2023]
Abstract
The reaction of o-halobenzoic acid with aniline derivatives and their subsequent cyclization reaction yielded the acridone derivatives. The series of nitro acridone derivatives were prepared by Ullmann condensation in presence of copper as catalyst and were characterized by FTIR, (1)H, (13)C NMR and mass spectra. The structure of 5-nitro-(2-phenyl amino) benzoic acid (4) was confirmed by X-ray crystallography and was found to crystallize in P21/c space group. The in vitro efficacy of the compounds for their acetylcholinesterase (AChE) and antimicrobial inhibitory activities have been evaluated against the standard drugs Ampicillin and Gentamicin against Gram positive and Gram negative bacteria. 1,7-Dinitroacridone was found to be the most potent AChE inhibitor (IC50=0.22μM). Moreover, the compounds have been screened for their antioxidant activity using the DPPH assay. Also, docking study results were found to be in good agreement with the results obtained through in vitro experiments. The docking study further predicted possible binding conformation.
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Affiliation(s)
- Mehtab Parveen
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India.
| | - Afroz Aslam
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India
| | - Shahab A A Nami
- Department of Kulliyat, Faculty of Unani Medicine, Aligarh Muslim University, Aligarh 202002, India
| | - Ali Mohammed Malla
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India
| | - Mahboob Alam
- Division of Bioscience, Dongguk University, Gyeongju 780-714, Republic of Korea
| | - Dong-Ung Lee
- Division of Bioscience, Dongguk University, Gyeongju 780-714, Republic of Korea
| | - Sumbul Rehman
- Department of Ilmul Advia, Faculty of Unani Medicine, Aligarh Muslim University, Aligarh 202002, India
| | - P S Pereira Silva
- CEMDRX, Physics Department, University of Coimbra, P-3004-516 Coimbra, Portugal
| | - M Ramos Silva
- CEMDRX, Physics Department, University of Coimbra, P-3004-516 Coimbra, Portugal
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Thimmaiah K, Ugarkar AG, Martis EF, Shaikh MS, Coutinho EC, Yergeri MC. Drug-DNA Interaction Studies of Acridone-Based Derivatives. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 34:309-31. [PMID: 25874941 DOI: 10.1080/15257770.2014.992531] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
N10-alkylated 2-bromoacridones are a novel series of potent antitumor compounds. DNA binding studies of these compounds were carried out using spectrophotometric titrations, Circular dichroism (CD) measurements using Calf Thymus DNA (CT DNA). The binding constants were identified at a range of K=0.3 to 3.9×10(5) M(-1) and the percentage of hypochromism from the spectral titrations at 28-54%. This study has identified a compound 9 with the good binding affinity of K=0.39768×10(5) M(-1) with CT DNA. Molecular dynamics (MD) simulations have investigated the changes in structural and dynamic features of native DNA on binding to the active compound 9. All the synthesized compounds have increased the uptake of Vinblastine in MDR KBChR-8-5 cells to an extent of 1.25- to1.9-fold than standard modulator Verapamil of similar concentration. These findings allowed us to draw preliminary conclusions about the structural features of 2-bromoacridones and further chemical enhancement will improve the binding affinity of the acridone derivatives to CT-DNA for better drug-DNA interaction. The molecular modeling studies have shown mechanism of action and the binding modes of the acridones to DNA.
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Effect of intercalator substituent and nucleotide sequence on the stability of DNA- and RNA-naphthalimide complexes. Bioorg Med Chem 2015; 23:3586-91. [PMID: 25960324 DOI: 10.1016/j.bmc.2015.04.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/30/2015] [Accepted: 04/09/2015] [Indexed: 01/02/2023]
Abstract
DNA intercalators are commonly used as anti-cancer and anti-tumor agents. As a result, it is imperative to understand how changes in intercalator structure affect binding affinity to DNA. Amonafide and mitonafide, two naphthalimide derivatives that are active against HeLa and KB cells in vitro, were previously shown to intercalate into DNA. Here, a systematic study was undertaken to change the 3-substituent on the aromatic intercalator 1,8-naphthalimide to determine how 11 different functional groups with a variety of physical and electronic properties affect binding of the naphthalimide to DNA and RNA duplexes of different sequence compositions and lengths. Wavelength scans, NMR titrations, and circular dichroism were used to investigate the binding mode of 1,8-naphthalimide derivatives to short synthetic DNA. Optical melting experiments were used to measure the change in melting temperature of the DNA and RNA duplexes due to intercalation, which ranged from 0 to 19.4°C. Thermal stabilities were affected by changing the substituent, and several patterns and idiosyncrasies were identified. By systematically varying the 3-substituent, the binding strength of the same derivative to various DNA and RNA duplexes was compared. The binding strength of different derivatives to the same DNA and RNA sequences was also compared. The results of these comparisons shed light on the complexities of site specificity and binding strength in DNA-intercalator complexes. For example, the consequences of adding a 5'-TpG-3' or 5'-GpT-3' step to a duplex is dependent on the sequence composition of the duplex. When added to a poly-AT duplex, naphthalimide binding was enhanced by 5.6-11.5°C, but when added to a poly-GC duplex, naphthalimide binding was diminished by 3.2-6.9°C.
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12
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Hájková A, Barek J, Vyskočil V. Voltammetric Determination of 2-Aminofluoren-9-one and Investigation of Its Interaction with DNA on a Glassy Carbon Electrode. ELECTROANAL 2014. [DOI: 10.1002/elan.201400427] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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13
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Stockert JC. Predictive binding geometry of ligands to DNA minor groove: isohelicity and hydrogen-bonding pattern. Methods Mol Biol 2014; 1094:1-12. [PMID: 24162975 DOI: 10.1007/978-1-62703-706-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The interaction of drugs and dyes with nucleic acids, particularly when binding to DNA minor groove occurs, has increasing importance in biomedical sciences. This is due to the resulting biological activity and to the possibility of recognizing AT and GC base pairs. In such cases, DNA binding can be predicted if appropriate helical and hydrogen-bonding parameters are deduced from DNA models, and a simplified geometrical rule in the form of a stencil is then applied on computer-drawn molecules of interest. Relevant structure parameter values for minor groove binders are the length (4.6 < L < 5.4 Å) and angle (152 < σ < 156.5°) between three consecutive units, measured at the level of hydrogen donor or acceptor groups. Application of the stencil shows that predictive methods can aid in the design of new compounds, by checking the possible binding of isohelical sequence-specific ligands along the DNA minor groove.
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Affiliation(s)
- Juan C Stockert
- Department of Biology, Faculty of Sciences, Autonomous University of Madrid, Cantoblanco, Madrid, Spain
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14
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Raman N, Rajakumar R. Bis-amide transition metal complexes: isomerism and DNA interaction study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 120:428-436. [PMID: 24211801 DOI: 10.1016/j.saa.2013.10.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Revised: 10/01/2013] [Accepted: 10/09/2013] [Indexed: 06/02/2023]
Abstract
A quatridentate bis-amide ligand, N,N'-propylenebis(salicylamide) H2pbs, and its transition metal complexes [M(pbs)(H2O)2], where M=Co(II), Ni(II), Cu(II), and Zn(II) have been synthesized and characterized by elemental analysis, UV-Vis, IR, NMR, Mass, EPR, molar conductivity, magnetic moment values and thermal analysis. The NMR spectrum of ligand evidences the E/Z isomerism. All the evidences reveal that the metal ions adopt octahedral geometry with metal:ligand:solvent ratio 1:1:2. The conductivity measurements exhibit that the complexes are non-electrolytes. DNA binding properties of these complexes have been explored by UV-Vis and cyclic voltammetry. The results indicate that these complexes are good intercalators.
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Affiliation(s)
- Natarajan Raman
- Research Department of Chemistry, VHNSN College, Virudhunagar 626 001, India.
| | - Ramasubbu Rajakumar
- Research Department of Chemistry, VHNSN College, Virudhunagar 626 001, India
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15
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Malinovskii VL, Nussbaumer AL, Häner R. Oligopyrenotides: chiral nanoscale templates for chromophore assembly. Angew Chem Int Ed Engl 2012; 51:4905-8. [PMID: 22492542 DOI: 10.1002/anie.201201352] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Indexed: 01/29/2023]
Abstract
Getting organized: DNA-like supramolecular polymers formed of short oligopyrenotides serve as a helical scaffold for the molecular assembly of ligands. The cationic porphyrin meso-tetrakis(1-methylpyridin-4-yl)porphyrin interacts with the helical polymers in a similar way as with poly(dA:dT).
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16
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Malinovskii VL, Nussbaumer AL, Häner R. Oligopyrenotides: Chiral Nanoscale Templates for Chromophore Assembly. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201352] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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17
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Javed F, Altaf AA, Badshah A, Tahir MN, Siddiq M, Shah A, Ullah S, Lal B. New supramolecular ferrocenyl amides: synthesis, characterization, and preliminary DNA-binding studies. J COORD CHEM 2012. [DOI: 10.1080/00958972.2012.664769] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Fatima Javed
- a Department of Chemistry , Quaid-i-Azam University , Islamabad-45320 , Pakistan
| | - Ataf Ali Altaf
- a Department of Chemistry , Quaid-i-Azam University , Islamabad-45320 , Pakistan
| | - Amin Badshah
- a Department of Chemistry , Quaid-i-Azam University , Islamabad-45320 , Pakistan
| | | | - Muhammad Siddiq
- a Department of Chemistry , Quaid-i-Azam University , Islamabad-45320 , Pakistan
| | - Afzal Shah
- a Department of Chemistry , Quaid-i-Azam University , Islamabad-45320 , Pakistan
| | - Shafiq Ullah
- a Department of Chemistry , Quaid-i-Azam University , Islamabad-45320 , Pakistan
| | - Bhajan Lal
- a Department of Chemistry , Quaid-i-Azam University , Islamabad-45320 , Pakistan
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Wang Y, Wang J, Yang F, Yang X. Probing Biomolecular Interactions with Dual Polarization Interferometry: Real-Time and Label-Free Coralyne Detection by Use of Homoadenine DNA Oligonucleotide. Anal Chem 2011; 84:924-30. [DOI: 10.1021/ac2019443] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yong Wang
- State Key
Laboratory of Electroanalytical
Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022,
China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039,
China
| | - Juan Wang
- State Key
Laboratory of Electroanalytical
Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022,
China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039,
China
| | - Fan Yang
- State Key
Laboratory of Electroanalytical
Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022,
China
| | - Xiurong Yang
- State Key
Laboratory of Electroanalytical
Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022,
China
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Varvaresou A, Iakovou K. Molecular modeling study of intercalation complexes of tricyclic carboxamides with d(CCGGCGCCGG)₂ and d(CGCGAATTCGCG)₂. J Mol Model 2010; 17:2041-50. [PMID: 21153908 DOI: 10.1007/s00894-010-0891-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2010] [Accepted: 10/29/2010] [Indexed: 11/25/2022]
Abstract
Tricyclic dyes with different mesoatoms such as xanthenes (fluorescein, eosin) anthracenes and acridines (proflavine) approved by the Food and Drug Administration (FDA) for use in foods, pharmaceuticals and cosmetic preparations interact with DNA, and some of them do so through intercalation. Hyperchem 7.5, Spartan 04, Yasara 10.5.14 program packages and molecular modeling, molecular mechanics and dynamics techniques with the oligonucleotides d(CCGGCGCCGG)2 and d(CGCGAATTCGCG)2 were utilized in order to examine the mode of binding to DNA of a range of tricyclic carboxamides bearing N,N-dimethylaminoethyl side chain, i.e., 9-amino-DACA, anthracene, acridine-1-carboxamide, acridine-4-carboxamide (DACA), azacridine, phenazine, pyridoquinoxaline, oxopyridoquinoxaline, phenoxazine and xanthenone or N,N-dimethylaminobutyl moiety, i.e., phenazine and acridine. The bicyclic quinoline-8-carboxamide was also examined for comparison reasons. On the basis of our data, prerequisite for the interaction between protonated N,N-dimethylaminoethyl moiety and guanine is the formation of only one internal hydrogen bond between carboxamide and peri NH + in the case of 9-amino-DACA or peri N in the cases of DACA, azacridine, phenazine and pyridoquinoxaline. The presence of an additional internal hydrogen bond between oxygen carboxamide and protonated N,N-dimethylamino group in the cases of tricyclic systems bearing peri NH (phenoxazine) or O (xanthenone) group, prevents the interaction between side chain and guanine. Also, the formation of one internal hydrogen bond between oxygen carboxamide and protonated N,N-dimethylamino group inhibits the interaction between side chain and guanine in the case of acridine-1-carboxamide. Our findings are in accordance with previously reported results obtained from the kinetic studies of the binding of acridine and related tricyclic carboxamides to DNA.
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Affiliation(s)
- Athanasia Varvaresou
- Laboratory of Cosmetology, Department of Aesthetics and Cosmetology, Technological Educational Institution of Athens, Ag. Spyridona, Egaleo, 12 210 Athens, Greece.
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Del Castillo P, Horobin RW, Blázquez-Castro A, Stockert JC. Binding of cationic dyes to DNA: distinguishing intercalation and groove binding mechanisms using simple experimental and numerical models. Biotech Histochem 2010; 85:247-56. [DOI: 10.3109/10520290903149620] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Bhadra K, Kumar GS. Therapeutic potential of nucleic acid-binding isoquinoline alkaloids: Binding aspects and implications for drug design. Med Res Rev 2010; 31:821-62. [DOI: 10.1002/med.20202] [Citation(s) in RCA: 219] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Maiti M, Kumar GS. Polymorphic nucleic Acid binding of bioactive isoquinoline alkaloids and their role in cancer. J Nucleic Acids 2009; 2010. [PMID: 20814427 PMCID: PMC2915887 DOI: 10.4061/2010/593408] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Revised: 09/11/2009] [Accepted: 09/14/2009] [Indexed: 12/20/2022] Open
Abstract
Bioactive alkaloids occupy an important position in applied chemistry and play an indispensable role in medicinal chemistry. Amongst them, isoquinoline alkaloids like berberine, palmatine and coralyne of protoberberine group, sanguinarine of the benzophenanthridine group, and their derivatives represent an important class of molecules for their broad range of clinical and pharmacological utility. In view of their extensive occurrence in various plant species and significantly low toxicities, prospective development and use of these alkaloids as effective anticancer agents are matters of great current interest. This review has focused on the interaction of these alkaloids with polymorphic nucleic acid structures (B-form, A-form, Z-form, HL-form, triple helical form, quadruplex form) and their topoisomerase inhibitory activity reported by several research groups using various biophysical techniques like spectrophotometry, spectrofluorimetry, thermal melting, circular dichroism, NMR spectroscopy, electrospray ionization mass spectroscopy, viscosity, isothermal titration calorimetry, differential scanning calorimetry, molecular modeling studies, and so forth, to elucidate their mode and mechanism of action for structure-activity relationships. The DNA binding of the planar sanguinarine and coralyne are found to be stronger and thermodynamically more favoured compared to the buckled structure of berberine and palmatine and correlate well with the intercalative mechanism of sanguinarine and coralyne and the partial intercalation by berberine and palmatine. Nucleic acid binding properties are also interpreted in relation to their anticancer activity.
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Affiliation(s)
- Motilal Maiti
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology (CSIR), Kolkata 700032, India
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Wanunu M, Sutin J, Meller A. DNA profiling using solid-state nanopores: detection of DNA-binding molecules. NANO LETTERS 2009; 9:3498-502. [PMID: 19585985 PMCID: PMC2871189 DOI: 10.1021/nl901691v] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We present a novel single-molecule method for rapidly evaluating small-molecule binding to individual DNA molecules using nanopores fabricated in ultrathin silicon membranes. A measurable shift in the residual ion current through a approximately 3.5 nm pore results from threading of a dye-intercalated DNA molecule, as compared to the typical residual current of native DNA. The average level of the residual current can be used to directly quantify the fraction of bound molecules to DNA, providing a new way to determine binding isotherms. Spatial sensitivity is also demonstrated by designing a two-segment DNA molecule that contains small-molecule binding sites in one of its two segments. Translocations of such molecules exhibit two current levels upon incubation with a DNA-binding dye, caused by selectively bound dye in one of the DNA segments. Our results, as shown here with four different dyes, coincide well with bulk fluorescence measurements performed under identical conditions. The nanopore approach for "reading-out" molecular binding along a DNA molecule, combined with the miniscule amounts of DNA required and the potential for scalability using nanopore arrays, provide a novel platform for future applications in analytical drug screening.
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Riahi S, Ganjali MR, Bagheri M. Theoretical investigation of interaction between Gatifloxacin and DNA: Implications for anticancer drug design. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2009. [DOI: 10.1016/j.msec.2009.02.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Liu CS, Zhang H, Chen R, Shi XS, Bu XH, Yang M. Two New Co(II) and Ni(II) Complexes with 3-(2-Pyridyl)pyrazole-Based Ligand: Synthesis, Crystal Structures, and Bioactivities. Chem Pharm Bull (Tokyo) 2007; 55:996-1001. [PMID: 17603188 DOI: 10.1248/cpb.55.996] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Two new Co(II) and Ni(II) complexes exhibiting DNA cytotoxic activities with 3-(2-pyridyl)pyrazole-based ligand, [Co(L)(3)](ClO(4))(2) (1) and [Ni(L)(3)](ClO(4))(2) (2) (L=1-[3-(2-pyridyl)-pyrazol-1-ylmethyl]-naphthalene) were synthesized and structurally characterized. Both 1 and 2 crystallized in the monoclinic system, space group P2(1)/c, for 1, a=12.8324(8), b=12.1205(8), c=33.27(2) A, beta=93.92(3) degrees and Z=4; for 2, a=12.8764(3), b=12.1015(3), c=33.2415(9) A, beta=93.998(1) degrees and Z=4. Among them, the Co(II) and Ni(II) ions were all coordinated by six N donors from three distinct L ligands. In addition, the cytotoxic activities of 1, 2 and L in vitro were evaluated against three different cancer cell lines HL-60 (human leukemia), BGC-823 (stomach cancer) and MDA-MB-435 (mammary cancer), respectively. The results showed that 1 exhibited significantly high cytotoxic activities against HL-60 and moderate activities against BGC-823 and MDA-MB-435. In order to further investigate the relationships between structures and DNA-binding behaviors of these complexes, the interactions of 1, 2 and L with calf thymus DNA (CT-DNA) were then subjected to thermal denaturation, viscosity measurements and spectrophotometric methods. The results indicated that 1 and 2 intercalated with DNA via L ligand. The intrinsic binding constants of 1, 2 and L with DNA were 1.6x10(4), 5.6x10(3) and 2.76x10(3) M(-1), respectively.
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Affiliation(s)
- Chun-Sen Liu
- Department of Chemistry, Nankai University, Tianjin, PR, China
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Maiti M, Kumar GS. Molecular aspects on the interaction of protoberberine, benzophenanthridine, and aristolochia group of alkaloids with nucleic acid structures and biological perspectives. Med Res Rev 2007; 27:649-95. [PMID: 16894530 DOI: 10.1002/med.20087] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Alkaloids occupy an important position in chemistry and pharmacology. Among the various alkaloids, berberine and coralyne of the protoberberine group, sanguinarine of the benzophenanthridine group, and aristololactam-beta-d-glucoside of the aristolochia group have potential to form molecular complexes with nucleic acid structures and have attracted recent attention for their prospective clinical and pharmacological utility. This review highlights (i) the physicochemical properties of these alkaloids under various environmental conditions, (ii) the structure and functional aspects of various forms of deoxyribonucleic acid (DNA) (B-form, Z-form, H(L)-form, protonated form, and triple helical form) and ribonucleic acid (RNA) (A-form, protonated form, and triple helical form), and (iii) the interaction of these alkaloids with various polymorphic DNA and RNA structures reported by several research groups employing various analytical techniques like absorbance, fluorescence, circular dichroism, and NMR spectroscopy; electrospray ionization mass spectrometry, thermal melting, viscosity, and DNase footprinting as well as molecular modeling and thermodynamic studies to provide detailed binding mechanism at the molecular level for structure-activity relationship. Nucleic acids binding properties of these alkaloids are interpreted in relation to their biological activity.
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Affiliation(s)
- Motilal Maiti
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Kolkata 700 032, India.
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Arakelyan VB, Babayan SY, Tairyan VI, Arakelyan HV, Parsadanyan MA, Vardevanyan PO. Kinetics of ligand binding to nucleic acids at arbitrary occupancy. Biophysics (Nagoya-shi) 2006. [DOI: 10.1134/s0006350906030067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Arakelyan VB, Babayan SY, Tairyan VI, Arakelyan AV, Parsadanyan MA, Vardevanyan PO. Kinetics of Ligand Binding to Nucleic Acids. J Biomol Struct Dyn 2006; 23:479-84. [PMID: 16363882 DOI: 10.1080/07391102.2006.10507073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Ligand binding to nucleic acids (NA) is considered as a stationary Markov process. It is shown that the probabilistic description of ligand-NA binding allows one to describe not only the kinetics of the change of number of bound ligands at arbitrary fillings but also to calculate stationary values of the number of bound ligands and its dispersion. The general analysis of absorption isotherms and kinetics of ligand binding to NA make it possible to determine of rate constants of ligand-NA complex formation and dissociation.
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Affiliation(s)
- V B Arakelyan
- Yerevan Physics Institute, 2, Alikhanian Brothers Str., Yerevan, 375036 Armenia.
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29
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Martin JN, Muñoz EM, Schwergold C, Souard F, Asensio JL, Jiménez-Barbero J, Cañada J, Vicent C. Carbohydrate-based DNA ligands: sugar-oligoamides as a tool to study carbohydrate-nucleic acid interactions. J Am Chem Soc 2005; 127:9518-33. [PMID: 15984879 DOI: 10.1021/ja050794n] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sugar-oligoamides have been designed and synthesized as structurally simple carbohydrate-based ligands to study carbohydrate-DNA interactions. The general design of the ligands 1-3 has been done as to favor the bound conformation of Distamycin-type gamma-linked covalent dimers which is a hairpin conformation. Indeed, NMR analysis of the sugar-oligoamides in the free state has indicated the presence of a percentage of a hairpin conformation in aqueous solution. The DNA binding activity of compounds 1-3 was confirmed by calf thymus DNA (ct-DNA) NMR titration. Interestingly, the binding of the different sugar-oligoamides seems to be modulated by the sugar configuration. Semiquantitative structural information about the DNA ligand complexes has been derived from NMR data. A competition experiment with Netropsin suggested that the sugar-oligoamide 3 bind to DNA in the minor groove. The NMR titrations of 1-3 with poly(dA-dT) and poly(dG-dC) suggested preferential binding to the ATAT sequence. TR-NOE NMR experiments for the sugar-oligoamide 3-ct-DNA complex both in D(2)O and H(2)O have confirmed the complex formation and given information on the conformation of the ligand in the bound state. The data confirmed that the sugar-oligoamide ligand is a hairpin in the bound state. Even more relevant to our goal, structural information on the conformation around the N-glycosidic linkage has been accessed. Thus, the sugar asymmetric centers pointing to the NH-amide and N-methyl rims of the molecule have been characterized.
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Affiliation(s)
- Jason N Martin
- Instituto de Química Orgánica, CSIC, c/ Juan de la Cierva 3, Madrid 28006, Spain
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Rauf S, Gooding JJ, Akhtar K, Ghauri MA, Rahman M, Anwar MA, Khalid AM. Electrochemical approach of anticancer drugs--DNA interaction. J Pharm Biomed Anal 2005; 37:205-17. [PMID: 15708659 DOI: 10.1016/j.jpba.2004.10.037] [Citation(s) in RCA: 232] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2004] [Accepted: 10/28/2004] [Indexed: 11/18/2022]
Abstract
The interaction of drugs with DNA is among the most important aspects of biological studies in drug discovery and pharmaceutical development processes. In recent years there has been a growing interest in the electrochemical investigation of interaction between anticancer drugs and DNA. Observing the pre and post electrochemical signals of DNA or drug interaction provides good evidence for the interaction mechanism to be elucidated. Also this interaction could be used for the quantification of these drugs and for the determination of new drugs targeting DNA. Electrochemical approach can provide new insight into rational drug design and would lead to further understanding of the interaction mechanism between anticancer drugs and DNA.
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Affiliation(s)
- S Rauf
- Bioprocess Technology Division, National Institute for Biotechnology and Genetic Engineering, P.O. Box 577, Jhang Road, Faisalabad, Pakistan
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31
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Di Tullio A, Reale S, De Angelis F. Molecular recognition by mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2005; 40:845-65. [PMID: 16034845 DOI: 10.1002/jms.896] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
A recent major advance in the field of mass spectrometry in the biomolecular sciences is represented by the study of the supramolecular interactions among two or more partners in the gas phase. A great deal of chemistry and most of biochemistry concerns molecular interactions taking place in solution. The electrospray technique, which allows direct sampling from solution, and soft ionization of the solute without deposition into the analyte of large amounts of energy, guarantees in many cases the survival of noncovalent bondings and, hence, the direct analysis of the supramolecular complexes present in the condensed phase. The proper preparation of the solution to be studied and also the expert and accurate setting and use of the instrumental parameters are the prerequisites for gaining results as to the specific interactions between, for instance, a protein conformationally modified by its specific metal ion, eventually, and a ligand molecule. The analysis of the charge state of the protein itself and of the modifications of the complex integrity by activating collisions are also methods for studying the biomolecule-molecule interactions. Accordingly, this new mass spectrometric approach to the supramolecular chemistry, which could be also defined as 'supramolecular mass spectrometry', allows the study of ion-protein, protein-protein, protein-ligand and DNA-drug interactions. Chiral recognition can also be performed in the gas phase, studying by electrospray mass spectrometry the fragmentation of diastereomeric complex ions. Not the least, a deep insight can also be obtained into the formation and nature of inclusion complexes like those formed with crown ethers, cyclodextrins and calixarenes as host molecules. All these topics are treated to a certain extent in this special feature article.
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Affiliation(s)
- Alessandra Di Tullio
- Department of Chemistry, Chemical Engineering and Material, University of L'Aquila, Via Vetoio Coppito II, I-67010 Coppito L'Aquila Italy
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32
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Stockert JC, Pinna-Senn E, Bella JL, Lisanti JA. DNA-binding fluorochromes: correlation between C-banding of mouse metaphase chromosomes and hydrogen bonding to adenine-thymine base pairs. Acta Histochem 2005; 106:413-20. [PMID: 15707650 DOI: 10.1016/j.acthis.2004.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2004] [Revised: 09/08/2004] [Accepted: 09/12/2004] [Indexed: 11/16/2022]
Abstract
Numerous non-rigid and bow-shaped cationic fluorochromes exist which bind to chromatin DNA, but only some of them are able to selectively label pericentromeric heterochromatin (C-bands) in metaphase chromosomes. Likewise, some DNA ligands allow the recognition of adenine-thymine sequences establishing hydrogen bonds with acceptor atoms in the minor groove. In the present study, we have employed cationic fluorochromes based on a variety of chemical groups to analyze comparatively their potential to demonstrate C-bands, as well as the relationship between this feature and structural parameters of fluorochromes such as curvature radius and hydrogen-bonding ability. Only fluorochromes that bind DNA by hydrogen bonds demonstrated the characteristic C-banding pattern in mouse metaphase chromosomes (together with a weak G/Q-banding), whereas the other (non-hydrogen-bonding) cationic fluorochromes produced uniform emission without any visible banding.
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Affiliation(s)
- Juan C Stockert
- Department of Biology, Faculty of Sciences, Autonomous University of Madrid, Cantoblanco, 28049-Madrid, Spain.
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33
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Flader W, Wellenzohn B, Winger RH, Hallbrucker A, Mayer E, Liedl KR. Stepwise induced fit in the pico- to nanosecond time scale governs the complexation of the even-skipped transcriptional repressor homeodomain to DNA. Biopolymers 2003; 68:139-49. [PMID: 12548619 DOI: 10.1002/bip.10242] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Induced fit effects in the complex of a DNA decamer with two even-skipped transcriptional repressor homeodomain molecules were investigated by means of molecular dynamics simulations. Dynamics of these effects are found to be in the time scale from pico- to nanoseconds. First steps are made by the fast-moving DNA backbone phosphates, which upon binding change their B(I)/B(II) substate distribution. Further rearrangements in the DNA double helix induced upon complexation, like bending of the helix axis, changes of the minor groove width, and of different helical parameters, are slower and occur within a few nanoseconds. The flexibility of the DNA, especially of its backbone, seems thereby to play an important role for specific DNA ligand recognition.
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Affiliation(s)
- Wolfgang Flader
- Institute of General, Inorganic and Theoretical Chemistry University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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Wellenzohn B, Loferer MJ, Trieb M, Rauch C, Winger RH, Mayer E, Liedl KR. Hydration of hydroxypyrrole influences binding of ImHpPyPy-beta-Dp polyamide to DNA. J Am Chem Soc 2003; 125:1088-95. [PMID: 12537509 DOI: 10.1021/ja0277778] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ligands which are able to recognize DNA sequence specifically are of fundamental interest as transcription controlling drugs. Recently a polyamide ligand was developed (ImHpPyPy-beta-Dp) which differentiates in a dimeric arrangement between all four possible base pair steps in the minor groove. This is a landmark for the design of DNA binding drugs because it was believed that such a recognition could only be possible in the major groove of DNA. Although the OH groups of the hydroxypyrrole (Hp) moieties of the ligands are responsible for this sequence discrimination, experiments showed that this OH group also reduces the absolute binding constant. We performed a free energy calculation by means of thermodynamic integration in order to find out the influence of this single hydroxyl on DNA binding. In our simulation, we found that the hydroxyl group reduces binding by about 1.3 kcal/mol, which is in excellent agreement with the experimentally determined value of 1.2 kcal/mol. In further MD simulations, the structural reasons for this reduction was estimated. The results of these simulations qualitatively agree with the X-ray structures, but in contrast, in the simulations both (ImHpPyPy-beta-Dp and ImPyPyPy-beta-Dp) ligand-DNA (d(CCAGTACTGG)(2)) complexes exhibit only slight structural differences. This is consistent with a recently published second pair of similar polyamide DNA crystal structures. Thus, we believe that the explanations resulting from the X-ray structures must be modified. We attribute the large structural differences between the two polyamide DNA complexes to a buffer molecule which binds only in the case of the ImHpPyPy-beta-Dp-DNA complex at the region of interest. We propose that the differential hydration of both ligands in the unbound state is responsible for the reduction of the binding constant. Additionally, we suggest an indirect readout of DNA, because of a lengthening of the Watson-Crick base pairs, which possibly contributes to the differentiation between T.A, A.T from G.C, C.G base pairs.
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Affiliation(s)
- Bernd Wellenzohn
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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Wellenzohn B, Flader W, Winger RH, Hallbrucker A, Mayer E, Liedl KR. Influence of netropsin's charges on the minor groove width of d(CGCGAATTCGCG)2. Biopolymers 2002; 61:276-86. [PMID: 12115142 DOI: 10.1002/bip.10156] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The exact understanding of the interaction of minor groove binding drugs with DNA is of interest due to their importance as transcription controlling drugs. In this study we performed four molecular dynamics simulations, one of the uncomplexed d(CGCGAATTCGCG)(2) dodecamer and three simulations of the DNA complexed with the minor groove binder netropsin. The charged guanidinium and amidinium ends of the small ligand were in one simulation formally uncharged, in the second one normally charged, and in the third simulation we doubled the charges of the two ends. So we are able to filter out the influence the charges exert on the DNA structure. The positive charges reduce the width of the minor groove showing that charges are able to modify the groove width by charge neutralization of the negative phosphate groups. The quality of the used force field was successfully tested by comparing the results of the uncomplexed dodecamer with already reported NMR and x-ray studies. Thus our simulations should be able to describe the minor groove width of DNA in a correct manner underlying the validity of the results.
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Affiliation(s)
- B Wellenzohn
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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Sperandio O, Fan BT, Zakrzewska K, Jia ZJ, Zheng RL, Panaye A, Doucet JP, El Fassi N. Theoretical study of fast repair of DNA damage by cistanoside C and analogs: mechanism and docking. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2002; 13:243-260. [PMID: 12071653 DOI: 10.1080/10629360290002749] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Experiments show that the natural substances phenylpropanoid glycosides (PPGs) extracted from pelicularis spicata are capable of repairing DNA damaged by oxygen radicals. Based on kinetic measurements and experiments on tumor cells, a theoretical study of the interaction between PPG molecules and isolated DNA bases, as well as a DNA fragment has been performed. An interaction mechanism reported early has been refined. The docking calculations performed using junction minimization of nucleic acids (JUMNA) software showed that the PPG molecules can be docked into the minor groove of DNA and form complexes with the geometry suitable for an electron transfer between guanine radical and the ligand. Such complexes can be formed without major distortions of DNA structure and are further stabilized by the interaction with the rhamnosyl side-groups.
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Affiliation(s)
- O Sperandio
- Institut de Topologie de Dynamique des Systèmes, CNRS ESA7986, Université Paris7-Denis-Diderot, France
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Flader W, Wellenzohn B, Winger RH, Hallbrucker A, Mayer E, Liedl KR. BI ⇌ BII Substate Transitions Induce Changes in the Hydration of B-DNA, Potentially Mediating Signal Transduction from the Minor to Major Groove. J Phys Chem B 2001. [DOI: 10.1021/jp004046q] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Wolfgang Flader
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Bernd Wellenzohn
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Rudolf H. Winger
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Andreas Hallbrucker
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Erwin Mayer
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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Wellenzohn B, Flader W, Winger RH, Hallbrucker A, Mayer E, Liedl KR. Complex of B-DNA with polyamides freezes DNA backbone flexibility. J Am Chem Soc 2001; 123:5044-9. [PMID: 11457333 DOI: 10.1021/ja003639b] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The development of sequence-specific minor groove binding ligands is a modern and rapidly growing field of research because of their extraordinary importance as transcription-controlling drugs. We performed three molecular dynamics simulations in order to clarify the influence of minor groove binding of two ImHpPyPy-beta-Dp polyamides to the d(CCAGTACTGG)(2) decamer in the B-form. This decamer contains the recognition sequence for the trp repressor (5'-GTACT-3'), and it was investigated recently by X-ray crystallography. On one hand we are able to reproduce X-ray-determined DNA--drug contacts, and on the other hand we provide new contact information which is important for the development of potential ligands. The new insights show how the beta-tail of the polyamide ligands contributes to binding. Our simulations also indicate that complexation freezes the DNA backbone in a specific B(I) or B(II) substate conformation and thus optimizes nonbonded contacts. The existence of this distinct B(I)/B(II) substate pattern also allows the formation of water-mediated contacts. Thus, we suggest the B(I) <==> B(II) substate behavior to be an important part of the indirect readout of DNA.
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Affiliation(s)
- B Wellenzohn
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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Haq I, Jenkins TC, Chowdhry BZ, Ren J, Chaires JB. Parsing free energies of drug-DNA interactions. Methods Enzymol 2001; 323:373-405. [PMID: 10944760 DOI: 10.1016/s0076-6879(00)23374-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- I Haq
- Krebs Institute for Biomolecular Sciences, Department of Chemistry, University of Sheffield, United Kingdom
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40
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Arakelyan V, Babayan Y, Potikyan G. Determination of constant rates of adsorption of ligand on DNA: analysis of correlation functions. J Biomol Struct Dyn 2000; 18:231-5. [PMID: 11089644 DOI: 10.1080/07391102.2000.10506661] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Correlation functions and spectral density of the number of molecules of ligand bound to DNA are calculated theoretically. Kinetics of rates of formation and decomposition of the complex are determined by calculating the dependence of correlation function on concentration of ligand in solution. The analysis of spectral density allows to distinguish "fast" and "slow" adsorption of ligands on macromolecule.
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Abstract
Understanding the thermodynamics of drug binding to DNA is of both practical and fundamental interest. The practical interest lies in the contribution that thermodynamics can make to the rational design process for the development of new DNA targeted drugs. Thermodynamics offer key insights into the molecular forces that drive complex formation that cannot be obtained by structural or computational studies alone. The fundamental interest in these interactions lies in what they can reveal about the general problems of parsing and predicting ligand binding free energies. For these problems, drug-DNA interactions offer several distinct advantages, among them being that the structures of many drug-DNA complexes are known at high resolution and that such structures reveal that in many cases the drug acts as a rigid body, with little conformational change upon binding. Complete thermodynamic profiles (delta G, delta H, delta S, delta Cp) for numerous drug-DNA interactions have been obtained, with the help of high-sensitivity microcalorimetry. The purpose of this article is to offer a perspective on the interpretation of these thermodynamics parameters, and in particular how they might be correlated with known structural features. Obligatory conformational changes in the DNA to accommodate intercalators and the loss of translational and rotational freedom upon complex formation both present unfavorable free energy barriers for binding. Such barriers must be overcome by favorable free energy contributions from the hydrophobic transfer of ligand from solution into the binding site, polyelectrolyte contributions from coupled ion release, and molecular interactions (hydrogen and ionic bonds, van der Waals interactions) that form within the binding site. Theoretical and semiempirical tools that allow estimates of these contributions to be made will be discussed, and their use in dissecting experimental data illustrated. This process, even at the current level of approximation, can shed considerable light on the drug-DNA binding process.
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Affiliation(s)
- J B Chaires
- Department of Biochemistry, University of Mississippi, Medical Center, Jackson 39216-4505, USA
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Wellenzohn B, Winger RH, Hallbrucker A, Mayer E, Liedl KR. Simulation of EcoRI Dodecamer Netropsin Complex Confirms Class I Complexation Mode. J Am Chem Soc 2000. [DOI: 10.1021/ja993759n] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bernd Wellenzohn
- Contribution from the Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Rudolf H. Winger
- Contribution from the Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Andreas Hallbrucker
- Contribution from the Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Erwin Mayer
- Contribution from the Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Contribution from the Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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Wan KX, Shibue T, Gross ML. Non-Covalent Complexes between DNA-Binding Drugs and Double-Stranded Oligodeoxynucleotides: A Study by ESI Ion-Trap Mass Spectrometry. J Am Chem Soc 2000. [DOI: 10.1021/ja990684e] [Citation(s) in RCA: 152] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Meresse P, Bertounesque E, Imbert T, Monneret C. Synthetic approaches to condensed aromatic analogues from etoposide. Synthesis of A-ring pyridazine picroetoposide. Tetrahedron 1999. [DOI: 10.1016/s0040-4020(99)00756-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Castelli F, De Guidi G, Giuffrida S, Miano P, Sortino S. Molecular mechanisms of photosensitization XIII: a combined differential scanning calorimetry and DNA photosensitization study in non steroidal antiinflammatory drugs-DNA interaction. Int J Pharm 1999; 184:21-33. [PMID: 10425348 DOI: 10.1016/s0378-5173(99)00094-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
A combined differential scanning calorimetry (DSC) and photosensitization study has been carried out on the interaction of several NSAID on DNA, both from calf thymus and pBR 322 plasmid. The investigated compounds were both non-steroidal anti-inflammatory drugs as well as compounds related to NSAIDs for structural similar properties, to find evidence for their ability to interact with DNA as a function of steric hindrance and polarity of the chemical structures. The considered NSAIDs were diflunisal (DFN, a salicylic derivative), naproxen (NAP), ketoprofen (KPF), suprofen (SPF) and tiaprofenic acid (TIA, arylpropionic acids). The structural criterion used was related to three different aromatic groups, biphenyl, naphthalene and benzophenone (BZP). In fact drug-DNA interaction can be revealed by variations of the enthalpies and temperatures of unfolding of DNA obtained by comparison of calorimetric peaks, where a decrease of the enthalpy is associated with the drug-DNA interaction, by engaging electrostatic bonds. Testing their ability in inducing DNA cleavage when UVA irradiated can evidence the photosensitizing properties of the drug. A good correlation was found between calorimetric and photosensitization studies. From the results obtained it can be reasonably supposed that the photocleavage depends only on the drug molecules bound to DNA.
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Affiliation(s)
- F Castelli
- Dipartimento di Scienze Chimiche, Università di Catania, Viale A. Doria 8, 95125, Catania, Italy.
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Molina A, Vaquero JJ, Garcia-Navio JL, Alvarez-Builla J, de Pascual-Teresa B, Gago F, Rodrigo MM. Novel DNA Intercalators Based on the Pyridazino[1‘,6‘:1,2]pyrido[4,3-b]indol-5-inium System. J Org Chem 1999. [DOI: 10.1021/jo982216d] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Andrés Molina
- Departamento de Química Orgánica, Departamento de Farmacología, and Departamento de Química-Física, Universidad de Alcalá, 28871-Alcalá de Henares, Madrid, Spain
| | - Juan J. Vaquero
- Departamento de Química Orgánica, Departamento de Farmacología, and Departamento de Química-Física, Universidad de Alcalá, 28871-Alcalá de Henares, Madrid, Spain
| | - José L. Garcia-Navio
- Departamento de Química Orgánica, Departamento de Farmacología, and Departamento de Química-Física, Universidad de Alcalá, 28871-Alcalá de Henares, Madrid, Spain
| | - Julio Alvarez-Builla
- Departamento de Química Orgánica, Departamento de Farmacología, and Departamento de Química-Física, Universidad de Alcalá, 28871-Alcalá de Henares, Madrid, Spain
| | - Beatriz de Pascual-Teresa
- Departamento de Química Orgánica, Departamento de Farmacología, and Departamento de Química-Física, Universidad de Alcalá, 28871-Alcalá de Henares, Madrid, Spain
| | - Federico Gago
- Departamento de Química Orgánica, Departamento de Farmacología, and Departamento de Química-Física, Universidad de Alcalá, 28871-Alcalá de Henares, Madrid, Spain
| | - María M. Rodrigo
- Departamento de Química Orgánica, Departamento de Farmacología, and Departamento de Química-Física, Universidad de Alcalá, 28871-Alcalá de Henares, Madrid, Spain
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Marzilli LA, Wang D, Kobertz WR, Essigmann JM, Vouros P. Mass spectral identification and positional mapping of aflatoxin B1-guanine adducts in oligonucleotides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 1998; 9:676-682. [PMID: 9879377 DOI: 10.1016/s1044-0305(98)00039-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The biological consequences of a carcinogen-DNA adduct are defined by the structure of the lesion and its position within the genome. Electrospray ionization ion trap mass spectrometry (ESI-ITMS) is shown here to be a sensitive and rapid approach capable of defining both of these parameters. Three isomeric oligonucleotides of the sequence 5'-CCGGAGGCC modified by the potent human carcinogen aflatoxin B1 (AFB1) at different guanines were analyzed by ESI-ITMS. All three samples possessed the same molecular ion confirming the presence of an intact aflatoxin moiety in each oligonucleotide. In addition, each sample displayed a characteristic fragmentation pattern that permitted unambiguous identification of the site of modification within the sequence. Furthermore, an AFB1-modified oligonucleotide was converted under alkaline conditions to its more stable formamidopyrimidine (FAPY) derivative. Analysis of this sample revealed the presence of a molecular ion corresponding to the presence of the FAPY adduct and a distinctive fragmentation pattern that paralleled the known chemical stability of the FAPY metabolite. This approach should be of general use in the determination of not only the nature and site of covalent modifications, but also the chemical stability of DNA adducts.
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Affiliation(s)
- L A Marzilli
- Department of Chemistry, Northeastern University, Boston, Massachusetts 02115, USA
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Abstract
Significant progress has been made over the past few years in studies of drug-DNA interactions. Structure-based design strategies have yielded new DNA-binding agents with clinical promise. The hairpin polyamides represent the result of a design strategy with outstanding potential. One specific molecule of this class has now been proven to inhibit the expression of a specific gene in vivo. A new bisintercalating anthracycline antibiotic binds with high affinity to DNA, and appears to overcome a specific form of multidrug resistance. Progress in fundamental studies of drug binding to DNA continues, with detailed thermodynamic studies providing new insights into the forces that drive complex formation. New tools have been developed in order to characterize both the binding mode and the sequence specificity of drug binding to DNA, tools that will enable the fundamental aspects of these biologically important reactions to be understood in more detail.
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Affiliation(s)
- J B Chaires
- Department of Biochemistry, University of Mississippi Medical Center, Jackson 39216-4505, USA.
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Bell A, Kittler L, Löber G, Zimmer C. DNA binding properties of minor groove binders and their influence on the topoisomerase II cleavage reaction. J Mol Recognit 1997; 10:245-55. [PMID: 9770648 DOI: 10.1002/(sici)1099-1352(199711/12)10:6<245::aid-jmr367>3.0.co;2-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We present titrations of the human delta beta-globin gene region with DNA minor groove binders netropsin, bisnetropsin, distamycin, chromomycin and four bis-quaternary ammonium compounds in the presence of calf thymus topoisomerase II and DNase I. With increasing ligand concentration, stimulation and inhibition of enzyme activity were detected and quantitatively evaluated. Additionally we show a second type of stimulation, the appearance of strong new topoisomerase II cleavage sites at high ligand concentrations. The specific binding sites of the minor groove binders of the DNA sequence and their microscopic binding constants were determined from DNase I footprints. A binding mechanism for minor groove binders is proposed in order to explain these results especially when ligand concentration is increased.
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Affiliation(s)
- A Bell
- Institut für Molekulare Biotechnologie e. V., Jena, Germany
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Pastor J, Siro JG, García-Navío JL, Vaquero JJ, Alvarez-Builla J, Gago F, de Pascual-Teresa B, Pastor M, Rodrigo MM. Azino-Fused Benzimidazolium Salts as DNA Intercalating Agents. 2. J Org Chem 1997. [DOI: 10.1021/jo962055i] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joaquín Pastor
- Departamento de Química Orgánica, Departamento de Química-Física, and Departamento de Farmacología, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
| | - Jorge G. Siro
- Departamento de Química Orgánica, Departamento de Química-Física, and Departamento de Farmacología, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
| | - José L. García-Navío
- Departamento de Química Orgánica, Departamento de Química-Física, and Departamento de Farmacología, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
| | - Juan J. Vaquero
- Departamento de Química Orgánica, Departamento de Química-Física, and Departamento de Farmacología, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
| | - Julio Alvarez-Builla
- Departamento de Química Orgánica, Departamento de Química-Física, and Departamento de Farmacología, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
| | - Federico Gago
- Departamento de Química Orgánica, Departamento de Química-Física, and Departamento de Farmacología, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
| | - Beatriz de Pascual-Teresa
- Departamento de Química Orgánica, Departamento de Química-Física, and Departamento de Farmacología, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
| | - Manuel Pastor
- Departamento de Química Orgánica, Departamento de Química-Física, and Departamento de Farmacología, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
| | - M. Melia Rodrigo
- Departamento de Química Orgánica, Departamento de Química-Física, and Departamento de Farmacología, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
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