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Hu W, Jing H, Fu W, Wang Z, Zhou J, Zhang N. Conversion to Trimolecular G-Quadruplex by Spontaneous Hoogsteen Pairing-Based Strand Displacement Reaction between Bimolecular G-Quadruplex and Double G-Rich Probes. J Am Chem Soc 2023; 145:18578-18590. [PMID: 37553999 DOI: 10.1021/jacs.3c05617] [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: 08/10/2023]
Abstract
Bimolecular or tetramolecular G-quadruplexes (GQs) are predominantly self-assembled by the same sequence-identical G-rich oligonucleotides and usually remain inert to the strand displacement reaction (SDR) with other short G-rich invading fragments of DNA or RNA. Appealingly, in this study, we demonstrate that a parallel homomeric bimolecular GQ target of Tub10 d(CAGGGAGGGT) as the starting reactant, although completely folded in K+ solution and sufficiently stable (melting temperature of 57.7 °C), can still spontaneously accept strand invasion by a pair of short G-rich invading probes of P1 d(TGGGA) near room temperature. The final SDR product is a novel parallel heteromeric trimolecular GQ (tri-GQ) of Tub10/2P1 reassembled between one Tub10 strand and two P1 strands. Here we present, to the best of our knowledge, the first NMR solution structure of such a discrete heteromeric tri-GQ and unveil a unique mode of two probes vs one target in mutual recognition among G-rich canonical DNA oligomers. As a model system, the short invading probe P1 can spontaneously trap G-rich target Tub10 from a Watson-Crick duplex completely hybridized between Tub10 and its fully complementary strand d(ACCCTCCCTG). The Tub10 sequence of d(CAGGGAGGGT) is a fragment from the G-rich promoter region of the human β2-tubulin gene. Our findings provide new insights into the Hoogsteen pairing-based SDR between a GQ target and double invading probes of short G-rich DNA fragments and are expected to grant access to increasingly complex architectures in GQ-based DNA nanotechnology.
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Affiliation(s)
- Wenxuan Hu
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Haitao Jing
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Wenqiang Fu
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Zengrong Wang
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Jiang Zhou
- Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Na Zhang
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- Key Laboratory of Anhui Province for High Field Magnetic Resonance Imaging, Hefei 230031, China
- High Magnetic Field Laboratory of Anhui Province, Hefei 230031, China
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
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2
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Roxo C, Pasternak A. Changes in physicochemical and anticancer properties modulated by chemically modified sugar moieties within sequence-related G-quadruplex structures. PLoS One 2022; 17:e0273528. [PMID: 35998148 PMCID: PMC9397905 DOI: 10.1371/journal.pone.0273528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/09/2022] [Indexed: 11/18/2022] Open
Abstract
We systematically investigated the influence of locked nucleic acid (LNA), unlock nucleic acid (UNA), and 2’-O-methyl-RNA (2’-O-Me-RNA) residues on the thermal stability, structure folding topology, biological activity and enzymatic resistance of three sequence-related DNA G-quadruplexes. In order to better understand the mechanism of action of the studied modifications, a single-position substitution in the loops or G-tetrads was performed and their influence was analyzed for a total of twenty-seven modified G-quadruplex variants. The studies show that the influence of each modification on the physicochemical properties of G-quadruplexes is position-dependent, due to mutual interactions between G-tetrads, loops, and additional guanosine at 5’ or 3’ end. Nevertheless, the anticancer activity of the modified G-quadruplexes is determined by their structure, thus also by the local changes of chemical character of sugar moieties, what might influence the specific interactions with therapeutic targets. In general, UNA modifications are efficient modulators of the G-quadruplex thermodynamic stability, however they are poor tools to improve the anticancer properties. In contrast, LNA and 2’-O-Me-RNA modified G-quadruplexes demonstrated certain antiproliferative potential and might be used as molecular tools for designing novel G-quadruplex-based therapeutics.
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Affiliation(s)
- Carolina Roxo
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Anna Pasternak
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- * E-mail:
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Reddy Peddi S, Kundenapally R, Kanth Sivan S, Somadi G, Manga V. A pragmatic pharmacophore informatics strategy to discover new potent inhibitors against pim-3. Struct Chem 2022. [DOI: 10.1007/s11224-022-01949-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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4
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Thermally Induced Transitions of d(G4T4G3) Quadruplexes Can Be Described as Kinetically Driven Processes. Life (Basel) 2022; 12:life12060825. [PMID: 35743856 PMCID: PMC9225023 DOI: 10.3390/life12060825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/24/2022] [Accepted: 05/27/2022] [Indexed: 11/16/2022] Open
Abstract
DNA sequences that are rich in guanines and can form four-stranded structures are called G-quadruplexes. Due to the growing evidence that they may play an important role in several key biological processes, the G-quadruplexes have captured the interest of several researchers. G-quadruplexes may form in the presence of different metal cations as polymorphic structures formed in kinetically governed processes. Here we investigate a complex polymorphism of d(G4T4G3) quadruplexes at different K+ concentrations. We show that population size of different d(G4T4G3) quadruplex conformations can be manipulated by cooling rate and/or K+ concentration. We use a kinetic model to describe data obtained from DSC, CD and UV spectroscopy and PAGE experiments. Our model is able to describe the observed thermally induced conformational transitions of d(G4T4G3) quadruplexes at different K+ concentrations.
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Maddah M, Karami L. An atomistic investigation on the interaction of distamycin A and its derivative with the telomeric G-Quadruplex as anticancer agents by molecular dynamics simulation. Arch Biochem Biophys 2021; 701:108797. [PMID: 33607110 DOI: 10.1016/j.abb.2021.108797] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/05/2021] [Accepted: 02/06/2021] [Indexed: 10/22/2022]
Abstract
Human telomerase that activates within cancer cells has a telomeric sequence at the 3' end. Each factor that stabilizes the G-quadruplex in guanine-rich telomeric sequences can inhibit the regular telomerase activity. Therefore, the telomeric G-quadruplex is known as a promising target in cancer treatment. In this work, we studied the binding of positively charged distamycin A and its uncharged derivative to the G-quadruplex in a solution environment by Molecular Dynamics (MD) simulation. The binding mechanism and subtle conformational changes were investigated as a result of the ligand attachment. Moreover, binding free energy and clustering analysis describe the stability and flexibility of G-quadruplexes upon ligand binding. Structural analyses displayed that the favorable binding of both ligands imposes significant stability and rigidity in G-quadruplex conformation compared to free G-quadruplex, especially charged distamycin. Hydration pattern and ion distribution were different for free G-quadruplex and both of the ligand complexes. Energy decomposition reveals the electrostatic effect on the stability of G-quadruplex. The radial distribution function displayed the solvent shell and ion moving away from the groove. The hydrogen bond played an essential role in the binding of both ligands, especially for the charged derivative. van der Waals interaction is the only factor that is more important in binding uncharged distamycin into G-quadruplex than the charged one. The calculated ΔGbind showed the stability of both ligands within grooves and good agreement with the experimental binding free energy data. Finally, the results suggest that ligand modification improves the binding mode toward stabilizing G-quadruplexes.
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Affiliation(s)
- Mina Maddah
- Depatment of Chemistry, K. N. Toosi University of Technology, Tehran, Iran; Super Computing Institute, University of Tehran, Tehran, Iran.
| | - Leila Karami
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran.
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Li K, Yatsunyk L, Neidle S. Water spines and networks in G-quadruplex structures. Nucleic Acids Res 2021; 49:519-528. [PMID: 33290519 PMCID: PMC7797044 DOI: 10.1093/nar/gkaa1177] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/15/2020] [Accepted: 11/17/2020] [Indexed: 12/12/2022] Open
Abstract
Quadruplex DNAs can fold into a variety of distinct topologies, depending in part on loop types and orientations of individual strands, as shown by high-resolution crystal and NMR structures. Crystal structures also show associated water molecules. We report here on an analysis of the hydration arrangements around selected folded quadruplex DNAs, which has revealed several prominent features that re-occur in related structures. Many of the primary-sphere water molecules are found in the grooves and loop regions of these structures. At least one groove in anti-parallel and hybrid quadruplex structures is long and narrow and contains an extensive spine of linked primary-sphere water molecules. This spine is analogous to but fundamentally distinct from the well-characterized spine observed in the minor groove of A/T-rich duplex DNA, in that every water molecule in the continuous quadruplex spines makes a direct hydrogen bond contact with groove atoms, principally phosphate oxygen atoms lining groove walls and guanine base nitrogen atoms on the groove floor. By contrast, parallel quadruplexes do not have extended grooves, but primary-sphere water molecules still cluster in them and are especially associated with the loops, helping to stabilize loop conformations.
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Affiliation(s)
- Kevin Li
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, USA
| | - Liliya Yatsunyk
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, USA
| | - Stephen Neidle
- UCL School of Pharmacy, University College London, London WC1N 1AX, UK
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Peddi SR, Peddi SR, Sivan S, Veerati R, Manga V. Integrated molecular docking, 3D QSAR and molecular dynamics simulation studies on indole derivatives for designing new Pim-1 inhibitors. J Recept Signal Transduct Res 2020; 40:1-14. [DOI: 10.1080/10799893.2020.1713809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Sudhir Reddy Peddi
- Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Saikiran Reddy Peddi
- Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Sreekanth Sivan
- Department of Chemistry, Nizam College, Osmania University, Hyderabad
| | - Radhika Veerati
- Department of Chemistry, S R Engineering College, Ananthasagar, India
| | - Vijjulatha Manga
- Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
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Sharmila DJS, Blessy JJ, Rapheal VS, Subramanian KS. Molecular dynamics investigations for the prediction of molecular interaction of cauliflower mosaic virus transmission helper component protein complex with Myzus persicae stylet's cuticular protein and its docking studies with annosquamosin-A encapsulated in nano-porous Silica. Virusdisease 2019; 30:413-425. [PMID: 31803809 PMCID: PMC6864000 DOI: 10.1007/s13337-019-00549-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/15/2019] [Indexed: 02/06/2023] Open
Abstract
Large numbers of bioactive natural products from plant species such as alkaloids, phenolics, terpenoids etc. are remaining unexplored for their potential as plant protective agents as inhibitors for viral and other pathogenic infections of plant. Myzus aphids are important plant pests and vectors for several plant viruses. Cauliflower mosaic virus (CaMV) belongs to the plant virus family Caulimoviridae which is transmitted "non-circulative" from plant to plant through an interaction with aphid insect vectors. This viral transmission process most likely involves a protein-protein binding interaction between aphid stylet receptor cuticular protein and viral proteins namely, CaMV aphid transmission Helper Component protein and virion associated protein. Aphid stylets are made of cuticle and little is known about the structure of cuticle protein of this insect group. The present study reports the molecular modeling of the structures of Myzus persicae aphid stylet's cuticular protein (MpsCP) and cauliflower mosaic virus aphid transmission Helper component protein (CaMV HCP). Protein-protein docking studies and molecular dynamics simulations are performed to establish the mode of binding of MpsCP with CaMV HCP. Molecular docking and molecular dynamics investigations of terpenoids Annosquamosin-A from Annona squamosa complex with CaMV transmitting aphid M. persicae stylet's cuticular protein revealed their means of interaction perhaps relates to restrain viral binding and transmission. QM/MM optimization of mesoporous silica nanopores composite with Annosquamosin-A for smart and safe delivery of bioactive is carried out to study their electronic parameters such as heat of formation, total energy, electronic energy, Ionization potential, Highest Occupied Molecular Orbital, Lowest Un-occupied Molecular Orbital and energy gaps.
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Affiliation(s)
- D. Jeya Sundara Sharmila
- Department of Nano Science and Technology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641003 India
| | - J. Jino Blessy
- Department of Nano Science and Technology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641003 India
| | - V. Stephen Rapheal
- Department of Biotechnology, Kumaraguru College of Technology, Coimbatore, Tamil Nadu 641049 India
| | - K. S. Subramanian
- Department of Nano Science and Technology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641003 India
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S A, Matchado MS, Snijesh V, Kumar A, Singh S. An insight into anti-arthritic property OF C25H34O7 for Rheumatoid arthritis using molecular modelling and molecular dynamics approach. INFORMATICS IN MEDICINE UNLOCKED 2019. [DOI: 10.1016/j.imu.2018.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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11
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The estimation of H-bond and metal ion-ligand interaction energies in the G-Quadruplex ⋯ Mn+ complexes. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.02.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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12
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Rational design of methicillin resistance staphylococcus aureus inhibitors through 3D-QSAR, molecular docking and molecular dynamics simulations. Comput Biol Chem 2018; 73:95-104. [DOI: 10.1016/j.compbiolchem.2017.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 12/11/2017] [Accepted: 12/17/2017] [Indexed: 12/27/2022]
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13
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Ballu S, Itteboina R, Sivan SK, Manga V. Structural insights of Staphylococcus aureus FtsZ inhibitors through molecular docking, 3D-QSAR and molecular dynamics simulations. J Recept Signal Transduct Res 2018; 38:61-70. [DOI: 10.1080/10799893.2018.1426607] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Srilata Ballu
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Ramesh Itteboina
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Sree Kanth Sivan
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Vijjulatha Manga
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
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14
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Pharmacophore modeling, 3D-QSAR, docking, and molecular dynamics simulation on topoisomerase IV inhibitors of wild type Staphylococcus aureus. Struct Chem 2017. [DOI: 10.1007/s11224-017-1056-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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García-Arriaga M, Acosta-Santiago M, Cruz A, Rivera-Rivera JM, López GE, Rivera JM. Probing the Limits of Supramolecular G-Quadruplexes Using Atomistic Molecular Dynamics Simulations. Inorganica Chim Acta 2017; 468:209-222. [PMID: 29062143 PMCID: PMC5649357 DOI: 10.1016/j.ica.2017.08.051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Guanosine and related derivatives self-assemble in the presence of cations like potassium into supramolecular G-quadruplexes (SGQs), where four guanine moieties form planar tetrads (T) that coaxially stack into columnar aggregates with broad size distributions. However, SGQs made from 8-aryl-2'-deoxyguanosine derivatives (8ArGs), form mostly octamers, or two-tetrad (2T)-SGQs, while some form dodecamers (3T-SGQs), or hexadecamers (4T-SGQs), and none reported to date form higher assemblies. A theoretical model that addresses the configurational space available for the multiple pathways available for 8ArGs to self-assemble into SGQs is used to frame a series of molecular dynamics simulations (MDS) with selected SGQs. Some key insights from this work include: (a) The predicted entropic costs are not significantly higher for SGQs with more subunits due to their hierarchical assembly pathways; (b) The multiple isomeric SGQs vary in the interfacial contacts between consecutive tetrads, due to their two distinct sides (head, h; tail, t), with the MDS supporting the predicted order of stability of hh > ht > tt for octamers. (c) Such order also applies to dodecamers and hexadecamers, but with context-dependent exceptions due to strong allosteric effects. (d) The main factor disfavoring the tt interface is the repulsive dipolar interactions between the O4' from ribose moieties on adjacent tetrads. (e) SGQs with 5 or more tetrads are disfavored because the attractive interactions are not large or strong enough to overcome the many repulsive forces resulting from the addition of further tetrads. We expect these findings provide some guidelines to enable the further development of SGQs into functional materials.
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Affiliation(s)
- Marilyn García-Arriaga
- Department of Chemistry and Molecular Sciences Research Center, University of Puerto Rico at Río Piedras, San Juan, PR, 00926
| | - Maxier Acosta-Santiago
- Department of Chemistry and Molecular Sciences Research Center, University of Puerto Rico at Río Piedras, San Juan, PR, 00926
| | - Antony Cruz
- School of Natural and Social Sciences, Department of Chemistry, Lehman College-CUNY, Bronx, NY 10468
| | - José M Rivera-Rivera
- Department of Chemistry and Molecular Sciences Research Center, University of Puerto Rico at Río Piedras, San Juan, PR, 00926
| | - Gustavo E López
- School of Natural and Social Sciences, Department of Chemistry, Lehman College-CUNY, Bronx, NY 10468
| | - José M Rivera
- Department of Chemistry and Molecular Sciences Research Center, University of Puerto Rico at Río Piedras, San Juan, PR, 00926
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16
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Jia WQ, Jing Z, Liu X, Feng XY, Liu YY, Wang SQ, Xu WR, Liu JW, Cheng XC. Virtual identification of novel PPARα/γ dual agonists by scaffold hopping of saroglitazar. J Biomol Struct Dyn 2017; 36:3496-3512. [DOI: 10.1080/07391102.2017.1392363] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Wen-Qing Jia
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Zhi Jing
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Xin Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Xiao-Yan Feng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ya-Ya Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Shu-Qing Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wei-Ren Xu
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, China
| | - Jian-Wen Liu
- State Key Laboratory of Bioreactor Engineering & Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xian-Chao Cheng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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Determination of Structural Requirements of N-Substituted Tetrahydro-β-Carboline Imidazolium Salt Derivatives Using in Silico Approaches for Designing MEK-1 Inhibitors. Molecules 2017. [PMID: 28629184 PMCID: PMC6152744 DOI: 10.3390/molecules22061020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Novel N-substituted tetrahydro-β-carboline imidazolium salt derivatives proved to have potent antitumor activity in past research. The Topomer CoMFA and CoMSIA function in Sybyl-X 2.0 software was applied for the identification of important features of N-substituted tetrahydro-β-carboline-imidazolium salt derivative moieties. In the case of Topomer CoMFA, all the compounds were split into two fragments which were used to generate a 3D invariant representation, the statistical results of the Topomer CoMFA model: q2 value of 0.700; r2 value of 0.954; with 5 optimum components. The database alignment was utilized for building the CoMSIA model, and the CoMSIA model had q2 and r2 values of 0.615 and 0.897, with 4 optimum components. Target fishing of the PharmMapper platform was utilised for finding potential targets, the human mitogen-activated protein kinase 1 (MEK-1) was found to be the primary potential target for the three compounds with the fit scores of 6.288, 5.741, and 6.721. The molecular docking technique of MOE 2015 was carried out to identify the interactions of amino acids surrounding the ligand, and correlating QASR contour maps were used to identify structural requirements of N-substituted tetrahydro-β-carboline imidazolium salt moieties. Molecular dynamics and simulation studies proved that the target protein was stable for 0.8–5 ns. The pivotal moieties of N-substituted tetrahydro-β-carboline imidazolium salt derivatives and its potential targets were verified by the QASR study, PharmMapper, and the molecular docking study which would be helpful to design novel MEK-1 inhibitors for anticancer drugs.
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Peddi SR, Sivan SK, Manga V. Molecular dynamics and MM/GBSA-integrated protocol probing the correlation between biological activities and binding free energies of HIV-1 TAR RNA inhibitors. J Biomol Struct Dyn 2017; 36:486-503. [PMID: 28081678 DOI: 10.1080/07391102.2017.1281762] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The interaction of HIV-1 transactivator protein Tat with its cognate transactivation response (TAR) RNA has emerged as a promising target for developing antiviral compounds and treating HIV infection, since it is a crucial step for efficient transcription and replication. In the present study, molecular dynamics (MD) simulations and MM/GBSA calculations have been performed on a series of neamine derivatives in order to estimate appropriate MD simulation time for acceptable correlation between ΔGbind and experimental pIC50 values. Initially, all inhibitors were docked into the active site of HIV-1 TAR RNA. Later to explore various conformations and examine the docking results, MD simulations were carried out. Finally, binding free energies were calculated using MM/GBSA method and were correlated with experimental pIC50 values at different time scales (0-1 to 0-10 ns). From this study, it is clear that in case of neamine derivatives as simulation time increased the correlation between binding free energy and experimental pIC50 values increased correspondingly. Therefore, the binding energies which can be interpreted at longer simulation times can be used to predict the bioactivity of new neamine derivatives. Moreover, in this work, we have identified some plausible critical nucleotide interactions with neamine derivatives that are responsible for potent inhibitory activity. Furthermore, we also provide some insights into a new class of oxadiazole-based back bone cyclic peptides designed by incorporating the structural features of neamine derivatives. On the whole, this approach can provide a valuable guidance for designing new potent inhibitors and modify the existing compounds targeting HIV-1 TAR RNA.
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Affiliation(s)
- Saikiran Reddy Peddi
- a Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry , University College of Science, Osmania University , Hyderabad 500 007 , Telangana , India
| | - Sree Kanth Sivan
- b Department of Chemistry , Nizam College, Osmania University , Hyderabad 500 001 , Telangana , India
| | - Vijjulatha Manga
- a Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry , University College of Science, Osmania University , Hyderabad 500 007 , Telangana , India
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19
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Itteboina R, Ballu S, Sivan SK, Manga V. Molecular docking, 3D QSAR and dynamics simulation studies of imidazo-pyrrolopyridines as janus kinase 1 (JAK 1) inhibitors. Comput Biol Chem 2016; 64:33-46. [DOI: 10.1016/j.compbiolchem.2016.04.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 04/16/2016] [Accepted: 04/26/2016] [Indexed: 01/30/2023]
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20
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Bhattacharyya D, Mirihana Arachchilage G, Basu S. Metal Cations in G-Quadruplex Folding and Stability. Front Chem 2016; 4:38. [PMID: 27668212 PMCID: PMC5016522 DOI: 10.3389/fchem.2016.00038] [Citation(s) in RCA: 381] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/25/2016] [Indexed: 12/23/2022] Open
Abstract
This review is focused on the structural and physicochemical aspects of metal cation coordination to G-Quadruplexes (GQ) and their effects on GQ stability and conformation. G-quadruplex structures are non-canonical secondary structures formed by both DNA and RNA. G-quadruplexes regulate a wide range of important biochemical processes. Besides the sequence requirements, the coordination of monovalent cations in the GQ is essential for its formation and determines the stability and polymorphism of GQ structures. The nature, location, and dynamics of the cation coordination and their impact on the overall GQ stability are dependent on several factors such as the ionic radii, hydration energy, and the bonding strength to the O6 of guanines. The intracellular monovalent cation concentration and the localized ion concentrations determine the formation of GQs and can potentially dictate their regulatory roles. A wide range of biochemical and biophysical studies on an array of GQ enabling sequences have generated at a minimum the knowledge base that allows us to often predict the stability of GQs in the presence of the physiologically relevant metal ions, however, prediction of conformation of such GQs is still out of the realm.
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Affiliation(s)
| | | | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State UniversityKent, OH, USA
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Peddi SR, Sivan SK, Manga V. An integrated molecular modeling approach for in silico design of new tetracyclic derivatives as ALK inhibitors. J Recept Signal Transduct Res 2016; 36:488-504. [PMID: 26758803 DOI: 10.3109/10799893.2015.1130057] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Anaplastic lymphoma kinase (ALK), a promising therapeutic target for treatment of human cancers, is a receptor tyrosine kinase that instigates the activation of several signal transduction pathways. In the present study, in silico methods have been employed in order to explore the structural features and functionalities of a series of tetracyclic derivatives displaying potent inhibitory activity toward ALK. Initially docking was performed using GLIDE 5.6 to probe the bioactive conformation of all the compounds and to understand the binding modes of inhibitors. The docking results revealed that ligand interaction with Met 1199 plays a crucial role in binding of inhibitors to ALK. Further to establish a robust 3D-QSAR model using CoMFA and CoMSIA methods, the whole dataset was divided into three splits. Model obtained from Split 3 showed high accuracy ([Formula: see text] of 0.700 and 0.682, [Formula: see text] of 0.971 and 0.974, [Formula: see text] of 0.673 and 0.811, respectively for CoMFA and CoMSIA). The key structural requirements for enhancing the inhibitory activity were derived from CoMFA and CoMSIA contours in combination with site map analysis. Substituting small electronegative groups at Position 8 by replacing either morpholine or piperidine rings and maintaining hydrophobic character at Position 9 in tetracyclic derivatives can enhance the inhibitory potential. Finally, we performed molecular dynamics simulations in order to investigate the stability of protein ligand interactions and MM/GBSA calculations to compare binding free energies of co-crystal ligand and newly designed molecule N1. Based on the coherence of outcome of various molecular modeling studies, a set of 11 new molecules having potential predicted inhibitory activity were designed.
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Affiliation(s)
- Saikiran Reddy Peddi
- a Department of Chemistry , University College of Science, Osmania University , Hyderabad , India and
| | | | - Vijjulatha Manga
- a Department of Chemistry , University College of Science, Osmania University , Hyderabad , India and
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Sharmila DJS, Jino Blessy J. Molecular dynamics of sialic acid analogues complex with cholera toxin and DFT optimization of ethylene glycol-mediated zinc nanocluster conjugation. J Biomol Struct Dyn 2016; 35:182-206. [PMID: 26733187 DOI: 10.1080/07391102.2015.1136689] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Cholera is an infectious disease caused by cholera toxin (CT) protein of bacterium Vibrio cholerae. A sequence of sialic acid (N-acetylneuraminic acid, NeuNAc or Neu5Ac) analogues modified in its C-5 position is modelled using molecular modelling techniques and docked against the CT followed by molecular dynamics simulations. Docking results suggest better binding affinity of NeuNAc analogue towards the binding site of CT. The NeuNAc analogues interact with the active site residues GLU:11, TYR:12, HIS:13, GLY:33, LYS:34, GLU:51, GLN:56, HIE:57, ILE:58, GLN:61, TRP:88, ASN:90 and LYS:91 through intermolecular hydrogen bonding. Analogues N-glycolyl-NeuNAc, N-Pentanoyl-NeuNAc and N-Propanoyl-NeuNAc show the least XPGscore (docking score) of -9.90, -9.16, and -8.91, respectively, and glide energy of -45.99, -42.14 and -41.66 kcal/mol, respectively. Stable nature of CT-N-glycolyl-NeuNAc, CT-N-Pentanoyl-NeuNAc and CT-N-Propanoyl-NeuNAc complexes was verified through molecular dynamics simulations, each for 40 ns using the software Desmond. All the nine NeuNAc analogues show better score for drug-like properties, so could be considered as suitable candidates for drug development for cholera infection. To improve the enhanced binding mode of NeuNAc analogues towards CT, the nine NeuNAc analogues are conjugated with Zn nanoclusters through ethylene glycol (EG) as carriers. The NeuNAc analogues conjugated with EG-Zn nanoclusters show better binding energy towards CT than the unconjugated nine NeuNAc analogues. The electronic structural optimization of EG-Zn nanoclusters was carried out for optimizing their performance as better delivery vehicles for NeuNAc analogues through density functional theory calculations. These sialic acid analogues may be considered as novel leads for the design of drug against cholera and the EG-Zn nanocluster may be a suitable carrier for sialic acid analogues.
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Affiliation(s)
- D Jeya Sundara Sharmila
- a Department of Nano Science and Technology , Tamil Nadu Agricultural University , Coimbatore 641003 , Tamil Nadu , India
| | - J Jino Blessy
- b Department of Bioinformatics , Karunya University , Karunya Nagar, Coimbatore 641 114 , Tamil Nadu , India
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Abstract
Metal ions are essential cofactors for the structure and functions of nucleic acids. Yet, the early discovery in the 70s of the crucial role of Mg(2+) in stabilizing tRNA structures has occulted for a long time the importance of monovalent cations. Renewed interest in these ions was brought in the late 90s by the discovery of specific potassium metal ions in the core of a group I intron. Their importance in nucleic acid folding and catalytic activity is now well established. However, detection of K(+) and Na(+) ions is notoriously problematic and the question about their specificity is recurrent. Here we review the different methods that can be used to detect K(+) and Na(+) ions in nucleic acid structures such as X-ray crystallography, nuclear magnetic resonance or molecular dynamics simulations. We also discuss specific versus non-specific binding to different structures through various examples.
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Affiliation(s)
- Pascal Auffinger
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC, CNRS, 15 rue René Descartes, F-67084, Strasbourg, France.
| | - Luigi D'Ascenzo
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC, CNRS, 15 rue René Descartes, F-67084, Strasbourg, France.
| | - Eric Ennifar
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC, CNRS, 15 rue René Descartes, F-67084, Strasbourg, France.
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Exploring the Molecular Interactions of 7,8-Dihydroxyflavone and Its Derivatives with TrkB and VEGFR2 Proteins. Int J Mol Sci 2015; 16:21087-108. [PMID: 26404256 PMCID: PMC4613243 DOI: 10.3390/ijms160921087] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 08/21/2015] [Accepted: 08/26/2015] [Indexed: 11/16/2022] Open
Abstract
7,8-dihydroxyflavone (7,8-DHF) is a TrkB receptor agonist, and treatment with this flavonoid derivative brings about an enhanced TrkB phosphorylation and promotes downstream cellular signalling. Flavonoids are also known to exert an inhibitory effect on the vascular endothelial growth factor receptor (VEGFR) family of tyrosine kinase receptors. VEGFR2 is one of the important receptors involved in the regulation of vasculogenesis and angiogenesis and has also been implicated to exhibit various neuroprotective roles. Its upregulation and uncontrolled activity is associated with a range of pathological conditions such as age-related macular degeneration and various proliferative disorders. In this study, we investigated molecular interactions of 7,8-DHF and its derivatives with both the TrkB receptor as well as VEGFR2. Using a combination of molecular docking and computational mapping tools involving molecular dynamics approaches we have elucidated additional residues and binding energies involved in 7,8-DHF interactions with the TrkB Ig2 domain and VEGFR2. Our investigations have revealed for the first time that 7,8-DHF has dual biochemical action and its treatment may have divergent effects on the TrkB via its extracellular Ig2 domain and on the VEGFR2 receptor through the intracellular kinase domain. Contrary to its agonistic effects on the TrkB receptor, 7,8-DHF was found to downregulate VEGFR2 phosphorylation both in 661W photoreceptor cells and in retinal tissue.
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König SLB, Evans AC, Huppert JL. Seven essential questions on G-quadruplexes. Biomol Concepts 2015; 1:197-213. [PMID: 25961997 DOI: 10.1515/bmc.2010.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The helical duplex architecture of DNA was discovered by Francis Crick and James Watson in 1951 and is well known and understood. However, nucleic acids can also adopt alternative structural conformations that are less familiar, although no less biologically relevant, such as the G-quadruplex. G-quadruplexes continue to be the subject of a rapidly expanding area of research, owing to their significant potential as therapeutic targets and their unique biophysical properties. This review begins by focusing on G-quadruplex structure, elucidating the intermolecular and intramolecular interactions underlying its formation and highlighting several substructural variants. A variety of methods used to characterize these structures are also outlined. The current state of G-quadruplex research is then addressed by proffering seven pertinent questions for discussion. This review concludes with an overview of possible directions for future research trajectories in this exciting and relevant field.
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Blessy JJ, Sharmila DJS. Molecular modeling of methyl-α-Neu5Ac analogues docked against cholera toxin - a molecular dynamics study. Glycoconj J 2015; 32:49-67. [DOI: 10.1007/s10719-014-9570-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 11/26/2014] [Accepted: 11/27/2014] [Indexed: 10/24/2022]
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Ho J, Newcomer MB, Ragain CM, Gascon JA, Batista ER, Loria JP, Batista VS. MoD-QM/MM Structural Refinement Method: Characterization of Hydrogen Bonding in the Oxytricha nova G-Quadruplex. J Chem Theory Comput 2014; 10:5125-35. [PMID: 26584390 PMCID: PMC5304451 DOI: 10.1021/ct500571k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A generalization of the Moving-Domain Quantum Mechanics/Molecular Mechanics (MoD-QM/MM) hybrid method [Gascon, J. A.; Leung, S. S. F.; Batista, E. R.; Batista, V. S. J. Chem. Theory Comput. 2006, 2, 175-186] is introduced to provide a self-consistent computational protocol for structural refinement of extended systems. The method partitions the system into molecular domains that are iteratively optimized as quantum mechanical (QM) layers embedded in their surrounding molecular environment to obtain an ab initio quality description of the geometry and the molecular electrostatic potential of the extended system composed of those constituent fragments. The resulting methodology is benchmarked as applied to model systems that allow for full QM optimization as well as through refinement of the hydrogen bonding geometry in Oxytricha nova guanine quadruplex for which several studies have been reported, including the X-ray structure and NMR data. Calculations of (1)H NMR chemical shifts based on the gauge independent atomic orbital (GIAO) method and direct comparisons with experiments show that solvated MoD-QM/MM structures, sampled from explicit solvent molecular dynamics simulations, allow for NMR simulations in much improved agreement with experimental data than models based on the X-ray structure or those optimized using classical molecular mechanics force fields.
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Affiliation(s)
- Junming Ho
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Michael B. Newcomer
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Christina M. Ragain
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Jose A. Gascon
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Enrique R. Batista
- Theoretical Division, Los Alamos National Laboratory, MS-B214, Los Alamos, New Mexico 87545, United States
| | - J. Patrick Loria
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, United States
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Victor S. Batista
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, United States
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A combined experimental and computational study of Vam3, a derivative of resveratrol, and Syk interaction. Int J Mol Sci 2014; 15:17188-203. [PMID: 25257535 PMCID: PMC4200806 DOI: 10.3390/ijms150917188] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 09/18/2014] [Accepted: 09/22/2014] [Indexed: 01/02/2023] Open
Abstract
Spleen tyrosine kinase (Syk) plays an indispensable role through preliminary extracellular antigen-induced crosslinking of Fc receptor (FcR) in the pathogenesis of autoimmune disorders, such as rheumatoid arthritis. In this study, we identify Vam3, a dimeric derivative of resveratrol isolated from grapes, as an ATP-competitive inhibitor of Syk with an IC50 of 62.95 nM in an in vitro kinase assay. Moreover, docking and molecular dynamics simulation approaches were performed to get more detailed information about the binding mode of Vam3 and Syk. The results show that 11b-OH on ring-C and 4b-OH on ring-D could form two hydrogen bonds with Glu449 and Phe382 of Syk, respectively. In addition, arene-cation interaction between ring-D of Vam3 and Lys402 of Syk was also observed. These results indicate that ring-C and D play an essential role in Vam3–Syk interaction. Our studies may be helpful in the structural optimization of Vam3, and also aid the design of novel Syk inhibitors in the future.
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Blessy JJ, Sharmila DJS. Molecular simulation of N-acetylneuraminic acid analogs and molecular dynamics studies of cholera toxin-Neu5Gc complex. J Biomol Struct Dyn 2014; 33:1126-39. [DOI: 10.1080/07391102.2014.931825] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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30
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Gupta MK, Misra K. Atom-based 3D-QSAR, molecular docking and molecular dynamics simulation assessment of inhibitors for thyroid hormone receptor α and β. J Mol Model 2014; 20:2286. [DOI: 10.1007/s00894-014-2286-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 05/01/2014] [Indexed: 12/27/2022]
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Mahesh Kumar J, Idris MM, Srinivas G, Vinay Kumar P, Meghah V, Kavitha M, Reddy CR, Mainkar PS, Pal B, Chandrasekar S, Nagesh N. Phenyl 1,2,3-triazole-thymidine ligands stabilize G-quadruplex DNA, inhibit DNA synthesis and potentially reduce tumor cell proliferation over 3'-azido deoxythymidine. PLoS One 2013; 8:e70798. [PMID: 23976957 PMCID: PMC3747139 DOI: 10.1371/journal.pone.0070798] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Accepted: 06/24/2013] [Indexed: 01/10/2023] Open
Abstract
Triazoles are known for their non-toxicity, higher stability and therapeutic activity. Few nucleoside (L1, L2 and L3) and non-nucleoside 1,2,3-triazoles (L4-L14) were synthesised using click chemistry and they were screened for tumor cell cytotoxicity and proliferation. Among these triazole ligands studied, nucleoside ligands exhibited higher potential than non-nucleoside ligands. The nucleoside triazole analogues, 3'-Phenyl-1,2,3- triazole-thymidine (L2) and 3'-4-Chlorophenyl-1,2,3-triazole-thymidine (L3), demonstrated higher cytotoxicity in tumor cells than in normal cells. The IC₅₀ value for L3 was lowest (50 µM) among the ligands studied. L3 terminated cell cycle at S, G2/M phases and enhanced sub-G1 populations, manifesting induction of apoptosis in tumor cells. Confocal studies indicated that nucleoside triazole ligands (L2/L3) cause higher DNA fragmentation than other ligands. Preclinical experiments with tumor-induced mice showed greater reduction in tumor size with L3. In vitro DNA synthesis reaction with L3 exhibited higher DNA synthesis inhibition with quadruplex forming DNA (QF DNA) than non quadruplex forming DNA (NQF DNA). T(m) of quadruplex DNA increased in the presence of L3, indicating its ability to enhance stability of quadruplex DNA at elevated temperature and the results indicate that it had higher affinity towards quadruplex DNA than the other forms of DNA (like dsDNA and ssDNA). From western blot experiment, it was noticed that telomerase expression levels in the tissues of tumor-induced mice were found to be reduced on L3 treatment. Microcalorimetry results emphasise that two nucleoside triazole ligands (L2/L3) interact with quadruplex DNA with significantly higher affinity (K(d)≈10⁻⁷ M). Interestingly the addition of an electronegative moiety to the phenyl group of L2 enhanced its anti-proliferative activity. Though IC₅₀ values are not significantly low with L3, the studies on series of synthetic 1,2,3-triazole ligands are useful for improving and building potential pro-apoptotic ligands.
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Affiliation(s)
| | | | - Gunda Srinivas
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | | | - Mitta Kavitha
- CSIR-Indian Institute of Chemical Technology, Hyderabad, India
| | | | | | - Biswajit Pal
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Narayana Nagesh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
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A combination of 3D-QSAR, molecular docking and molecular dynamics simulation studies of benzimidazole-quinolinone derivatives as iNOS inhibitors. Int J Mol Sci 2012; 13:11210-11227. [PMID: 23109848 PMCID: PMC3472740 DOI: 10.3390/ijms130911210] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 07/16/2012] [Accepted: 07/30/2012] [Indexed: 12/14/2022] Open
Abstract
Inducible Nitric Oxide Synthase (iNOS) has been involved in a variety of diseases, and thus it is interesting to discover and optimize new iNOS inhibitors. In previous studies, a series of benzimidazole-quinolinone derivatives with high inhibitory activity against human iNOS were discovered. In this work, three-dimensional quantitative structure-activity relationships (3D-QSAR), molecular docking and molecular dynamics (MD) simulation approaches were applied to investigate the functionalities of active molecular interaction between these active ligands and iNOS. A QSAR model with R2 of 0.9356, Q2 of 0.8373 and Pearson-R value of 0.9406 was constructed, which presents a good predictive ability in both internal and external validation. Furthermore, a combined analysis incorporating the obtained model and the MD results indicates: (1) compounds with the proper-size hydrophobic substituents at position 3 in ring-C (R3 substituent), hydrophilic substituents near the X6 of ring-D and hydrophilic or H-bond acceptor groups at position 2 in ring-B show enhanced biological activities; (2) Met368, Trp366, Gly365, Tyr367, Phe363, Pro344, Gln257, Val346, Asn364, Met349, Thr370, Glu371 and Tyr485 are key amino acids in the active pocket, and activities of iNOS inhibitors are consistent with their capability to alter the position of these important residues, especially Glu371 and Thr370. The results provide a set of useful guidelines for the rational design of novel iNOS inhibitors.
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Akhshi P, Acton G, Wu G. Molecular dynamics simulations to provide new insights into the asymmetrical ammonium ion movement inside of the [d(G3T4G4)]2 G-quadruplex DNA structure. J Phys Chem B 2012; 116:9363-70. [PMID: 22780684 DOI: 10.1021/jp304760k] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We have used both adaptive biasing force (ABF) and regular molecular dynamics (MD) simulations to investigate the asymmetrical NH(4)(+) ion movement inside of a bimolecular G-quadruplex DNA structure [d(G(3)T(4)G(4))](2). The free-energy landscapes obtained from ABF MD simulations suggest that the NH(4)(+) ion exiting the [d(G(3)T(4)G(4))](2) G-quadruplex stem in the direction toward the edge-type loop (denoted as the upper direction) experiences a lower free-energy barrier than that toward the diagonal loop (denoted as the lower direction) by approximately 3-4 kcal mol(-1). This result is in qualitative agreement with the previous discovery made by Šket and Plavec on the same G-quadruplex structure from (15)N NMR experiments (J. Am. Chem. Soc. 2007, 129, 8794). In the Na(+) form of the same G-quadruplex, Na(+) ion movement was found to be symmetrical, with a free-energy barrier of only 5-7 kcal mol(-1) to cross all three G-quartets, that is, [d(G(3)T(4)G(4))](2) still exhibits ion-channel-like behaviors for Na(+) ions. On the basis of the new computational results, we hypothesize that the stiffness of a G-quartet is primarily determined by the base stacking interactions within the G-quadruplex stem. Therefore, the structural origin for the asymmetrical NH(4)(+) ion movement in [d(G(3)T(4)G(4))](2) is the presence of two different modes of base stacking around the NH(4)(+) binding sites, a more stable 5'-syn-anti mode between lower and central G-quartets and a less stable 5'-anti-anti mode between upper and central G-quartets. Simulations also suggest that loop topology at the end of a G-quadruplex stem only controls the direction at which an exiting NH(4)(+) ion reaches bulk solution but does not impose significant free-energy barriers.
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Affiliation(s)
- Parisa Akhshi
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario, Canada K7L 3N6
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šponer J, Cang X, Cheatham TE. Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures. Methods 2012; 57:25-39. [PMID: 22525788 PMCID: PMC3775459 DOI: 10.1016/j.ymeth.2012.04.005] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Revised: 04/04/2012] [Accepted: 04/06/2012] [Indexed: 11/29/2022] Open
Abstract
The article reviews the application of biomolecular simulation methods to understand the structure, dynamics and interactions of nucleic acids with a focus on explicit solvent molecular dynamics simulations of guanine quadruplex (G-DNA and G-RNA) molecules. While primarily dealing with these exciting and highly relevant four-stranded systems, where recent and past simulations have provided several interesting results and novel insight into G-DNA structure, the review provides some general perspectives on the applicability of the simulation techniques to nucleic acids.
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Affiliation(s)
- Jiří šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
- CEITEC – Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Xiaohui Cang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Thomas E. Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, Skaggs Hall 201, 2000 East 30 South, University of Utah, Salt Lake City, UT 84112, United States
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FAN WENJIE, ZHANG RUIQIN. COMPUTATION OF LARGE SYSTEMS WITH AN ECONOMIC BASIS SET: AB INITIO CALCULATIONS OF BIOLOGICAL NUCLEIC ACID BASE PAIRS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633606002350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We show that an economic basis set, in which the polarization functions are considered only for oxygen and nitrogen atoms of strong electronegativity, can be used to determine reliable structures of nucleic acid base pairs. Mulliken charge analysis and the HOMO-LUMO gap in single-point energy calculations using standard basis sets on the geometric structures optimized with the economic basis set found reasonable agreements with the ones of standard calculations. This study is expected to provide a general guideline for basis set selection in the computation of large biological systems being performed with considerable high accuracy, using a low cost computation resource.
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Affiliation(s)
- WENJIE FAN
- Center of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, Hong Kong SAR, P. R. China
- Department of Physics and Materials Science, City University of Hong Kong, Hong Kong SAR, P. R. China
| | - RUIQIN ZHANG
- Center of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, Hong Kong SAR, P. R. China
- Department of Physics and Materials Science, City University of Hong Kong, Hong Kong SAR, P. R. China
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Fadrná E, Špačková N, Sarzyñska J, Koča J, Orozco M, Cheatham TE, Kulinski T, Šponer J. Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields. J Chem Theory Comput 2009; 5:2514-30. [DOI: 10.1021/ct900200k] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Eva Fadrná
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
| | - Nad’a Špačková
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
| | - Joanna Sarzyñska
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
| | - Jaroslav Koča
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
| | - Modesto Orozco
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
| | - Thomas E. Cheatham
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
| | - Tadeusz Kulinski
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
| | - Jiří Šponer
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
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Snoussi K, Halle B. Internal sodium ions and water molecules in guanine quadruplexes: magnetic relaxation dispersion studies of [d(G3T4G3)]2 and [d(G4T4G4)]2. Biochemistry 2008; 47:12219-29. [PMID: 18950191 DOI: 10.1021/bi801657s] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The structural stability of guanine quadruplexes depends critically on an unusual configuration of dehydrated Na (+) or K (+) ions, closely spaced along the central axis of the quadruplex. Crystallography and NMR spectroscopy indicate that these internal ions can be located between the G-quartet planes as well as in the thymine loops, but the precise ion coordination has been firmly established in only a few cases. Here, we examine the bimolecular diagonal-looped foldback quadruplexes [d(G 3T 4G 3)] 2 (Q3) and [d(G 4T 4G 4)] 2 (Q4) by (2)H, (17)O, and (23)Na magnetic relaxation dispersion (MRD). The MRD data indicate that both quadruplexes contain Na (+) ions between the T 4 loops and the terminal G-quartets and that these ions have one water ligand. These ions exchange with external ions on a time scale of 10-60 mus at 27 degrees C, while their highly ordered water ligands have residence times in the range 10 (-8)-10 (-6) s. The MRD data indicate that Q4 contains three Na (+) ions in the stem sites, in agreement with previous solid-state (23)Na NMR findings but contrary to the only crystal structure of this quadruplex. For Q3, the MRD data suggest a less symmetric coordination of the two stem ions. In both quadruplexes, the stem ions have residence times of 0.6-1.0 ms at 27 degrees C. The equilibrium constant for Na (+) --> K (+) exchange is approximately 4 for both loop and stem sites in Q3, in agreement with previous (1)H NMR findings.
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Affiliation(s)
- Karim Snoussi
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, SE-22100 Lund, Sweden.
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Agrawal S, Ojha RP, Maiti S. Energetics of the human Tel-22 quadruplex-telomestatin interaction: a molecular dynamics study. J Phys Chem B 2008; 112:6828-36. [PMID: 18461983 DOI: 10.1021/jp7102676] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The formation and stabilization of telomeric quadruplexes has been shown to inhibit the activity of telomerase, thus establishing telomeric DNA quadruplex as an attractive target for cancer therapeutic intervention. In this context, telomestatin, a G-quadruplex-specific ligand known to bind and stabilize G-quadruplex, is of great interest. Knowledge of the three-dimensional structure of telomeric quadruplex and its complex with telomestatin in solution is a prerequisite for structure-based rational drug design. Here, we report the relative stabilities of human telomeric quadruplex (AG3[T2AG3]3) structures under K+ ion conditions and their binding interaction with telomestatin, as determined by molecular dynamics simulations followed by energy calculations. The energetics study shows that, in the presence of K+ ions, mixed hybrid-type Tel-22 quadruplex conformations are more stable than other conformations. The binding free energy for quadruplex-telomestatin interactions suggests that 1:2 binding is favored over 1:1 binding. To further substantiate our results, we also calculated the change in solvent-accessible surface area (DeltaSASA) and heat capacity (DeltaCp) associated with 1:1 and 1:2 binding modes. The extensive investigation performed for quadruplex-telomestatin interaction will assist in understanding the parameters influencing the quadruplex-ligand interaction and will serve as a platform for rational drug design.
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Affiliation(s)
- Saurabh Agrawal
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, New Delhi 110007, India
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Kumar A, Sevilla MD, Suhai S. Microhydration of the guanine-cytosine (GC) base pair in the neutral and anionic radical states: a density functional study. J Phys Chem B 2008; 112:5189-98. [PMID: 18380501 DOI: 10.1021/jp710957p] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A density functional study of the effects of microhydration on the guanine-cytosine (GC) base pair and its anion radical is presented. Geometries of the GC base pair in the presence of 6 and 11 water molecules were fully optimized in the neutral (GC-nH2O) and anion radical [(GC-nH2O)*-] (n = 6 and 11) states using the B3LYP method and the 6-31+G** basis set. Further, vibrational frequency analysis at the same level of theory (B3LYP/6-31+G**) was also performed to ensure the existence of local minima in these hydrated structures. It was found that water molecules surrounding the GC base pair have significant effects on the geometry of the GC base pair and promote nonplanarity in the GC base pair. The calculated structures were found to be in good agreement with those observed experimentally and obtained in molecular dynamics (MD) simulation studies. The water molecules in neutral GC-nH2O complexes lie near the ring plane of the GC base pair where they undergo hydrogen bonding with both GC and each other. However, in the GC anion radical complexes (GC-nH2O, n = 6, 11), the water molecules are displaced substantially from the GC ring plane. For GC-11H2O*-, a water molecule is hydrogen-bonded with the C6 atom of the cytosine base. We found that the hydration shell initially destabilizes the GC base pair toward electron capture as a transient anion. Energetically unstable diffuse states in the hydration shell are suggested to provide an intermediate state for the excess electron before molecular reorganization of the water molecules and the base pair results in a stable anion formation. The singly occupied molecular orbital (SOMO) in the anion radical complexes clearly shows that an excess electron localizes into a pi orbital of cytosine. The zero-point-energy (ZPE-) corrected adiabatic electron affinities (AEAs) of the GC-6H2O and GC-11H2O complexes, at the B3LYP/6-31+G** level of theory, were found to be 0.74 and 0.95 eV, respectively. However, the incorporation of bulk water as a solvent using the polarized continuum model (PCM) increases the EAs of these complexes to 1.77 eV.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, USA
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40
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Ida R, Wu G. Direct NMR detection of alkali metal ions bound to G-quadruplex DNA. J Am Chem Soc 2008; 130:3590-602. [PMID: 18293981 DOI: 10.1021/ja709975z] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe a general multinuclear (1H, 23Na, 87Rb) NMR approach for direct detection of alkali metal ions bound to G-quadruplex DNA. This study is motivated by our recent discovery that alkali metal ions (Na+, K+, Rb+) tightly bound to G-quadruplex DNA are actually "NMR visible" in solution (Wong, A.; Ida, R.; Wu, G. Biochem. Biophys. Res. Commun. 2005, 337, 363). Here solution and solid-state NMR methods are developed for studying ion binding to the classic G-quadruplex structures formed by three DNA oligomers: d(TG4T), d(G4T3G4), and d(G4T4G4). The present study yields the following major findings. (1) Alkali metal ions tightly bound to G-quadruplex DNA can be directly observed by NMR in solution. (2) Competitive ion binding to the G-quadruplex channel site can be directly monitored by simultaneous NMR detection of the two competing ions. (3) Na+ ions are found to locate in the diagonal T4 loop region of the G-quadruplex formed by two strands of d(G4T4G4). This is the first time that direct NMR evidence has been found for alkali metal ion binding to the diagonal T4 loop in solution. We propose that the loop Na+ ion is located above the terminal G-quartet, coordinating to four guanine O6 atoms from the terminal G-quartet and one O2 atom from a loop thymine base and one water molecule. This Na+ ion coordination is supported by quantum chemical calculations on 23Na chemical shifts. Variable-temperature 23Na NMR results have revealed that the channel and loop Na+ ions in d(G4T4G4) exhibit very different ion mobilities. The loop Na+ ions have a residence lifetime of 220 micros at 15 degrees C, whereas the residence lifetime of Na+ ions residing inside the G-quadruplex channel is 2 orders of magnitude longer. (4) We have found direct 23Na NMR evidence that mixed K+ and Na+ ions occupy the d(G4T4G4) G-quadruplex channel when both Na+ and K+ ions are present in solution. (5) The high spectral resolution observed in this study is unprecedented in solution 23Na NMR studies of biological macromolecules. Our results strongly suggest that multinuclear NMR is a viable technique for studying ion binding to G-quadruplex DNA.
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Affiliation(s)
- Ramsey Ida
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario, Canada K7L 3N6
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Rachwal PA, Findlow IS, Werner JM, Brown T, Fox KR. Intramolecular DNA quadruplexes with different arrangements of short and long loops. Nucleic Acids Res 2007; 35:4214-22. [PMID: 17576685 PMCID: PMC1919480 DOI: 10.1093/nar/gkm316] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
We have examined the folding, stability and kinetics of intramolecular quadruplexes formed by DNA sequences containing four G3 tracts separated by either single T or T4 loops. All these sequences fold to form intramolecular quadruplexes and 1D-NMR spectra suggest that they each adopt unique structures (with the exception of the sequence with all three loops containing T4, which is polymorphic). The stability increases with the number of single T loops, though the arrangement of different length loops has little effect. In the presence of potassium ions, the oligonucleotides that contain at least one single T loop exhibit similar CD spectra, which are indicative of a parallel topology. In contrast, when all three loops are substituted with T4 the CD spectrum is typical of an antiparallel arrangement. In the presence of sodium ions, the sequences with two and three single T loops also adopt a parallel folded structure. Kinetic studies on the complexes with one or two T4 loops in the presence of potassium ions reveal that sequences with longer loops display slower folding rates.
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Affiliation(s)
- Phillip A. Rachwal
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK and School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - I. Stuart Findlow
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK and School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Joern M. Werner
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK and School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Tom Brown
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK and School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Keith R. Fox
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK and School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
- *To whom correspondence should be addressed. +44 23 8059 4374+44 23 8059 4459
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Podbevšek P, Hud NV, Plavec J. NMR evaluation of ammonium ion movement within a unimolecular G-quadruplex in solution. Nucleic Acids Res 2007; 35:2554-63. [PMID: 17412708 PMCID: PMC1895886 DOI: 10.1093/nar/gkm138] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
d[G4(T4G4)3] has been folded into a unimolecular G-quadruplex in the presence of 15NH4+ ions. NMR spectroscopy confirmed that its topology is the same as the solution state structure determined earlier by Wang and Patel (J. Mol. Biol., 1995; 251: 76-94) in the presence of Na+ ions. The d[G4(T4G4)3] G-quadruplex exhibits four G-quartets with three 15NH4+-ion-binding sites (O1, I and O2). Quantitative analysis utilizing 15NH4+ ions as a NMR probe clearly demonstrates that there is no unidirectional 15NH4+ ion movement through the central cavity of the G-quadruplex. 15NH4+ ions move back and forth between the binding sites within the G-quadruplex and exchange with ions in bulk solution. 15NH4+ ion movement is controlled by the thermodynamic preferences of individual binding sites, steric restraints of the G-quartets for 15NH4+ ion passage and diagonal versus edge-type arrangement of the T4 loops. The movement of 15NH4+ ions from the interior of the G-quadruplex to bulk solution is faster than exchange within the G-quadruplex. The structural details of the G-quadruplex define stiffness of individual G-quartets that intimately affects 15NH4+ ion movement. The stiffness of G-quartets and steric hindrance imposed by thymine residues in the loops contribute to the 5-fold difference in the exchange rate constants through the outer G-quartets.
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Affiliation(s)
- Peter Podbevšek
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia and School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Nicholas V. Hud
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia and School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia and School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
- *To whom correspondence should be addressed +1-386 1-47-60-353+386 1-47-60-300
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Abstract
Stabilization of nucleic acid structures results from a balance of multiple interactions, including electrostatics, base stacking, hydrophobic interactions, hydrogen bonding, van der Waals forces, etc. Nucleic acid quadruplexes are unusual structures in that their formation is driven by specific binding of metal ions. This unique mode of metal binding, which is tightly coupled to oligonucleotide folding, can engender correspondingly unique solution behavior. In particular, we show that addition of many cosolvents, such as primary aliphatic alcohols, increases the thermal stability of quadruplexes, as determined by melting temperature, Tm, in direct contrast to the response of duplexes to the same admixture of solvents. Thermal stability is observed to increase as the dielectric constant of the composite solvent decreases. This behavior suggests a dominant role for electrostatics in quadruplex formation and stability. Additional studies done with other cosolvents and solutes suggest that, in some cases, other forces may come into play, including the possibility of direct interaction with the quadruplex structure. Nonetheless, many cosolvents and small molecules, such as ethanol, dimethylformamide, and betaine, stabilize the quadruplex conformation in sharp distinction to their destabilization of DNA duplexes.
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Affiliation(s)
- Ivan V Smirnov
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143-0446, USA
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45
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Yu HQ, Miyoshi D, Sugimoto N. Characterization of structure and stability of long telomeric DNA G-quadruplexes. J Am Chem Soc 2007; 128:15461-8. [PMID: 17132013 DOI: 10.1021/ja064536h] [Citation(s) in RCA: 150] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the current study, we used a combination of gel electrophoresis, circular dichroism, and UV melting analysis to investigate the structure and stability of G-quadruplexes formed by long telomeric DNAs from Oxytricha and human, where the length of the repeat (n)=4 to 12. We found that the Oxytricha telomeric DNAs, which have the sequence (TTTTGGGG)n, folded into intramolecular and intermolecular G-quadruplexes depending on the ionic conditions, whereas human telomeric DNAs, which have the sequence (TTAGGG)n, formed only intramolecular G-quadruplexes in all the tested conditions. We further estimated the thermodynamic parameters of the intramolecular G-quadruplex. We found that thermodynamic stabilities of G-quadruplex structures of long telomeric DNAs (n=5 to 12) are mostly independent of sequence length, although telomeric DNAs are more stable when n=4 than when n>or=5. Most importantly, when n is a multiple of four, the change in enthalpy and entropy for G-quadruplex formation increased gradually, demonstrating that the individual G-quadruplex units are composed of four repeats and that the individual units do not interact. Therefore, we propose that the G-quadruplexes formed by long telomeric DNAs (n>or=8) are bead-on-a-string structures in which the G-quadruplex units are connected by one TTTT (Oxytricha) or TTA (human) linker. These results should be useful for understanding the structure and function of telomeres and for developing improved therapeutic agents targeting telomeric DNAs.
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Affiliation(s)
- Hai-Qing Yu
- Frontier Institute for Biomolecular Engineering Research (FIBER) and Department of Chemistry, Faculty of Science and Engineering, Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan
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46
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Cavallari M, Calzolari A, Garbesi A, Di Felice R. Stability and migration of metal ions in G4-wires by molecular dynamics simulations. J Phys Chem B 2007; 110:26337-48. [PMID: 17181293 DOI: 10.1021/jp064522y] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We present a molecular dynamics investigation of guanine quadruple helices based on classical force fields. We analyze the dependence of the helical conformation on various compositional factors, such as the length of the G4-wire, as well as the incorporation into the helix channel of alkali ions of different species and in different amounts. In compliance with previous indications, our results suggest that monovalent alkali cations assist the stability of the quadruplex arrangement against disruption on the few nanoseconds time scale in the order of increasing van der Waals radius. Whereas very short G4-wire fragments immediately unfold in the absence of coordinating metal ions or in the presence of tiny ions (e.g., Li+) in agreement with the experimental evidence that empty short guanine quadruplexes are not formed in any synthetic conditions, our simulations show that longer empty helices do not discompose. This finding supports the possibility of producing long G4-wires with different guanine-cation stoichiometries than those routinely known. The classical trajectories allow us to identify different stationary axial sites for the different metal species, which are confirmed by complementary quantum calculations.
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Affiliation(s)
- Manuela Cavallari
- National Center on nanoStructures and bioSystems at Surfaces (S3) of INFM-CNR, Dipartimento di Fisica, Università di Modena e Reggio Emilia, Via Campi 213/A, 41100 Modena, Italy. cavallari.
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47
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Fan WJ, Zhang RQ, Liu S. Computation of large systems with an economic basis set: Structures and reactivity indices of nucleic acid base pairs from density functional theory. J Comput Chem 2007; 28:967-74. [PMID: 17269120 DOI: 10.1002/jcc.20670] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We show here that an economic basis set can describe nucleic acid base pairs involving the hydrogen bond interactions in density functional calculations. The economic basis set in which the polarization function is added only to oxygen and nitrogen atoms of strong electronegativity can predict reliable geometric structures and dipole moment of nucleic acid base pairs, comparable to those obtained from the basis set of 6-31G* in B3LYP calculations. Combining single point calculations with the standard basis set on the geometric structures optimized by the economic basis set, the present approach has predicted accurate natural bond orbital charge, binding energy, electronegativity, hardness, softness, and electrophilicity index. The principle for basis selection presented in this study can be regarded as a general guideline in the computation of large biological systems with considerably high accuracy and low computational expense.
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Affiliation(s)
- W J Fan
- Center of Super-Diamond and Advanced Films (COSDAF) & Department of Physics and Materials Science, City University of Hong Kong, Hong Kong SAR, People's Republic of China
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Burge S, Parkinson GN, Hazel P, Todd AK, Neidle S. Quadruplex DNA: sequence, topology and structure. Nucleic Acids Res 2006; 34:5402-15. [PMID: 17012276 PMCID: PMC1636468 DOI: 10.1093/nar/gkl655] [Citation(s) in RCA: 1810] [Impact Index Per Article: 100.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
G-quadruplexes are higher-order DNA and RNA structures formed from G-rich sequences that are built around tetrads of hydrogen-bonded guanine bases. Potential quadruplex sequences have been identified in G-rich eukaryotic telomeres, and more recently in non-telomeric genomic DNA, e.g. in nuclease-hypersensitive promoter regions. The natural role and biological validation of these structures is starting to be explored, and there is particular interest in them as targets for therapeutic intervention. This survey focuses on the folding and structural features on quadruplexes formed from telomeric and non-telomeric DNA sequences, and examines fundamental aspects of topology and the emerging relationships with sequence. Emphasis is placed on information from the high-resolution methods of X-ray crystallography and NMR, and their scope and current limitations are discussed. Such information, together with biological insights, will be important for the discovery of drugs targeting quadruplexes from particular genes.
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Affiliation(s)
| | | | | | | | - Stephen Neidle
- To whom correspondence should be addressed. Tel: +44 207 753 5969; Fax: +44 207 753 5970;
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Guzmán MR, Liquier J, Brahmachari SK, Taillandier E. Characterization of parallel and antiparallel G-tetraplex structures by vibrational spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2006; 64:495-503. [PMID: 16384730 DOI: 10.1016/j.saa.2005.07.049] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2005] [Accepted: 07/25/2005] [Indexed: 05/05/2023]
Abstract
A series of G-rich oligonucleotides able to form tetraplexes has been studied by FTIR spectroscopy. Characteristic markers of the formation of guanine tetrads are given. Moreover, we propose a new marker discriminating between parallel and antiparallel tetraplexes: the position of the C6O6 guanine carbonyl stretching vibration. In intermolecular parallel tetrameric structures formed by four separate strands this absorption is observed at 1693 cm-1 while for antiparallel tetrameric structures, either intramolecular or formed by dimerization of hairpins, this vibrational mode is observed at 1682 cm-1. These shifts to higher wavenumbers, when compared to the position of a free guanine C6O6 carbonyl stretching vibration observed at 1666 cm-1(Deltanu=27 cm-1 for parallel tetraplexes and Deltanu=16 cm-1 for antiparallel tetraplexes) reflect different strand orientations in the structures. This marker has been used to evidence the possibility of an antiparallel-parallel tetraplex reorganization for Oxytricha nova d(G4T4G4) and d((G4T4)3G4) and human d(G3T2AG3) telomeric sequences induced by Na+/K+ or Na+/Ca2+ ion exchange. Formation of the guanine tetrads, characterization of the phosphate geometries and of the sugar conformations have also been obtained by FTIR for the different tetraplexes.
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Affiliation(s)
- M Romero Guzmán
- Laboratoire BioMoCeTi, UMR CNRS 7033, Université Paris 13, 74, rue Marcel Cachin, F93017 Bobigny Cedex, France
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Hazel P, Parkinson GN, Neidle S. Predictive modelling of topology and loop variations in dimeric DNA quadruplex structures. Nucleic Acids Res 2006; 34:2117-27. [PMID: 16641317 PMCID: PMC1449907 DOI: 10.1093/nar/gkl182] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have used a combination of simulated annealing (SA), molecular dynamics (MD) and locally enhanced sampling (LES) methods in order to predict the favourable topologies and loop conformations of dimeric DNA quadruplexes with T2 or T3 loops. This follows on from our previous MD simulation studies on the influence of loop lengths on the topology of intramolecular quadruplex structures [P. Hazel et al. (2004) J. Am. Chem. Soc., 126, 16 405–16 415], which provided results consistent with biophysical data. The recent crystal structures of d(G4T3G4)2 and d(G4BrUT2G4) (P. Hazel et al. (2006) J. Am. Chem. Soc., in press) and the NMR-determined topology of d(TG4T2G4T)2 [A.T. Phan et al. (2004) J. Mol. Biol., 338, 93–102] have been used in the present study for comparison with simulation results. These together with MM-PBSA free-energy calculations indicate that lateral T3 loops are favoured over diagonal loops, in accordance with the experimental structures; however, distinct loop conformations have been predicted to be favoured compared to those found experimentally. Several lateral and diagonal loop conformations have been found to be similar in energy. The simulations suggest an explanation for the distinct patterns of observed dimer topology for sequences with T3 and T2 loops, which depend on the loop lengths, rather than only on G-quartet stability.
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Affiliation(s)
| | | | - Stephen Neidle
- To whom correspondence should be addressed. Tel: 44 207 753 5969; Fax: 44 207 753 5970;
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