1
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Brossard EE, Corcelli SA. Mechanism of Daunomycin Intercalation into DNA from Enhanced Sampling Simulations. J Phys Chem Lett 2024; 15:5770-5778. [PMID: 38776167 DOI: 10.1021/acs.jpclett.4c00961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
Daunomycin is a widely used anticancer drug, yet the mechanism underlying how it binds to DNA remains contested. 469 all-atom trajectories of daunomycin binding to the DNA oligonucleotide d(GCG CAC GTG CGC) were collected using weighted ensemble (WE)-enhanced sampling. Mechanistic insights were revealed through analysis of the ensemble of trajectories. Initially, the binding process involves a ubiquitous hydrogen bond between the DNA backbone and the NH3+ group on daunomycin. During the binding process, most trajectories exhibited similar structural changes to DNA, including DNA base pair rise, bending, and minor groove width changes. Variability within the ensemble of binding trajectories illuminates differences in the orientation of daunomycin as it initially intercalates; around 10% of trajectories needed minimal rearrangement from intercalation to reaching the fully bound configuration, whereas most needed an additional 1-5 ns to rearrange. The results here emphasize the utility of generating an ensemble of trajectories to discern biomolecular binding mechanisms.
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Affiliation(s)
- E E Brossard
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - S A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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2
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Brossard EE, Corcelli SA. Molecular Mechanism of Ligand Binding to the Minor Groove of DNA. J Phys Chem Lett 2023; 14:4583-4590. [PMID: 37163748 DOI: 10.1021/acs.jpclett.3c00635] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Although DNA-ligand binding is pervasive in biology, little is known about molecular-level binding mechanisms. Using all-atom, explicit-solvent molecular dynamics simulations in conjunction with weighted ensemble (WE)-enhanced sampling, an ensemble of 2562 binding trajectories of Hoechst 33258 (H33258) to d(CGC AAA TTT GCG) was generated from which the binding mechanism was extracted. In particular, the electrostatic interaction between the positively charged H33258 and the negatively charged DNA backbone drives the formation of initial H33258-DNA contacts. After this initial contact, a hinge-like intermediate state is formed in which one end of H33258 inserts into the minor groove of DNA. Following hinge state formation is a concerted motion whereby the second end of H33258 swings into the minor groove and the spine of hydration along the minor groove causing dehydration. This study illustrates how WE-enhanced simulations of biomolecular ligation processes can offer novel mechanistic insights by generating ensembles of binding events.
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Affiliation(s)
- E E Brossard
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - S A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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3
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Vianney YM, Weisz K. High-affinity binding at quadruplex-duplex junctions: rather the rule than the exception. Nucleic Acids Res 2022; 50:11948-11964. [PMID: 36416262 PMCID: PMC9723630 DOI: 10.1093/nar/gkac1088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/19/2022] [Accepted: 10/26/2022] [Indexed: 11/24/2022] Open
Abstract
Quadruplex-duplex (Q-D) junctions constitute unique structural motifs in genomic sequences. Through comprehensive calorimetric as well as high-resolution NMR structural studies, Q-D junctions with a hairpin-type snapback loop coaxially stacked onto an outer G-tetrad were identified to be most effective binding sites for various polycyclic quadruplex ligands. The Q-D interface is readily recognized by intercalation of the ligand aromatic core structure between G-tetrad and the neighboring base pair. Based on the thermodynamic and structural data, guidelines for the design of ligands with enhanced selectivity towards a Q-D interface emerge. Whereas intercalation at Q-D junctions mostly outcompete stacking at the quadruplex free outer tetrad or intercalation between duplex base pairs to varying degrees, ligand side chains considerably contribute to the selectivity for a Q-D target over other binding sites. In contrast to common perceptions, an appended side chain that additionally interacts within the duplex minor groove may confer only poor selectivity. Rather, the Q-D selectivity is suggested to benefit from an extension of the side chain towards the exposed part of the G-tetrad at the junction. The presented results will support the design of selective high-affinity binding ligands for targeting Q-D interfaces in medicinal but also technological applications.
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Affiliation(s)
- Yoanes Maria Vianney
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, D-17489 Greifswald, Germany
| | - Klaus Weisz
- To whom correspondence should be addressed. Tel: +49 3834 420 4426; Fax: +49 3834 420 4427;
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4
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Rozza AM, Bakó I, Oláh J. Theoretical insights into water network of B-DNA duplex with Watson-Crick and Hoogsteen base pairing geometries. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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5
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Sinha R, Chatterjee A, Purkayastha P. Graphene Quantum Dot Assisted Translocation of Daunomycin through an Ordered Lipid Membrane: A Study by Fluorescence Lifetime Imaging Microscopy and Resonance Energy Transfer. J Phys Chem B 2022; 126:1232-1241. [PMID: 35129981 DOI: 10.1021/acs.jpcb.1c09376] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Daunomycin (DN) is a well-known chemotherapy drug frequently used in treating acute myeloid and lymphoblastic leukemia. It needs to be delivered to the therapeutic target by a delivering agent that beats the blood-brain barrier. DN is known to be specifically located at the membrane surface and scantly to the bilayer. Penetration of DN into the membrane bilayer depends on the molecular packing of the lipid. It does not travel promptly to the interior of the cells and needs a carrier to serve the purpose. Here, we have demonstrated, by fluorescence lifetime imaging spectroscopy (FLIM) and resonance energy transfer (RET) phenomenon, that ultrasmall graphene quantum dots (GQDs) can be internalized into the aqueous pool of giant unilamellar vesicles (GUVs) made from dipalmitoylphosphatidylcholine (DPPC) lipids, which, in turn, help in fast translocation of DN through the membrane without any delivery vehicle.
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Affiliation(s)
- Riya Sinha
- Department of Chemical Sciences and Centre for Advanced Functional Materials (CAFM), Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, WB, India
| | - Arunavo Chatterjee
- Department of Chemical Sciences and Centre for Advanced Functional Materials (CAFM), Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, WB, India
| | - Pradipta Purkayastha
- Department of Chemical Sciences and Centre for Advanced Functional Materials (CAFM), Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, WB, India
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6
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Wakchaure PD, Ganguly B. Deciphering the mechanism of action of 5FDQD and the design of new neutral analogues for the FMN riboswitch: a well-tempered metadynamics simulation study. Phys Chem Chem Phys 2022; 24:817-828. [PMID: 34928280 DOI: 10.1039/d1cp01348c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The FMN riboswitch is a novel drug target for the design of new antibiotics, and efforts have been made to design new charged and uncharged ligands. Uncharged ligands have shown advantages of not requiring any transporter for intracellular transport or proteins for their phosphorylation. 5FDQD (5-(3-(4-fluorophenyl)butyl)-7,8-dimethylpyrido(3,4-b)quinoxaline-1,3(2H,5H)-dione) is a recently reported neutral ligand for the FMN riboswitch active against Clostridium difficile infection in mice. However, the crystal structure of the 5FDQD bound FMN riboswitch is not available, and the mechanism of ligand binding and triggering the function of the riboswitch is not well understood. We have examined 5FDQD for its binding affinity with the FMN riboswitch using the well-tempered metadynamics (WT-MtD) simulation technique. The crystal structure of the FMN riboswitch shows that the FMN interacts with the J4/5 region through the phosphate group with G62; however, the uncharged ligands take advantage of π-π stacking interactions with the same residue of the riboswitch observed from the WT-MtD simulation results. The simulation results show that the presence of fluorine on the phenyl ring in 5FDQD is important to enhance the binding affinity of the neutral ligands with the FMN riboswitch. The WT-MtD results showed that the 1,2-difluoro substitution on the phenyl ring in 5FDQD (FMN-difluoro2) and the 1,3 positions in the phenyl ring (FMN-difluoro1) showed weaker binding energy with the FMN riboswitch compared to 5FDQD. The substitution of another fluorine atom at the 5-position of the phenyl ring (FMN-trifluoro) showed a comparable binding affinity (∼-31.4 kcal mol-1) to 5FDQD. Electron-donating substitution on the phenyl ring such as the amino group also lowered the binding affinity (-28.8 kcal mol-1) with the riboswitch compared to 5FDQD. The computed results suggest that the position and nature of substitution in the phenyl ring of the uncharged ligands affect the overall binding and such a delicate balance is important to achieve superior binding affinity with the FMN riboswitch.
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Affiliation(s)
- Padmaja D Wakchaure
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar-364002, Gujarat, India.,Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh-201 002, India.
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar-364002, Gujarat, India.,Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh-201 002, India.
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7
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Majumder R, Das CK, Banerjee I, Chandra Jena B, Mandal A, Das P, Pradhan AK, Das S, Basak P, Das SK, Emdad L, Fisher PB, Mandal M. Screening of the Prime bioactive compounds from Aloe vera as potential anti-proliferative agents targeting DNA. Comput Biol Med 2021; 141:105052. [PMID: 34836625 DOI: 10.1016/j.compbiomed.2021.105052] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/31/2021] [Accepted: 11/16/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND Aloe vera extract and its bioactive compounds possess anti-proliferative properties against cancer cells. However, no detailed molecular mechanism of action studies has been reported. We have now employed a computational approach to scrutinize the molecular mechanism of lead bioactive compounds from Aloe vera that potentially inhibit DNA synthesis. METHODS Initially, the anti-proliferative activity of Aloe vera extract was examined in human breast cancer cells (in vitro/in vivo). Later on, computational screening of bioactive compounds from Aloe vera targeting DNA was performed by molecular docking and molecular dynamics simulation. RESULTS In-vitro and in-vivo studies confirm that Aloe vera extract effectively suppresses the growth of breast cancer cells without significant cytotoxicity towards non-cancerous normal immortal cells. Computational screening predicts that growth suppression may be due to the presence of DNA intercalating bioactive compounds (riboflavin, daidzin, aloin, etc.) contained in Aloe vera. MM/PBSA calculation showed that riboflavin has a higher binding affinity at the DNA binding sites compared to standard drug daunorubicin. CONCLUSIONS These observations support the hypothesis that riboflavin may be exploited as an anti-proliferative DNA intercalating agent to prevent cancer and is worthy of testing for the management of cancer by performing more extensive pre-clinical and if validated clinical trials.
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Affiliation(s)
- Ranabir Majumder
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Bengal, India
| | - Chandan Kanta Das
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Bengal, India
| | - Indranil Banerjee
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Bengal, India
| | - Bikash Chandra Jena
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Bengal, India
| | - Anik Mandal
- Electronics and Electrical Communication Engineering, Indian Institute of Technology Kharagpur, West Bengal, India
| | - Pratik Das
- School of Bioscience and Engineering, Jadavpur University, Kolkata, West Bengal, India
| | - Anjan Kumar Pradhan
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA, 23298, USA
| | - Subhasis Das
- Patient-Derived Models Core Lab, University of Illinois Cancer Center and Department of Surgery, College of Medicine, University of Illinois at Chicago, Chicago, 60612, USA
| | - Piyali Basak
- School of Bioscience and Engineering, Jadavpur University, Kolkata, West Bengal, India
| | - Swadesh K Das
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA, 23298, USA
| | - Luni Emdad
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA, 23298, USA
| | - Paul B Fisher
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA, 23298, USA
| | - Mahitosh Mandal
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Bengal, India.
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8
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Singh AK, Wen C, Cheng S, Vinh NQ. Long-range DNA-water interactions. Biophys J 2021; 120:4966-4979. [PMID: 34687717 DOI: 10.1016/j.bpj.2021.10.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/14/2021] [Accepted: 10/18/2021] [Indexed: 11/18/2022] Open
Abstract
DNA functions only in aqueous environments and adopts different conformations depending on the hydration level. The dynamics of hydration water and hydrated DNA leads to rotating and oscillating dipoles that, in turn, give rise to a strong megahertz to terahertz absorption. Investigating the impact of hydration on DNA dynamics and the spectral features of water molecules influenced by DNA, however, is extremely challenging because of the strong absorption of water in the megahertz to terahertz frequency range. In response, we have employed a high-precision megahertz to terahertz dielectric spectrometer, assisted by molecular dynamics simulations, to investigate the dynamics of water molecules within the hydration shells of DNA as well as the collective vibrational motions of hydrated DNA, which are vital to DNA conformation and functionality. Our results reveal that the dynamics of water molecules in a DNA solution is heterogeneous, exhibiting a hierarchy of four distinct relaxation times ranging from ∼8 ps to 1 ns, and the hydration structure of a DNA chain can extend to as far as ∼18 Å from its surface. The low-frequency collective vibrational modes of hydrated DNA have been identified and found to be sensitive to environmental conditions including temperature and hydration level. The results reveal critical information on hydrated DNA dynamics and DNA-water interfaces, which impact the biochemical functions and reactivity of DNA.
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Affiliation(s)
- Abhishek K Singh
- Department of Physics and Center for Soft Matter and Biological Physics, Blacksburg, Virginia
| | - Chengyuan Wen
- Department of Physics and Center for Soft Matter and Biological Physics, Blacksburg, Virginia
| | - Shengfeng Cheng
- Department of Physics and Center for Soft Matter and Biological Physics, Blacksburg, Virginia; Macromolecules Innovation Institute, Blacksburg, Virginia; Department of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia
| | - Nguyen Q Vinh
- Department of Physics and Center for Soft Matter and Biological Physics, Blacksburg, Virginia; Macromolecules Innovation Institute, Blacksburg, Virginia; Department of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia.
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9
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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.
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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
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10
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Aggarwal A, Sahoo AK, Bag S, Kaliginedi V, Jain M, Maiti PK. Fine-tuning the DNA conductance by intercalation of drug molecules. Phys Rev E 2021; 103:032411. [PMID: 33862831 DOI: 10.1103/physreve.103.032411] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 03/08/2021] [Indexed: 11/07/2022]
Abstract
In this work we study the structure-transport property relationships of small ligand intercalated DNA molecules using a multiscale modeling approach where extensive ab initio calculations are performed on numerous MD-simulated configurations of dsDNA and dsDNA intercalated with two different intercalators, ethidium and daunomycin. DNA conductance is found to increase by one order of magnitude upon drug intercalation due to the local unwinding of the DNA base pairs adjacent to the intercalated sites, which leads to modifications of the density of states in the near-Fermi-energy region of the ligand-DNA complex. Our study suggests that the intercalators can be used to enhance or tune the DNA conductance, which opens new possibilities for their potential applications in nanoelectronics.
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Affiliation(s)
- Abhishek Aggarwal
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Anil Kumar Sahoo
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Saientan Bag
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Veerabhadrarao Kaliginedi
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Manish Jain
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
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11
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Zhao L, Gu Z. Potential Unwinding of Double-Stranded DNA upon Binding to a Carbon Nitride Polyaniline (C 3N) Nanosheet. J Phys Chem B 2021; 125:2258-2265. [PMID: 33625858 DOI: 10.1021/acs.jpcb.0c11288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recently, carbon nitride polyaniline (C3N) had attracted considerable attention from many scientific fields after its successful synthesis. However, thus far, limited efforts were devoted to reveal its potential effect to biomolecules, which correlated intimately with its further utilization. In this study, by using a molecular dynamics (MD) simulation approach, we investigated in detail the interaction between C3N and a double-stranded DNA (dsDNA) segment to expose the underlying biological effect of C3N to dsDNA and the corresponding molecular basis. MD simulation results demonstrated that dsDNA presented serious damages upon adsorption onto a C3N nanosheet with the terminal base pairs denaturized, unwound, and directly packing on the C3N surface, which implied that C3N was potentially deleterious to biomolecules. This binding/unwinding process was mainly guided by a combination of van der Waals and π-π stacking interactions together with a continuous lateral migration of dsDNA. Moreover, the nanoscale dewetting also played an important role during the adsorption. These findings revealed the potential bio-effect of the C3N nanomaterial and its molecular mechanism, which might benefit the future applications of C3N-based nanostructures.
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Affiliation(s)
- Liang Zhao
- College of Physical Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Zonglin Gu
- College of Physical Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
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12
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Cárdenas G, Nogueira JJ. Stacking Effects on Anthraquinone/DNA Charge-Transfer Electronically Excited States. Molecules 2020; 25:E5927. [PMID: 33333751 PMCID: PMC7765225 DOI: 10.3390/molecules25245927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/03/2020] [Accepted: 12/13/2020] [Indexed: 12/14/2022] Open
Abstract
The design of more efficient photosensitizers is a matter of great importance in the field of cancer treatment by means of photodynamic therapy. One of the main processes involved in the activation of apoptosis in cancer cells is the oxidative stress on DNA once a photosensitizer is excited by light. As a consequence, it is very relevant to investigate in detail the binding modes of the chromophore with DNA, and the nature of the electronically excited states that participate in the induction of DNA damage, for example, charge-transfer states. In this work, we investigate the electronic structure of the anthraquinone photosensitizer intercalated into a double-stranded poly(dG-dC) decamer model of DNA. First, the different geometric configurations are analyzed by means of classical molecular dynamics simulations. Then, the excited states for the most relevant poses of anthraquinone inside the binding pocket are computed by an electrostatic-embedding quantum mechanics/molecular mechanics approach, where anthraquinone and one of the nearby guanine residues are described quantum mechanically to take into account intermolecular charge-transfer states. The excited states are characterized as monomer, exciton, excimer, and charge-transfer states based on the analysis of the transition density matrix, and each of these contributions to the total density of states and absorption spectrum is discussed in terms of the stacking interactions. These results are relevant as they represent the footing for future studies on the reactivity of anthraquinone derivatives with DNA and give insights on possible geometrical configurations that potentially favor the oxidative stress of DNA.
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Affiliation(s)
- Gustavo Cárdenas
- Chemistry Department, Universidad Autónoma de Madrid, Calle Francisco Tomás y Valiente, 7, 28049 Madrid, Spain;
| | - Juan J. Nogueira
- Chemistry Department, Universidad Autónoma de Madrid, Calle Francisco Tomás y Valiente, 7, 28049 Madrid, Spain;
- IADCHEM, Institute for Advanced Research in Chemistry, Universidad Autónoma de Madrid, Calle Francisco Tomás y Valiente, 7, 28049 Madrid, Spain
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13
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Decherchi S, Cavalli A. Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation. Chem Rev 2020; 120:12788-12833. [PMID: 33006893 PMCID: PMC8011912 DOI: 10.1021/acs.chemrev.0c00534] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Indexed: 12/19/2022]
Abstract
Computational studies play an increasingly important role in chemistry and biophysics, mainly thanks to improvements in hardware and algorithms. In drug discovery and development, computational studies can reduce the costs and risks of bringing a new medicine to market. Computational simulations are mainly used to optimize promising new compounds by estimating their binding affinity to proteins. This is challenging due to the complexity of the simulated system. To assess the present and future value of simulation for drug discovery, we review key applications of advanced methods for sampling complex free-energy landscapes at near nonergodicity conditions and for estimating the rate coefficients of very slow processes of pharmacological interest. We outline the statistical mechanics and computational background behind this research, including methods such as steered molecular dynamics and metadynamics. We review recent applications to pharmacology and drug discovery and discuss possible guidelines for the practitioner. Recent trends in machine learning are also briefly discussed. Thanks to the rapid development of methods for characterizing and quantifying rare events, simulation's role in drug discovery is likely to expand, making it a valuable complement to experimental and clinical approaches.
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Affiliation(s)
- Sergio Decherchi
- Computational
and Chemical Biology, Fondazione Istituto
Italiano di Tecnologia, 16163 Genoa, Italy
| | - Andrea Cavalli
- Computational
and Chemical Biology, Fondazione Istituto
Italiano di Tecnologia, 16163 Genoa, Italy
- Department
of Pharmacy and Biotechnology, University
of Bologna, 40126 Bologna, Italy
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14
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Abstract
The solvation properties of liquid water originate from the transient network of hydrogen-bonded molecules. In order to probe the coupling between the different modes of this network, nonlinear terahertz (THz) spectroscopy techniques are required. Ideally, these techniques should use a minimal volume and capitalize on sensitive field-resolved detection. Here we performed open aperture z-scan transmission experiments on static liquid cells, and detect the THz fields with electro-optical techniques. We show that it is possible to quantify the nonlinear response of liquid water at ~1 THz even when large signals originate from the sample holder windows.
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15
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Novelli F, Guchhait B, Havenith M. Towards Intense THz Spectroscopy on Water: Characterization of Optical Rectification by GaP, OH1, and DSTMS at OPA Wavelengths. MATERIALS (BASEL, SWITZERLAND) 2020; 13:E1311. [PMID: 32183131 PMCID: PMC7143731 DOI: 10.3390/ma13061311] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/05/2020] [Accepted: 03/10/2020] [Indexed: 12/02/2022]
Abstract
Water is the most prominent solvent. The unique properties of water are rooted in the dynamical hydrogen-bonded network. While TeraHertz (THz) radiation can probe directly the collective molecular network, several open issues remain about the interpretation of these highly anharmonic, coupled bands. In order to address this problem, we need intense THz radiation able to drive the liquid into the nonlinear response regime. Firstly, in this study, we summarize the available brilliant THz sources and compare their emission properties. Secondly, we characterize the THz emission by Gallium Phosphide (GaP), 2-{3-(4-hydroxystyryl)-5,5-dimethylcyclohex-2-enylidene}malononitrile (OH1), and 4-N,N-dimethylamino-4'-N'-methyl-stilbazolium 2,4,6-trimethylbenzenesulfonate (DSTMS) crystals pumped by an amplified near-infrared (NIR) laser with tunable wavelength. We found that both OH1 as well as DSTMS could convert NIR laser radiation between 1200 and 2500 nm into THz radiation with high efficiency (> 2 × 10-4), resulting in THz peak fields exceeding 0.1 MV/cm for modest pump excitation (~ mJ/cm2). DSTMS emits the broadest spectrum, covering the entire bandwidth of our detector from ca. 0.5 to ~7 THz, also at a laser wavelength of 2100 nm. Future improvements will require handling the photothermal damage of these delicate organic crystals, and increasing the THz frequency.
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Affiliation(s)
- Fabio Novelli
- Department of Physical Chemistry II, Ruhr University Bochum, 44801 Bochum, Germany;
| | - Biswajit Guchhait
- Department of Physical Chemistry II, Ruhr University Bochum, 44801 Bochum, Germany;
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Greater Noida, Uttar Pradesh 201314, India
| | - Martina Havenith
- Department of Physical Chemistry II, Ruhr University Bochum, 44801 Bochum, Germany;
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16
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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.
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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
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17
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Maganti L, Bhattacharyya D. Sequence specificity in DNA–drug intercalation: MD simulation and density functional theory approaches. J Comput Aided Mol Des 2019; 34:83-95. [DOI: 10.1007/s10822-019-00268-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/29/2019] [Indexed: 12/14/2022]
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18
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Sahoo AK, Bagchi B, Maiti PK. Understanding enhanced mechanical stability of DNA in the presence of intercalated anticancer drug: Implications for DNA associated processes. J Chem Phys 2019; 151:164902. [PMID: 31675856 DOI: 10.1063/1.5117163] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Most of the anticancer drugs bind to double-stranded DNA (dsDNA) by intercalative-binding mode. Although experimental studies have become available recently, a molecular-level understanding of the interactions between the drug and dsDNA that lead to the stability of the intercalated drug is lacking. Of particular interest are the modifications of the mechanical properties of dsDNA observed in experiments. The latter could affect many biological functions, such as DNA transcription and replication. Here, we probe, via all-atom molecular dynamics (MD) simulations, the change in the mechanical properties of intercalated drug-DNA complexes for two intercalators, daunomycin and ethidium. We find that, upon drug intercalation, the stretch modulus of DNA increases significantly, whereas its persistence length and bending modulus decrease. Steered MD simulations reveal that it requires higher forces to stretch the intercalated dsDNA complexes than the normal dsDNA. Adopting various pulling protocols to study force-induced DNA melting, we find that the dissociation of dsDNA becomes difficult in the presence of intercalators. The results obtained here provide a plausible mechanism of function of the anticancer drugs, i.e., via altering the mechanical properties of DNA. We also discuss long-time consequences of using these drugs, which require further in vivo investigations.
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Affiliation(s)
- Anil Kumar Sahoo
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
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19
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Sardana D, Yadav K, Shweta H, Clovis NS, Alam P, Sen S. Origin of Slow Solvation Dynamics in DNA: DAPI in Minor Groove of Dickerson-Drew DNA. J Phys Chem B 2019; 123:10202-10216. [PMID: 31589442 DOI: 10.1021/acs.jpcb.9b09275] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The measurement and understanding of collective solvation dynamics in DNA have vital biological implications, as protein and ligand binding to DNA can be directly controlled by complex electrostatic interactions of anionic DNA and surrounding dipolar water, and ions. Time-resolved fluorescence Stokes shift (TRFSS) experiments revealed anomalously slow solvation dynamics in DNA much beyond 100 ps that follow either power-law or slow multiexponential decay over several nanoseconds. The origin of such dispersed dynamics remains difficult to understand. Here we compare results of TRFSS experiments to molecular dynamics (MD) simulations of well-known 4',6-diamidino-2-phenylindole (DAPI)/Dickerson-Drew DNA complex over five decades of time from 100 fs to 10 ns to understand the origin of such dispersed dynamics. We show that the solvation time-correlation function (TCF) calculated from 200 ns simulation trajectory (total 800 ns) captures most features of slow dynamics as measured in TRFSS experiments. Decomposition of TCF into individual components unravels that slow dynamics originating from dynamically coupled DNA-water motion, although contribution from coupled water-Na+ motion is non-negligible. The analysis of residence time of water molecules around the probe (DAPI) reveals broad distribution from ∼6 ps to ∼3.5 ns: Several (49 nos.) water molecules show residences time greater than 500 ps, of which at least 14 water molecules show residence times of more than 1 ns in the first solvation shell of DAPI. Most of these slow water molecules are found to occupy two hydration sites in the minor groove near DAPI binding site. The residence time of Na+, however, is found to vary within ∼17-120 ps. Remarkably, we find that freezing the DNA fluctuations in simulation eliminates slower dynamics beyond ∼100 ps, where water and Na+ dynamics become faster, although strong anticorrelation exists between them. These results indicate that primary origin of slow dynamics lies within the slow fluctuations of DNA parts that couple with nearby slow water and ions to control the dispersed collective solvation dynamics in DNA minor groove.
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Affiliation(s)
- Deepika Sardana
- Spectroscopy Laboratory, School of Physical Sciences , Jawaharlal Nehru University , New Delhi 110067 , India
| | - Kavita Yadav
- Spectroscopy Laboratory, School of Physical Sciences , Jawaharlal Nehru University , New Delhi 110067 , India
| | - Him Shweta
- Spectroscopy Laboratory, School of Physical Sciences , Jawaharlal Nehru University , New Delhi 110067 , India
| | - Ndege Simisi Clovis
- Spectroscopy Laboratory, School of Physical Sciences , Jawaharlal Nehru University , New Delhi 110067 , India
| | - Parvez Alam
- Spectroscopy Laboratory, School of Physical Sciences , Jawaharlal Nehru University , New Delhi 110067 , India
| | - Sobhan Sen
- Spectroscopy Laboratory, School of Physical Sciences , Jawaharlal Nehru University , New Delhi 110067 , India
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20
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Roque Marques KM, do Desterro MR, de Arruda SM, de Araújo Neto LN, do Carmo Alves de Lima M, de Almeida SMV, da Silva ECD, de Aquino TM, da Silva-Júnior EF, de Araújo-Júnior JX, de M Silva M, de A Dantas MD, Santos JCC, Figueiredo IM, Bazin MA, Marchand P, da Silva TG, Mendonça Junior FJB. 5-Nitro-Thiophene-Thiosemicarbazone Derivatives Present Antitumor Activity Mediated by Apoptosis and DNA Intercalation. Curr Top Med Chem 2019; 19:1075-1091. [PMID: 31223089 DOI: 10.2174/1568026619666190621120304] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 03/12/2019] [Accepted: 04/02/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND Considering the need for the development of new antitumor drugs, associated with the great antitumor potential of thiophene and thiosemicarbazonic derivatives, in this work we promote molecular hybridization approach to synthesize new compounds with increased anticancer activity. OBJECTIVE Investigate the antitumor activity and their likely mechanisms of action of a series of N-substituted 2-(5-nitro-thiophene)-thiosemicarbazone derivatives. METHODS Methods were performed in vitro (cytotoxicity, cell cycle progression, morphological analysis, mitochondrial membrane potential evaluation and topoisomerase assay), spectroscopic (DNA interaction studies), and in silico studies (docking and molecular modelling). RESULTS Most of the compounds presented significant inhibitory activity; the NCIH-292 cell line was the most resistant, and the HL-60 cell line was the most sensitive. The most promising compound was LNN-05 with IC50 values ranging from 0.5 to 1.9 µg.mL-1. The in vitro studies revealed that LNN-05 was able to depolarize (dose-dependently) the mitochondrial membrane, induceG1 phase cell cycle arrest noticeably, promote morphological cell changes associated with apoptosis in chronic human myelocytic leukaemia (K-562) cells, and presented no topoisomerase II inhibition. Spectroscopic UV-vis and molecular fluorescence studies showed that LNN compounds interact with ctDNA forming supramolecular complexes. Intercalation between nitrogenous bases was revealed through KI quenching and competitive ethidium bromide assays. Docking and Molecular Dynamics suggested that 5-nitro-thiophene-thiosemicarbazone compounds interact against the larger DNA groove, and corroborating the spectroscopic results, may assume an intercalating interaction mode. CONCLUSION Our findings highlight 5-nitro-thiophene-thiosemicarbazone derivatives, especially LNN-05, as a promising new class of compounds for further studies to provide new anticancer therapies.
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Affiliation(s)
- Karla Mirella Roque Marques
- Bioactive Products Prospecting Laboratory, Department of Antibiotics, Federal University of Pernambuco, Recife-PE, Brazil
| | - Maria Rodrigues do Desterro
- Bioactive Products Prospecting Laboratory, Department of Antibiotics, Federal University of Pernambuco, Recife-PE, Brazil
| | - Sandrine Maria de Arruda
- Bioactive Products Prospecting Laboratory, Department of Antibiotics, Federal University of Pernambuco, Recife-PE, Brazil
| | - Luiz Nascimento de Araújo Neto
- Laboratory of Chemistry and Therapeutic Innovation, Department of Antibiotics, Federal University of Pernambuco, Recife-PE, Brazil
| | - Maria do Carmo Alves de Lima
- Laboratory of Chemistry and Therapeutic Innovation, Department of Antibiotics, Federal University of Pernambuco, Recife-PE, Brazil
| | | | - Edjan Carlos Dantas da Silva
- Laboratory of Medicinal Chemistry, Nursing and Pharmacy School, Federal University of Alagoas, Maceio-AL, Brazil
| | - Thiago Mendonça de Aquino
- Laboratory of Medicinal Chemistry, Nursing and Pharmacy School, Federal University of Alagoas, Maceio-AL, Brazil
| | | | - João Xavier de Araújo-Júnior
- Laboratory of Medicinal Chemistry, Nursing and Pharmacy School, Federal University of Alagoas, Maceio-AL, Brazil
| | - Marina de M Silva
- Laboratory of Development and Instrumentation in Analytical Chemistry, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Maceio-AL, Brazil
| | - Maria Dayanne de A Dantas
- Laboratory of Development and Instrumentation in Analytical Chemistry, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Maceio-AL, Brazil
| | - Josué Carinhanha C Santos
- Laboratory of Development and Instrumentation in Analytical Chemistry, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Maceio-AL, Brazil
| | - Isis M Figueiredo
- Laboratory of Development and Instrumentation in Analytical Chemistry, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Maceio-AL, Brazil
| | - Marc-Antoine Bazin
- Universite de Nantes, Cibles et medicaments des infections et du cancer, IICiMed, EA1155, F-44000 Nantes, France
| | - Pascal Marchand
- Universite de Nantes, Cibles et medicaments des infections et du cancer, IICiMed, EA1155, F-44000 Nantes, France
| | - Teresinha Gonçalves da Silva
- Bioactive Products Prospecting Laboratory, Department of Antibiotics, Federal University of Pernambuco, Recife-PE, Brazil
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21
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Sheu SY, Liu YC, Zhou JK, Schlag EW, Yang DY. Surface Topography Effects of Globular Biomolecules on Hydration Water. J Phys Chem B 2019; 123:6917-6932. [PMID: 31282162 DOI: 10.1021/acs.jpcb.9b03734] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hydration water serves as a microscopic manifestation of structural stability and functions of biomolecules. To develop bio-nanomaterials in applications, it is important to study how the surface topography and heterogeneity of biomolecules result in their diversity of the hydration dynamics and energetics. We here performed molecular dynamics simulations combined with the steered molecular dynamics and umbrella sampling to investigate the dynamics and escape process associated with the free energy change of water molecules close to a globular biomolecule, i.e., hemoglobin (Hb) and G-quadruplex DNA (GDNA). The residence time, power of long-time tail, and dipole relaxation time were found to display drastic changes within the averaged hydration shell of 3.0-5.0 Å. Compared with bulk water, in the inner hydration shell, the water dipole moment displays a slower relaxation process and is more oriented toward GDNA than toward Hb, forming a hedgehog-like structure when it surrounds GDNA. In particular, a spine water structure is observed in the GDNA narrow groove. The water isotope effect not only prolongs the dynamic time scales of libration motion in the inner hydration shell and the dipole relaxation processes in the bulk but also strengthens the DNA spine water structure. The potential of the mean force profile reflects the integrity of the hydration shell structure and enables us to obtain detailed insights into the structures formed by water, such as the caged H-bond network and the edge bridge structures; it also reveals that local hydration shell free energy (LHSFE) depends on H-bond rupture processes and ranges from 0.2 to 4.2 kcal/mol. Our results demonstrate that the surface topography of a biomolecule influences the integrity of the hydration shell structure and LHSFE. Our studies are able to identify various further applications in the areas of microfluid devices and nano-dewetting on bioinspired surfaces.
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Affiliation(s)
- Sheh-Yi Sheu
- Department of Life Sciences and Institute of Genome Sciences , National Yang-Ming University , Taipei 112 , Taiwan.,Institute of Biomedical Informatics , National Yang-Ming University , Taipei 112 , Taiwan
| | - Yu-Cheng Liu
- Institute of Biomedical Informatics , National Yang-Ming University , Taipei 112 , Taiwan
| | - Jia-Kai Zhou
- Department of Life Sciences and Institute of Genome Sciences , National Yang-Ming University , Taipei 112 , Taiwan
| | - Edward W Schlag
- Institut für Physikalische und Theoretische Chemie , TU-München , Lichtenbergstr. 4 , 85748 Garching , Germany
| | - Dah-Yen Yang
- Institute of Atomic and Molecular Sciences , Academia Sinica , Taipei 106 , Taiwan
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22
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Avagliano D, Sánchez-Murcia PA, González L. DNA-binding mechanism of spiropyran photoswitches: the role of electrostatics. Phys Chem Chem Phys 2019; 21:8614-8618. [PMID: 30801589 PMCID: PMC6484825 DOI: 10.1039/c8cp07508e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The binding mechanism of the protonated open form of three spiropyran derivatives into a 12-mer (poly-dAT)2 has been unveiled by means of computational methods.
The binding mechanism of the protonated open form of three spiropyran derivatives into a 12-mer (poly-dAT)2 has been unveiled by means of computational methods. It is found that the electrostatic term in the probe:DNA binding energy, modulates the binding mode, providing new guidelines for the design of spiropyran photoswitches with specific binding modes to DNA.
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Affiliation(s)
- Davide Avagliano
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090, Vienna, Austria.
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23
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Jawad B, Poudel L, Podgornik R, Steinmetz NF, Ching WY. Molecular mechanism and binding free energy of doxorubicin intercalation in DNA. Phys Chem Chem Phys 2019; 21:3877-3893. [PMID: 30702122 DOI: 10.1039/c8cp06776g] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The intercalation process of binding doxorubicin (DOX) in DNA is studied by extensive MD simulations. Many molecular factors that control the binding affinity of DOX to DNA to form a stable complex are inspected and quantified by employing continuum solvation models for estimating the binding free energy. The modified MM-PB(GB)SA methodology provides a complete energetic profile of ΔGele, ΔGvDW, ΔGpolar, ΔGnon-polar, TΔStotal, ΔGdeform, ΔGcon, and ΔGion. To identify the sequence specificity of DOX, two different DNA sequences, d(CGATCG) or DNA1 and d(CGTACG) or DNA2, with one molecule (1 : 1 complex) or two molecule (2 : 1 complex) configurations of DOX were selected in this study. Our results show that the DNA deformation energy (ΔGdeform), the energy cost from translational and rotational entropic contributions (TΔStran+rot), the total electrostatic interactions (ΔGpolar-PB/GB + ΔGele) of incorporation, the intramolecular electrostatic interactions (ΔGele) and electrostatic polar solvation interactions (ΔGpolar-PB/GB) are all unfavorable to the binding of DOX to DNA. However, they are overcome by at least five favorable interactions: the van der Waals interactions (ΔGvDW), the non-polar solvation interaction (ΔGnon-polar), the vibrational entropic contribution (TΔSvib), and the standard concentration dependent free energies of DOX (ΔGcon) and the ionic solution (ΔGion). Specifically, the van der Waals interaction appears to be the major driving force to form a stable DOX-DNA complex. We also predict that DOX has stronger binding to DNA1 than DNA2. The DNA deformation penalty and entropy cost in the 2 : 1 complex are less than those in the 1 : 1 complex, thus they indicate that the 2 : 1 complex is more stable than the 1 : 1 complex. We have calculated the total binding free energy (BFE) (ΔGt-sim) using both MM-PBSA and MM-GBSA methods, which suggests a more stable DOX-DNA complex at lower ionic concentration. The calculated BFE from the modified MM-GBSA method for DOX-DNA1 and DOX-DNA2 in the 1 : 1 complex is -9.1 and -5.1 kcal mol-1 respectively. The same quantities from the modified MM-PBSA method are -12.74 and -8.35 kcal mol-1 respectively. The value of the total BFE ΔGt-sim in the 1 : 1 complex is in reasonable agreement with the experimental value of -7.7 ± 0.3 kcal mol-1.
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Affiliation(s)
- Bahaa Jawad
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, Missouri 64110, USA.
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24
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Wang J, Deng C, Zhang Q, Chai Y. Tuning the Chemoselectivity of Silyl Protected Rhamnals by Temperature and Brønsted Acidity: Kinetically Controlled 1,2-Addition vs Thermodynamically Controlled Ferrier Rearrangement. Org Lett 2019; 21:1103-1107. [PMID: 30714737 DOI: 10.1021/acs.orglett.9b00009] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An acidity- and temperature-dependent chemoselective glycosylation of silyl-protected rhamnals with alcohols has been revealed. The reaction undergoes a 1,2-addition pathway with (±)-CSA as the catalyst at rt, affording kinetically controlled 2-deoxyl rhamnosides. In contrast, only thermodynamically controlled 2,3-unsaturated rhamnosides are formed via Ferrier rearrangement when elevating reaction temperature to 85 °C or using CF3SO3H instead. This tunable glycosylation allows facile and practical access to both 2-deoxyl and 2,3-unsaturated rhamnosides with excellent yields and high α-stereoselectivity.
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Affiliation(s)
- Jincai Wang
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Xi'an , Shaanxi 710119 , P. R. China.,School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an , Shaanxi 710119 , P. R. China
| | - Chuqiao Deng
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Xi'an , Shaanxi 710119 , P. R. China.,School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an , Shaanxi 710119 , P. R. China
| | - Qi Zhang
- School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an , Shaanxi 710119 , P. R. China
| | - Yonghai Chai
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Xi'an , Shaanxi 710119 , P. R. China.,School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an , Shaanxi 710119 , P. R. China
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25
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Mondal S, Samajdar RN, Mukherjee S, Bhattacharyya AJ, Bagchi B. Unique Features of Metformin: A Combined Experimental, Theoretical, and Simulation Study of Its Structure, Dynamics, and Interaction Energetics with DNA Grooves. J Phys Chem B 2018; 122:2227-2242. [DOI: 10.1021/acs.jpcb.7b11928] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Sayantan Mondal
- Solid State and Structural
Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Rudra N. Samajdar
- Solid State and Structural
Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Saumyak Mukherjee
- Solid State and Structural
Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Aninda J. Bhattacharyya
- Solid State and Structural
Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Biman Bagchi
- Solid State and Structural
Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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26
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Dhusia K, Bajpai A, Ramteke PW. Overcoming antibiotic resistance: Is siderophore Trojan horse conjugation an answer to evolving resistance in microbial pathogens? J Control Release 2017; 269:63-87. [PMID: 29129658 DOI: 10.1016/j.jconrel.2017.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/30/2017] [Accepted: 11/01/2017] [Indexed: 01/11/2023]
Abstract
Comparative study of siderophore biosynthesis pathway in pathogens provides potential targets for antibiotics and host drug delivery as a part of computationally feasible microbial therapy. Iron acquisition using siderophore models is an essential and well established model in all microorganisms and microbial infections a known to cause great havoc to both plant and animal. Rapid development of antibiotic resistance in bacterial as well as fungal pathogens has drawn us at a verge where one has to get rid of the traditional way of obstructing pathogen using single or multiple antibiotic/chemical inhibitors or drugs. 'Trojan horse' strategy is an answer to this imperative call where antibiotic are by far sneaked into the pathogenic cell via the siderophore receptors at cell and outer membrane. This antibiotic once gets inside, generates a 'black hole' scenario within the opportunistic pathogens via iron scarcity. For pathogens whose siderophore are not compatible to smuggle drug due to their complex conformation and stiff valence bonds, there is another approach. By means of the siderophore biosynthesis pathways, potential targets for inhibition of these siderophores in pathogenic bacteria could be achieved and thus control pathogenic virulence. Method to design artificial exogenous siderophores for pathogens that would compete and succeed the battle of intake is also covered with this review. These manipulated siderophore would enter pathogenic cell like any other siderophore but will not disperse iron due to which iron inadequacy and hence pathogens control be accomplished. The aim of this review is to offer strategies to overcome the microbial infections/pathogens using siderophore.
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Affiliation(s)
- Kalyani Dhusia
- Deptartment of Computational Biology and Bioinformatics, Jacob Institute of Biotechnology and Bio-Engineering, Sam Higginbottom University of Agriculture, Technology and Sciences (SHUATS), Allahabad-211007 (U.P.), India
| | - Archana Bajpai
- Laboratory for Disease Systems Modeling, Center for Integrative Medical Sciences, RIKEN, Yokohama City, Kanagawa, 230-0045, Japan
| | - P W Ramteke
- Deptartment of Computational Biology and Bioinformatics, Jacob Institute of Biotechnology and Bio-Engineering, Sam Higginbottom University of Agriculture, Technology and Sciences (SHUATS), Allahabad-211007 (U.P.), India
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27
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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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28
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Griesser H, Schwenger A, Richert C. Encapsulating Active Pharmaceutical Ingredients in Self-Assembling Adamantanes with Short DNA Zippers. ChemMedChem 2017; 12:1759-1767. [PMID: 28914989 PMCID: PMC5698727 DOI: 10.1002/cmdc.201700466] [Citation(s) in RCA: 6] [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: 08/07/2017] [Revised: 09/06/2017] [Indexed: 11/23/2022]
Abstract
Formulating pharmaceutically active ingredients for drug delivery is a challenge. There is a need for new drug delivery systems that take up therapeutic molecules and release them into biological systems. We propose a novel mode of encapsulation that involves matrices formed through co-assembly of drugs with adamantane hybrids that feature four CG dimers as sticky ends. Such adamantanes are accessible via inexpensive solution-phase syntheses, and the resulting materials show attractive properties for controlled release. This is demonstrated for two different hybrids and a series of drugs, including anticancer drugs, antibiotics, and cyclosporin. Up to 20 molar equivalents of active pharmaceutical ingredients (APIs) are encapsulated in hybrid materials. Encapsulation is demonstrated for DNA-binding and several non-DNA binding compounds. Nanoparticles were detected that range in size from 114-835 nm average diameter, and ζ potentials were found to be between -29 and +28 mV. Release of doxorubicin into serum at near-constant rates for 10 days was shown, demonstrating the potential for slow release. The encapsulation and release in self-assembling matrices of dinucleotide-bearing adamantanes appears to be broadly applicable and may thus lead to new drug delivery systems for APIs.
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Affiliation(s)
- Helmut Griesser
- Institute of Organic ChemistryUniversity of StuttgartPfaffenwaldring 5570569StuttgartGermany
| | - Alexander Schwenger
- Institute of Organic ChemistryUniversity of StuttgartPfaffenwaldring 5570569StuttgartGermany
| | - Clemens Richert
- Institute of Organic ChemistryUniversity of StuttgartPfaffenwaldring 5570569StuttgartGermany
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29
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Bignon E, Dršata T, Morell C, Lankaš F, Dumont E. Interstrand cross-linking implies contrasting structural consequences for DNA: insights from molecular dynamics. Nucleic Acids Res 2017; 45:2188-2195. [PMID: 27986856 PMCID: PMC5389527 DOI: 10.1093/nar/gkw1253] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/05/2016] [Indexed: 01/17/2023] Open
Abstract
Oxidatively-generated interstrand cross-links rank among the most deleterious DNA lesions. They originate from abasic sites, whose aldehyde group can form a covalent adduct after condensation with the exocyclic amino group of purines, sometimes with remarkably high yields. We use explicit solvent molecular dynamics simulations to unravel the structures and mechanical properties of two DNA sequences containing an interstrand cross-link. Our simulations palliate the absence of experimental structural and stiffness information for such DNA lesions and provide an unprecedented insight into the DNA embedding of lesions that represent a major challenge for DNA replication, transcription and gene regulation by preventing strand separation. Our results based on quantum chemical calculations also suggest that the embedding of the ICL within the duplex can tune the reaction profile, and hence can be responsible for the high difference in yields of formation.
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Affiliation(s)
- Emmanuelle Bignon
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France.,Univ Lyon, Ens de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
| | - Tomáš Dršata
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Christophe Morell
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Filip Lankaš
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic.,Laboratory of Informatics and Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28 Praha 6, Czech Republic
| | - Elise Dumont
- Univ Lyon, Ens de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
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30
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Bignon E, Chan CH, Morell C, Monari A, Ravanat JL, Dumont E. Molecular Dynamics Insights into Polyamine-DNA Binding Modes: Implications for Cross-Link Selectivity. Chemistry 2017; 23:12845-12852. [DOI: 10.1002/chem.201702065] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Emmanuelle Bignon
- Institut des Sciences Analytiques, UMR 5280; Université de Lyon 1 (UCBL) CNRS, ENS Lyon; Lyon France
- Laboratoire de Chimie; Univ Lyon; Ecole Normale Supérieure de Lyon, CNRS UMR 5182; Université Lyon 1; Laboratoire de Chimie; 46 allée d'Italie 69364 Lyon France
| | - Chen-Hui Chan
- Laboratoire de Chimie; Univ Lyon; Ecole Normale Supérieure de Lyon, CNRS UMR 5182; Université Lyon 1; Laboratoire de Chimie; 46 allée d'Italie 69364 Lyon France
| | - Christophe Morell
- Institut des Sciences Analytiques, UMR 5280; Université de Lyon 1 (UCBL) CNRS, ENS Lyon; Lyon France
| | - Antonio Monari
- Université de Lorraine Nancy; Theory-Modeling-Simulation, SRSMC; 54506 Vandoeuvre-lès-Nancy France
- CNRS; UMR 7565, SRSMC; 54506 Vandoeuvre-lès- Nancy France
| | - Jean-Luc Ravanat
- CEA and Université Grenoble Alpes, INAC-SyMMES; 38000 Grenoble France
| | - Elise Dumont
- Laboratoire de Chimie; Univ Lyon; Ecole Normale Supérieure de Lyon, CNRS UMR 5182; Université Lyon 1; Laboratoire de Chimie; 46 allée d'Italie 69364 Lyon France
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31
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Shen Z, Mulholland KA, Zheng Y, Wu C. Binding of anticancer drug daunomycin to a TGGGGT G-quadruplex DNA probed by all-atom molecular dynamics simulations: additional pure groove binding mode and implications on designing more selective G-quadruplex ligands. J Mol Model 2017; 23:256. [PMID: 28785893 DOI: 10.1007/s00894-017-3417-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 07/12/2017] [Indexed: 12/12/2022]
Abstract
DNA G-quadruplex structures are emerging cancer-specific targets for chemotherapeutics. Ligands that bind to and stabilize DNA G-quadruplexes have the potential to be anti-cancer drugs. Lack of binding selectivity to DNA G-quadruplex over DNA duplex remains a major challenge when attempting to develop G-quadruplex ligands into successful anti-cancer drugs. Thorough understanding of the binding nature of existing non-selective ligands that bind to both DNA quadruplex and DNA duplex will help to address this challenge. Daunomycin and doxorubicin, two commonly used anticancer drugs, are examples of non-selective DNA ligands. In this study, we extended our early all-atom binding simulation studies between doxorubicin and a DNA duplex (d(CGATCG)2) to probe the binding between daunomycin and a parallel DNA quadruplex (d(TGGGGT)4) and DNA duplex. In addition to the end stacking mode, which mimics the mode in the crystal structure, a pure groove binding mode was observed in our free binding simulations. The dynamic and energetic properties of these two binding modes are thoroughly examined, and a detailed comparison is made between DNA quadruplex binding modes and DNA duplex binding modes. Implications on the design of more selective DNA quadruplex ligands are also discussed. Graphical abstract Top stacking and groov binding modes from the MD simulations.
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Affiliation(s)
- Zhanhang Shen
- School of Physics, Shandong University, Jinan, 250100, China
| | - Kelly A Mulholland
- College of Science and Mathematics, Rowan University, Glassboro, NJ, 08028, USA
| | - Yujun Zheng
- School of Physics, Shandong University, Jinan, 250100, China.
| | - Chun Wu
- College of Science and Mathematics, Rowan University, Glassboro, NJ, 08028, USA.
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32
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Nutho B, Nunthaboot N, Wolschann P, Kungwan N, Rungrotmongkol T. Metadynamics supports molecular dynamics simulation-based binding affinities of eucalyptol and beta-cyclodextrin inclusion complexes. RSC Adv 2017. [DOI: 10.1039/c7ra09387j] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The development of various molecular dynamics methods enables the detailed investigation of association processes, like host–guest complexes, including their dynamics and, additionally, the release of the guest compound.
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Affiliation(s)
- Bodee Nutho
- Program in Biotechnology
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330
- Thailand
| | - Nadtanet Nunthaboot
- Department of Chemistry
- Center of Excellence for Innovation in Chemistry
- Faculty of Science
- Mahasarakham University
- Mahasarakham 44150
| | - Peter Wolschann
- Structural and Computational Biology Research Group
- Department of Biochemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330
| | - Nawee Kungwan
- Department of Chemistry
- Faculty of Science
- Chiang Mai University
- Chiang Mai 50200
- Thailand
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Research Group
- Department of Biochemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330
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33
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Salvadori A, Del Frate G, Pagliai M, Mancini G, Barone V. Immersive virtual reality in computational chemistry: Applications to the analysis of QM and MM data. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 2016; 116:1731-1746. [PMID: 27867214 PMCID: PMC5101850 DOI: 10.1002/qua.25207] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/21/2016] [Accepted: 06/24/2016] [Indexed: 05/31/2023]
Abstract
The role of Virtual Reality (VR) tools in molecular sciences is analyzed in this contribution through the presentation of the Caffeine software to the quantum chemistry community. Caffeine, developed at Scuola Normale Superiore, is specifically tailored for molecular representation and data visualization with VR systems, such as VR theaters and helmets. Usefulness and advantages that can be gained by exploiting VR are here reported, considering few examples specifically selected to illustrate different level of theory and molecular representation.
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Affiliation(s)
- Andrea Salvadori
- Scuola Normale Superiore Piazza dei Cavalieri 7 Pisa I-56126 Italy
| | | | - Marco Pagliai
- Scuola Normale Superiore Piazza dei Cavalieri 7 Pisa I-56126 Italy
| | - Giordano Mancini
- Scuola Normale Superiore Piazza dei Cavalieri 7 Pisa I-56126 Italy
| | - Vincenzo Barone
- Scuola Normale Superiore Piazza dei Cavalieri 7 Pisa I-56126 Italy
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34
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Duboué-Dijon E, Fogarty AC, Hynes JT, Laage D. Dynamical Disorder in the DNA Hydration Shell. J Am Chem Soc 2016; 138:7610-20. [DOI: 10.1021/jacs.6b02715] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Elise Duboué-Dijon
- École Normale
Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS,
Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités,
UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Aoife C. Fogarty
- École Normale
Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS,
Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités,
UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - James T. Hynes
- École Normale
Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS,
Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités,
UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
- Department
of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, United States
| | - Damien Laage
- École Normale
Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS,
Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités,
UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
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35
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von Hippel PH, Johnson NP, Marcus AH. Fifty years of DNA "breathing": Reflections on old and new approaches. Biopolymers 2016; 99:923-54. [PMID: 23840028 DOI: 10.1002/bip.22347] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 07/02/2013] [Indexed: 12/20/2022]
Abstract
The coding sequences for genes, and much other regulatory information involved in genome expression, are located 'inside' the DNA duplex. Thus the "macromolecular machines" that read-out this information from the base sequence of the DNA must somehow access the DNA "interior." Double-stranded (ds) DNA is a highly structured and cooperatively stabilized system at physiological temperatures, but is also only marginally stable and undergoes a cooperative "melting phase transition" at temperatures not far above physiological. Furthermore, due to its length and heterogeneous sequence, with AT-rich segments being less stable than GC-rich segments, the DNA genome 'melts' in a multistate fashion. Therefore the DNA genome must also manifest thermally driven structural ("breathing") fluctuations at physiological temperatures that should reflect the heterogeneity of the dsDNA stability near the melting temperature. Thus many of the breathing fluctuations of dsDNA are likely also to be sequence dependent, and could well contain information that should be "readable" and useable by regulatory proteins and protein complexes in site-specific binding reactions involving dsDNA "opening." Our laboratory has been involved in studying the breathing fluctuations of duplex DNA for about 50 years. In this "Reflections" article we present a relatively chronological overview of these studies, starting with the use of simple chemical probes (such as hydrogen exchange, formaldehyde, and simple DNA "melting" proteins) to examine the local stability of the dsDNA structure, and culminating in sophisticated spectroscopic approaches that can be used to monitor the breathing-dependent interactions of regulatory complexes with their duplex DNA targets in "real time."
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Affiliation(s)
- Peter H von Hippel
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403; Department of Chemistry, University of Oregon, Eugene, OR, 97403
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36
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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.
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Affiliation(s)
- Wilbee D Sasikala
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Maharashtra 411021, India.
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37
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Scaglioni L, Mondelli R, Artali R, Sirtori FR, Mazzini S. Nemorubicin and doxorubicin bind the G-quadruplex sequences of the human telomeres and of the c-MYC promoter element Pu22. Biochim Biophys Acta Gen Subj 2016; 1860:1129-38. [PMID: 26922833 DOI: 10.1016/j.bbagen.2016.02.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 02/12/2016] [Accepted: 02/21/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND Intra-molecular G-quadruplex structures are present in the guanine rich regions of human telomeres and were found to be prevalent in gene promoters. More recently, the targeting of c-MYC transcriptional control has been suggested, because the over expression of the c-MYC oncogene is one of the most common aberration found in a wide range of human tumors. METHODS The interaction of nemorubicin and doxorubicin with DNA G-quadruplex structures has been studied by NMR, ESI-MS and molecular modelling, in order to obtain further information about the complex and the multiple mechanisms of action of these drugs. RESULTS AND CONCLUSIONS Nemorubicin intercalates between A3 and G4 of d(TTAGGGT)4 and form cap-complex at the G6pT7 site. The presence of the adenine in this sequence is important for the stabilization of the complex, as was shown by the interaction with d(TTGGGTT)4 and d(TTTGGGT)4, which form only a 1:1 complex. The interaction of doxorubicin with d(TTAGGGT)4 is similar, but the complex appears less stable. Nemorubicin also binds with high efficiency the c-MYC G-quadruplex sequence Pu22, to form a very well defined complex. Two nemorubicin molecules bind to the 3'-end and to the 5'-end, forming an additional plane of stacking over each external G-tetrad. The wild type c-MYCPu22 sequence forms with nemorubicin the same complex. GENERAL SIGNIFICANCE Nemorubicin and doxorubicin, not only intercalate into the duplex DNA, but also result in significant ligands for G-quadruplex DNA segments, stabilizing their structure; this may in part explain the multiple mechanisms of action of their antitumor activity.
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Affiliation(s)
- Leonardo Scaglioni
- Department of Food, Environmental and Nutritional Sciences, Division of Chemistry and Molecular Biology, University of Milan, Via Celoria 2, 20133 Milano, Italy
| | - Rosanna Mondelli
- Department of Food, Environmental and Nutritional Sciences, Division of Chemistry and Molecular Biology, University of Milan, Via Celoria 2, 20133 Milano, Italy
| | | | - Federico Riccardi Sirtori
- Nerviano, Medical Sciences, Oncology-Chemical Core, Technologies Department, viale Pasteur, 10, 20014 Nerviano, Milano, Italy
| | - Stefania Mazzini
- Department of Food, Environmental and Nutritional Sciences, Division of Chemistry and Molecular Biology, University of Milan, Via Celoria 2, 20133 Milano, Italy.
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38
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Halley PD, Lucas CR, McWilliams EM, Webber MJ, Patton RA, Kural C, Lucas DM, Byrd JC, Castro CE. Daunorubicin-Loaded DNA Origami Nanostructures Circumvent Drug-Resistance Mechanisms in a Leukemia Model. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:308-20. [PMID: 26583570 PMCID: PMC4879968 DOI: 10.1002/smll.201502118] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 10/06/2015] [Indexed: 05/02/2023]
Abstract
Many cancers show primary or acquired drug resistance due to the overexpression of efflux pumps. A novel mechanism to circumvent this is to integrate drugs, such as anthracycline antibiotics, with nanoparticle delivery vehicles that can bypass intrinsic tumor drug-resistance mechanisms. DNA nanoparticles serve as an efficient binding platform for intercalating drugs (e.g., anthracyclines doxorubicin and daunorubicin, which are widely used to treat acute leukemias) and enable precise structure design and chemical modifications, for example, for incorporating targeting capabilities. Here, DNA nanostructures are utilized to circumvent daunorubicin drug resistance at clinically relevant doses in a leukemia cell line model. The fabrication of a rod-like DNA origami drug carrier is reported that can be controllably loaded with daunorubicin. It is further directly verified that nanostructure-mediated daunorubicin delivery leads to increased drug entry and retention in cells relative to free daunorubicin at equal concentrations, which yields significantly enhanced drug efficacy. Our results indicate that DNA origami nanostructures can circumvent efflux-pump-mediated drug resistance in leukemia cells at clinically relevant drug concentrations and provide a robust DNA nanostructure design that could be implemented in a wide range of cellular applications due to its remarkably fast self-assembly (≈5 min) and excellent stability in cell culture conditions.
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Affiliation(s)
| | | | - Emily M. McWilliams
- Biomedical Sciences Graduate Program, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH 43210, United States
| | - Matthew J. Webber
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, United States
| | - Randy A. Patton
- Department of Mechanical and Aerospace Engineering, College of Engineering, The Ohio State University, Columbus, OH 43210, United States
| | - Comert Kural
- Biophysics Graduate Program, Department of Physics, The Ohio State University, Columbus, OH 43210, United States
| | - David M. Lucas
- Department of Internal Medicine, College of Medicine, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - John C. Byrd
- Department of Internal Medicine, College of Medicine, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Carlos E. Castro
- Correspondence: Prof. Carlos E. Castro, Department of Mechanical and Aerospace Engineering, The Ohio State University, E328 Scott Laboratory, Peter L & C, 201 W 19th Ave. Columbus, OH 43210,
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39
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A computational approach to the resonance Raman spectrum of doxorubicin in aqueous solution. Theor Chem Acc 2016. [DOI: 10.1007/s00214-015-1781-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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40
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Kocak A, Yilmaz H, Faiz O, Andac O. Experimental and theoretical studies on Cu(II) complex of N,N′-disalicylidene-2,3-diaminopyridine ligand reveal indirect evidence for DNA intercalation. Polyhedron 2016. [DOI: 10.1016/j.poly.2015.11.037] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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41
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Mondal A, Bhattacherjee A. Searching target sites on DNA by proteins: Role of DNA dynamics under confinement. Nucleic Acids Res 2015; 43:9176-86. [PMID: 26400158 PMCID: PMC4627088 DOI: 10.1093/nar/gkv931] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/15/2015] [Accepted: 09/07/2015] [Indexed: 02/07/2023] Open
Abstract
DNA-binding proteins (DBPs) rapidly search and specifically bind to their target sites on genomic DNA in order to trigger many cellular regulatory processes. It has been suggested that the facilitation of search dynamics is achieved by combining 3D diffusion with one-dimensional sliding and hopping dynamics of interacting proteins. Although, recent studies have advanced the knowledge of molecular determinants that affect one-dimensional search efficiency, the role of DNA molecule is poorly understood. In this study, by using coarse-grained simulations, we propose that dynamics of DNA molecule and its degree of confinement due to cellular crowding concertedly regulate its groove geometry and modulate the inter-communication with DBPs. Under weak confinement, DNA dynamics promotes many short, rotation-decoupled sliding events interspersed by hopping dynamics. While this results in faster 1D diffusion, associated probability of missing targets by jumping over them increases. In contrast, strong confinement favours rotation-coupled sliding to locate targets but lacks structural flexibility to achieve desired specificity. By testing under physiological crowding, our study provides a plausible mechanism on how DNA molecule may help in maintaining an optimal balance between fast hopping and rotation-coupled sliding dynamics, to locate target sites rapidly and form specific complexes precisely.
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Affiliation(s)
- Anupam Mondal
- Center for Computational Biology, Indraprastha Institute of Information Technology (IIIT) Delhi, New Delhi-110020, India
| | - Arnab Bhattacherjee
- Center for Computational Biology, Indraprastha Institute of Information Technology (IIIT) Delhi, New Delhi-110020, India
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42
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Yang D, Boyer B, Prévost C, Danilowicz C, Prentiss M. Integrating multi-scale data on homologous recombination into a new recognition mechanism based on simulations of the RecA-ssDNA/dsDNA structure. Nucleic Acids Res 2015; 43:10251-63. [PMID: 26384422 PMCID: PMC4666392 DOI: 10.1093/nar/gkv883] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 08/23/2015] [Indexed: 12/11/2022] Open
Abstract
RecA protein is the prototypical recombinase. Members of the recombinase family can accurately repair double strand breaks in DNA. They also provide crucial links between pairs of sister chromatids in eukaryotic meiosis. A very broad outline of how these proteins align homologous sequences and promote DNA strand exchange has long been known, as are the crystal structures of the RecA-DNA pre- and postsynaptic complexes; however, little is known about the homology searching conformations and the details of how DNA in bacterial genomes is rapidly searched until homologous alignment is achieved. By integrating a physical model of recognition to new modeling work based on docking exploration and molecular dynamics simulation, we present a detailed structure/function model of homology recognition that reconciles extremely quick searching with the efficient and stringent formation of stable strand exchange products and which is consistent with a vast body of previously unexplained experimental results.
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Affiliation(s)
- Darren Yang
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Benjamin Boyer
- Laboratoire de Biochimie Théorique, CNRS UPR 9080, Univ Paris Diderot, Sorbonne Paris Cité, IBPC, Paris, France
| | - Chantal Prévost
- Laboratoire de Biochimie Théorique, CNRS UPR 9080, Univ Paris Diderot, Sorbonne Paris Cité, IBPC, Paris, France
| | | | - Mara Prentiss
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
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43
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Singh RK, Sasikala WD, Mukherjee A. Molecular Origin of DNA Kinking by Transcription Factors. J Phys Chem B 2015; 119:11590-6. [PMID: 26258468 DOI: 10.1021/acs.jpcb.5b06229] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Binding of transcription factor (TF) proteins with DNA may cause severe kinks in the latter. Here, we investigate the molecular origin of the DNA kinks observed in the TF-DNA complexes using small molecule intercalation pathway, crystallographic analysis, and free energy calculations involving four different transcription factor (TF) protein-DNA complexes. We find that although protein binding may bend the DNA, bending alone is not sufficient to kink the DNA. We show that partial, not complete, intercalation is required to form the kink at a particular place in the DNA. It turns out that while amino acid alone can induce the desired kink through partial intercalation, protein provides thermodynamic stabilization of the kinked state in TF-DNA complexes.
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Affiliation(s)
- Reman Kumar Singh
- Department of Chemistry, Indian Institute of Science Education and Research , Pune, Maharashtra 411021, India
| | - Wilbee D Sasikala
- Department of Chemistry, Indian Institute of Science Education and Research , Pune, Maharashtra 411021, India
| | - Arnab Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research , Pune, Maharashtra 411021, India
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Huynh TP, Sharma PS, Sosnowska M, D'Souza F, Kutner W. Functionalized polythiophenes: Recognition materials for chemosensors and biosensors of superior sensitivity, selectivity, and detectability. Prog Polym Sci 2015. [DOI: 10.1016/j.progpolymsci.2015.04.009] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Bouvier B, Cézard C, Sonnet P. Selectivity of pyoverdine recognition by the FpvA receptor of Pseudomonas aeruginosa from molecular dynamics simulations. Phys Chem Chem Phys 2015; 17:18022-34. [PMID: 26098682 DOI: 10.1039/c5cp02939b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Gram-negative bacterium Pseudomonas aeruginosa, a ubiquitous human opportunistic pathogen, has developed resistances to multiple antibiotics. It uses its primary native siderophore, pyoverdine, to scavenge the iron essential to its growth in the outside medium and transport it back into its cytoplasm. The FpvA receptor on the bacterial outer membrane recognizes and internalizes pyoverdine bearing its iron payload, but can also bind pyoverdines from other Pseudomonads or synthetic analogues. Pyoverdine derivatives could therefore be used as vectors to deliver antibiotics into the bacterium. In this study, we use molecular dynamics and free energy calculations to characterize the mechanisms and thermodynamics of the recognition of the native pyoverdines of P. aeruginosa and P. fluorescens by FpvA. Based on these results, we delineate the features that pyoverdines with high affinity for FpvA should possess. In particular, we show that (i) the dynamics and interaction of the unbound pyoverdines with water should be optimized with equal care as the interface contacts in the complex with FpvA; (ii) the C-terminal extremity of the pyoverdine chain, which appears to play no role in the bound complex, is involved in the intermediate stages of recognition; and (iii) the length and cyclicity of the pyoverdine chain can be used to fine-tune the kinetics of the recognition mechanism.
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Affiliation(s)
- Benjamin Bouvier
- Laboratoire de Glycochimie, des Antimicrobiens et des Agroressources, CNRS FRE3517/Université de Picardie Jules Verne, 1, rue des Louvels, 80037 Amiens Cedex 1, France.
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Dumont E, Monari A. Understanding DNA under oxidative stress and sensitization: the role of molecular modeling. Front Chem 2015; 3:43. [PMID: 26236706 PMCID: PMC4500984 DOI: 10.3389/fchem.2015.00043] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/29/2015] [Indexed: 12/12/2022] Open
Abstract
DNA is constantly exposed to damaging threats coming from oxidative stress, i.e., from the presence of free radicals and reactive oxygen species. Sensitization from exogenous and endogenous compounds that strongly enhance the frequency of light-induced lesions also plays an important role. The experimental determination of DNA lesions, though a difficult subject, is somehow well established and allows to elucidate even extremely rare DNA lesions. In parallel, molecular modeling has become fundamental to clearly understand the fine mechanisms related to DNA defects induction. Indeed, it offers an unprecedented possibility to get access to an atomistic or even electronic resolution. Ab initio molecular dynamics may also describe the time-evolution of the molecular system and its reactivity. Yet the modeling of DNA (photo-)reactions does necessitate elaborate multi-scale methodologies to tackle a damage induction reactivity that takes place in a complex environment. The double-stranded DNA environment is first characterized by a very high flexibility, but also a strongly inhomogeneous electrostatic embedding. Additionally, one aims at capturing more subtle effects, such as the sequence selectivity which is of critical important for DNA damage. The structure and dynamics of the DNA/sensitizers complexes, as well as the photo-induced electron- and energy-transfer phenomena taking place upon sensitization, should be carefully modeled. Finally the factors inducing different repair ratios for different lesions should also be rationalized. In this review we will critically analyze the different computational strategies used to model DNA lesions. A clear picture of the complex interplay between reactivity and structural factors will be sketched. The use of proper multi-scale modeling leads to the in-depth comprehension of DNA lesions mechanisms and also to the rational design of new chemo-therapeutic agents.
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Affiliation(s)
- Elise Dumont
- Laboratoire de Chimie, UMR 5182 Centre National de la Recherche Scientifique, École Normale Supérieure de Lyon Lyon, France
| | - Antonio Monari
- Université de Lorraine - Nancy, Theory-Modeling-Simulation, Structure et Réactivité des Systèmes Moléculaires Complexes (SRSMC) Vandoeuvre-les-Nancy, France ; Centre National de la Recherche Scientifique, Theory-Modeling-Simulation, Structure et Réactivité des Systèmes Moléculaires Complexes (SRSMC) Vandoeuvre-les-Nancy, France
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47
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Galindo-Murillo R, García-Ramos JC, Ruiz-Azuara L, Cheatham TE, Cortés-Guzmán F. Intercalation processes of copper complexes in DNA. Nucleic Acids Res 2015; 43:5364-76. [PMID: 25958394 PMCID: PMC4477671 DOI: 10.1093/nar/gkv467] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 04/28/2015] [Indexed: 11/25/2022] Open
Abstract
The family of anticancer complexes that include the transition metal copper known as Casiopeínas® shows promising results. Two of these complexes are currently in clinical trials. The interaction of these compounds with DNA has been observed experimentally and several hypotheses regarding the mechanism of action have been developed, and these include the generation of reactive oxygen species, phosphate hydrolysis and/or base-pair intercalation. To advance in the understanding on how these ligands interact with DNA, we present a molecular dynamics study of 21 Casiopeínas with a DNA dodecamer using 10 μs of simulation time for each compound. All the complexes were manually inserted into the minor groove as the starting point of the simulations. The binding energy of each complex and the observed representative type of interaction between the ligand and the DNA is reported. With this extended sampling time, we found that four of the compounds spontaneously flipped open a base pair and moved inside the resulting cavity and four compounds formed stacking interactions with the terminal base pairs. The complexes that formed the intercalation pocket led to more stable interactions.
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Affiliation(s)
- Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, College of Pharmacy, Skaggs Hall 201, University of Utah, Salt Lake City, UT 84112, USA
| | - Juan Carlos García-Ramos
- Departamento de Química Inorgánica y Nuclear, Facultad de Química, Universidad Nacional Autónoma de México. Avenida Universidad 3000, 04510 México City, Mexico
| | - Lena Ruiz-Azuara
- Departamento de Química Inorgánica y Nuclear, Facultad de Química, Universidad Nacional Autónoma de México. Avenida Universidad 3000, 04510 México City, Mexico
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, Skaggs Hall 201, University of Utah, Salt Lake City, UT 84112, USA
| | - Fernando Cortés-Guzmán
- Instituto de Química, Universidad Nacional Autónoma de México, DF 04510, Mexico Centro Conjunto de Investigación en Química Sustentable UAEMex-UNAM, carretera Toluca-Atlacomulco km 14.5, Toluca, México 50200, Mexico
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Hynes JT. Molecules in Motion: Chemical Reaction and Allied Dynamics in Solution and Elsewhere. Annu Rev Phys Chem 2015; 66:1-20. [DOI: 10.1146/annurev-physchem-040214-121833] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- James T. Hynes
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309;
- Department of Chemistry, UMR ENS-CNRS-UPMC-8640, Ecole Normale Supérieure, Paris, France 75005
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Deligkaris C, Ascone AT, Sweeney KJ, Greene AJQ. Validation of a computational docking methodology to identify the non-covalent binding site of ligands to DNA. MOLECULAR BIOSYSTEMS 2015; 10:2106-25. [PMID: 24853173 DOI: 10.1039/c4mb00239c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Despite the biomedical consequences of carcinogen-DNA interactions and the potential of DNA as a drug target in medicinal chemistry, only a small number of studies have validated or used docking methods for the prediction of the physical binding of small molecules to DNA. Knowledge of the DNA-physically-bound ligand geometry can lead to the elucidation of the molecular-level mechanism of drugs as well as predicting the subsequent chemical interactions that lead to DNA damage from carcinogens. We sought to validate AutoDock 4.2, a docking method that includes a physics-based free energy function and a Lamarckian Genetic Algorithm, for the prediction of ligand geometries upon physical binding to DNA. We performed simulations by systematically changing the length of the search process for a comprehensive set of 32 ligand-DNA molecular systems with different physico-chemical properties, and we used a free-energy-based convergence criterion to terminate our simulations. For 11 out of 28 molecular systems for which convergence was achieved, the lowest binding free energy geometries were within 2 Å of the experimentally determined geometry. Considering all predicted sites with free energy changes within 20% of the lowest binding free energy site, we found a site within 2 Å of the experimentally determined geometry for 24 out of the 28 systems. However, the predicted hydrogen bonding interactions were different for most molecular systems compared to the same interactions in the experimentally determined geometry. We discuss reasons for the successes and failures, implications, and the importance of ensuring an adequate search in docking calculations. Overall, we concluded that AutoDock 4.2 can be used to predict the non-covalent binding geometry of a small molecule to DNA with some limitations.
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Tsoneva Y, Jonker HRA, Wagner M, Tadjer A, Lelle M, Peneva K, Ivanova A. Molecular Structure and Pronounced Conformational Flexibility of Doxorubicin in Free and Conjugated State within a Drug–Peptide Compound. J Phys Chem B 2015; 119:3001-13. [DOI: 10.1021/jp509320q] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yana Tsoneva
- University of Sofia, Faculty of Chemistry and Pharmacy,
Department of Physical Chemistry, 1 James Bourchier Avenue, 1164 Sofia, Bulgaria
| | - Hendrik R. A. Jonker
- Goethe University Frankfurt, Institute for Organic
Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Max von Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Manfred Wagner
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Alia Tadjer
- University of Sofia, Faculty of Chemistry and Pharmacy,
Department of Physical Chemistry, 1 James Bourchier Avenue, 1164 Sofia, Bulgaria
| | - Marco Lelle
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Kalina Peneva
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Anela Ivanova
- University of Sofia, Faculty of Chemistry and Pharmacy,
Department of Physical Chemistry, 1 James Bourchier Avenue, 1164 Sofia, Bulgaria
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