1
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Khatun M, Jana GC, Nayim S, Dhal A, Patra A, Hossain M. Evaluation of the size effect of hydrophobic ring substitution on 9-O position of berberine on DNA binding. J Biomol Struct Dyn 2023; 41:14299-14307. [PMID: 38073529 DOI: 10.1080/07391102.2023.2180436] [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: 12/22/2022] [Accepted: 02/08/2023] [Indexed: 02/25/2023]
Abstract
The interaction of deoxyribonucleic acid (DNA) with medicinally significant small molecules has long piqued the interest of researchers because its applications are directly related to the discovery of new classes of drugs. Keeping this in mind, here we report berberine derivatives and their interaction with calf thymus DNA (CT-DNA). In this report we discussed on the structural perspectives and thermodynamic characteristics of the interaction of four 9-O-substituted berberines (BRDR1 to BRDR4) with CT-DNA. The binding affinity of BRDR-DNA complexes increased with increasing the cycloalkane ring size of the substitution except BRDR2. The binding constant value obtained from UV-Visible spectral analysis was 1.12 × 106 for BRDR1, 0.37 × 106 for BRDR2, 1.72 × 106 for BRDR3 and 3.20 × 106 for BRDR4. Ferrocyanide quenching experiments revealed unequivocally that the analogues except BRDR2 had a partly intercalative binding to DNA. From the ITC experiment it was found that the bindings of BRDR1, BRDR3 and BRDR4 to DNA was favoured by negative enthalpy and positive entropy while BRDR2 was driven by positive enthalpy and positive entropy. In all cases the hydrophobic interaction plays a crucial role. Thus, the complete multispectroscopic and thermodynamic binding studies may be useful for new drug design and development.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Munira Khatun
- Department of Chemistry, Vidyasagar University, Midnapore, West Bengal, India
| | - Gopal Chandra Jana
- Department of Chemistry, Vidyasagar University, Midnapore, West Bengal, India
| | - Sk Nayim
- Department of Chemistry, Vidyasagar University, Midnapore, West Bengal, India
| | - Asima Dhal
- Department of Chemistry, Vidyasagar University, Midnapore, West Bengal, India
| | - Anirudha Patra
- Department of Chemistry, Vidyasagar University, Midnapore, West Bengal, India
| | - Maidul Hossain
- Department of Chemistry, Vidyasagar University, Midnapore, West Bengal, India
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2
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Han JH, Kim JH, Jung M, Kim SK, Jang YJ. Effects of the Ligand Structure of Cu(
II
) Complexes on Oxidative
DNA
Cleavage. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ji Hoon Han
- Department of Chemistry Yeungnam University Gyeongsan City 38541 Republic of Korea
- Present address: Department of Applied Chemistry Andong National University Andong‐si 1375 Republic of Korea
| | - Ji Hoon Kim
- Department of Chemistry Yeungnam University Gyeongsan City 38541 Republic of Korea
| | - Maeng‐Joon Jung
- Department of Chemistry Kyungpook National University Daegu 41566 Republic of Korea
| | - Seog K. Kim
- Department of Chemistry Yeungnam University Gyeongsan City 38541 Republic of Korea
| | - Yoon Jung Jang
- College of Basic Education Yeungnam University Gyeongsan City 38541 Republic of Korea
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3
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Senapati S, Upadhyaya A, Dhruw S, Giri D, Maiti P. Controlled DNA Delivery Using Poly(lactide) Nanoparticles and Understanding the Binding Interactions. J Phys Chem B 2021; 125:10009-10017. [PMID: 34436883 DOI: 10.1021/acs.jpcb.1c06520] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cationic polymer-based gene delivery vectors suffer from several limitations such as low DNA-loading capacity, poor transfection, toxicity, environmental degradations, etc. Again, very limited works are available addressing the binding interactions in detail at the atomic level explaining the loading capacity, protection ability against harsh environments, and controlled release behavior of the DNA-encapsulated vehicles. Here, a poly(l-lactide) (PLA) nanoparticle-based controlled DNA release system is proposed. The developed vehicle possesses a high DNA-loading capacity and can release the loaded DNA in a controlled manner. Spectroscopic, physicochemical, and molecular simulation techniques (AM1 and atomistic molecular dynamics) have been employed to understand the binding interactions between PLA and DNA molecules enabling high DNA loading, protection against external harsh environments, and controlled DNA release behavior. Methyl thiazolyl tetrazolium (MTT) assay experiments confirm the biocompatible nature of the vehicle. Cellular uptake efficiency and endo-lysosomal escape capabilities have been investigated against HeLA cells. This study, therefore, demonstrates the development of a promising nonviral DNA delivery vector and includes a detailed investigation of the atomic-level interaction behavior between PLA and DNA molecules.
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Affiliation(s)
- Sudipta Senapati
- School of Materials Science and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221 005, India
| | - Anurag Upadhyaya
- Department of Physics, Institute of Science, Banaras Hindu University, Varanasi 221 005, India
| | - Somnath Dhruw
- School of Materials Science and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221 005, India
| | - Debaprasad Giri
- Department of Physics, Indian Institute of Technology (Banaras Hindu University), Varanasi 221 005, India
| | - Pralay Maiti
- School of Materials Science and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221 005, India
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4
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Sharma SK, Poonam. Molecular Interaction Studies of Doxycycline Hyclate in Aqueous Glycine or l-Alanine by Using Volumetric and Ultrasonic Parameters. J SOLUTION CHEM 2021. [DOI: 10.1007/s10953-020-01038-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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5
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Pant P, Fisher M. Marshall's nucleic acid: From double-helical structure to a potent intercalator. Biophys Chem 2021; 269:106525. [PMID: 33352335 DOI: 10.1016/j.bpc.2020.106525] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 02/06/2023]
Abstract
Deoxyribonucleic acid (DNA) not only stores genetic information but also emerged as a popular drug target. Modified nucleotides/nucleosides have been extensively studied in recent years wherein the sugar/nucleobase/phosphate-backbone has been altered. Several such molecules are FDA approved, capable of targeting nucleic acids and proteins. In this article, we modified negatively charged phosphate backbone to marshall's acid-based neutral backbone and analyzed the resultant structures by utilizing Gaussian accelerated molecular dynamics simulations (1 μs) in aqueous media at 150 mM salt concentration. We noted that the double-helical marshall's nucleic acid structure was partially denatured during the course of simulations, however, after using conformationally locked sugar, the marshall's nucleic acid (hereby called MNA) maintained the double-helical structure throughout the simulations. Despite the fact that MNA has a more extended backbone than the regular DNA, surprisingly, both showed similar helical rise (~3.4 Å) along with a comparable Watson-Crick hydrogen bond profile. The backbone difference was majorly compensated in terms of helical twist (~56° (MNA) and ~ 35° (control DNA)). Further, we examined a few MNA based ss-dinucleotides as intercalating ligands for a regular B-DNA. Quite strikingly, the ligands unwinded the DNA and showed intercalating properties with high DNA binding affinities. Hence, the use of small fragments of MNA based molecules in DNA targeted drug discovery is foreseen.
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Affiliation(s)
- Pradeep Pant
- Department of Chemistry, Indian Institute of Technology Delhi, India.
| | - Maria Fisher
- Department of Biosciences, University of Helsinki, Finland
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6
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Understanding the role of hydrogen bonds in destruction of DNA by screening interactions of Flutamide anticancer drug with nucleotides bases: DFT perspective, MD simulation and free energy calculation. ADSORPTION 2019. [DOI: 10.1007/s10450-019-00179-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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7
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Kinyanyi D, Amwayi P, Wamalwa M, Obiero G. Comparative in silico study of congocidine congeners as potential inhibitors of African swine fever virus. PLoS One 2019; 14:e0221175. [PMID: 31461446 PMCID: PMC6713398 DOI: 10.1371/journal.pone.0221175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/31/2019] [Indexed: 01/08/2023] Open
Abstract
African swine fever virus (ASFV) infection is fatal in domesticated pigs, with a mortality rate approaching 100%. This may result in economic losses and threats to food security. Currently, there are no approved vaccines or antiviral therapies for ASFV. Therefore, in this study, we evaluated congocidine congeners and a tris-benzimidazole as potential inhibitors of ASFV transcription using an in silico approach. We applied redocking of congocidine and docking of its congeners and a tris-benzimidazole to a receptor containing B-DNA with AT-motifs as a target to mimic conserved ASFV late gene promoters. Subsequently, the binding scores of DNA-ligand docked complexes were evaluated and their binding affinity was estimated. Molecular dynamics (MD) simulation was then used to assess ligand behavior within the minor groove. From our results, it is evident the less toxic congocidine congeners and tris-benzimidazole could dock to AT-rich regions significantly. Additionally, the predicted binding affinities had suitable values comparable to other experimentally determined minor groove binders, MD simulation of the docked DNA-ligand complexes and subsequent molecular trajectory visualization further showed that the ligands remained embedded in the minor groove during the time course of simulation, indicating that these ligands may have potential applications in abrogating ASFV transcription.
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Affiliation(s)
- Dickson Kinyanyi
- Department of Biochemistry and Biotechnology, Technical University of Kenya, Nairobi, Kenya
- * E-mail:
| | - Peris Amwayi
- Department of Biochemistry and Biotechnology, Technical University of Kenya, Nairobi, Kenya
| | - Mark Wamalwa
- Department of Biochemistry and Biotechnology, Kenyatta University, Nairobi, Kenya
| | - George Obiero
- Center for Biotechnology and Bioinformatics, University of Nairobi, Nairobi, Kenya
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8
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Sakthikumar K, Solomon RV, Raja JD. Spectro-electrochemical assessments of DNA/BSA interactions, cytotoxicity, radical scavenging and pharmacological implications of biosensitive and biologically active morpholine-based metal(ii) complexes: a combined experimental and computational investigation. RSC Adv 2019; 9:14220-14241. [PMID: 35519345 PMCID: PMC9064050 DOI: 10.1039/c8ra09218d] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 04/07/2019] [Indexed: 12/12/2022] Open
Abstract
Biosensitive and biologically active morpholine-based transition metal(ii) complexes (1-5) were constructed as [MII(L) AcO]·nH2O {where M = Cu (1) n = 1; Co (2), Mn (3), Ni (4), n = 4 and Zn (5) n = 2}, which were synthesized from 2-(-(2-morpholinoethylimino) methyl)-4-bromophenol ligand (HL) and structurally characterized by various analytical and spectroscopic techniques, which proposed a square planar and tetrahedral geometry around the central metal ion with lattice water molecules. The gel electrophoresis results revealed that complexes 1 and 5 had more potent DNA cleavage efficacy in the presence of an oxidizing agent (H2O2) as compared to the others. The observed DNA binding results for all the compounds as determined by spectro-electrochemical and hydrodynamic techniques were in the order 3.36 (1) > 3.06 (2) > 2.73 (4) > 2.61 (5) > 1.84 (3) > 1.00 (HL) × 104 M-1. The obtained bovine serum albumin (BSA) protein binding constant (K b) results put forward the following order 2.38 (1) > 2.21 (2) > 2.18 (5) > 1.76 (4) > 1.40 (3) > 1.26 (HL) × 104 M-1. Also, the biothermodynamic parameters (, , ΔH° and ΔS°) and binding results divulged that all the complexes (1-5) could bind to DNA via intercalation in a spontaneous manner. Density functional theory calculations were employed to optimize the structure of ligand (HL) and its complexes (1-5) to gain insights into their electronic structures. Molecular docking analysis was carried out to identify the preferential binding modes of these complexes toward DNA and BSA protein. The theoretical observations of all cases were found to be very close to the experimental observations. Among the radical scavenging activity results for all the cases toward DPPH, hydroxyl radical, superoxide, nitric oxide and ferric reducing agents, complex (1) revealed a superior scavenging potency over the other compounds. In the screened antimicrobial reports against 10 different selected pathogenic species, although all the complexes (1-5) exhibited a greater significant inhibitory effect than the free ligand, complexes 4 and 5 achieved the best potency over standard drugs. The observed percentage of growth inhibition for all the compounds against the A549, HepG2, MCF-7 and NHDF cell lines suggested that complex 1 had enhanced growth-inhibitory potency over the other compounds and slightly affected normal cells as compared to the standard drug cisplatin, which may lead to its investigation as a promising anticancer agent in future research.
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Affiliation(s)
- Karunganathan Sakthikumar
- Chemistry Research Centre, Mohamed Sathak Engineering College Kilakarai, Ramanathapuram 623 806 Tamil Nadu India +91 9751054202
| | - Rajadurai Vijay Solomon
- Department of Chemistry, Madras Christian College (Autonomous) Tambaram East Chennai 600 059 Tamil Nadu India +91 9944804597
| | - Jeyaraj Dhaveethu Raja
- Department of Chemistry, The American College (Autonomous) Madurai 625 002 Tamil Nadu India +91 94876 82202 +91 90925 61924
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9
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Khalid S, Rodger P. Molecular Dynamics Simulations of Dna and Its Complexes. PROGRESS IN REACTION KINETICS AND MECHANISM 2019. [DOI: 10.3184/007967404777726232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This article describes how classical molecular simulation methods are being used to gain a molecular-level understanding of the interaction mechanisms responsible for DNA–ligand recognition, and that govern the response of DNA to ligand binding. Case studies using a variety of different ligands—including small pharmaceutical drugs, proteins and lipids—are used to illustrate the power of modern molecular dynamics simulation methods for understanding how we may control the function and structure of DNA.
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Affiliation(s)
- Syma Khalid
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
- Current address: Laboratory of Molecular Biophysics, University of Oxford, South Parks Rd, Oxford, OX1 3QU, UK
| | - P.Mark Rodger
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
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10
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Alam MF, Varshney S, Khan MA, Laskar AA, Younus H. In vitro DNA binding studies of therapeutic and prophylactic drug citral. Int J Biol Macromol 2018; 113:300-308. [DOI: 10.1016/j.ijbiomac.2018.02.098] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 02/10/2018] [Accepted: 02/14/2018] [Indexed: 01/09/2023]
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11
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Abstract
Matrix metalloproteinases (MMPs) are a family of zinc-containing enzymes required for homeostasis. These enzymes are an important class of drug targets as their over expression is associated with many disease states. Most of the inhibitors reported against this class of proteins have failed in clinical trials due to lack of specificity. In order to assist in drug design endeavors for MMP targets, a computationally tractable pathway is presented, comprising, (1) docking of small molecule inhibitors against the target MMPs, (2) derivation of quantum mechanical charges on the zinc ion in the active site and the amino acids coordinating with zinc including the inhibitor molecule, (3) molecular dynamics simulations on the docked ligand-MMP complexes, and (4) evaluation of binding affinities of the ligand-MMP complexes via an accurate scoring function for zinc containing metalloprotein-ligand complexes. The above pathway was applied to study the interaction of the inhibitor Batimastat with MMPs, which resulted in a high correlation between the predicted and experimental binding free energies, suggesting the potential applicability of the pathway.
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12
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Shakibapour N, Dehghani Sani F, Beigoli S, Sadeghian H, Chamani J. Multi-spectroscopic and molecular modeling studies to reveal the interaction between propyl acridone and calf thymus DNA in the presence of histone H1: binary and ternary approaches. J Biomol Struct Dyn 2018; 37:359-371. [DOI: 10.1080/07391102.2018.1427629] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Niloufar Shakibapour
- Faculty of Sciences, Department of Biology, Islamic Azad University, Mashhad Branch, Mashhad, Iran
| | - Farzad Dehghani Sani
- Faculty of Sciences, Department of Biology, Islamic Azad University, Mashhad Branch, Mashhad, Iran
| | - Sima Beigoli
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Hamid Sadeghian
- Neurogenic Inflammation Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Laboratory Sciences, School of Paramedical Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jamshidkhan Chamani
- Faculty of Sciences, Department of Biology, Islamic Azad University, Mashhad Branch, Mashhad, Iran
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13
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Pramanik S, Chatterjee S, Suresh Kumar G, Sujatha Devi P. Egg-shell derived carbon dots for base pair selective DNA binding and recognition. Phys Chem Chem Phys 2018; 20:20476-20488. [DOI: 10.1039/c8cp02872a] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Here, we have used food waste derived chicken egg shell membrane as a cost effective carbon source for the synthesis of heteroatom doped fluorescent carbon dots. We are able to apply these synthesized carbon dots as a new fluorescent probe for label free base pair selective and sequence specific double stranded DNA binding.
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Affiliation(s)
- Srikrishna Pramanik
- Sensor and Actuator Division
- CSIR-Central Glass and Ceramic Research Institute
- Kolkata 700 032
- India
| | - Sabyasachi Chatterjee
- Biophysical Chemistry Laboratory
- Organic and Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700 032
- India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory
- Organic and Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700 032
- India
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14
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Mishra A, Pant P, Mrinal N, Jayaram B. A computational protocol for the discovery of lead molecules targeting DNA unique to pathogens. Methods 2017; 131:4-9. [PMID: 28733089 DOI: 10.1016/j.ymeth.2017.07.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 07/11/2017] [Accepted: 07/18/2017] [Indexed: 12/19/2022] Open
Abstract
With the rapid emergence of drug resistant pathogens, it has become imperative to develop alternative medications as well as find new drug targets to overcome this crisis. Hence, this has become prime focus of several academic laboratories and pharmaceutical companies. Here, we report a computational protocol for identifying unique DNA sequence(s) in the pathogen which is absent in human and related non-pathogenic strains of the microbe. In order to use the unique sequence as drug target, the protocol, in the second step, uses virtual screening against a million compound library to identify candidate small molecules which can bind to these unique DNA targets in the pathogen only. Theoretically the molecules identified after screening should not bind to human DNA. This methodology is demonstrated on Mycobacterium tuberculosis H37Rv, wherein a new octamer sequence present only in H37Rv has been identified and a few candidate small molecules as potential drug have been proposed. Being fast and cost effective, this protocol could be of importance in generating new potential drug candidates against infectious organisms for further experimental studies. This methodology is freely available at http://www.scfbio-iitd.res.in/PSDDF/.
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Affiliation(s)
- Akhilesh Mishra
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, India; Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, India
| | - Pradeep Pant
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, India; Department of Chemistry, Indian Institute of Technology Delhi, India
| | - Nirotpal Mrinal
- Laboratory of Molecular Biology, South Asian University, New Delhi, India
| | - B Jayaram
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, India; Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, India; Department of Chemistry, Indian Institute of Technology Delhi, India.
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15
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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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16
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Pant P, Afshan Shaikh S, Jayaram B. Design and characterization of symmetric nucleic acids via molecular dynamics simulations. Biopolymers 2017; 107. [PMID: 27861723 DOI: 10.1002/bip.23002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 11/05/2016] [Accepted: 11/07/2016] [Indexed: 12/15/2022]
Abstract
Asymmetry (5'→3') associated with each strand of the deoxyribonucleic acid (DNA) is inherent in the sugar-phosphate backbone connectivity and is essential for replication and transcription. We note that this asymmetry is due to one single chemical bond (C3' to C2' ) in each nucleotide unit, and the absence of this bond results in directionally symmetric nucleic acids. We also discovered that creation of an extra chemical bond (C5' to C2' ) can lead to a symmetric backbone. Keeping their potential synthetic and therapeutic interest in mind, we designed a few novel symmetric nucleic acids. We investigated their conformational stability and flexibility via detailed all atom explicit solvent 100-ns long molecular dynamics simulations and compared the resulting structures with that of regular B-DNA. Quite interestingly, some of the symmetric nucleic acids retain the overall double helical structure indicating their potential for integration in physiological DNA without causing major structural perturbations.
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Affiliation(s)
- Pradeep Pant
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.,Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Saher Afshan Shaikh
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.,Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - B Jayaram
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.,Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.,Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
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17
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Li A, Gao K. Accurate estimation of electrostatic binding energy with Poisson-Boltzmann equation solver DelPhi program. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2016. [DOI: 10.1142/s0219633616500711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Poisson–Boltzmann (PB) model is a widely used implicit solvent approximation in biophysical modeling because of its ability to provide accurate and reliable PB electrostatic salvation free energies ([Formula: see text] as well as electrostatic binding free energy ([Formula: see text] estimations. However, a recent study has warned that the 0.5[Formula: see text]Å grid spacing which is normally adopted can produce unacceptable errors in [Formula: see text] estimation with the solvent excluded surface (SES) (Harris RC, Boschitsch AH and Fenley MO, Influence of grid spacing in Poisson–Boltzmann equation binding energy estimation, J Chem Theory Comput 19: 3677–3685, 2013). In this work, we investigate the grid dependence of the widely used PB solver DelPhi v6.2 with molecular surface (MS) for estimating both electrostatic solvation free energies and electrostatic binding free energies. Our results indicate that, for the molecular complex and components the absolute errors of [Formula: see text] are smaller than that of [Formula: see text], and grid spacing of 0.8[Formula: see text]Å with DelPhi program ensures the accuracy and reliability of [Formula: see text]; however, the accuracy of [Formula: see text] largely relies on the order of magnitude of [Formula: see text] itself rather than that of [Formula: see text] or [Formula: see text]. Our findings suggest that grid spacing of 0.5[Formula: see text]Å is enough to produce accurate [Formula: see text] for molecules whose [Formula: see text] are large, but finer grids are needed when [Formula: see text] is very small.
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Affiliation(s)
- Anbang Li
- College of Physics Science and Technology, Central China Normal University, Wuhan, P.R. China, 430079, P.R. China
| | - Kaifu Gao
- College of Physics Science and Technology, Central China Normal University, Wuhan, P.R. China, 430079, P.R. China
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18
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Sato Y, Saito H, Aoki D, Teramae N, Nishizawa S. Lysine linkage in abasic site-binding ligand-thiazole orange conjugates for improved binding affinity to orphan nucleobases in DNA/RNA hybrids. Chem Commun (Camb) 2016; 52:14446-14449. [PMID: 27901527 DOI: 10.1039/c6cc07236d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Introduction of lysine linkage in the conjugate between abasic site-binding ligands and thiazole orange significantly improved the binding affinity for target orphan adenine or uracil nucleobase in DNA/RNA hybrids.
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Affiliation(s)
- Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Hiroki Saito
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Daisuke Aoki
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Norio Teramae
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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19
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Tomar N, Mishra A, Mrinal N, Jayaram B. Onco-Regulon: an integrated database and software suite for site specific targeting of transcription factors of cancer genes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw116. [PMID: 27515825 PMCID: PMC4980569 DOI: 10.1093/database/baw116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 07/13/2016] [Indexed: 11/13/2022]
Abstract
Transcription factors (TFs) bind at multiple sites in the genome and regulate expression of many genes. Regulating TF binding in a gene specific manner remains a formidable challenge in drug discovery because the same binding motif may be present at multiple locations in the genome. Here, we present Onco-Regulon (http://www.scfbio-iitd.res.in/software/onco/NavSite/index.htm), an integrated database of regulatory motifs of cancer genes clubbed with Unique Sequence-Predictor (USP) a software suite that identifies unique sequences for each of these regulatory DNA motifs at the specified position in the genome. USP works by extending a given DNA motif, in 5′→3′, 3′ →5′ or both directions by adding one nucleotide at each step, and calculates the frequency of each extended motif in the genome by Frequency Counter programme. This step is iterated till the frequency of the extended motif becomes unity in the genome. Thus, for each given motif, we get three possible unique sequences. Closest Sequence Finder program predicts off-target drug binding in the genome. Inclusion of DNA-Protein structural information further makes Onco-Regulon a highly informative repository for gene specific drug development. We believe that Onco-Regulon will help researchers to design drugs which will bind to an exclusive site in the genome with no off-target effects, theoretically. Database URL:http://www.scfbio-iitd.res.in/software/onco/NavSite/index.htm
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Affiliation(s)
- Navneet Tomar
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology-Delhi, New Delhi, India
| | - Akhilesh Mishra
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology-Delhi, New Delhi, India Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, Delhi, India
| | - Nirotpal Mrinal
- Labaratory of Molecular Biology, South Asian University, New Delhi, India
| | - B Jayaram
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology-Delhi, New Delhi, India Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, Delhi, India Department of Chemistry, Indian Institute of Technology-Delhi, Delhi
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20
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Laxmi SV, Anil P, Rajitha G, Rao AJ, Crooks PA, Rajitha B. Synthesis of thiazolidine-2,4-dione derivatives: anticancer, antimicrobial and DNA cleavage studies. J Chem Biol 2016; 9:97-106. [PMID: 27698947 DOI: 10.1007/s12154-016-0154-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 07/05/2016] [Indexed: 01/08/2023] Open
Abstract
In the search of efficient anticancer agents, here, new 5-(4-alkylbenzyledene)thiazolidine-2,4-dione derivatives (5a-g) have been successfully synthesized and characterized and are evaluated for anticancer and antimicrobial activities using DNA cleavage studies. In vitro studies on anticancer activity of compound 5d (NSC: 768619/1) was done against the full panel of 60 human tumor cell lines. The five-level dose activity results revealed that, the compound 5d was active against all the cell lines, it has shown potential activity against leukemia SR (GI50: 2.04 μM), non-small cell lung cancer NCI-H522 (GI50: 1.36 μM), colon cancer COLO 205 (GI50: 1.64 μM), CNS cancer SF-539 (GI50: 1.87 μM), melanoma SK-MEL-2 (GI50: 1.64 μM), ovarian cancer OVCAR-3 (GI50: 1.87 μM), renal cancer RXF 393 (GI50: 1.15 μM), prostate cancer PC-3 (GI50: 1.90 μM), and breast cancer MDA-MB-468(GI50: 1.11 μM). DNA cleavage studies revealed that at 50 μg/mL concentration, partial DNA digestion was observed and when the concentration is increasing to threefold (150 μg/mL), complete linear DNA digestion and partial supercoiled DNA digestion was observed. Further antimicrobial studies indicate that all the synthesized compounds except compound 5a possess prominent activity against all the screened microbial species. This study throws a ray of light in the field of anticancer drugs.
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Affiliation(s)
- S Vijaya Laxmi
- Department of Chemistry, K L University, Guntur, 522502 India
| | - P Anil
- Department of Chemistry, K L University, Guntur, 522502 India
| | - G Rajitha
- Department of Chemistry, National Institute of Technology, Warangal, 506004 India
| | - Asha Jyothi Rao
- Department of Zoology, Bhavan's College, Andheri(W), Mumbai, 400058 India
| | - Peter A Crooks
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for medical Sciences, Little Rock, AR 72205 USA
| | - B Rajitha
- Department of Chemistry, National Institute of Technology, Warangal, 506004 India
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21
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Sargolzaei M, Afshar M, Jorabchi MN. Binding of 1-substituted carbazolyl-3,4-dihydro-β-carbolines with DNA: Molecular dynamics simulation and MM-GBSA analysis. Mol Biol 2016. [DOI: 10.1134/s0026893316020205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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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]
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23
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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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24
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Benz[c,d]indolium-containing Monomethine Cyanine Dyes: Synthesis and Photophysical Properties. Molecules 2015; 21:E23. [PMID: 26712725 PMCID: PMC6274575 DOI: 10.3390/molecules21010023] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 12/17/2015] [Accepted: 12/18/2015] [Indexed: 01/24/2023] Open
Abstract
Asymmetric monomethine cyanines have been extensively used as probes for nucleic acids among other biological systems. Herein we report the synthesis of seven monomethine cyanine dyes that have been successfully prepared with various heterocyclic moieties such as quinoline, benzoxazole, benzothiazole, dimethyl indole, and benz[e]indole adjoining benz[c,d]indol-1-ium, which was found to directly influence their optical and energy profiles. In this study the optical properties vs. structural changes were investigated using nuclear magnetic resonance and computational approaches. The twisted conformation unique to monomethine cyanines was exploited in DNA binding studies where the newly designed sensor displayed an increase in fluorescence when bound in the DNA grooves compared to the unbound form.
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25
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Singh T, Adekoya OA, Jayaram B. Understanding the binding of inhibitors of matrix metalloproteinases by molecular docking, quantum mechanical calculations, molecular dynamics simulations, and a MMGBSA/MMBappl study. MOLECULAR BIOSYSTEMS 2015; 11:1041-51. [PMID: 25611160 DOI: 10.1039/c5mb00003c] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Matrix metalloproteinases (MMPs) consist of a class of proteins required for normal tissue function. Their over expression is associated with many disease states and hence the interest in MMPs as drug targets. Almost all MMP inhibitors have been reported to fail in clinical trials due to lack of specificity. Zinc in the binding site of metalloproteinases performs essential biological functions and contributes to the binding affinity of inhibitors. The multiple possibilities for coordination geometry and the consequent charge on the zinc atom indicate that parameters developed are not directly transferable across different families of zinc metalloproteinases with different zinc coordination geometries, active sites and ligand architectures which makes it difficult to evaluate metal-ligand interactions. In order to assist in drug design endeavors for MMP targets, a computationally tractable pathway is presented, comprising docking of small molecule inhibitors against the target MMPs, derivation of quantum mechanical charges on the zinc ion in the active site and the amino acids coordinating with zinc including the inhibitor molecule, molecular dynamics simulations on the docked ligand-MMP complexes and evaluation of binding affinities of the ligand-MMP complexes via an accurate scoring function for zinc containing metalloprotein-ligand complexes. The above pathway was applied to study the interaction of inhibitor Batimastat with MMPs, which resulted in a high correlation between the predicted binding free energies and experiment, suggesting the potential applicability of the pathway. We then proceeded to formulate a few design principles which identify the key protein residues for generating molecules with high affinity and specificity against each of the MMPs.
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Affiliation(s)
- Tanya Singh
- Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi-110016, India.
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26
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Deng Y, Roux B. Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant. J Chem Theory Comput 2015; 2:1255-73. [PMID: 26626834 DOI: 10.1021/ct060037v] [Citation(s) in RCA: 224] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Calculations of the binding free energy of various nonpolar aromatic ligands with the L99A mutant of T4 lysozyme using molecular dynamics (MD) simulation are presented. To ensure better convergence, biasing potentials are used to restrain the ligand orientation and center-of-mass movement relative to the binding site when the ligand is decoupled from its environment in the binding pocket. The bias introduced by the restraint potentials is removed once the ligand fully interacts with the rest of the system and the calculated binding free energy is independent of the applied restraints. To decrease the computational cost, the simulations are generated with a reduced system in which protein and water atoms within a 15 Å-radius sphere around the ligand are included explicitly, while the rest of the system is treated with the generalized solvent boundary potential (GSBP). For all the ligands, the precision of the calculated free energy is less than 0.5 kcal/mol. For small nonpolar ligands such as benzene, toluene, and ethylbenzene, the calculated binding free energies are within 1.1 kcal/mol of the experimental values. For larger ligands, the computed binding free energies are slightly more favorable than the experimental values. The nonbinding polar molecule, phenol, has a calculated binding free energy of -0.88 kcal/mol. The simulation protocol presented here provides a way to calculate the binding free energy of small molecules to receptors at moderate computational cost.
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Affiliation(s)
- Yuqing Deng
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Building 221, Argonne, Illinois 60439, and Institute of Molecular Pediatric Sciences, Gordon Center for Integrative Sciences, University of Chicago, 929 East 57th Street, Room W323B, Chicago, Illinois 60637
| | - Benoît Roux
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Building 221, Argonne, Illinois 60439, and Institute of Molecular Pediatric Sciences, Gordon Center for Integrative Sciences, University of Chicago, 929 East 57th Street, Room W323B, Chicago, Illinois 60637
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27
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Furusawa H, Nakayama H, Funasaki M, Okahata Y. Kinetic characterization of small DNA-binding molecules interacting with a DNA strand on a quartz crystal microbalance. Anal Biochem 2015; 492:34-42. [PMID: 26408811 DOI: 10.1016/j.ab.2015.09.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 08/25/2015] [Accepted: 09/15/2015] [Indexed: 11/18/2022]
Abstract
Quantitative studies of the binding of various DNA-binding antibiotics with dsDNA are useful for drug design, not only for effective antibiotics, but also for antitumor drugs. We studied the binding kinetics, association and dissociation rate constants, and association constants (kon, koff, and Ka, respectively) of intercalators and groove binders, including various antibiotics, to double-stranded DNA (dA30·dT30 and dG30·dC30) immobilized on a highly sensitive 27 MHz quartz-crystal microbalance (QCM) in aqueous solution. Although a simple ethidium bromide intercalator bound to both dA30·dT30 and dG30·dC30, antibiotics that are side-binding intercalators, such as daunomycin, aclacinomycin A, and actinomycin D, with sugar or peptide moieties on the intercalator parts selectively bound to dG30·dC30 with high Ka and small koff values. Nogalamycin, a dumbbell-shaped penetrating intercalator, showed low kon and koff values owing to slow duplex unwinding during the penetration process. Groove binders (Hoechst 33258, distamycin A, and mithramycin) had high Ka values owing to the high kon values. Kinetic parameters depended largely on molecular shapes and DNA-binding molecule binding modes.
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Affiliation(s)
- Hiroyuki Furusawa
- Innovative Flex Course for Frontier Organic Material Systems (iFront), Graduate School of Science and Engineering, Yamagata University, 4-3-16 Jonan, Yonezawa, Yamagata, Japan; Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259, Nagatsuda, Midori-ku, Yokohama, Japan.
| | - Hajime Nakayama
- Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259, Nagatsuda, Midori-ku, Yokohama, Japan
| | - Mariko Funasaki
- Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259, Nagatsuda, Midori-ku, Yokohama, Japan
| | - Yoshio Okahata
- Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259, Nagatsuda, Midori-ku, Yokohama, Japan
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28
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Siboni RB, Bodner MJ, Khalifa MM, Docter AG, Choi JY, Nakamori M, Haley MM, Berglund JA. Biological Efficacy and Toxicity of Diamidines in Myotonic Dystrophy Type 1 Models. J Med Chem 2015; 58:5770-80. [PMID: 26103061 PMCID: PMC4972181 DOI: 10.1021/acs.jmedchem.5b00356] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Myotonic dystrophy type 1 (DM1) is a disease characterized by errors in alternative splicing, or "mis-splicing". The causative agent of mis-splicing in DM1 is an inherited CTG repeat expansion located in the 3' untranslated region of the DM protein kinase gene. When transcribed, CUG repeat expansion RNA sequesters muscleblind-like (MBNL) proteins, which constitute an important family of alternative splicing regulators. Sequestration of MBNL proteins results in the mis-splicing of its regulated transcripts. Previous work has demonstrated that pentamidine, a diamidine which is currently FDA-approved as an antiparasitic agent, was able to partially reverse mis-splicing in multiple DM1 models, albeit at toxic concentrations. In this study, we characterized a series of pentamidine analogues to determine their ability to reverse mis-splicing and their toxicity in vivo. Experiments in cell and mouse models demonstrated that compound 13, also known as furamidine, effectively reversed mis-splicing with equal efficacy and reduced toxicity compared to pentamidine.
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Affiliation(s)
| | | | | | | | | | - Masayuki Nakamori
- §Department of Neurology, University of Osaka Graduate School of Medicine, Osaka 565-0871, Japan
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29
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Pabbathi A, Samanta A. Spectroscopic and Molecular Docking Study of the Interaction of DNA with a Morpholinium Ionic Liquid. J Phys Chem B 2015; 119:11099-105. [PMID: 26061788 DOI: 10.1021/acs.jpcb.5b02939] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structural integrity of a nucleic acid under various conditions determines its utility in biocatalysis and biotechnology. Exploration of the ionic liquids (ILs) for extraction of DNA and other nucleic acid based applications requires an understanding of the nature of interaction between the IL and DNA. Considering these aspects, we have studied the interaction between calf-thymus DNA and a less toxic morpholinium IL, [Mor1,2][Br], employing fluorescence correlation spectroscopy (FCS), conventional steady state and time-resolved fluorescence, circular dichroism (CD) and molecular docking techniques. While the CD spectra indicate the stability of DNA and retention of its B-form in the presence of the morpholinium IL, the docking study reveals that [Mor1,2](+) binds to the minor groove of DNA with a binding energy of -4.57 kcal mol(-1). The groove binding of the cationic component of the IL is corroborated by the steady state fluorescence data, which indicated displacement of a known minor groove binder, DAPI, from its DNA-bound state on addition of [Mor1,2][Br]. The FCS measurements show that the hydrodynamic radius of DNA remains more or less constant in the presence of [Mor1,2][Br], thus suggesting that the structure of DNA is retained in the presence of the IL. DNA melting experiments show that the thermal stability of DNA is enhanced in the presence of morpholinium IL.
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Affiliation(s)
- Ashok Pabbathi
- School of Chemistry, University of Hyderabad , Hyderabad 500046, India
| | - Anunay Samanta
- School of Chemistry, University of Hyderabad , Hyderabad 500046, India
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30
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Eslami Moghadam M, Saidifar M, Divsalar A, Mansouri-Torshizi H, Saboury AA, Farhangian H, Ghadamgahi M. Rich spectroscopic and molecular dynamic studies on the interaction of cytotoxic Pt(II) and Pd(II) complexes of glycine derivatives with calf thymus DNA. J Biomol Struct Dyn 2015; 34:206-22. [DOI: 10.1080/07391102.2015.1015056] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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31
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Masum AA, Chakraborty M, Pandya P, Halder UC, Islam MM, Mukhopadhyay S. Thermodynamic Study of Rhodamine 123-Calf Thymus DNA Interaction: Determination of Calorimetric Enthalpy by Optical Melting Study. J Phys Chem B 2014; 118:13151-61. [DOI: 10.1021/jp509326r] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Abdulla Al Masum
- Department
of Chemistry, Aliah University, Sector V, Salt Lake City, Kolkata 700 091, India
| | | | - Prateek Pandya
- Department
of Chemistry, University of Rajasthan, Jaipur 302 004, India
| | | | - Md. Maidul Islam
- Department
of Chemistry, Aliah University, Sector V, Salt Lake City, Kolkata 700 091, India
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32
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Tumbi KM, Nandekar PP, Shaikh N, Kesharwani SS, Sangamwar AT. Molecular dynamics simulation studies for DNA sequence recognition by reactive metabolites of anticancer compounds. J Mol Recognit 2014; 27:138-50. [PMID: 24446378 DOI: 10.1002/jmr.2342] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 11/19/2013] [Accepted: 11/20/2013] [Indexed: 01/12/2023]
Abstract
The discovery of novel anticancer molecules 5F-203 (NSC703786) and 5-aminoflavone (5-AMF, NSC686288) has addressed the issues of toxicity and reduced efficacy by targeting over expressed Cytochrome P450 1A1 (CYP1A1) in cancer cells. CYP1A1 metabolizes these compounds into their reactive metabolites, which are proven to mediate their anticancer effect through DNA adduct formation. However, the drug metabolite-DNA binding has not been explored so far. Hence, understanding the binding characteristics and molecular recognition for drug metabolites with DNA is of practical and fundamental interest. The present study is aimed to model binding preference shown by reactive metabolites of 5F-203 and 5-AMF with DNA in forming DNA adducts. To perform this, three different DNA crystal structures covering sequence diversity were selected, and 12 DNA-reactive metabolite complexes were generated. Molecular dynamics simulations for all complexes were performed using AMBER 11 software after development of protocol for DNA-reactive metabolite system. Furthermore, the MM-PBSA/GBSA energy calculation, per-nucleotide energy decomposition, and Molecular Electrostatic Surface Potential analysis were performed. The results obtained from present study clearly indicate that minor groove in DNA is preferable for binding of reactive metabolites of anticancer compounds. The binding preferences shown by reactive metabolites were also governed by specific nucleotide sequence and distribution of electrostatic charges in major and minor groove of DNA structure. Overall, our study provides useful insights into the initial step of mechanism of reactive metabolite binding to the DNA and the guidelines for designing of sequence specific DNA interacting anticancer agents.
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Affiliation(s)
- Khaled M Tumbi
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER) S.A.S. Nagar, Punjab, India
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33
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Kostjukov VV, Rogova OV, Evstigneev MP. General features of the energetics of complex formation between ligand and nucleic acids. Biophysics (Nagoya-shi) 2014. [DOI: 10.1134/s0006350914040149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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34
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Kostjukov VV, Evstigneev MP. Energy analysis of non-covalent ligand binding to nucleic acids: Present and future. Biophysics (Nagoya-shi) 2014. [DOI: 10.1134/s0006350914040150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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35
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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]
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36
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Abstract
While the Watson-Crick base pairs are known to stabilize the DNA double helix and play a vital role in storage/replication of genetic information, their replacement with non-Watson-Crick base pairs has recently been shown to have interesting practical applications. Nowadays, theoretical calculations are routinely performed on very complex systems to gain a better understanding of how molecules interact with each other. We not only bring together some of the basic concepts of how mispaired or unnatural nucleobases interact with each other but also look at how such an understanding influences the prediction of novel properties and development of new materials. We highlight the recent developments in this field of research. In this Perspective, we discuss the success of DFT methods, particularly, dispersion-corrected DFT, for applications such as pH-controlled molecular switching, electric-field-induced stacking of disk-like molecules with guanine quartets, and optical birefringence of alkali-metal-coordinated guanine quartets. The synergy between theoretical models and real applications is highlighted.
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Affiliation(s)
- A K Jissy
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur 700032 West Bengal, India
| | - Ayan Datta
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur 700032 West Bengal, India
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37
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Chattopadhyay SK, Kundu I, Maitra R. The coumarin–pterocarpan conjugate – a natural product inspired hybrid molecular probe for DNA recognition. Org Biomol Chem 2014; 12:8087-93. [DOI: 10.1039/c4ob01360c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thermally induced cascade sigmatropic rearrangement of a butynyloxycoumarin derivative has led to a quick access to the coumarin–pterocarpan hybrid molecule. Biophysical studies together with molecular modeling show that this nature-inspired hybrid molecule is capable of binding to the minor groove of DNA as a non-conventional entity.
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Affiliation(s)
| | - Indranil Kundu
- Department of Chemistry
- University of Kalyani
- Nadia-742135, India
| | - Ratnava Maitra
- Department of Chemistry
- University of Kalyani
- Nadia-742135, India
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38
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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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39
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Al-Mudaris ZA, Majid ASA, Ji D, Al-Mudarris BA, Chen SH, Liang PH, Osman H, Jamal Din SKK, Abdul Majid AMS. Conjugation of benzylvanillin and benzimidazole structure improves DNA binding with enhanced antileukemic properties. PLoS One 2013; 8:e80983. [PMID: 24260527 PMCID: PMC3829952 DOI: 10.1371/journal.pone.0080983] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 10/18/2013] [Indexed: 11/19/2022] Open
Abstract
Benzyl-o-vanillin and benzimidazole nucleus serve as important pharmacophore in drug discovery. The benzyl vanillin (2-(benzyloxy)-3-methoxybenzaldehyde) compound shows anti-proliferative activity in HL60 leukemia cancer cells and can effect cell cycle progression at G2/M phase. Its apoptosis activity was due to disruption of mitochondrial functioning. In this study, we have studied a series of compounds consisting of benzyl vanillin and benzimidazole structures. We hypothesize that by fusing these two structures we can produce compounds that have better anticancer activity with improved specificity particularly towards the leukemia cell line. Here we explored the anticancer activity of three compounds namely 2-(2-benzyloxy-3-methoxyphenyl)-1H-benzimidazole, 2MP, N-1-(2-benzyloxy-3-methoxybenzyl)-2-(2-benzyloxy-3-methoxyphenyl)-1H-benzimidazole, 2XP, and (R) and (S)-1-(2-benzyloxy-3-methoxyphenyl)-2, 2, 2-trichloroethyl benzenesulfonate, 3BS and compared their activity to 2-benzyloxy-3-methoxybenzaldehyde, (Bn1), the parent compound. 2XP and 3BS induces cell death of U937 leukemic cell line through DNA fragmentation that lead to the intrinsic caspase 9 activation. DNA binding study primarily by the equilibrium binding titration assay followed by the Viscosity study reveal the DNA binding through groove region with intrinsic binding constant 7.39 µM/bp and 6.86 µM/bp for 3BS and 2XP respectively. 2XP and 3BS showed strong DNA binding activity by the UV titration method with the computational drug modeling showed that both 2XP and 3BS failed to form any electrostatic linkages except via hydrophobic interaction through the minor groove region of the nucleic acid. The benzylvanillin alone (Bn1) has weak anticancer activity even after it was combined with the benzimidazole (2MP), but after addition of another benzylvanillin structure (2XP), stronger activity was observed. Also, the combination of benzylvanillin with benzenesulfonate (3BS) significantly improved the anticancer activity of Bn1. The present study provides a new insight of benzyl vanillin derivatives as potential anti-leukemic agent.
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Affiliation(s)
- Zena A. Al-Mudaris
- School of Pharmaceutical Sciences, University Sains Malaysia, Minden, Penang, Malaysia
| | - Aman S. A. Majid
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bandar Putra Bertam, Penang, Malaysia
| | - Dan Ji
- Key Laboratory of Visual Damage and Regeneration & Restoration of Chongqing, Southwest Eye Hospital, Southwest Hospital, The Third Military Medical University, Chongqing, P.R.China
| | - Ban A. Al-Mudarris
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bandar Putra Bertam, Penang, Malaysia
- College of Dentistry, Ajman University, Ajman, UAE
| | - Shih-Hsun Chen
- Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan
| | - Po-Huang Liang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Hasnah Osman
- School of Chemical Sciences, University Sains Malaysia, Minden, Penang, Malaysia
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Shahabadi N, Fili SM, Kheirdoosh F. Study on the interaction of the drug mesalamine with calf thymus DNA using molecular docking and spectroscopic techniques. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2013; 128:20-6. [DOI: 10.1016/j.jphotobiol.2013.08.005] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 07/31/2013] [Accepted: 08/04/2013] [Indexed: 01/14/2023]
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Dumat B, Bordeau G, Faurel-Paul E, Mahuteau-Betzer F, Saettel N, Metge G, Fiorini-Debuisschert C, Charra F, Teulade-Fichou MP. DNA Switches on the Two-Photon Efficiency of an Ultrabright Triphenylamine Fluorescent Probe Specific of AT Regions. J Am Chem Soc 2013; 135:12697-706. [DOI: 10.1021/ja404422z] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Blaise Dumat
- Institut Curie, CNRS UMR-176, Centre Universitaire d’Orsay, Paris-Sud 91405
Orsay Cedex France
| | - Guillaume Bordeau
- Institut Curie, CNRS UMR-176, Centre Universitaire d’Orsay, Paris-Sud 91405
Orsay Cedex France
| | - Elodie Faurel-Paul
- Institut Curie, CNRS UMR-176, Centre Universitaire d’Orsay, Paris-Sud 91405
Orsay Cedex France
| | | | - Nicolas Saettel
- Institut Curie, CNRS UMR-176, Centre Universitaire d’Orsay, Paris-Sud 91405
Orsay Cedex France
| | - Germain Metge
- CEA-
Saclay, DSM-IRAMIS/SPCSI/Laboratoire NanoPhotonique, 91191 Gif-sur-Yvette, France
| | | | - Fabrice Charra
- CEA-
Saclay, DSM-IRAMIS/SPCSI/Laboratoire NanoPhotonique, 91191 Gif-sur-Yvette, France
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Sen A, Sahu D, Ganguly B. In silico studies toward understanding the interactions of DNA base pairs with protonated linear/cyclic diamines. J Phys Chem B 2013; 117:9840-50. [PMID: 23909683 DOI: 10.1021/jp402847u] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protonated amino groups are ubiquitous in nature and important in the fields of chemistry and biology. In search of efficient polyamine analogues, we have performed DFT calculations on the interactions of some simple cyclic and constrained protonated diamines with the DNA base pairs and compared the results with those obtained for the corresponding interactions involving linear diamines, which mimic biogenic polyamines such as spermine. The interactions are mainly governed by the strong hydrogen bonding between the ligand and the DNA base pairs. The DFT calculations suggest that the major-groove N7 interaction (GC base pair) with linear diamine is energetically more favored than other possible interactions, as reported with spermine. The cyclic diamines exhibited better interactions with the N7 site of the AT and GC base pairs of DNA than the linear diamines. The net atomic charges calculated for the protonated amine hydrogens were higher for the cyclic systems than for the linear diamines, inducing better binding affinity with the DNA base pairs. The stable conformers of cyclic diamines were predicted using the MP2/aug-cc-pVDZ level of theory. The positions of the protonated diamine groups in these cyclic systems are crucial for effective binding with the DNA base pairs. The DFT-calculated results show that diequatorial (ee) 1,2-cyclohexadiamine (CHDA) is a promising candidate as a polyamine analogue for biogenic polyamines. Molecular dynamics simulations were performed using explicit water molecules for the interaction of representative ligands with the DNA base pairs to examine the influence of solvent molecules on such interactions.
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Affiliation(s)
- Anik Sen
- Computation and Simulation Unit, Analytical Discipline & Centralized Instrument Facility, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat 364002, India
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Samanta SK, Dutta D, Roy S, Bhattacharya K, Sarkar S, Dasgupta AK, Pal BC, Mandal C, Mandal C. Mahanine, A DNA Minor Groove Binding Agent Exerts Cellular Cytotoxicity with Involvement of C-7-OH and −NH Functional Groups. J Med Chem 2013; 56:5709-21. [DOI: 10.1021/jm400290q] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Suman K. Samanta
- Cancer Biology and Inflammatory
Disorder Division, Council of Scientific and Industrial Research—Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, India
| | - Devawati Dutta
- Cancer Biology and Inflammatory
Disorder Division, Council of Scientific and Industrial Research—Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, India
| | - Sarita Roy
- Department of Biochemistry, University of Calcutta, 35 Ballygunge Circular Road,
Kolkata 700019, India
| | - Kaushik Bhattacharya
- Cancer Biology and Inflammatory
Disorder Division, Council of Scientific and Industrial Research—Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, India
| | - Sayantani Sarkar
- Cancer Biology and Inflammatory
Disorder Division, Council of Scientific and Industrial Research—Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, India
| | - Anjan K. Dasgupta
- Department of Biochemistry, University of Calcutta, 35 Ballygunge Circular Road,
Kolkata 700019, India
| | - Bikas C. Pal
- National Institute of Pharmaceutical Education and Research, Kolkata, 4
Raja S. C. Mullick Road, Kolkata 700032, India
| | - Chhabinath Mandal
- National Institute of Pharmaceutical Education and Research, Kolkata, 4
Raja S. C. Mullick Road, Kolkata 700032, India
| | - Chitra Mandal
- Cancer Biology and Inflammatory
Disorder Division, Council of Scientific and Industrial Research—Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, India
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Studies on the interaction mechanism of aminopyrene derivatives with human tumor-related DNA. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2013; 123:32-40. [DOI: 10.1016/j.jphotobiol.2013.03.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 03/05/2013] [Accepted: 03/24/2013] [Indexed: 11/20/2022]
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Soni A, Pandey KM, Ray P, Jayaram B. Genomes to hits in silico - a country path today, a highway tomorrow: a case study of chikungunya. Curr Pharm Des 2013; 19:4687-700. [PMID: 23260020 PMCID: PMC3831887 DOI: 10.2174/13816128113199990379] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Accepted: 12/17/2012] [Indexed: 12/11/2022]
Abstract
These are exciting times for bioinformaticians, computational biologists and drug designers with the genome and proteome sequences and related structural databases growing at an accelerated pace. The post-genomic era has triggered high expectations for a rapid and successful treatment of diseases. However, in this biological information rich and functional knowledge poor scenario, the challenges are indeed grand, no less than the assembly of the genome of the whole organism. These include functional annotation of genes, identification of druggable targets, prediction of three-dimensional structures of protein targets from their amino acid sequences, arriving at lead compounds for these targets followed by a transition from bench to bedside. We propose here a "Genome to Hits In Silico" strategy (called Dhanvantari) and illustrate it on Chikungunya virus (CHIKV). "Genome to hits" is a novel pathway incorporating a series of steps such as gene prediction, protein tertiary structure determination, active site identification, hit molecule generation, docking and scoring of hits to arrive at lead compounds. The current state of the art for each of the steps in the pathway is high-lighted and the feasibility of creating an automated genome to hits assembly line is discussed.
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Affiliation(s)
- Anjali Soni
- Department of Chemistry, Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, Hauz Khas, New Delhi-110016, India.
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Mukherjee G, Jayaram B. A rapid identification of hit molecules for target proteins via physico-chemical descriptors. Phys Chem Chem Phys 2013; 15:9107-16. [DOI: 10.1039/c3cp44697b] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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47
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Ning J, Chen W, Li J, Peng Z, Wang J, Ni Z. Structural and energetic insights into sequence-specific interaction in DNA–drug recognition: development of affinity predictor and analysis of binding selectivity. J Mol Model 2012; 19:1573-82. [DOI: 10.1007/s00894-012-1722-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 12/03/2012] [Indexed: 11/28/2022]
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Jayaram B, Singh T, Mukherjee G, Mathur A, Shekhar S, Shekhar V. Sanjeevini: a freely accessible web-server for target directed lead molecule discovery. BMC Bioinformatics 2012; 13 Suppl 17:S7. [PMID: 23282245 PMCID: PMC3521208 DOI: 10.1186/1471-2105-13-s17-s7] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Background Computational methods utilizing the structural and functional information help to understand specific molecular recognition events between the target biomolecule and candidate hits and make it possible to design improved lead molecules for the target. Results Sanjeevini represents a massive on-going scientific endeavor to provide to the user, a freely accessible state of the art software suite for protein and DNA targeted lead molecule discovery. It builds in several features, including automated detection of active sites, scanning against a million compound library for identifying hit molecules, all atom based docking and scoring and various other utilities to design molecules with desired affinity and specificity against biomolecular targets. Each of the modules is thoroughly validated on a large dataset of protein/DNA drug targets. Conclusions The article presents Sanjeevini, a freely accessible user friendly web-server, to aid in drug discovery. It is implemented on a tera flop cluster and made accessible via a web-interface at http://www.scfbio-iitd.res.in/sanjeevini/sanjeevini.jsp. A brief description of various modules, their scientific basis, validation, and how to use the server to develop in silico suggestions of lead molecules is provided.
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Affiliation(s)
- B Jayaram
- Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi-110016, India.
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Abstract
Pyrene derivatives can be carcinogenic, teratogenic and mutagenic, thus having the potential to cause malignant diseases. In this work, the interactions of two selected pyrene derivatives (1-OHP and 1-PBO) and human tumor-related DNA (p53 DNA and C-myc DNA) are investigated by spectroscopic and non-native polyacrylamide gel electrophoresis (PAGE) methods. Using fluorescence spectrometry and circular dichroism (CD), DNA interactions of pyrene derivatives are confirmed to occur mainly via the groove binding mode supported by the intercalation into the base pairs of DNA. There is an obvious binding order of pyrene derivatives to the targeted DNA, 1-OHP > 1-PBO. The binding constants of 1-OHP are 1.16 × 106 L·mol−1 and 4.04 × 105 L·mol−1 for p53 DNA and C-myc DNA, respectively, while that of 1-PBO are only 2.04 × 103 L·mol−1 and 1.39 × 103 L·mol−1 for p53 DNA and C-myc DNA, respectively. Besides, the binding of pyrene derivatives to p53 DNA is stronger than that for C-myc DNA. CD and PAGE results indicate that the binding of pyrene derivatives can affect the helical structures of DNA and further induce the formation of double-chain antiparallel G-quadruplex DNA of hybrid G-rich sequences.
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50
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Zhu X, Schatz GC. Molecular dynamics study of the role of the spine of hydration in DNA A-tracts in determining nucleosome occupancy. J Phys Chem B 2012; 116:13672-81. [PMID: 23102092 PMCID: PMC3508256 DOI: 10.1021/jp3084887] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A-tracts in DNA are generally associated with reduced nucleosome occupancy relative to other sequences, such that the longer the A-tract, the less likely that nucleosomes are found. In this paper, we use molecular dynamics methods to study the structural properties of A-tracts, and in particular the role that the spine of hydration in A-tracts plays in allowing DNA to distort to the highly bent structure needed to form nucleosomes. This study includes a careful assessment of the ability of the Amber (parmbsc0), CHARMM27, and BMS force fields to describe these structural waters for the AAATTT sequence (here capped with CGC and GCG), including comparisons with X-ray results. All three force fields show a spine of hydration, but BMS and Amber show better correlation with measured properties, such as in narrowing of the minor groove width associated with the A-tract. We have used Amber to study the spine properties for several 6 and 14 base-pair A-tracts (all capped with CGC and GCG). These calculations show that the structural waters are tightly bound for "pure" A-tracts that allow for A-water-T links, and for AT steps that allow for a T-water-T link, but other sequences disfavor structural water, especially those that lead to A-water-A, G-water-G, and C-water-A structures. In addition, we show that pure A-tracts favor roll values close to the Watson-Crick value for linear DNA, while A-tract sequences containing embedded T's, C's, or G's that are less favorable to structural water are more flexible. This implies the essential role of the spine of hydration in disfavoring nucleosome formation.
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Affiliation(s)
- Xiao Zhu
- Texas Advanced Computing Center, Austin, Texas 78758-4497, USA
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