1
|
Ponkarpagam S, Vennila KN, Elango KP. Molecular spectroscopic and molecular simulation studies on the interaction of oral contraceptive drug Ormeloxifene with CT-DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 278:121351. [PMID: 35567820 DOI: 10.1016/j.saa.2022.121351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 06/15/2023]
Abstract
The interaction between oral contraceptive drug Ormeloxifene (ORM) and calf thymus DNA (CT-DNA) was studied using UV-Vis, fluorescence, circular dichroism (CD) and 1H NMR spectral techniques under physiological buffer (pH 7.4). Competitive binding assays with ethidium bromide (EB) and Hoechst 33258, viscosity measurements, KI quenching studies, molecular docking and metadynamics simulation studies were also substantiated the spectroscopic results. ORM is found to binds in the minor groove of CT-DNA as evidenced by: (1) non-displacement of EB from EB/CT-DNA complex; (2) appreciable displacement of Hoechst 33258 from its CT-DNA complex; (3) slight alteration in the CD signal; (4) small shifts (Δδ < 0.033 ppm) without broadening in 1H NMR signals and (5) the nearly equal extent of quenching of fluorescence of ORM by KI in the absence and presence of CT-DNA. Negative values of both enthalpy and entropy changes pointed out that the interaction between ORM and CT-DNA is governed mainly by H-bonding and van der Waals forces. Negative free energy change suggested a spontaneous interaction between ORM and CT-DNA. The free energy landscape of the binding process was computed using metadynamics simulation. The simulation study results disclosed that ORM binds to the minor groove of DNA through H-bonding and π-π stacking interactions. The results of molecular docking and simulation studies corroborate the available experimental data.
Collapse
Affiliation(s)
- S Ponkarpagam
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram 624302, India
| | - K N Vennila
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram 624302, India
| | - Kuppanagounder P Elango
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram 624302, India.
| |
Collapse
|
2
|
Datar A, Paithankar H, Deb P, Chugh J, Bagchi S, Mukherjee A, Hazra A. Water-Controlled Keto-Enol Tautomerization of a Prebiotic Nucleobase. J Phys Chem B 2022; 126:5735-5743. [PMID: 35895006 DOI: 10.1021/acs.jpcb.2c02507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Barbituric acid is believed to be a proto-RNA nucleobase that was used for biological information transfer on prebiotic earth before DNA and RNA in their present forms evolved. Nucleobases have various tautomeric forms and the relative stability of these forms is critical to their biological function. It has been shown that barbituric acid has a tri-keto form in the gas phase and an enol form in the solid state. However, its dominant tautomeric form in aqueous medium that is most relevant for biology has been investigated only to a limited extent and the findings are inconclusive. We have used multiple approaches, namely, molecular dynamics, quantum chemistry, NMR, and IR spectroscopy to determine the most stable tautomer of barbituric acid in solution. We find a delicate balance in the stability of the two tautomers, tri-keto and enol, which is tipped toward the enol as the extent of solvation by water increases.
Collapse
Affiliation(s)
- Avdhoot Datar
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | | | - Pranab Deb
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | | | - Sayan Bagchi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | | | | |
Collapse
|
3
|
Sánchez‐González Á, Grenut P, Gil A. Influence of conventional hydrogen bonds in the intercalation of phenanthroline derivatives with DNA: The important role of the sugar and phosphate backbone. J Comput Chem 2022; 43:804-821. [PMID: 35297513 PMCID: PMC9313584 DOI: 10.1002/jcc.26836] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/28/2022] [Indexed: 12/14/2022]
Abstract
The influence of hydrogen bonds in model intercalated systems between guanine-cytosine and adenine-thymine DNA base pairs (bps) was analyzed with the popular intercalator 1,10-phenanthroline (phen) and derivatives obtained by substitution with OH and NH2 groups in positions 4 and 7. Semiempirical and Density Functional Theory (DFT) methods were used both including dispersion effects: PM6-DH2, M06-2X and B3LYP-D3 along with the recently developed near linear-scaling coupled cluster method DLPNO-CCSD(T) for benchmark calculations. Our results given by QTAIM and non-covalent interaction analysis confirmed the existence of hydrogen bonds created by OH and NH2 . The trends in the energy decomposition analysis for the interaction energy, ΔEint , showed that the ΔEelstat contributions are equal or even a little bit higher than the values for ΔEdisp . Such important ΔEelstat attractive contribution comes mainly from the conventional hydrogen bonds formed by OH and NH2 functional groups with DNA not only with bps but specially with the sugar and phosphate backbone. This behavior is very different from that of phen and other classical intercalators that cannot form conventional hydrogen bonds, where the ΔEdisp is the most important attractive contribution to the ΔEint . The inclusion of explicit water molecules in molecular dynamics simulations showed, as a general trend, that the hydrogen bonds with the bps disappear during the simulations but those with the sugar and phosphate backbone remain in time, which highlights the important role of the sugar and phosphate backbone in the stabilization of these systems.
Collapse
Affiliation(s)
- Ángel Sánchez‐González
- BioISI—Biosystems and Integrative Sciences Institute, Departamento de Química e Bioquímica, Faculdade de CiênciasUniversidade de Lisboa, Campo GrandeLisbonPortugal
| | - Pierre Grenut
- BioISI—Biosystems and Integrative Sciences Institute, Departamento de Química e Bioquímica, Faculdade de CiênciasUniversidade de Lisboa, Campo GrandeLisbonPortugal
| | - Adrià Gil
- BioISI—Biosystems and Integrative Sciences Institute, Departamento de Química e Bioquímica, Faculdade de CiênciasUniversidade de Lisboa, Campo GrandeLisbonPortugal
- ARAID FoundationZaragozaSpain
- Departamento de Química InorgánicaInstituto de Síntesis Química y Catálisis Homogénea (ISQCH) CSIC‐Universidad de Zaragoza, c/ Pedro Cerbuna 12ZaragozaSpain
| |
Collapse
|
4
|
Das A, Banik BK. Advances in heterocycles as DNA intercalating cancer drugs. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2021-0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The insertion of a molecule between the bases of DNA is known as intercalation. A molecule is able to interact with DNA in different ways. DNA intercalators are generally aromatic, planar, and polycyclic. In chemotherapeutic treatment, to suppress DNA replication in cancer cells, intercalators are used. In this article, we discuss the anticancer activity of 10 intensively studied DNA intercalators as drugs. The list includes proflavine, ethidium bromide, doxorubicin, dactinomycin, bleomycin, epirubicin, mitoxantrone, ellipticine, elinafide, and echinomycin. Considerable structural diversities are seen in these molecules. Besides, some examples of the metallo-intercalators are presented at the end of the chapter. These molecules have other crucial properties that are also useful in the treatment of cancers. The successes and limitations of these molecules are also presented.
Collapse
Affiliation(s)
- Aparna Das
- Department of Mathematics and Natural Sciences , College of Sciences and Human Studies, Prince Mohammad Bin Fahd University , Al Khobar 31952 , Kingdom of Saudi Arabia
| | - Bimal Krishna Banik
- Department of Mathematics and Natural Sciences , College of Sciences and Human Studies, Prince Mohammad Bin Fahd University , Al Khobar 31952 , Kingdom of Saudi Arabia
| |
Collapse
|
5
|
Sánchez-González Á, Castro TG, Melle-Franco M, Gil A. From groove binding to intercalation: unravelling the weak interactions and other factors modulating the modes of interaction between methylated phenanthroline-based drugs and duplex DNA. Phys Chem Chem Phys 2021; 23:26680-26695. [PMID: 34825685 DOI: 10.1039/d1cp04529f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Several antitumor drugs base their cytotoxicity on their capacity to intercalate between base pairs of DNA. Nevertheless, it has been established that the mechanism of intercalation of drugs in DNA starts with the prior groove binding mode of interaction of the drug with DNA. Sometimes, for some kind of flat small molecules, groove binding does not produce any cytotoxic effect and the fast transition of such flat small molecules to the cytotoxic intercalation mode is desirable. This is the case of methylated phenanthroline (phen) derivatives, where, changes in the substitution in the position and number of methyl groups determine their capability as cytotoxic compounds and, therefore, it is a way for the modulation of cytotoxic effects. In this work, we studied this modulation by means of the interaction of the [Pt(en)(phen)]2+ complex and several derivatives by methylation of phen in different number and position and the d(GTCGAC)2 DNA hexamer via groove binding using PM6-DH2 and DFT-D methods. The analysis of the geometries, electronic structure and energetics of the studied systems was compared to experimental works to gain insight into the relation structure-interaction for the studied systems with cytotoxicity. The trends are explained by means of the Non-Covalent Interaction (NCI) index, the Energy Decomposition Analysis (EDA) and solvation contributions. Our results are in agreement with the experiments, in which the methylation of position 4 of phen seems to favour the interaction via groove binding thus making the transition to the intercalation cytotoxic mode difficult. Looking at the NCI results, these interactions come not only from the CH/π and CH/n interactions of the methyl group in position 4 but also from the ethylenediamine (en) ligand, whose orientation in the Pt complex was found in such a way that it produces a high number of weak interactions with DNA, especially with the sugar and phosphate backbone.
Collapse
Affiliation(s)
- Ángel Sánchez-González
- Centro de Química e Bioquímica and BioISI - Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande 1749-016, Lisboa, Portugal.
| | - Tarsila G Castro
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Manuel Melle-Franco
- CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Adrià Gil
- Centro de Química e Bioquímica and BioISI - Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande 1749-016, Lisboa, Portugal. .,CIC nanoGUNE BRTA, Tolosa Hiribidea 76, E-20018 Donostia - San Sebastian, Euskadi, Spain
| |
Collapse
|
6
|
Sánchez-González Á, Bandeira NAG, Ortiz de Luzuriaga I, Martins FF, Elleuchi S, Jarraya K, Lanuza J, Lopez X, Calhorda MJ, Gil A. New Insights on the Interaction of Phenanthroline Based Ligands and Metal Complexes and Polyoxometalates with Duplex DNA and G-Quadruplexes. Molecules 2021; 26:4737. [PMID: 34443326 PMCID: PMC8397986 DOI: 10.3390/molecules26164737] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 12/24/2022] Open
Abstract
This work provides new insights from our team regarding advances in targeting canonical and non-canonical nucleic acid structures. This modality of medical treatment is used as a form of molecular medicine specifically against the growth of cancer cells. Nevertheless, because of increasing concerns about bacterial antibiotic resistance, this medical strategy is also being explored in this field. Up to three strategies for the use of DNA as target have been studied in our research lines during the last few years: (1) the intercalation of phenanthroline derivatives with duplex DNA; (2) the interaction of metal complexes containing phenanthroline with G-quadruplexes; and (3) the activity of Mo polyoxometalates and other Mo-oxo species as artificial phosphoesterases to catalyze the hydrolysis of phosphoester bonds in DNA. We demonstrate some promising computational results concerning the favorable interaction of these small molecules with DNA that could correspond to cytotoxic effects against tumoral cells and microorganisms. Therefore, our results open the door for the pharmaceutical and medical applications of the compounds we propose.
Collapse
Affiliation(s)
- Ángel Sánchez-González
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; (Á.S.-G.); (N.A.G.B.); (F.F.M.); (M.J.C.)
| | - Nuno A. G. Bandeira
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; (Á.S.-G.); (N.A.G.B.); (F.F.M.); (M.J.C.)
| | - Iker Ortiz de Luzuriaga
- CIC nanoGUNE BRTA, Tolosa Hiribidea 76, Euskadi, 20018 Donostia-San Sebastián, Spain;
- Polimero eta Material Aurreratuak, Fisika, Kimika eta Teknologia Saila, Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), Paseo Manuel de Lardizabal 3, 20018 Donostia-San Sebastián, Spain; (J.L.); (X.L.)
| | - Frederico F. Martins
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; (Á.S.-G.); (N.A.G.B.); (F.F.M.); (M.J.C.)
| | - Sawssen Elleuchi
- Laboratoire de Chimie Inorganique, LR17ES07, Faculté de Sciences de Sfax, Université de Sfax, Sfax 3000, Tunisia; (S.E.); (K.J.)
| | - Khaled Jarraya
- Laboratoire de Chimie Inorganique, LR17ES07, Faculté de Sciences de Sfax, Université de Sfax, Sfax 3000, Tunisia; (S.E.); (K.J.)
| | - Jose Lanuza
- Polimero eta Material Aurreratuak, Fisika, Kimika eta Teknologia Saila, Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), Paseo Manuel de Lardizabal 3, 20018 Donostia-San Sebastián, Spain; (J.L.); (X.L.)
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián, Spain
| | - Xabier Lopez
- Polimero eta Material Aurreratuak, Fisika, Kimika eta Teknologia Saila, Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), Paseo Manuel de Lardizabal 3, 20018 Donostia-San Sebastián, Spain; (J.L.); (X.L.)
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián, Spain
| | - Maria José Calhorda
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; (Á.S.-G.); (N.A.G.B.); (F.F.M.); (M.J.C.)
| | - Adrià Gil
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; (Á.S.-G.); (N.A.G.B.); (F.F.M.); (M.J.C.)
- CIC nanoGUNE BRTA, Tolosa Hiribidea 76, Euskadi, 20018 Donostia-San Sebastián, Spain;
| |
Collapse
|
7
|
Mohammad H, Demir B, Akin C, Luan B, Hihath J, Oren EE, Anantram MP. Role of intercalation in the electrical properties of nucleic acids for use in molecular electronics. NANOSCALE HORIZONS 2021; 6:651-660. [PMID: 34190284 DOI: 10.1039/d1nh00211b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Intercalating ds-DNA/RNA with small molecules can play an essential role in controlling the electron transmission probability for molecular electronics applications such as biosensors, single-molecule transistors, and data storage. However, its applications are limited due to a lack of understanding of the nature of intercalation and electron transport mechanisms. We addressed this long-standing problem by studying the effect of intercalation on both the molecular structure and charge transport along the nucleic acids using molecular dynamics simulations and first-principles calculations coupled with the Green's function method, respectively. The study on anthraquinone and anthraquinone-neomycin conjugate intercalation into short nucleic acids reveals some universal features: (1) the intercalation affects the transmission by two mechanisms: (a) inducing energy levels within the bandgap and (b) shifting the location of the Fermi energy with respect to the molecular orbitals of the nucleic acid, (2) the effect of intercalation was found to be dependent on the redox state of the intercalator: while oxidized anthraquinone decreases, reduced anthraquinone increases the conductance, and (3) the sequence of the intercalated nucleic acid further affects the transmission: lowering the AT-region length was found to enhance the electronic coupling of the intercalator with GC bases, hence yielding an increase of more than four times in conductance. We anticipate our study to inspire designing intercalator-nucleic acid complexes for potential use in molecular electronics via creating a multi-level gating effect.
Collapse
Affiliation(s)
- Hashem Mohammad
- Department of Electrical Engineering, University of Washington, Seattle, WA, USA.
| | - Busra Demir
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara, Turkey. and Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara, Turkey
| | - Caglanaz Akin
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara, Turkey. and Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara, Turkey
| | - Binquan Luan
- Computational Biological Center, IBM Thomas J. Watson Research, Yorktown Heights, NY 10598, USA
| | - Joshua Hihath
- Electrical and Computer Engineering Department, University of California Davis, Davis, CA, USA
| | - Ersin Emre Oren
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara, Turkey. and Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara, Turkey
| | - M P Anantram
- Department of Electrical Engineering, University of Washington, Seattle, WA, USA.
| |
Collapse
|
8
|
Chowdhury R, Sai Sreyas Adury V, Vijay A, Singh RK, Mukherjee A. Atomistic De-novo Inhibitor Generation-Guided Drug Repurposing for SARS-CoV-2 Spike Protein with Free-Energy Validation by Well-Tempered Metadynamics. Chem Asian J 2021; 16:1634-1642. [PMID: 33949124 PMCID: PMC8207131 DOI: 10.1002/asia.202100268] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/20/2021] [Indexed: 12/13/2022]
Abstract
Computational drug design is increasingly becoming important with new and unforeseen diseases like COVID-19. In this study, we present a new computational de novo drug design and repurposing method and applied it to find plausible drug candidates for the receptor binding domain (RBD) of SARS-CoV-2 (COVID-19). Our study comprises three steps: atom-by-atom generation of new molecules around a receptor, structural similarity mapping to existing approved and investigational drugs, and validation of their binding strengths to the viral spike proteins based on rigorous all-atom, explicit-water well-tempered metadynamics free energy calculations. By choosing the receptor binding domain of the viral spike protein, we showed that some of our new molecules and some of the repurposable drugs have stronger binding to RBD than hACE2. To validate our approach, we also calculated the free energy of hACE2 and RBD, and found it to be in an excellent agreement with experiments. These pool of drugs will allow strategic repurposing against COVID-19 for a particular prevailing conditions.
Collapse
Affiliation(s)
- Rituparno Chowdhury
- Department of ChemistryIndian Institute of Science Education and Research PuneMaharashtraIndia
- Department of Chemical SciencesIndian Institute of Science Education and Research KolkataWest BengalIndia
| | | | - Amal Vijay
- Department of ChemistryIndian Institute of Science Education and Research PuneMaharashtraIndia
| | - Reman K. Singh
- Department of ChemistryIndian Institute of Science Education and Research PuneMaharashtraIndia
| | - Arnab Mukherjee
- Department of ChemistryIndian Institute of Science Education and Research PuneMaharashtraIndia
| |
Collapse
|
9
|
Ponkarpagam S, Mahalakshmi G, Vennila KN, Elango KP. Concentration-dependent mode of binding of drug oxatomide with DNA: multi-spectroscopic, voltammetric and metadynamics simulation analysis. J Biomol Struct Dyn 2021; 40:8394-8404. [PMID: 33896411 DOI: 10.1080/07391102.2021.1911860] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The interaction between antihistaminic drug oxatomide (OXT) and calf-thymus DNA (CT-DNA) has been investigated in a physiological buffer (pH 7.4) using UV-Vis, fluorescence, 1H NMR and circular dichroism spectral techniques coupled with viscosity measurements, KI quenching, voltammetry and in silico molecular modeling studies. OXT binds with CT-DNA in a concentration-dependent manner. At a lower [Drug]/[CT-DNA] molar ratio (0.6-0.1), OXT intercalates into the base pairs of CT-DNA, while at a higher [Drug]/[CT-DNA] molar ratio (13-6), the drug binds in the minor grooves of CT-DNA. The binding constants for the interaction are found to be in the order of 103-105 M-1, and the groove binding mode of interaction exhibits a slightly higher binding constant than that of intercalative mode. Thermodynamic analysis of binding constants at three different temperatures suggests that both these modes of binding are mainly driven by hydrophobic interactions (ΔHo > 0 and ΔSo > 0). Voltammetric investigations indicate that the electro-reduction of OXT is an adsorption controlled process and shifts in reduction peak potentials reiterate the concentration-dependent mode of binding of the drug with CT-DNA. The free energy landscape obtained at the all-atom level, using metadynamics simulation studies, revealed two major binding forces: partial intercalation and minor groove binding, which corroborate well with the experimental results.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Sundararajan Ponkarpagam
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram, India
| | - Govindaraj Mahalakshmi
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram, India
| | - Kailasam N Vennila
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram, India
| | - Kuppanagounder P Elango
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram, India
| |
Collapse
|
10
|
Khan MI, Gulzar S, Majid A, Noor I. A computational study of intercalation of streptozotocin (STZ) into DNA base pairs. J Mol Model 2021; 27:78. [PMID: 33558970 DOI: 10.1007/s00894-020-04620-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 11/26/2020] [Indexed: 11/28/2022]
Abstract
Deoxyribonucleic acid (DNA) drug intercalation is a well-known phenomenon for the treatment of cancer. Streptozotocin (STZ) is a drug agent containing toxic properties that make it good in the pancreatic cancer. The main objective of this study is the intercalation of the anticancer drug into the stacked base pair of DNA sequence with ATGC using a density functional theory (DFT) code named as ADF-Molecule. ADF code implements DFT using the Slater-type orbitals (STO) for computational analysis of atomic and molecular structures. All the calculations were carried out with the GGA and hybrid exchange correlation functional with TZ2P basis sets. It was captivatingly studied that during the intercalation process, the bonds between the DNA base pairs broken. Moreover, during the process of intercalation, the free radicals are considered responsible for disturbance in the base configurations. It was determined that the disturbances that occurred in the base pairs lead to discontinuity in the replication of that particular sequence in the DNA strand.
Collapse
Affiliation(s)
| | - Salma Gulzar
- Department of Physics, University of Gujrat, Gujrat, Pakistan
| | - Abdul Majid
- Department of Physics, University of Gujrat, Gujrat, Pakistan
| | - Irum Noor
- Quaid e Azam Medical College, Bahawalpur, Pakistan
| |
Collapse
|
11
|
Zhang L, Luo K, Li D, Zhang Y, Zeng Y, Li J. Chiral molecular imprinted sensor for highly selective determination of D-carnitine in enantiomers via dsDNA-assisted conformation immobilization. Anal Chim Acta 2020; 1136:82-90. [PMID: 33081952 DOI: 10.1016/j.aca.2020.08.046] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/03/2020] [Accepted: 08/22/2020] [Indexed: 02/08/2023]
Abstract
In this paper, a novel approach was established on the basis of a molecularly imprinted technique with the aid of double-stranded deoxyribonucleic acid (dsDNA) embedded in a molecularly imprinted polymer (MIP) membrane as a new functional unit with chiral recognition for highly specific chiral recognition. The chiral molecules were immobilized and anchored in the cavities of the MIP membrane on the basis of the three-dimensional structure of a molecule determined by the functional groups, spatial characterization of the cavities of MIPs, and the spatial orientation with dsDNA embedded in MIPs. D-carnitine was selected as an example of a chiral molecular template, which intercalated into dsDNA immobilized on the gold electrode surface to form dsDNA-D-carnitine complex, and then the complex was embedded in the MIP during electropolymerization. After elution, the stereo-selective cavities were obtained. Our findings have shown that AAAA-TTTT base sequence had high affinity for D-carnitine intercalation. Combined with the electrochemical detection method, MIP sensor was prepared. The selectivity of the MIP sensor to ultratrace D-carnitine was significantly improved; the sensor had remarkable stereo-selectivity and highly chiral specific recognition to D-carnitine, and L-carnitine with a concentration of 10,000 times D-carnitine did not interfere with the detection of D-carnitine in the assay of raceme. The sensor also exhibited high sensitivity to ultratrace D-carnitine determination with a linear response to the concentration of D-carnitine in the range of 3.0 × 10-16 mol/L to 4.0 × 10-13 mol/L, with a detection limit of 2.24 × 10-16 mol/L. The mechanism of chiral recognition was studied, and result showed that apart from the recognition effect of imprinted cavities, dsDNA provided chiral selectivity to the spatial orientation of chiral molecules via the intercalation of chiral molecules with dsDNA and electrostatic interaction with groups of DNA base.
Collapse
Affiliation(s)
- Lianming Zhang
- Guangxi Colleges and Universities Key Laboratory of Food Safety and Detection, Guangxi Key Laboratory of Electrochemical and Magnetochemical Functional Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, 541004, PR China; College of Material and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu, 610000, PR China
| | - Kui Luo
- Guangxi Colleges and Universities Key Laboratory of Food Safety and Detection, Guangxi Key Laboratory of Electrochemical and Magnetochemical Functional Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, 541004, PR China
| | - Dan Li
- Guangxi Colleges and Universities Key Laboratory of Food Safety and Detection, Guangxi Key Laboratory of Electrochemical and Magnetochemical Functional Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, 541004, PR China
| | - Yufu Zhang
- Guangxi Colleges and Universities Key Laboratory of Food Safety and Detection, Guangxi Key Laboratory of Electrochemical and Magnetochemical Functional Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, 541004, PR China
| | - Ying Zeng
- College of Material and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu, 610000, PR China
| | - Jianping Li
- Guangxi Colleges and Universities Key Laboratory of Food Safety and Detection, Guangxi Key Laboratory of Electrochemical and Magnetochemical Functional Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, 541004, PR China.
| |
Collapse
|
12
|
Elleuchi S, Ortiz de Luzuriaga I, Sanchez-Gonzalez Á, Lopez X, Jarraya K, Calhorda MJ, Gil A. Computational Studies on the Binding Preferences of Molybdenum(II) Phenanthroline Complexes with Duplex DNA. The Important Role of the Ancillary Ligands. Inorg Chem 2020; 59:12711-12721. [DOI: 10.1021/acs.inorgchem.0c01793] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Sawssen Elleuchi
- Laboratoire de Chimie Inorganique, LR17ES07, Université de Sfax, Faculté de Sciences de Sfax, Route de Soukra Km 3.5, BP 1171, 3000 Sfax, Tunisia
| | - Iker Ortiz de Luzuriaga
- CIC nanoGUNE BRTA, Tolosa Hiribidea 76, E-20018 Donostia, San Sebastián, Euskadi, Spain
- Kimika Fakultatea, Euskal Herriko Unibertsitatea, P.K. 107, 20018 Donostia, San Sebastián, Euskadi, Spain
| | - Ángel Sanchez-Gonzalez
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal
| | - Xabier Lopez
- Kimika Fakultatea, Euskal Herriko Unibertsitatea, P.K. 107, 20018 Donostia, San Sebastián, Euskadi, Spain
- Donostia International Physics Center, P.K. 1072, 20080 Donostia, San Sebastián, Euskadi, Spain
| | - Khaled Jarraya
- Laboratoire de Chimie Inorganique, LR17ES07, Université de Sfax, Faculté de Sciences de Sfax, Route de Soukra Km 3.5, BP 1171, 3000 Sfax, Tunisia
| | - Maria José Calhorda
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal
| | - Adrià Gil
- CIC nanoGUNE BRTA, Tolosa Hiribidea 76, E-20018 Donostia, San Sebastián, Euskadi, Spain
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal
| |
Collapse
|
13
|
Hridya VM, Hynes JT, Mukherjee A. Dynamical Recrossing in the Intercalation Process of the Anticancer Agent Proflavine into DNA. J Phys Chem B 2019; 123:10904-10914. [PMID: 31671261 DOI: 10.1021/acs.jpcb.9b08470] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Intercalation into DNA is the interaction mode of some anthracycline antibiotics. Recently, the molecular mechanism of this process was explored using the static free energy landscape. Here we explore the dynamical effects in the intercalation of proflavine into DNA by calculating the transmission coefficient κ-providing a measure of the departure from transition state theory for the reaction rate constant-by examination of the recrossing events at the transition state. For that purpose, we first found the accurate transition state of this complex system-as judged by a committor analysis-using a set of all-atom simulations of total length 6.3 ms. In a subsequent calculation of the transmission coefficient κ in another extensive set of simulations the small value κ = 0.1 was found, indicating a significant departure from TST. Comparison of this result with Grote-Hynes and Kramers theories shows that neither theory is able to capture this complex system's recrossing events; the source of this striking failure is discussed, as are related aspects of the mechanism. This study suggests that, for biomolecular processes similar to this, dynamical effects essential for the process are complex in nature and require novel approaches for their elucidation.
Collapse
Affiliation(s)
- V M Hridya
- Department of Chemistry , Indian Institute of Science Education and Research , Pune 411008 , India
| | - James T Hynes
- Department of Chemistry , University of Colorado , Boulder , Colorado 80309-0215 , United States.,PASTEUR, Department of Chemistry, École normale supérieure , PSL University, Sorbonne Université, CNRS , 75005 Paris , France
| | - Arnab Mukherjee
- Department of Chemistry , Indian Institute of Science Education and Research , Pune 411008 , India
| |
Collapse
|
14
|
Jin B, Sung GW, Jang YJ. Binding mode of proflavine to DNA probed by polarized light spectroscopy. J CHIN CHEM SOC-TAIP 2018. [DOI: 10.1002/jccs.201800246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Biao Jin
- Instrumental Analysis CenterYanbian University Yanji City Jilin Province China
| | - Gi Woong Sung
- Department of ChemistryYeungnam University Dae‐dong Gyeongsan City Gyeong‐buk Republic of Korea
| | - Yoon Jung Jang
- College of Basic Education, Yeungnam University Dae‐dong Gyeongsan City Gyeong‐buk Republic of Korea
| |
Collapse
|
15
|
Prasher P, Sharma M. Medicinal chemistry of acridine and its analogues. MEDCHEMCOMM 2018; 9:1589-1618. [PMID: 30429967 PMCID: PMC6195008 DOI: 10.1039/c8md00384j] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 08/14/2018] [Indexed: 02/01/2023]
Abstract
'Acridine' along with its functional analogue 'Acridone' is the most privileged pharmacophore in medicinal chemistry with diverse applications ranging from DNA intercalators, endonuclease mimics, ratiometric selective ion sensors, and P-glycoprotein inhibitors in countering the multi-drug resistance, enzyme inhibitors, and reversals of neurodegenerative disorders. Their interaction with DNA and ability of selectively identifying numerous biologically useful ions has cemented exploitability of the acridone nucleus in modern day therapeutics. Additionally, most derivatives and salts of acridine are planar, crystalline, and stable displaying a strong fluorescence which, when coupled with their marked bio selectivity and low cytotoxicity, enables the studying and monitoring of several biochemical, metabolic, and pharmacological processes. In this review, a detailed picture covering the important therapeutic aspects of the acridone nucleus and its functional analogues is discussed.
Collapse
Affiliation(s)
- Parteek Prasher
- UGC Sponsored Centre for Advanced Studies , Department of Chemistry , Guru Nanak Dev University , Amritsar 143005 , India
- Department of Chemistry , University of Petroleum & Energy Studies , Dehradun 248007 , India . ;
| | - Mousmee Sharma
- UGC Sponsored Centre for Advanced Studies , Department of Chemistry , Guru Nanak Dev University , Amritsar 143005 , India
| |
Collapse
|
16
|
Biswas R, Bagchi B. Anomalous water dynamics at surfaces and interfaces: synergistic effects of confinement and surface interactions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:013001. [PMID: 29205175 DOI: 10.1088/1361-648x/aa9b1d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In nature, water is often found in contact with surfaces that are extended on the scale of molecule size but small on a macroscopic scale. Examples include lipid bilayers and reverse micelles as well as biomolecules like proteins, DNA and zeolites, to name a few. While the presence of surfaces and interfaces interrupts the continuous hydrogen bond network of liquid water, confinement on a mesoscopic scale introduces new features. Even when extended on a molecular scale, natural and biological surfaces often have features (like charge, hydrophobicity) that vary on the scale of the molecular diameter of water. As a result, many new and exotic features, which are not seen in the bulk, appear in the dynamics of water close to the surface. These different behaviors bear the signature of both water-surface interactions and of confinement. In other words, the altered properties are the result of the synergistic effects of surface-water interactions and confinement. Ultrafast spectroscopy, theoretical modeling and computer simulations together form powerful synergistic approaches towards an understanding of the properties of confined water in such systems as nanocavities, reverse micelles (RMs), water inside and outside biomolecules like proteins and DNA, and also between two hydrophobic walls. We shall review the experimental results and place them in the context of theory and simulations. For water confined within RMs, we discuss the possible interference effects propagating from opposite surfaces. Similar interference is found to give rise to an effective attractive force between two hydrophobic surfaces immersed and kept fixed at a separation of d, with the force showing an exponential dependence on this distance. For protein and DNA hydration, we shall examine a multitude of timescales that arise from frustration effects due to the inherent heterogeneity of these surfaces. We pay particular attention to the role of orientational correlations and modification of the same due to interaction with the surfaces.
Collapse
|
17
|
Harada K, Imai T, Kizu J, Mochizuki M, Inami K. DNA interaction of bromomethyl-substituted acridines. Med Chem Res 2017. [DOI: 10.1007/s00044-017-2030-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
18
|
Lauria A, Mingoia F, García-Argáez AN, Delisi R, Martorana A, Dalla Via L. New insights into the mechanism of action of pyrazolo[1,2-a]benzo[1,2,3,4]tetrazin-3-one derivatives endowed with anticancer potential. Chem Biol Drug Des 2017; 91:463-477. [PMID: 28905525 DOI: 10.1111/cbdd.13108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/28/2017] [Accepted: 08/11/2017] [Indexed: 12/20/2022]
Abstract
Due to the scarce biological profile, the pyrazolo[1,2-a]benzo[1,2,3,4]tetrazine-3-one scaffold (PBT) has been recently explored as promising core for potential anticancer candidates. Several suitably decorated derivatives (PBTs) exhibited antiproliferative activity in the low-micromolar range associated with apoptosis induction and cell cycle arrest on S phase. Herein, we selected the most active derivatives and submitted them to further biological explorations to deepen the mechanism of action. At first, a DNA targeting is approached by means of flow Linear Dichroism experiments so as to evaluate how small planar molecules might interact with DNA, including the interference with the catalytic cycle of topoisomerase II and the influence on the cleavable complex stabilization (poisoning effect). In support of the experimental data, in silico studies have been achieved to better understand the chemical space of the interactions. Interestingly some meaningful structural features, useful for further developments, were found. The 8,9-di-Cl substituted derivative revealed as the most effective in the intercalative process, as well as on the inhibition of catalytic activity of topoisomerase II. Predicted ADME studies confirm that PBTs are promising as potential drug candidates.
Collapse
Affiliation(s)
- Antonino Lauria
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche "STEBICEF", University of Palermo, Palermo, Italy
| | - Francesco Mingoia
- Istituto per lo Studio dei Materiali Nanostrutturati (ISMN), Consiglio Nazionale delle Ricerche (CNR), Palermo, Italy
| | - Aída Nelly García-Argáez
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy.,Fondazione per la Biologia e la Medicina della Rigenerazione T.E.S.-Tissue Engineering and Signalling Onlus, Padova, Italy
| | - Riccardo Delisi
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche "STEBICEF", University of Palermo, Palermo, Italy
| | - Annamaria Martorana
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche "STEBICEF", University of Palermo, Palermo, Italy
| | - Lisa Dalla Via
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| |
Collapse
|
19
|
Galliot A, Gil A, Calhorda MJ. Effects of oxygenation on the intercalation of 1,10-phenanthroline-5,6/4,7-dione between DNA base pairs: a computational study. Phys Chem Chem Phys 2017. [PMID: 28621352 DOI: 10.1039/c7cp00532f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The effects of oxygen in positions 4,7 and 5,6 of phenanthroline have been studied computationally when this ligand intercalates between DNA base pairs. Our results indicate that solvation energy could be the driving force of the process and thus, it can be also related with the cytotoxicity of the drug.
Collapse
Affiliation(s)
- Aurellia Galliot
- Centro de Química e Bioquímica
- DQB
- Faculdade de Ciências
- Universidade de Lisboa
- Campo Grande 1749-016 Lisboa
| | - Adrià Gil
- Centro de Química e Bioquímica
- DQB
- Faculdade de Ciências
- Universidade de Lisboa
- Campo Grande 1749-016 Lisboa
| | - Maria José Calhorda
- Centro de Química e Bioquímica
- DQB
- Faculdade de Ciências
- Universidade de Lisboa
- Campo Grande 1749-016 Lisboa
| |
Collapse
|
20
|
Mahata T, Kanungo A, Ganguly S, Modugula EK, Choudhury S, Pal SK, Basu G, Dutta S. The Benzyl Moiety in a Quinoxaline-Based Scaffold Acts as a DNA Intercalation Switch. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511881] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Tridib Mahata
- Department of Organic and Medicinal Chemistry; CSIR-Indian Institute of Chemical Biology; 4 Raja S. C. Mullick Road Kolkata 700032 WB India
| | - Ajay Kanungo
- Department of Organic and Medicinal Chemistry; CSIR-Indian Institute of Chemical Biology; 4 Raja S. C. Mullick Road Kolkata 700032 WB India
| | - Sudakshina Ganguly
- Department of Biophysics; Bose Institute; P-1/12 CIT Scheme VIIM Kolkata 700054 India
| | - Eswar Kalyan Modugula
- Department of Biophysics; Bose Institute; P-1/12 CIT Scheme VIIM Kolkata 700054 India
| | - Susobhan Choudhury
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III SaltLake; Kolkata 700 098 India
| | - Samir Kumar Pal
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III SaltLake; Kolkata 700 098 India
| | - Gautam Basu
- Department of Biophysics; Bose Institute; P-1/12 CIT Scheme VIIM Kolkata 700054 India
| | - Sanjay Dutta
- Department of Organic and Medicinal Chemistry; CSIR-Indian Institute of Chemical Biology; 4 Raja S. C. Mullick Road Kolkata 700032 WB India
| |
Collapse
|
21
|
Mahata T, Kanungo A, Ganguly S, Modugula EK, Choudhury S, Pal SK, Basu G, Dutta S. The Benzyl Moiety in a Quinoxaline-Based Scaffold Acts as a DNA Intercalation Switch. Angew Chem Int Ed Engl 2016; 55:7733-6. [DOI: 10.1002/anie.201511881] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 02/09/2016] [Indexed: 01/28/2023]
Affiliation(s)
- Tridib Mahata
- Department of Organic and Medicinal Chemistry; CSIR-Indian Institute of Chemical Biology; 4 Raja S. C. Mullick Road Kolkata 700032 WB India
| | - Ajay Kanungo
- Department of Organic and Medicinal Chemistry; CSIR-Indian Institute of Chemical Biology; 4 Raja S. C. Mullick Road Kolkata 700032 WB India
| | - Sudakshina Ganguly
- Department of Biophysics; Bose Institute; P-1/12 CIT Scheme VIIM Kolkata 700054 India
| | - Eswar Kalyan Modugula
- Department of Biophysics; Bose Institute; P-1/12 CIT Scheme VIIM Kolkata 700054 India
| | - Susobhan Choudhury
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III SaltLake; Kolkata 700 098 India
| | - Samir Kumar Pal
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III SaltLake; Kolkata 700 098 India
| | - Gautam Basu
- Department of Biophysics; Bose Institute; P-1/12 CIT Scheme VIIM Kolkata 700054 India
| | - Sanjay Dutta
- Department of Organic and Medicinal Chemistry; CSIR-Indian Institute of Chemical Biology; 4 Raja S. C. Mullick Road Kolkata 700032 WB India
| |
Collapse
|
22
|
Sasikala WD, Mukherjee A. Structure and dynamics of proflavine association around DNA. Phys Chem Chem Phys 2016; 18:10383-91. [PMID: 27030311 DOI: 10.1039/c5cp07789c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proflavine is a small molecule that intercalates into DNA and, thereby, acts as an anticancer agent. Intercalation of proflavine is shown to be a two-step process in which the first step is believed to be the formation of a pre-intercalative outside bound state. Experimental studies so far have been unable to capture the nature of the outside bound state. However, the sub-millisecond timescale observed in fluorescence kinetic experiments is often attributed to the binding of proflavine outside of DNA. Here, we have performed molecular dynamics simulations with multiple proflavine molecules to study the structure and dynamics of the formation of the outside bound state of DNA at different ion concentrations. We observed that the timescale of the outside bound state formation is, at least, five orders of magnitude faster (in nanoseconds) than the experimentally reported timescale (sub-milliseconds) attributed to binding outside DNA. Moreover, we also observed the stacked arrangement of proflavine all around DNA, which is different from the experimentally predicted stacking arrangement perpendicular to the helical axis of DNA in the close vicinity of the phosphate groups. This study, therefore, provides insight into the molecular structure and dynamics of the pre-intercalative outside bound state and will help in understanding the overall intercalation mechanism.
Collapse
Affiliation(s)
- Wilbee D Sasikala
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Maharashtra 411021, India.
| | | |
Collapse
|
23
|
Patra A, Hazra S, Samanta N, Suresh Kumar G, Mitra RK. Micelle induced dissociation of DNA–ligand complexes: The effect of ligand binding specificity. Int J Biol Macromol 2016; 82:418-24. [DOI: 10.1016/j.ijbiomac.2015.11.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 10/19/2015] [Accepted: 11/05/2015] [Indexed: 11/16/2022]
|
24
|
Gil A, Branchadell V, Calhorda MJ. A theoretical study of methylation and CH/π interactions in DNA intercalation: methylated 1,10-phenanthroline in adenine–thymine base pairs. RSC Adv 2016. [DOI: 10.1039/c6ra15495f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
This work shows that quality is better that quantity to estabilize the intercalation of methylated phen.
Collapse
Affiliation(s)
- A. Gil
- Centro de Química e Bioquímica
- Faculdade de Ciências
- Universidade de Lisboa
- 1749-016 Lisboa
- Portugal
| | - V. Branchadell
- Departament de Química
- Universitat Autònoma de Barcelona
- Barcelona
- Spain
| | - M. J. Calhorda
- Centro de Química e Bioquímica
- Faculdade de Ciências
- Universidade de Lisboa
- 1749-016 Lisboa
- Portugal
| |
Collapse
|
25
|
Miroshnychenko KV, Shestopalova AV. Molecular Docking of Biologically Active Substances to Double Helical Nucleic Acids. ACTA ACUST UNITED AC 2016. [DOI: 10.4018/978-1-5225-0362-0.ch005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
Molecular docking of ligands to DNA-targets is of great importance for the design of new anticancer drugs. Unfortunately, most docking programs were developed for protein-ligand docking which raises a question about their applicability for the DNA-ligand docking. In this study, the popular docking programs AutoDock Vina, AutoDock4 and AutoDock3 were compared for a test set of 50 DNA-ligand complexes taken from the Nucleic Acid Database. It was shown that the version 3.05 of the AutoDock program was the most successful in reproducing the structures of intercalation and minor-groove complexes. The program AutoDock4 was able to re-dock to within 2 Å RMSD most of the intercalation complexes of the test set, but showed poor performance for minor groove binders. While Vina, on the contrary, failed to construct six intercalation complexes of the test set, but showed satisfactory results for DNA-ligand minor-groove complexes when small search space was used.
Collapse
Affiliation(s)
| | - Anna V. Shestopalova
- O. Ya. Usikov Institute for Radiophysics and Electronics of NAS of Ukraine, Ukraine
| |
Collapse
|
26
|
DNA intercalation studies and antimicrobial activity of Ag@ZrO2 core-shell nanoparticles in vitro. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2015; 59:1063-1068. [PMID: 26652465 DOI: 10.1016/j.msec.2015.11.027] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 10/19/2015] [Accepted: 11/09/2015] [Indexed: 11/20/2022]
Abstract
Ag@ZrO2 core-shell nanoparticles were prepared by one pot simultaneous reduction of AgNO3 and hydrolysis of zirconium (IV) isopropoxide. The formation of core-shell nanoparticles was confirmed by absorption, XRD, and HR-TEM techniques. The antibacterial activity of Ag@ZrO2 core-shell nanoparticles against Escherichia coli and Staphylococcus aureus and the antifungal properties against Candida albicans, Candida glabrata, Aspergillus niger and Aspergillus flavus were examined by the agar diffusion method. DNA intercalation studies were carried out in CT-DNA. As a result ZrO2 supported on the surface of AgNPs not only prevented aggregation, but also proved to have enhanced antimicrobial activity and DNA intercalation than the Ag nanoparticles.
Collapse
|
27
|
Gil A, Melle-Franco M, Branchadell V, Calhorda MJ. How the Intercalation of Phenanthroline Affects the Structure, Energetics, and Bond Properties of DNA Base Pairs: Theoretical Study Applied to Adenine–Thymine and Guanine–Cytosine Tetramers. J Chem Theory Comput 2015; 11:2714-28. [DOI: 10.1021/ct5006104] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Adrià Gil
- Centro
de Química e Bioquímica, DQB, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | | | - Vicenç Branchadell
- Departament
de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Maria José Calhorda
- Centro
de Química e Bioquímica, DQB, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| |
Collapse
|
28
|
Prieto SP, Powless AJ, Boice JW, Sharma SG, Muldoon TJ. Proflavine Hemisulfate as a Fluorescent Contrast Agent for Point-of-Care Cytology. PLoS One 2015; 10:e0125598. [PMID: 25962131 PMCID: PMC4427403 DOI: 10.1371/journal.pone.0125598] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 03/24/2015] [Indexed: 11/19/2022] Open
Abstract
Proflavine hemisulfate, an acridine-derived fluorescent dye, can be used as a rapid stain for cytologic examination of biological specimens. Proflavine fluorescently stains cell nuclei and cytoplasmic structures, owing to its small amphipathic structure and ability to intercalate DNA. In this manuscript, we demonstrated the use of proflavine as a rapid cytologic dye on a number of specimens, including normal exfoliated oral squamous cells, cultured human oral squamous carcinoma cells, and leukocytes derived from whole blood specimens using a custom-built, portable, LED-illuminated fluorescence microscope. No incubation time was needed after suspending cells in 0.01% (w/v) proflavine diluted in saline. Images of proflavine stained oral cells had clearly visible nuclei as well as granular cytoplasm, while stained leukocytes exhibited bright nuclei, and highlighted the multilobar nature of nuclei in neutrophils. We also demonstrated the utility of quantitative analysis of digital images of proflavine stained cells, which can be used to detect significant morphological differences between different cell types. Proflavine stained oral cells have well-defined nuclei and cell membranes which allowed for quantitative analysis of nuclear to cytoplasmic ratios, as well as image texture analysis to extract quantitative image features.
Collapse
Affiliation(s)
- Sandra P. Prieto
- Biomedical Engineering Department, University of Arkansas, Fayetteville, Arkansas 72701, United States of America
| | - Amy J. Powless
- Biomedical Engineering Department, University of Arkansas, Fayetteville, Arkansas 72701, United States of America
| | - Jackson W. Boice
- Biomedical Engineering Department, University of Arkansas, Fayetteville, Arkansas 72701, United States of America
| | - Shree G. Sharma
- 10810 Executive Center Dr., Nephropath Ste. 100, Little Rock, Arkansas 72211, United States of America
| | - Timothy J. Muldoon
- Biomedical Engineering Department, University of Arkansas, Fayetteville, Arkansas 72701, United States of America
| |
Collapse
|
29
|
Vargiu AV, Magistrato A. Atomistic-Level Portrayal of Drug-DNA Interplay: A History of Courtships and Meetings Revealed by Molecular Simulations. ChemMedChem 2014; 9:1966-81. [DOI: 10.1002/cmdc.201402203] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Indexed: 12/19/2022]
|
30
|
Franco D, Vargiu AV, Magistrato A. Ru[(bpy)2(dppz)]2+ and Rh[(bpy)2(chrysi)]3+ Targeting Double Strand DNA: The Shape of the Intercalating Ligand Tunes the Free Energy Landscape of Deintercalation. Inorg Chem 2014; 53:7999-8008. [DOI: 10.1021/ic5008523] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Duvan Franco
- International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136, Trieste, Italy
| | - Attilio V. Vargiu
- Dipartimento
di Fisica, Università di Cagliari, s.p. Monserrato-Sestu km 0.700, I-09042 Monserrato, Italy
| | - Alessandra Magistrato
- CNR-IOM-DEMOCRITOS c/o International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136, Trieste, Italy
| |
Collapse
|
31
|
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.
Collapse
Affiliation(s)
- Barbara Fresch
- Department of Chemistry, B6c, University of Liege, B4000 Liege, Belgium.
| | | |
Collapse
|
32
|
Rescifina A, Zagni C, Varrica MG, Pistarà V, Corsaro A. Recent advances in small organic molecules as DNA intercalating agents: synthesis, activity, and modeling. Eur J Med Chem 2014; 74:95-115. [PMID: 24448420 DOI: 10.1016/j.ejmech.2013.11.029] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 11/26/2013] [Accepted: 11/28/2013] [Indexed: 11/28/2022]
Abstract
The interaction of small molecules with DNA plays an essential role in many biological processes. As DNA is often the target for majority of anticancer and antibiotic drugs, study about the interaction of drug and DNA has a key role in pharmacology. Moreover, understanding the interactions of small molecules with DNA is of prime significance in the rational design of more powerful and selective anticancer agents. Two of the most important and promising targets in cancer chemotherapy include DNA alkylating agents and DNA intercalators. For these last the DNA recognition is a critical step in their anti-tumor action and the intercalation is not only one kind of the interactions in DNA recognition but also a pivotal step of several clinically used anti-tumor drugs such as anthracyclines, acridines and anthraquinones. To push clinical cancer therapy, the discovery of new DNA intercalators has been considered a practical approach and a number of intercalators have been recently reported. The intercalative binding properties of such molecules can also be harnessed as diagnostic probes for DNA structure in addition to DNA-directed therapeutics. Moreover, the problem of intercalation site formation in the undistorted B-DNA of different length and sequence is matter of tremendous importance in molecular modeling studies and, nowadays, three models of DNA intercalation targets have been proposed that account for the binding features of intercalators. Finally, despite DNA being an important target for several drugs, most of the docking programs are validated only for proteins and their ligands. Therefore, a default protocol to identify DNA binding modes which uses a modified canonical DNA as receptor is needed.
Collapse
Affiliation(s)
- Antonio Rescifina
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy.
| | - Chiara Zagni
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Maria Giulia Varrica
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Venerando Pistarà
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Antonino Corsaro
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| |
Collapse
|
33
|
MoradpourHafshejani S, Hedley JH, Haigh AO, Pike AR, Tuite EM. Synthesis and binding of proflavine diazides as functional intercalators for directed assembly on DNA. RSC Adv 2013. [DOI: 10.1039/c3ra43090a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
|
34
|
Drug-DNA intercalation: from discovery to the molecular mechanism. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013; 92:1-62. [PMID: 23954098 DOI: 10.1016/b978-0-12-411636-8.00001-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The ability of small molecules to perturb the natural structure and dynamics of nucleic acids is intriguing and has potential applications in cancer therapeutics. Intercalation is a special binding mode where the planar aromatic moiety of a small molecule is inserted between a pair of base pairs, causing structural changes in the DNA and leading to its functional arrest. Enormous progress has been made to understand the nature of the intercalation process since its idealistic conception five decades ago. However, the biological functions were detected even earlier. In this review, we focus mainly on the acridine and anthracycline types of drugs and provide a brief overview of the development in the field through various experimental methods that led to our present understanding of the subject. Subsequently, we discuss the molecular mechanism of the intercalation process, free-energy landscapes, and kinetics that was revealed recently through detailed and rigorous computational studies.
Collapse
|