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Alniss HY, Al-Jubeh HM, Msallam YA, Siddiqui R, Makhlouf Z, Ravi A, Hamdy R, Soliman SSM, Khan NA. Structure-based drug design of DNA minor groove binders and evaluation of their antibacterial and anticancer properties. Eur J Med Chem 2024; 271:116440. [PMID: 38678825 DOI: 10.1016/j.ejmech.2024.116440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/09/2024] [Accepted: 04/18/2024] [Indexed: 05/01/2024]
Abstract
Antimicrobial and chemotherapy resistance are escalating medical problem of paramount importance. Yet, research for novel antimicrobial and anticancer agents remains lagging behind. With their reported medical applications, DNA minor groove binders (MGBs) are worthy of exploration. In this study, the approach of structure-based drug design was implemented to generate 11 MGB compounds including a novel class of bioactive alkyne-linked MGBs. The NCI screening protocol was utilized to evaluate the antitumor activity of the target MGBs. Furthermore, a variety of bactericidal, cytopathogenicity, MIC90, and cytotoxicity assays were carried out using these MGBs against 6 medically relevant bacteria: Salmonella enterica, Escherichia coli, Serratia marcescens, Bacillus cereus, Streptococcus pneumoniae and Streptococcus pyogenes. Moreover, molecular docking, molecular dynamic simulations, DNA melting, and isothermal titration calorimetry (ITC) analyses were utilized to explore the binding mode and interactions between the most potent MGBs and the DNA duplex d(CGACTAGTCG)2. NCI results showed that alkyne-linked MGBs (26 & 28) displayed the most significant growth inhibition among the NCI-60 panel. In addition, compounds MGB3, MGB4, MGB28, and MGB32 showed significant bactericidal effects, inhibited B. cereus and S. enterica-mediated cytopathogenicity, and exhibited low cytotoxicity. MGB28 and MGB32 demonstrated significant inhibition of S. pyogenes, whereas MGB28 notably inhibited S. marcescens and all four minor groove binders significantly inhibited B. cereus. The ability of these compounds to bind with DNA and distort its groove dimensions provides the molecular basis for the allosteric perturbation of proteins-DNA interactions by MGBs. This study shed light on the mechanism of action of MGBs and revealed the important structural features for their antitumor and antibacterial activities, which are important to guide future development of MGB derivatives as novel antibacterial and anticancer agents.
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Affiliation(s)
- Hasan Y Alniss
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, 27272, Sharjah, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates.
| | - Hadeel M Al-Jubeh
- Research Institute for Medical and Health Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Yousef A Msallam
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, 27272, Sharjah, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Ruqaiyyah Siddiqui
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University Edinburgh, EH14 4AS, United Kingdom; Department of Medical Biology, Faculty of Medicine, Istinye University, Istanbul, 34010, Turkey
| | - Zinb Makhlouf
- College of Medicine, Department of Clinical Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Anil Ravi
- Research Institute for Medical and Health Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Rania Hamdy
- Research Institute for Medical and Health Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Sameh S M Soliman
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, 27272, Sharjah, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Naveed A Khan
- Department of Medical Biology, Faculty of Medicine, Istinye University, Istanbul, 34010, Turkey.
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Alniss HY, Chu C, Ramadan WS, Msallam YA, Srinivasulu V, El-Awady R, Macgregor RB, Al-Tel TH. Interaction of an anticancer benzopyrane derivative with DNA: Biophysical, biochemical, and molecular modeling studies. Biochim Biophys Acta Gen Subj 2023; 1867:130347. [PMID: 36958685 DOI: 10.1016/j.bbagen.2023.130347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/09/2023] [Accepted: 03/20/2023] [Indexed: 03/25/2023]
Abstract
BACKGROUND SIMR1281 is a potent anticancer lead candidate with multi- target activity against several proteins; however, its mechanism of action at the molecular level is not fully understood. Revealing the mechanism and the origin of multitarget activity is important for the rational identification and optimization of multitarget drugs. METHODS We have used a variety of biophysical (circular dichroism, isothermal titration calorimetry, viscosity, and UV DNA melting), biochemical (topoisomerase I & II assays) and computational (molecular docking and MD simulations) methods to study the interaction of SIMR1281 with duplex DNA structures. RESULTS The biophysical results revealed that SIMR1281 binds to dsDNA via an intercalation-binding mode with an average binding constant of 3.1 × 106 M-1. This binding mode was confirmed by the topoisomerases' inhibition assays and molecular modeling simulations, which showed the intercalation of the benzopyrane moiety between DNA base pairs, while the remaining moieties (thiazole and phenyl rings) sit in the minor groove and interact with the flanking base pairs adjacent to the intercalation site. CONCLUSIONS The DNA binding characteristics of SIMR1281, which can disrupt/inhibit DNA function as confirmed by the topoisomerases' inhibition assays, indicate that the observed multi-target activity might originate from ligand intervention at nucleic acids level rather than due to direct interactions with multiple biological targets at the protein level. GENERAL SIGNIFICANCE The findings of this study could be helpful to guide future optimization of benzopyrane-based ligands for therapeutic purposes.
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Affiliation(s)
- Hasan Y Alniss
- College of Pharmacy, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
| | - Chen Chu
- Graduate Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Wafaa S Ramadan
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
| | - Yousef A Msallam
- College of Pharmacy, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
| | - Vunnam Srinivasulu
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
| | - Raafat El-Awady
- College of Pharmacy, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
| | - Robert B Macgregor
- Graduate Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Taleb H Al-Tel
- College of Pharmacy, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
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Kiruba Nesamalar E, SatheeshKumar J, Amudha T. Efficient DNA-ligand interaction framework using fuzzy C-means clustering based glowworm swarm optimization (FCMGSO) method. J Biomol Struct Dyn 2022:1-13. [PMID: 35930294 DOI: 10.1080/07391102.2022.2105958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Assessment of DNA and ligand interaction is a great challenge to the medical researchers and drug industries since the accurate mapping of DNA and ligand plays an important role in associating drugs for suitable diseases. The primary objective of this research work is to develop an efficient model for predicting the best DNA and Ligand mapping. In this research work, 500 instances of DNA and drugs used for cancer and non-cancer diseases from the National Centre for Biotechnology Information (NCBI) were considered for analysis. Binding energy is one of the important measures to predict and finalize the best DNA and ligand interaction. Existing methods used for the docking process such as Simulated Annealing (SA), Lamarckian Genetic Algorithm (LGA), Genetic Clustering (GC), Fuzzy C-means clustering (FCM), and Genetic Clustering with Multi swarm Optimization (GCMSO) were applied for all 500 instances. These algorithms failed to produce better binding energy due to a lack of optimization in the existing approaches. Optimization methods play a major role in predicting accurate DNA ligand docking. Hence, this research proposes an efficient architecture using Fuzzy C-Means Clustering with Glowworm Swarm (FCMGSO) optimization method for accurate analysis of the DNA-ligand docking process. Results are proving that the proposed FCMGSO algorithm shows less binding energy than other existing methods in all instances of samples considered from the NCBI dataset.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - J SatheeshKumar
- Department of Computer Applications, Bharathiar University, Coimbatore, India
| | - T Amudha
- Department of Computer Applications, Bharathiar University, Coimbatore, India
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Multitargeted anti-infective drugs: resilience to resistance in the antimicrobial resistance era. FUTURE DRUG DISCOVERY 2022; 4:FDD73. [PMID: 35600289 PMCID: PMC9112235 DOI: 10.4155/fdd-2022-0001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 04/08/2022] [Indexed: 12/23/2022] Open
Abstract
The standard drug discovery paradigm of single molecule – single biological target – single biological effect is perhaps particularly unsuitable for anti-infective drug discovery. This is due to the rapid evolution of resistance likely to be observed with single target drugs. Multitargeted anti-infective drugs are likely to be superior due to their lower susceptibility to target-related resistance mechanisms. Strathclyde minor groove binders are a class of compounds which have been developed by adopting the multitargeted anti-infective drugs paradigm, and their effectiveness against a wide range of pathogenic organisms is discussed. The renaming of this class to Strathclyde nucleic acid binders is also presented due to their likely targets including both DNA and RNA.
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Jiang Y, Chen SJ. RLDOCK method for predicting RNA-small molecule binding modes. Methods 2022; 197:97-105. [PMID: 33549725 PMCID: PMC8333169 DOI: 10.1016/j.ymeth.2021.01.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/24/2021] [Accepted: 01/27/2021] [Indexed: 01/03/2023] Open
Abstract
RNA molecules play critical roles in cellular functions at the level of gene expression and regulation. The intricate 3D structures and the functional roles of RNAs make RNA molecules ideal targets for therapeutic drugs. The rational design of RNA-targeted drug requires accurate modeling of RNA-ligand interactions. Recently a new computational tool, RLDOCK, was developed to predict ligand binding sites and binding poses. Using an iterative multiscale sampling and search algorithm and a energy-based evaluation of ligand poses, the method enables efficient and accurate predictions for RNA-ligand interactions. Here we present a detailed illustration of the computational procedure for the practical implementation of the RLDOCK method. Using Flavin mononucleotide (FMN) docking to F. nucleatum FMN riboswitch as an example, we illustrate the computational protocol for RLDOCK-based prediction of RNA- ligand interactions. The RLDOCK software is freely accessible at http://https://github.com/Vfold-RNA/RLDOCK.
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Affiliation(s)
- Yangwei Jiang
- Department of Physics, MU Institute for Data Science and Informatics, Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Shi-Jie Chen
- Department of Physics, MU Institute for Data Science and Informatics, Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
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Sun LZ, Jiang Y, Zhou Y, Chen SJ. RLDOCK: A New Method for Predicting RNA-Ligand Interactions. J Chem Theory Comput 2020; 16:7173-7183. [PMID: 33095555 DOI: 10.1021/acs.jctc.0c00798] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The ability to accurately predict the binding site, binding pose, and binding affinity for ligand-RNA binding is important for RNA-targeted drug design. Here, we describe a new computational method, RLDOCK, for predicting the binding site and binding pose for ligand-RNA binding. By developing an energy-based scoring function, we sample exhaustively all of the possible binding sites with flexible ligand conformations for a ligand-RNA pair based on the geometric and energetic scores. The model distinguishes from other approaches in three notable features. First, the model enables exhaustive scanning of all of the possible binding sites, including multiple alternative or coexisting binding sites, for a given ligand-RNA pair. Second, the model is based on a new energy-based scoring function developed here. Third, the model employs a novel multistep screening algorithm to improve computational efficiency. Specifically, first, for each binding site, we use a gird-based energy map to rank the binding sites according to the minimum Lennard-Jones potential energy for the different ligand poses. Second, for a given selected binding site, we predict the ligand pose using a two-step algorithm. In the first step, we quickly identify the probable ligand poses using a coarse-grained simplified energy function. In the second step, for each of the probable ligand poses, we predict the ligand poses using a refined energy function. Tests of the RLDOCK for a set of 230 RNA-ligand-bound structures indicate that RLDOCK can successfully predict ligand poses for 27.8, 58.3, and 69.6% of all of the test cases with the root-mean-square deviation within 1.0, 2.0, and 3.0 Å, respectively, for the top three predicted docking poses. The computational method presented here may enable the development of a new, more comprehensive framework for the prediction of ligand-RNA binding with an ensemble of RNA conformations and the metal-ion effects.
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Affiliation(s)
- Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.,Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, United States
| | - Yangwei Jiang
- Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, United States
| | - Yuanzhe Zhou
- Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, United States
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, United States
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González-Mundo I, Pérez-Vielma NM, Gómez-López M, Fleury A, Correa-Basurto J, Rosales-Hernández MC, Sixto-López Y, Martínez-Godinez MDLÁ, Domínguez-López A, Miliar-García A. DNA methylation of the RE-1 silencing transcription factor in peripheral blood mononuclear cells and gene expression of antioxidant enzyme in patients with late-onset Alzheimer disease. Exp Gerontol 2020; 136:110951. [DOI: 10.1016/j.exger.2020.110951] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 04/03/2020] [Accepted: 04/08/2020] [Indexed: 12/13/2022]
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8
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Yang B, Qin C, Hu X, Xia K, Lu C, Gudda FO, Ma Z, Gao Y. Enzymatic degradation of extracellular DNA exposed to chlorpyrifos and chlorpyrifos-methyl in an aqueous system. ENVIRONMENT INTERNATIONAL 2019; 132:105087. [PMID: 31430607 DOI: 10.1016/j.envint.2019.105087] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/30/2019] [Accepted: 08/07/2019] [Indexed: 05/25/2023]
Abstract
The persistence of extracellular DNA (eDNA) is crucial for ensuring species diversity and ecological function in aquatic systems. However, scarce information exists about the impact of pesticides on eDNA, although they often co-exist in the aquatic environment. Using a variety of spectroscopic analyses, eDNA degradation and the associated alterations in DNA secondary structure was investigated by exposing DNase I to tested DNA in the presence of chlorpyrifos, a commonly used organophosphate pesticide. Molecular dynamics simulation was used to explore the weak interactions between the tested DNA and chlorpyrifos. The results indicated that chlorpyrifos significantly enhanced DNA degradation without affecting the enzyme activity of DNase I in an aqueous system. Spectroscopic experiments confirmed that chlorpyrifos and the analog chlorpyrifos-methyl could bind with DNA to cause the bases noncovalent stacking interaction. Molecular simulations further demonstrated that pesticide binding with DNA molecules caused widening of the DNA grooves and destruction of the hydrated layer, which enhanced DNA degradation. The findings presented herein provide novel insight into the genotoxicity and ecotoxicity of chlorpyrifos and chlorpyrifos-methyl, as well as their impacts on DNA persistence in aquatic environments.
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Affiliation(s)
- Bing Yang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Chao Qin
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Xiaojie Hu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Kang Xia
- School of Plant and Soil Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States
| | - Chao Lu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Fredrick Owino Gudda
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Zhao Ma
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P.R. China.
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Alniss HY, Witzel II, Semreen MH, Panda PK, Mishra YK, Ahuja R, Parkinson JA. Investigation of the Factors That Dictate the Preferred Orientation of Lexitropsins in the Minor Groove of DNA. J Med Chem 2019; 62:10423-10440. [DOI: 10.1021/acs.jmedchem.9b01534] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Hasan Y. Alniss
- College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
- Sharjah Institute for Medical Research, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Ini-Isabée Witzel
- Core Technology Platform, New York University of Abu Dhabi, P.O. Box 129188, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Mohammad H. Semreen
- College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
- Sharjah Institute for Medical Research, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Pritam Kumar Panda
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-75120, Uppsala Sweden
| | - Yogendra Kumar Mishra
- Functional Nanomaterials, Institute for Materials Science, Kiel University, Kaiserstraße 2, D-24143 Kiel, Germany
| | - Rajeev Ahuja
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-75120, Uppsala Sweden
- Department of Materials and Engineering, Royal Institute of Technology (KTH), SE-10044 Stockholm Sweden
| | - John A. Parkinson
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
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Affiliation(s)
- Hasan Y. Alniss
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
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11
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Zhang H, Gattuso H, Dumont E, Cai W, Monari A, Chipot C, Dehez F. Accurate Estimation of the Standard Binding Free Energy of Netropsin with DNA. Molecules 2018; 23:molecules23020228. [PMID: 29370096 PMCID: PMC6017086 DOI: 10.3390/molecules23020228] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 01/14/2018] [Accepted: 01/19/2018] [Indexed: 12/12/2022] Open
Abstract
DNA is the target of chemical compounds (drugs, pollutants, photosensitizers, etc.), which bind through non-covalent interactions. Depending on their structure and their chemical properties, DNA binders can associate to the minor or to the major groove of double-stranded DNA. They can also intercalate between two adjacent base pairs, or even replace one or two base pairs within the DNA double helix. The subsequent biological effects are strongly dependent on the architecture of the binding motif. Discriminating between the different binding patterns is of paramount importance to predict and rationalize the effect of a given compound on DNA. The structural characterization of DNA complexes remains, however, cumbersome at the experimental level. In this contribution, we employed all-atom molecular dynamics simulations to determine the standard binding free energy of DNA with netropsin, a well-characterized antiviral and antimicrobial drug, which associates to the minor groove of double-stranded DNA. To overcome the sampling limitations of classical molecular dynamics simulations, which cannot capture the large change in configurational entropy that accompanies binding, we resort to a series of potentials of mean force calculations involving a set of geometrical restraints acting on collective variables.
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Affiliation(s)
- Hong Zhang
- Research Center for Analytical Sciences, College of Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin 300071, China.
| | - Hugo Gattuso
- UMR 7019, Theoretical Physics and Chemistry Department (LPCT), Université de Lorraine-Nancy, 54506 Vandoeuvre-lès-Nancy, France.
- UMR 7019, Theoretical Physics and Chemistry Department (LPCT), CNRS, 54506 Vandeouvre-lès-Nancy, France.
| | - Elise Dumont
- Univ Lyon, Ens de Lyon, CNRS UMR 5182, Laboratoire de Chimie, Université Claude Bernard Lyon 1, F-69342 Lyon, France.
| | - Wensheng Cai
- Research Center for Analytical Sciences, College of Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin 300071, China.
- Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China.
| | - Antonio Monari
- UMR 7019, Theoretical Physics and Chemistry Department (LPCT), Université de Lorraine-Nancy, 54506 Vandoeuvre-lès-Nancy, France.
- UMR 7019, Theoretical Physics and Chemistry Department (LPCT), CNRS, 54506 Vandeouvre-lès-Nancy, France.
| | - Christophe Chipot
- UMR 7019, Theoretical Physics and Chemistry Department (LPCT), Université de Lorraine-Nancy, 54506 Vandoeuvre-lès-Nancy, France.
- UMR 7019, Theoretical Physics and Chemistry Department (LPCT), CNRS, 54506 Vandeouvre-lès-Nancy, France.
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Champaign, Illinois, 54506 Vandeouvre-lès-Nancy, France.
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA.
| | - François Dehez
- UMR 7019, Theoretical Physics and Chemistry Department (LPCT), Université de Lorraine-Nancy, 54506 Vandoeuvre-lès-Nancy, France.
- UMR 7019, Theoretical Physics and Chemistry Department (LPCT), CNRS, 54506 Vandeouvre-lès-Nancy, France.
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Champaign, Illinois, 54506 Vandeouvre-lès-Nancy, France.
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Deng N, Wickstrom L, Cieplak P, Lin C, Yang D. Resolving the Ligand-Binding Specificity in c-MYC G-Quadruplex DNA: Absolute Binding Free Energy Calculations and SPR Experiment. J Phys Chem B 2017; 121:10484-10497. [PMID: 29086571 DOI: 10.1021/acs.jpcb.7b09406] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We report the absolute binding free energy calculation and surface plasmon resonance (SPR) experiment for ligand binding with the c-MYC G-quadruplex DNA. The unimolecular parallel DNA G-quadruplex formed in nuclease hypersensitivity element III1 of the c-MYC gene promoter regulates the c-MYC transcription and is recognized as an emerging drug target for cancer therapy. Quindoline derivatives have been shown to stabilize the G-quadruplex and inhibit the c-MYC expression in cancer cells. NMR revealed two binding sites located at the 5' and 3' termini of the G-quadruplex. Questions about which site is more favored and the basis for the ligand-induced binding site formation remain unresolved. Here, we employ two absolute binding free energy methods, the double decoupling and the potential of mean force methods, to dissect the ligand-binding specificity in the c-MYC G-quadruplex. The calculated absolute binding free energies are in general agreement with the SPR result and suggest that quindoline has a slight preference for the 5' site. The flanking residues around the two sites undergo significant reorganization as the ligand unbinds, which provides evidence for ligand-induced binding pocket formation. The results help interpret experimental data and inform rational design of small molecules targeting the c-MYC G-quadruplex.
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Affiliation(s)
- Nanjie Deng
- Department of Chemistry and Physical Sciences, Pace University , 1 Pace Plaza, New York, New York 10038, United States
| | - Lauren Wickstrom
- Department of Science, Borough of Manhattan Community College, the City University of New York , New York, New York 10007, United States
| | - Piotr Cieplak
- Sanford Burnham Prebys Medical Discovery Institute , La Jolla, San Diego, California 92037, United States
| | - Clement Lin
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University , West Lafayette, Indiana 47907, United States
| | - Danzhou Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University , West Lafayette, Indiana 47907, United States
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Kostjukov VV, Starodub MA, Evstigneev MP. Molecular Modeling-Based Energy Analysis of Dimeric Binding of Ligands to the Minor DNA Groove. Biophysics (Nagoya-shi) 2017. [DOI: 10.1134/s0006350917060100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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14
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Mary V, Haris P, Varghese MK, Aparna P, Sudarsanakumar C. Experimental Probing and Molecular Dynamics Simulation of the Molecular Recognition of DNA Duplexes by the Flavonoid Luteolin. J Chem Inf Model 2017; 57:2237-2249. [PMID: 28825481 DOI: 10.1021/acs.jcim.6b00747] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Luteolin (C15H10O6) is an important flavonoid found in many fruits, plants, medicinal herbs, and vegetables exhibiting many pharmacological properties. The anticancer, antitumor, antioxidant, and anti-inflammatory activities of luteolin have been reported. The pharmacological action of small molecules is dependent upon its interaction with biomacromolecules. The interactions of small molecules with DNA play a major role in the transcription and translation process. In this work, we explored the energetic profile of DNA-luteolin interaction by isothermal titration calorimetry (ITC). The effect of temperature and salt concentration on DNA binding was examined by UV-Vis method. The mode of interaction was further probed by UV melting temperature analysis and differential scanning calorimetry. An atomic level insight on the recognition of luteolin with DNA was achieved by employing molecular dynamics (MD) simulation on luteolin in complex with AT- and GC-rich DNA sequences. AMBER force field proves to be appropriate in providing an understanding on the binding mode and specificity of luteolin with duplex DNA. MD results suggest a minor groove binding of luteolin with DNA and the binding free energy obtained is in agreement with the experimental results.
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Affiliation(s)
- Varughese Mary
- School of Pure and Applied Physics, Mahatma Gandhi University , Kottayam, Kerala 686560, India
| | - P Haris
- School of Pure and Applied Physics, Mahatma Gandhi University , Kottayam, Kerala 686560, India
| | - Mathew K Varghese
- School of Pure and Applied Physics, Mahatma Gandhi University , Kottayam, Kerala 686560, India.,Department of Physics, Pavanatma College , Murickassery, Kerala 685604, India
| | - P Aparna
- School of Pure and Applied Physics, Mahatma Gandhi University , Kottayam, Kerala 686560, India
| | - C Sudarsanakumar
- School of Pure and Applied Physics, Mahatma Gandhi University , Kottayam, Kerala 686560, India.,Center for High Performance Computing, Mahatma Gandhi University , Kottayam, Kerala 686560, India
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15
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Yu T, Zhu Y, He Z, Chen SJ. Predicting Molecular Crowding Effects in Ion-RNA Interactions. J Phys Chem B 2016; 120:8837-44. [PMID: 27490487 DOI: 10.1021/acs.jpcb.6b05625] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We develop a new statistical mechanical model to predict the molecular crowding effects in ion-RNA interactions. By considering discrete distributions of the crowders, the model can treat the main crowder-induced effects, such as the competition with ions for RNA binding, changes of electrostatic interaction due to crowder-induced changes in the dielectric environment, and changes in the nonpolar hydration state of the crowder-RNA system. To enhance the computational efficiency, we sample the crowder distribution using a hybrid approach: For crowders in the close vicinity of RNA surface, we sample their discrete distributions; for crowders in the bulk solvent away from the RNA surface, we use a continuous mean-field distribution for the crowders. Moreover, using the tightly bound ion (TBI) model, we account for ion fluctuation and correlation effects in the calculation for ion-RNA interactions. Applications of the model to a variety of simple RNA structures such as RNA helices show a crowder-induced increase in free energy and decrease in ion binding. Such crowding effects tend to contribute to the destabilization of RNA structure. Further analysis indicates that these effects are associated with the crowder-ion competition in RNA binding and the effective decrease in the dielectric constant. This simple ion effect model may serve as a useful framework for modeling more realistic crowders with larger, more complex RNA structures.
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Affiliation(s)
- Tao Yu
- Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri , Columbia, Missouri 65211, United States.,Department of Physics, Jianghan University , Wuhan, Hubei 430056, China
| | - Yuhong Zhu
- Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri , Columbia, Missouri 65211, United States.,Department of Physics, Hangzhou Normal University , Hangzhou, Zhejiang 310036, China
| | - Zhaojian He
- Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri , Columbia, Missouri 65211, United States
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri , Columbia, Missouri 65211, United States
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16
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Scott FJ, Puig-Sellart M, Khalaf AI, Henderson CJ, Westrop G, Watson DG, Carter K, Grant MH, Suckling CJ. An evaluation of Minor Groove Binders as anti-lung cancer therapeutics. Bioorg Med Chem Lett 2016; 26:3478-86. [DOI: 10.1016/j.bmcl.2016.06.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 06/14/2016] [Accepted: 06/15/2016] [Indexed: 11/30/2022]
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17
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Gattuso H, Dumont E, Chipot C, Monari A, Dehez F. Thermodynamics of DNA: sensitizer recognition. Characterizing binding motifs with all-atom simulations. Phys Chem Chem Phys 2016; 18:33180-33186. [DOI: 10.1039/c6cp06078a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We report the investigation of the thermochemical properties of benzophenone interacting with B-DNA studied by all-atom molecular dynamic simulations.
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Affiliation(s)
- Hugo Gattuso
- Université de Lorraine – Nancy
- Theory-Modeling-Simulation
- UMR 7565
- Structure et Réactivité des Systémes Moléculaires Complexes (SRSMC)
- Vandoeuvre-les-Nancy
| | - Elise Dumont
- Laboratoire de Chimie
- UMR 5182
- Ecole Normale Supérieure de Lyon
- Lyon
- France
| | - Christophe Chipot
- Université de Lorraine – Nancy
- Theory-Modeling-Simulation
- UMR 7565
- Structure et Réactivité des Systémes Moléculaires Complexes (SRSMC)
- Vandoeuvre-les-Nancy
| | - Antonio Monari
- Université de Lorraine – Nancy
- Theory-Modeling-Simulation
- UMR 7565
- Structure et Réactivité des Systémes Moléculaires Complexes (SRSMC)
- Vandoeuvre-les-Nancy
| | - François Dehez
- Université de Lorraine – Nancy
- Theory-Modeling-Simulation
- UMR 7565
- Structure et Réactivité des Systémes Moléculaires Complexes (SRSMC)
- Vandoeuvre-les-Nancy
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18
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Lomzov AA, Vorobjev YN, Pyshnyi DV. Evaluation of the Gibbs Free Energy Changes and Melting Temperatures of DNA/DNA Duplexes Using Hybridization Enthalpy Calculated by Molecular Dynamics Simulation. J Phys Chem B 2015; 119:15221-34. [PMID: 26569147 DOI: 10.1021/acs.jpcb.5b09645] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A molecular dynamics simulation approach was applied for the prediction of the thermal stability of oligonucleotide duplexes. It was shown that the enthalpy of the DNA/DNA complex formation could be calculated using this approach. We have studied the influence of various simulation parameters on the secondary structure and the hybridization enthalpy value of Dickerson-Drew dodecamer. The optimal simulation parameters for the most reliable prediction of the enthalpy values were determined. The thermodynamic parameters (enthalpy and entropy changes) of a duplex formation were obtained experimentally for 305 oligonucleotides of various lengths and GC-content. The resulting database was studied with molecular dynamics (MD) simulation using the optimized simulation parameters. Gibbs free energy changes and the melting temperatures were evaluated using the experimental correlation between enthalpy and entropy changes of the duplex formation and the enthalpy values calculated by the MD simulation. The average errors in the predictions of enthalpy, the Gibbs free energy change, and the melting temperature of oligonucleotide complexes were 11%, 10%, and 4.4 °C, respectively. We have shown that the molecular dynamics simulation gives a possibility to calculate the thermal stability of native DNA/DNA complexes a priori with an unexpectedly high accuracy.
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Affiliation(s)
- Alexander A Lomzov
- Institute of Chemical Biology and Fundamental Medicine , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Yury N Vorobjev
- Institute of Chemical Biology and Fundamental Medicine , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
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19
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Haris P, Mary V, Haridas M, Sudarsanakumar C. Energetics, Thermodynamics, and Molecular Recognition of Piperine with DNA. J Chem Inf Model 2015; 55:2644-56. [DOI: 10.1021/acs.jcim.5b00514] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
| | | | - M. Haridas
- Inter
University Centre for Bioscience, Kannur University, Thalassery
Campus, Palayad, Kerala 670661, India
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20
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Probing the relationship between anti-Pneumocystis carinii activity and DNA binding of bisamidines by molecular dynamics simulations. Molecules 2015; 20:5942-64. [PMID: 25854757 PMCID: PMC6272165 DOI: 10.3390/molecules20045942] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 03/26/2015] [Accepted: 03/30/2015] [Indexed: 11/17/2022] Open
Abstract
The anti-Pneumocystis carinii activity of 13 synthetic pentamidine analogs was analyzed. The experimental differences in melting points of DNA dodecamer 5'-(CGCGAATTCGCG)2-3' complexes (ΔTm), and in the biological activity measured using ATP bioluminescence assay (IC50) together with the theoretical free energy of DNA-ligand binding estimated by the proposed computational protocol, showed that the experimental activity of the tested pentamidines appeared to be due to the binding to the DNA minor groove with extended AT sequences. The effect of heteroatoms in the aliphatic linker, and the sulfonamide or methoxy substituents on the compound inducing changes in the interactions with the DNA minor groove was examined and was correlated with biological activity. In computational analysis, the explicit solvent approximation with the discrete water molecules was taken into account, and the role of water molecules in the DNA-ligand complexes was defined.
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21
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Kachhap S, Singh B. Role of DNA conformation & energetic insights in Msx-1-DNA recognition as revealed by molecular dynamics studies on specific and nonspecific complexes. J Biomol Struct Dyn 2015; 33:2069-82. [PMID: 25484111 DOI: 10.1080/07391102.2014.995709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
In most of homeodomain-DNA complexes, glutamine or lysine is present at 50th position and interacts with 5th and 6th nucleotide of core recognition region. Molecular dynamics simulations of Msx-1-DNA complex (Q50-TG) and its variant complexes, that is specific (Q50K-CC), nonspecific (Q50-CC) having mutation in DNA and (Q50K-TG) in protein, have been carried out. Analysis of protein-DNA interactions and structure of DNA in specific and nonspecific complexes show that amino acid residues use sequence-dependent shape of DNA to interact. The binding free energies of all four complexes were analysed to define role of amino acid residue at 50th position in terms of binding strength considering the variation in DNA on stability of protein-DNA complexes. The order of stability of protein-DNA complexes shows that specific complexes are more stable than nonspecific ones. Decomposition analysis shows that N-terminal amino acid residues have been found to contribute maximally in binding free energy of protein-DNA complexes. Among specific protein-DNA complexes, K50 contributes more as compared to Q50 towards binding free energy in respective complexes. The sequence dependence of local conformation of DNA enables Q50/Q50K to make hydrogen bond with nucleotide(s) of DNA. The changes in amino acid sequence of protein are accommodated and stabilized around TAAT core region of DNA having variation in nucleotides.
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Affiliation(s)
- Sangita Kachhap
- a Bioinformatics Centre , CSIR-Institute of Microbial Technology , Sector 39A, Chandigarh , India
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22
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Stolić I, Čipčić Paljetak H, Perić M, Matijašić M, Stepanić V, Verbanac D, Bajić M. Synthesis and structure–activity relationship of amidine derivatives of 3,4-ethylenedioxythiophene as novel antibacterial agents. Eur J Med Chem 2015; 90:68-81. [DOI: 10.1016/j.ejmech.2014.11.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 10/28/2014] [Accepted: 11/01/2014] [Indexed: 12/20/2022]
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23
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Alniss HY, Salvia MV, Sadikov M, Golovchenko I, Anthony NG, Khalaf AI, MacKay SP, Suckling CJ, Parkinson JA. Recognition of the DNA minor groove by thiazotropsin analogues. Chembiochem 2014; 15:1978-90. [PMID: 25045155 DOI: 10.1002/cbic.201402202] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Indexed: 01/14/2023]
Abstract
Solution-phase self-association characteristics and DNA molecular-recognition properties are reported for three close analogues of minor-groove-binding ligands from the thiazotropsin class of lexitropsin molecules; they incorporate isopropyl thiazole as a lipophilic building block. Thiazotropsin B (AcImPy(iPr) ThDp) shows similar self-assembly characteristics to thiazotropsin A (FoPyPy(iPr) ThDp), although it is engineered, by incorporation of imidazole in place of N-methyl pyrrole, to swap its DNA recognition target from 5'-ACTAGT-3' to 5'-ACGCGT-3'. Replacement of the formamide head group in thiazotropsin A by nicotinamide in AIK-18/51 results in a measureable difference in solution-phase self-assembly character and substantially enhanced DNA association characteristics. The structures and associated thermodynamic parameters of self-assembled ligand aggregates and their complexes with their respective DNA targets are considered in the context of cluster targeting of DNA by minor-groove complexes.
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Affiliation(s)
- Hasan Y Alniss
- Department of Pharmacy, An-Najah National University, University Street, Nablus (Palestine); Present address: Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 2J7 (Canada)
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24
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Fresch B, Remacle F. Atomistic account of structural and dynamical changes induced by small binders in the double helix of a short DNA. Phys Chem Chem Phys 2014; 16:14070-82. [PMID: 24902052 DOI: 10.1039/c4cp01561d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nucleic acids are flexible molecules and their dynamical properties play a key role in molecular recognition events. Small binders interacting with DNA fragments induce both structural and dynamical changes in the double helix. We study the dynamics of a DNA dodecamer and of its complexes with Hoechst 33258, which is a minor groove binder, and with the ethidium cation, which is an intercalator, by molecular dynamics simulation. The thermodynamics of DNA-drug interaction is evaluated in connection with the structure and the dynamics of the resulting complexes. We identify and characterize the relevant changes in the configurational distribution of the DNA helix and relate them to the corresponding entropic contributions to the binding free energy. The binder Hoechst locks the breathing motion of the minor groove inducing a reduction of the configurational entropy of the helix, which amounts to 20 kcal mol(-1). In contrast, intercalations with the ethidium cation enhance the flexibility of the double helix. We show that the balance between the energy required to deform the helix for the intercalation and the gain in configurational entropy is the origin of cooperativity in the binding of a second ethidium and of anti-cooperativity in the binding of a third one. The results of our study provide an understanding of the relation between structure, dynamics and energetics in the interaction between DNA fragments and small binders, highlighting the role of dynamical changes and consequent variation of the configurational entropy of the DNA double helix for both types of binders.
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Affiliation(s)
- Barbara Fresch
- Department of Chemistry, B6c, University of Liege, B4000 Liege, Belgium.
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25
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Evstigneev MP, Shestopalova AV. Structure, Thermodynamics and Energetics of Drug-DNA Interactions: Computer Modeling and Experiment. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2014. [DOI: 10.1007/978-94-017-9257-8_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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26
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Despax S, Jia F, Pfeffer M, Hébraud P. Complexation of DNA with ruthenium organometallic compounds: the high complexation ratio limit. Phys Chem Chem Phys 2014; 16:10491-502. [DOI: 10.1039/c4cp00726c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Organometallic compounds possess two modes of interaction with DNA: intercalation at low complexation ratios and electrostatic adsorption at high ratios.
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Affiliation(s)
| | - Fuchao Jia
- IPCMS/CNRS
- Université de Strasbourg
- 67034 Strasbourg, France
| | - Michel Pfeffer
- Institut de Chimie
- CNRS
- UMR 7177
- Université de Strasbourg
- France
| | - Pascal Hébraud
- IPCMS/CNRS
- Université de Strasbourg
- 67034 Strasbourg, France
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27
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Yao XX, Ji CG, Xie DQ, Zhang JZ. Molecular dynamics study of DNA binding by INT-DBD under a polarized force field. J Comput Chem 2013; 34:1136-42. [DOI: 10.1002/jcc.23244] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 11/08/2012] [Accepted: 12/30/2012] [Indexed: 11/06/2022]
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28
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Parkinson JA, Scott FJ, Suckling CJ, Wilson G. Exceptionally strong intermolecular association in hydrophobic DNA minor groove binders and their potential therapeutic consequences. MEDCHEMCOMM 2013. [DOI: 10.1039/c3md00071k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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29
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Chandran A, Ghoshdastidar D, Senapati S. Groove binding mechanism of ionic liquids: a key factor in long-term stability of DNA in hydrated ionic liquids? J Am Chem Soc 2012. [PMID: 23181803 DOI: 10.1021/ja304519d] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Nucleic acid sample storage is of paramount importance in biotechnology and forensic sciences. Very recently, hydrated ionic liquids (ILs) have been identified as ideal media for long-term DNA storage. Hence, understanding the binding characteristics and molecular mechanism of interactions of ILs with DNA is of both practical and fundamental interest. Here, we employ molecular dynamics simulations and spectroscopic experiments to unravel the key factors that stabilize DNA in hydrated ILs. Both simulation and experimental results show that DNA maintains the native B-conformation in ILs. Simulation results further suggest that, apart from the electrostatic association of IL cations with the DNA backbone, groove binding of IL cations through hydrophobic and polar interactions contributes significantly to DNA stability. Circular dichroism spectral measurements and fluorescent dye displacement assay confirm the intrusion of IL molecules into the DNA minor groove. Very interestingly, the IL ions were seen to disrupt the water cage around DNA, including the spine of hydration in the minor groove. This partial dehydration by ILs likely prevents the hydrolytic reactions that denature DNA and helps stabilize DNA for the long term. The detailed understanding of IL-DNA interactions provided here could guide the future development of novel ILs, specific for nucleic acid solutes.
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Affiliation(s)
- Aneesh Chandran
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India
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30
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Khalaf AI, Bourdin C, Breen D, Donoghue G, Scott FJ, Suckling CJ, Macmillan D, Clements C, Fox K, Sekibo DAT. Design, synthesis and antibacterial activity of minor groove binders: the role of non-cationic tail groups. Eur J Med Chem 2012; 56:39-47. [PMID: 22948178 DOI: 10.1016/j.ejmech.2012.08.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 07/31/2012] [Accepted: 08/08/2012] [Indexed: 11/18/2022]
Abstract
The design and synthesis of a new class of minor groove binder (MGBs) in which, the cationic tail group has been replaced by a neutral, polar variant including cyanoguanidine, nitroalkene, and trifluoroacetamide groups. Antibacterial activity (against Gram positive bacteria) was found for both the nitroalkene and trifluoroacetamide groups. For the case of the nitroalkene tail group, strong binding of a minor groove binder containing this tail group was demonstrated by both DNA footprinting and melting temperature measurements, showing a correlation between DNA binding and antibacterial activity. The compounds have also been evaluated for binding to the hERG ion channel to determine whether non-cationic but polar substituents might have an advantage compared with conventional cationic tail groups in avoiding hERG binding. In this series of compounds, it was found that whilst non-cationic compounds generally had lower affinity to the hERG ion channel, all of the compounds studied bound weakly to the hERG ion channel, probably associated with the hydrophobic head groups.
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Affiliation(s)
- Abedawn I Khalaf
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK.
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31
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Ammar FF, Abdel-Azeim S, Zargarian L, Hobaika Z, Maroun RG, Fermandjian S. Unprocessed viral DNA could be the primary target of the HIV-1 integrase inhibitor raltegravir. PLoS One 2012; 7:e40223. [PMID: 22768342 PMCID: PMC3388078 DOI: 10.1371/journal.pone.0040223] [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: 04/26/2012] [Accepted: 06/02/2012] [Indexed: 12/18/2022] Open
Abstract
Integration of HIV DNA into host chromosome requires a 3'-processing (3'-P) and a strand transfer (ST) reactions catalyzed by virus integrase (IN). Raltegravir (RAL), commonly used in AIDS therapy, belongs to the family of IN ST inhibitors (INSTIs) acting on IN-viral DNA complexes (intasomes). However, studies show that RAL fails to bind IN alone, but nothing has been reported on the behaviour of RAL toward free viral DNA. Here, we assessed whether free viral DNA could be a primary target for RAL, assuming that the DNA molecule is a receptor for a huge number of pharmacological agents. Optical spectroscopy, molecular dynamics and free energy calculations, showed that RAL is a tight binder of both processed and unprocessed LTR (long terminal repeat) ends. Complex formation involved mainly van der Waals forces and was enthalpy driven. Dissociation constants (Kds) revealed that RAL affinity for unbound LTRs was stronger than for bound LTRs. Moreover, Kd value for binding of RAL to LTRs and IC50 value (half concentration for inhibition) were in same range, suggesting that RAL binding to DNA and ST inhibition are correlated events. Accommodation of RAL into terminal base-pairs of unprocessed LTR is facilitated by an extensive end fraying that lowers the RAL binding energy barrier. The RAL binding entails a weak damping of fraying and correlatively of 3'-P inhibition. Noteworthy, present calculated RAL structures bound to free viral DNA resemble those found in RAL-intasome crystals, especially concerning the contacts between the fluorobenzyl group and the conserved 5'C(4)pA(3)3' step. We propose that RAL inhibits IN, in binding first unprocessed DNA. Similarly to anticancer drug poisons acting on topoisomerases, its interaction with DNA does not alter the cut, but blocks the subsequent joining reaction. We also speculate that INSTIs having viral DNA rather IN as main target could induce less resistance.
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Affiliation(s)
- Farah F. Ammar
- LBPA, UMR8113 du CNRS, Ecole Normale Supérieure de Cachan, Cedex, Cachan, France
- Unité de Biochimie, Département SVT, Faculté des Sciences, Université Saint-Joseph, CST-Mar Roukoz, Beyrouth, Liban
| | - Safwat Abdel-Azeim
- LBPA, UMR8113 du CNRS, Ecole Normale Supérieure de Cachan, Cedex, Cachan, France
| | - Loussinée Zargarian
- LBPA, UMR8113 du CNRS, Ecole Normale Supérieure de Cachan, Cedex, Cachan, France
| | - Zeina Hobaika
- Unité de Biochimie, Département SVT, Faculté des Sciences, Université Saint-Joseph, CST-Mar Roukoz, Beyrouth, Liban
| | - Richard G. Maroun
- Unité de Biochimie, Département SVT, Faculté des Sciences, Université Saint-Joseph, CST-Mar Roukoz, Beyrouth, Liban
| | - Serge Fermandjian
- LBPA, UMR8113 du CNRS, Ecole Normale Supérieure de Cachan, Cedex, Cachan, France
- * E-mail:
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32
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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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33
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Kostjukov VV, Santiago AAH, Rodriguez FR, Castilla SR, Parkinson JA, Evstigneev MP. Energetics of ligand binding to the DNA minor groove. Phys Chem Chem Phys 2012; 14:5588-600. [DOI: 10.1039/c2cp40182g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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34
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Alniss HY, Anthony NG, Khalaf AI, Mackay SP, Suckling CJ, Waigh RD, Wheate NJ, Parkinson JA. Rationalising sequence selection by ligand assemblies in the DNA minor groove: the case for thiazotropsin A. Chem Sci 2012. [DOI: 10.1039/c2sc00630h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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35
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Galindo-Murillo R, Ruíz-Azuara L, Moreno-Esparza R, Cortés-Guzmán F. Molecular recognition between DNA and a copper-based anticancer complex. Phys Chem Chem Phys 2012; 14:15539-46. [DOI: 10.1039/c2cp42185b] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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36
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A revised treatment of the non-electrostatic contribution to the solvation free energy of DNA-binding ligands. J Mol Liq 2011. [DOI: 10.1016/j.molliq.2011.09.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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37
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Liu FF, Dong XY, He L, Middelberg APJ, Sun Y. Molecular insight into conformational transition of amyloid β-peptide 42 inhibited by (-)-epigallocatechin-3-gallate probed by molecular simulations. J Phys Chem B 2011; 115:11879-87. [PMID: 21899367 DOI: 10.1021/jp202640b] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Considerable experimental evidence indicates that (-)-epigallocatechin-3-gallate (EGCG) inhibits the fibrillogenesis of Aβ(42) and alleviates its associated cytotoxicity. However, the molecular mechanism of the inhibition effect of EGCG on the conformational transition of Aβ(42) remains unclear due to the limitations of current experimental techniques. In this work, molecular dynamics simulations and molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) analysis were coupled to better understand the issue. It was found that the direct interactions between EGCG and the peptide are the origin of its inhibition effects. Specifically, EGCG molecules expel water from the surface of the Aβ(42), cluster with each other, and interact directly with the peptide. The results of free energy decomposition calculated by MM-PBSA indicate that the nonpolar term contributes more than 71% to the binding free energy of the EGCG-Aβ(42) complex, while polar interactions (i.e., hydrogen bonding) play a minor role. It was identified that there are 12 important residues of Aβ(42) that strongly interact with EGCG (Phe4, Arg5, Phe19, Phe20, Glu22, Lys28, Gly29, Leu34-Gly37, and Ile41), while nonpolar interactions are mainly provided by the side chains of some hydrophobic residues (Phe, Met and Ile) and the main chains of some nonhydrophobic residues (Lys28 and Gly29). On the contrary, polar interactions are mainly formed by the main chain of Aβ(42), of which the main chains of Gly29 and Gly37 contribute greatly. The work has thus elucidated the molecular mechanism of the inhibition effect of EGCG on the conformational transition of Aβ(42), and the findings are considered critical for exploring more effective agents for the inhibition of Aβ(42) fibrillogenesis.
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Affiliation(s)
- Fu-Feng Liu
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
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Khalaf AI, Anthony N, Breen D, Donoghue G, Mackay SP, Scott FJ, Suckling CJ. Amide isosteres in structure-activity studies of antibacterial minor groove binders. Eur J Med Chem 2011; 46:5343-55. [PMID: 21908079 DOI: 10.1016/j.ejmech.2011.08.035] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 08/23/2011] [Indexed: 01/12/2023]
Abstract
Antibacterial minor groove binders related to the natural product, distamycin, are development candidates for novel antibiotics. Alkenes have been found to be effective substitutes for the isosteric amide links in some positions and alkyl groups larger than methyl have been found to increase binding to DNA in both selectivity and affinity. However the impact of other isosteres such as diazenes and the position of an alkyl group with respect to DNA binding and antibacterial activity are not known. The effects of some systematic variations in the structure of polyamide minor groove binders are investigated. Isosteres of the amide link (alkenes and diazenes) are compared: it is shown that all three are competent for binding to DNA but that alkene links give the tightest binding and highest antibacterial activity; no significant antibacterial activity was found for compounds with a diazene link. Within a series of alkene linked compounds, the effect of branched N-alkyl substituents on binding to DNA and antibacterial activity is investigated: it was found that C3 and C4 branched chains are acceptable at the central pyrrole residue but that at the pyrrole ring adjacent to the basic tail group, a C4 branched chain was too large both for DNA binding and for antibacterial activity. The active branched alkyl chain compounds were found to be especially active against Mycobacterium aurum, a bacterium related to the causative agent of tuberculosis.
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Affiliation(s)
- Abedawn I Khalaf
- WestCHEM Research School, Department of Pure & Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, Scotland, United Kingdom.
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Lo ATS, Salam NK, Hibbs DE, Rutledge PJ, Todd MH. Polyamide-scorpion cyclam lexitropsins selectively bind AT-rich DNA independently of the nature of the coordinated metal. PLoS One 2011; 6:e17446. [PMID: 21573061 PMCID: PMC3090394 DOI: 10.1371/journal.pone.0017446] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 02/03/2011] [Indexed: 01/17/2023] Open
Abstract
Cyclam was attached to 1-, 2- and 3-pyrrole lexitropsins for the first time through a synthetically facile copper-catalyzed "click" reaction. The corresponding copper and zinc complexes were synthesized and characterized. The ligand and its complexes bound AT-rich DNA selectively over GC-rich DNA, and the thermodynamic profile of the binding was evaluated by isothermal titration calorimetry. The metal, encapsulated in a scorpion azamacrocyclic complex, did not affect the binding, which was dominated by the organic tail.
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Affiliation(s)
- Anthony T. S. Lo
- School of Chemistry, University of Sydney, Sydney, New South Wales,
Australia
| | - Noeris K. Salam
- Schrödinger, Inc., New York, New York, United States of
America
| | - David E. Hibbs
- Faculty of Pharmacy, University of Sydney, Sydney, New South Wales,
Australia
| | - Peter J. Rutledge
- School of Chemistry, University of Sydney, Sydney, New South Wales,
Australia
| | - Matthew H. Todd
- School of Chemistry, University of Sydney, Sydney, New South Wales,
Australia
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40
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Falconer RJ, Collins BM. Survey of the year 2009: applications of isothermal titration calorimetry. J Mol Recognit 2010; 24:1-16. [DOI: 10.1002/jmr.1073] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Zuo Z, Gandhi NS, Mancera RL. Calculations of the Free Energy of Interaction of the c-Fos−c-Jun Coiled Coil: Effects of the Solvation Model and the Inclusion of Polarization Effects. J Chem Inf Model 2010; 50:2201-12. [DOI: 10.1021/ci100321h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhili Zuo
- Curtin Health Innovation Research Institute, Western Australian Biomedical Research Institute, School of Biomedical Sciences and School of Pharmacy, Curtin University, GPO Box U1987, Perth WA 6845, Australia
| | - Neha S. Gandhi
- Curtin Health Innovation Research Institute, Western Australian Biomedical Research Institute, School of Biomedical Sciences and School of Pharmacy, Curtin University, GPO Box U1987, Perth WA 6845, Australia
| | - Ricardo L. Mancera
- Curtin Health Innovation Research Institute, Western Australian Biomedical Research Institute, School of Biomedical Sciences and School of Pharmacy, Curtin University, GPO Box U1987, Perth WA 6845, Australia
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Wittayanarakul K, Anthony NG, Treesuwan W, Hannongbua S, Alniss H, Khalaf AI, Suckling CJ, Parkinson JA, Mackay SP. Ranking ligand affinity for the DNA minor groove by experiment and simulation. ACS Med Chem Lett 2010; 1:376-80. [PMID: 24900221 DOI: 10.1021/ml100047n] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2010] [Accepted: 07/12/2010] [Indexed: 11/30/2022] Open
Abstract
The structural and thermodynamic basis for the strength and selectivity of the interactions of minor groove binders (MGBs) with DNA is not fully understood. In 2003, we reported the first example of a thiazole-containing MGB that bound in a phase-shifted pattern that spanned six base pairs rather than the usual four (for tricyclic distamycin-like compounds). Since then, using DNA footprinting, NMR spectroscopy, isothermal titration calorimetry, and molecular dynamics, we have established that the flanking bases around the central four being read by the ligand have subtle effects on recognition. We have investigated the effect of these flanking sequences on binding and the reasons for the differences and established a computational method to rank ligand affinity against varying DNA sequences.
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Affiliation(s)
- Kitiyaporn Wittayanarakul
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 27 Taylor Street, Glasgow G4 0NR, United Kingdom
| | - Nahoum G. Anthony
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 27 Taylor Street, Glasgow G4 0NR, United Kingdom
| | - Witcha Treesuwan
- Chemistry Department and Center of Nanotechnology, Kasetsart University, Bangkok 10900, Thailand
| | - Supa Hannongbua
- Chemistry Department and Center of Nanotechnology, Kasetsart University, Bangkok 10900, Thailand
| | - Hasan Alniss
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 27 Taylor Street, Glasgow G4 0NR, United Kingdom
| | - Abedawn I. Khalaf
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Colin J. Suckling
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - John A Parkinson
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Simon P. Mackay
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 27 Taylor Street, Glasgow G4 0NR, United Kingdom
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Fenley MO, Harris RC, Jayaram B, Boschitsch AH. Revisiting the association of cationic groove-binding drugs to DNA using a Poisson-Boltzmann approach. Biophys J 2010; 99:879-86. [PMID: 20682266 DOI: 10.1016/j.bpj.2010.04.066] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 04/15/2010] [Accepted: 04/27/2010] [Indexed: 11/26/2022] Open
Abstract
Proper modeling of nonspecific salt-mediated electrostatic interactions is essential to understanding the binding of charged ligands to nucleic acids. Because the linear Poisson-Boltzmann equation (PBE) and the more approximate generalized Born approach are applied routinely to nucleic acids and their interactions with charged ligands, the reliability of these methods is examined vis-à-vis an efficient nonlinear PBE method. For moderate salt concentrations, the negative derivative, SK(pred), of the electrostatic binding free energy, DeltaG(el), with respect to the logarithm of the 1:1 salt concentration, [M(+)], for 33 cationic minor groove drugs binding to AT-rich DNA sequences is shown to be consistently negative and virtually constant over the salt range considered (0.1-0.4 M NaCl). The magnitude of SK(pred) is approximately equal to the charge on the drug, as predicted by counterion condensation theory (CCT) and observed in thermodynamic binding studies. The linear PBE is shown to overestimate the magnitude of SK(pred), whereas the nonlinear PBE closely matches the experimental results. The PBE predictions of SK(pred) were not correlated with DeltaG(el) in the presence of a dielectric discontinuity, as would be expected from the CCT. Because this correlation does not hold, parameterizing the PBE predictions of DeltaG(el) against the reported experimental data is not possible. Moreover, the common practice of extracting the electrostatic and nonelectrostatic contributions to the binding of charged ligands to biopolyelectrolytes based on the simple relation between experimental SK values and the electrostatic binding free energy that is based on CCT is called into question by the results presented here. Although the rigid-docking nonlinear PB calculations provide reliable predictions of SK(pred), at least for the charged ligand-nucleic acid complexes studied here, accurate estimates of DeltaG(el) will require further development in theoretical and experimental approaches.
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Affiliation(s)
- Marcia O Fenley
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA.
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