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Ghosal S, Bag S, Chinnadurai RK, Mukherjee M, Pramanik G, Bhowmik S. Investigating the preferential interaction between imatinib mesylate and VEGF G-quadruplex DNA as therapeutic strategies for cancer treatment: Biophysical and molecular modelling approaches. Comput Biol Med 2024; 177:108683. [PMID: 38838555 DOI: 10.1016/j.compbiomed.2024.108683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/07/2024]
Abstract
G-Quadruplex DNA (GQ-DNA) is one of the most important non-canonical nucleic acid structures. GQ-DNA forming sequences are present in different crucial genomic regions and are abundant in promoter regions of several oncogenes. Therefore, GQ-DNA is an important target for anticancer drugs and hence binding interactions between GQ-DNA and small molecule ligands are of great importance. Since GQ-DNA is a highly polymorphic structure, it is important to identify ligand molecules which preferentially target a particular quadruplex sequence. In this present study, we have used a FDA approved drug called imatinib mesylate (ligand) which is a selective tyrosine kinase inhibitor, successfully used for the treatment of chronic myelogenous leukaemia, gastrointestinal stromal tumours. Different spectroscopic techniques as well as molecular docking investigations and molecular simulations have been used to explore the interaction between imatinib mesylate with VEGF GQ DNA structures along with duplex DNA, C-Myc, H-Telo GQ DNA. We found that imatinib mesylate shows preferential interaction towards VEGF GQ DNA compared to C-Myc, H-Telo GQ and duplex DNA. Imatinib mesylate seems to be an efficient ligand for VEGF GQ DNA, suggesting that it might be used to regulate the expression of genes in cancerous cells.
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Affiliation(s)
- Souvik Ghosal
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to be University), Pondy-Cuddalore Main Road, Pillaiyarkuppam, Pondicherry, 607402, India
| | - Sagar Bag
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, A.P.C. Road, Kolkata, 700009, India
| | - Raj Kumar Chinnadurai
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to be University), Pondy-Cuddalore Main Road, Pillaiyarkuppam, Pondicherry, 607402, India
| | - Moupriya Mukherjee
- UGC-DAE Consortium for Scientific Research, Kolkata Centre, Sector III, LB-8, Bidhan Nagar, Kolkata, 700 106, India
| | - Goutam Pramanik
- UGC-DAE Consortium for Scientific Research, Kolkata Centre, Sector III, LB-8, Bidhan Nagar, Kolkata, 700 106, India
| | - Sudipta Bhowmik
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to be University), Pondy-Cuddalore Main Road, Pillaiyarkuppam, Pondicherry, 607402, India; Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, A.P.C. Road, Kolkata, 700009, India.
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Sun Z, He Q, Gong Z, Kalhor P, Huai Z, Liu Z. A General Picture of Cucurbit[8]uril Host–Guest Binding: Recalibrating Bonded Interactions. Molecules 2023; 28:molecules28073124. [PMID: 37049887 PMCID: PMC10095826 DOI: 10.3390/molecules28073124] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/15/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Atomic-level understanding of the dynamic feature of host–guest interactions remains a central challenge in supramolecular chemistry. The remarkable guest binding behavior of the Cucurbiturils family of supramolecular containers makes them promising drug carriers. Among Cucurbit[n]urils, Cucurbit[8]uril (CB8) has an intermediate portal size and cavity volume. It can exploit almost all host–guest recognition motifs formed by this host family. In our previous work, an extensive computational investigation of the binding of seven commonly abused and structurally diverse drugs to the CB8 host was performed, and a general dynamic binding picture of CB8-guest interactions was obtained. Further, two widely used fixed-charge models for drug-like molecules were investigated and compared in great detail, aiming at providing guidelines in choosing an appropriate charge scheme in host-guest modelling. Iterative refitting of atomic charges leads to improved binding thermodynamics and the best root-mean-squared deviation from the experimental reference is 2.6 kcal/mol. In this work, we focus on a thorough evaluation of the remaining parts of classical force fields, i.e., the bonded interactions. The widely used general Amber force fields are assessed and refitted with generalized force-matching to improve the intra-molecular conformational preference, and thus the description of inter-molecular host–guest interactions. The interaction pattern and binding thermodynamics show a significant dependence on the modelling parameters. The refitted system-specific parameter set improves the consistency of the modelling results and the experimental reference significantly. Finally, combining the previous charge-scheme comparison and the current force-field refitting, we provide general guidelines for the theoretical modelling of host–guest binding.
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Ortiz de Luzuriaga I, Sánchez-González Á, Synoradzki W, Lopez X, Gil A. Unravelling the binding affinity and selectivity of molybdenum(II) phenanthroline complexes with DNA G-quadruplexes by using linear-scaling DFT studies. The important role of ancillary ligands. Phys Chem Chem Phys 2022; 24:25918-25929. [PMID: 36260061 DOI: 10.1039/d2cp02241a] [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: 06/16/2023]
Abstract
We have used near linear-scaling density functional theory (LS-DFT) methods including dispersion, for the first time, to study the interaction of two isomers, equatorial (Eq) and axial (Ax), of the [Mo(η3-C3H5)Br(CO)2(phen)] metal complex with the DNA G-quadruplexes (GQ) to gain insight into its cytotoxicity. The LMKLL/DZDP level of calculation, which includes van der Waals contributions, with the SIESTA software was used to treat by means of first-principles computations the whole biological studied model system with ∼1000 atoms. Computed formation energies point to systems containing the Ax isomer as the most stable although the nearest system in energy containing the Eq isomer is only 7.5 kcal mol-1 above. On the other hand, the energy decomposition analysis (EDA) favours interaction energies for the systems containing the Eq isomer. However, when solvent effects are taken into account the systems containing the Ax isomer are again the most stable. This Ax isomer was found interacting by means of end-stacking with the GQ and surprisingly totally inside the non-canonical secondary structure, where all the ligands of the metal complex produce several weak interactions with the DNA structure. On the other hand, the Eq isomer prefers to interact from outside by means of intercalation in which the ancillary ligands also have some role in the interaction. Such features and comparison with the results regarding the interaction of the [Mo(η3-C3H5)Br(CO)2(phen)] metal complex with duplex DNA suggest that the [Mo(η3-C3H5)Br(CO)2(phen)] would have a higher affinity and eventual selectivity for non-canonical DNA GQ structures.
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Affiliation(s)
- Iker Ortiz de Luzuriaga
- CIC-nanoGUNE BRTA, Tolosa Hiribidea 76, E-20018, Donostia - San Sebastián, Euskadi, Spain.
- Polímero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea, UPV/EHU, 20080, Donostia, Euskadi, Spain
| | - Ángel Sánchez-González
- BioISI - Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Wojciech Synoradzki
- BioISI - Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Xabier Lopez
- Polímero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea, UPV/EHU, 20080, Donostia, Euskadi, Spain
- Donostia International Physics Center (DIPC), P. K. 1072, 20080, Donostia, Euskadi, Spain
| | - Adrià Gil
- CIC-nanoGUNE BRTA, Tolosa Hiribidea 76, E-20018, Donostia - San Sebastián, Euskadi, Spain.
- BioISI - Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
- ARAID Foundation, Zaragoza, Spain
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH) - Consejo Superior de Investigaciones Científicas (CSIC). Universidad de Zaragoza, c/Pedro Cerbuna 12, 50009, Zaragoza, Spain
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Göç YB, Poziemski J, Smolińska W, Suwała D, Wieczorek G, Niedzialek D. Tracking Topological and Electronic Effects on the Folding and Stability of Guanine-Deficient RNA G-Quadruplexes, Engineered with a New Computational Tool for De Novo Quadruplex Folding. Int J Mol Sci 2022; 23:ijms231910990. [PMID: 36232294 PMCID: PMC9570295 DOI: 10.3390/ijms231910990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
The initial aim of this work was to elucidate the mutual influence of different single-stranded segments (loops and caps) on the thermodynamic stability of RNA G-quadruplexes. To this end, we used a new NAB-GQ-builder software program, to construct dozens of two-tetrad G-quadruplex topologies, based on a designed library of sequences. Then, to probe the sequence–morphology–stability relationships of the designed topologies, we performed molecular dynamics simulations. Their results provide guidance for the design of G-quadruplexes with balanced structures, and in turn programmable physicochemical properties for applications as biomaterials. Moreover, by comparative examinations of the single-stranded segments of three oncogene promoter G-quadruplexes, we assess their druggability potential for future therapeutic strategies. Finally, on the basis of a thorough analysis at the quantum mechanical level of theory on a series of guanine assemblies, we demonstrate how a valence tautomerism, triggered by a coordination of cations, initiates the process of G-quadruplex folding, and we propose a sequential folding mechanism, otherwise dictated by the cancellation of the dipole moments on guanines.
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Affiliation(s)
- Yavuz Burak Göç
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland or
- Faculty of Chemistry, Biological & Chemical Research Center, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Jakub Poziemski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland or
| | - Weronika Smolińska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland or
- Faculty of Chemical and Process Engineering, Warsaw University of Technology, Waryńskiego 1, 00-645 Warsaw, Poland
| | - Dominik Suwała
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland or
- Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Grzegorz Wieczorek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland or
- Molecure SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Dorota Niedzialek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland or
- Correspondence:
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