1
|
Alexander A, Pillai AS, Akash BA, Ananthi N, Pal H, Enoch IV, Sayed M. Supramolecular association of a diguanidine derivative with a porphyrin-cyclodextrin conjugate and its binding to G-Quadruplex DNA. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
|
2
|
Pal S, Paul S. An in silico investigation of the binding modes and pathway of APTO-253 on c-KIT G-quadruplex DNA. Phys Chem Chem Phys 2021; 23:3361-3376. [PMID: 33502401 DOI: 10.1039/d0cp05210h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The stability of c-KIT G-quadruplex DNA via ligands has been a significant concern in the growing field of cancer therapy. Thus, it is very important to understand the mechanism behind the high binding affinity of the small drug molecules on the c-KIT G-quadruplex DNA. In this study, we have investigated the binding mode and pathway of the APTO-253 ligand on the c-KIT G-quadruplex DNA employing a total of 10 μs all atom molecular dynamics simulations and further 8.82 μs simulations via the umbrella sampling method using both OL15 and BSC1 latest force fields for DNA structures. From the cluster structure analysis, mainly three binding pathways i.e., top, bottom and side loop stacking modes are identified. Moreover, RMSD, RMSF and 2D-RMSD values indicate that the c-KIT G-quadruplex DNA and APTO-253 molecules are stable throughout the simulation run. Furthermore, the number of hydrogen bonds in each tetrad and the distance between the two central K+ cations confirm that the c-KIT G-quadruplex DNA maintains its conformation in the process of complex formation with the APTO-253 ligand. The binding free energies and the minimum values in the potential of mean forces suggest that the binding processes are energetically favorable. Furthermore, we have found that the bottom stacking mode is the most favorable binding mode among all the three modes for the OL15 force field. However, for the BSC1 force field, both the top and bottom binding modes of the APTO-253 ligand in c-KIT G-quadruplex DNA are comparable to each other. To investigate the driving force for the complex formation, we have noticed that the van der Waals (vdW) and π-π stacking interactions are mainly responsible. Our detailed studies provide useful information for the discovery of novel drugs in the field of stabilization of G-quadruplex DNAs.
Collapse
Affiliation(s)
- Saikat Pal
- Department of Chemistry, Indian Institute of Technology, Guwahati Assam, 781039, India.
| | | |
Collapse
|
3
|
Tyagi S, Saxena S, Srivastava P, Sharma T, Kundu N, Kaur S, Shankaraswamy J. Screening the binding potential of quercetin with parallel, antiparallel and mixed G-quadruplexes of human telomere and cancer protooncogenes using molecular docking approach. SN APPLIED SCIENCES 2020. [DOI: 10.1007/s42452-020-2280-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
|
4
|
Moghaddam KG, de Vries AH, Marrink SJ, Faraji S. Binding of quinazolinones to c-KIT G-quadruplex; an interplay between hydrogen bonding and π-π stacking. Biophys Chem 2019; 253:106220. [PMID: 31302375 DOI: 10.1016/j.bpc.2019.106220] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/04/2019] [Accepted: 07/04/2019] [Indexed: 12/18/2022]
Abstract
Stabilization of G-quadruplex structures in the c-KIT promoter with the aid of ligands has become an area of great interest in potential cancer therapeutics. Understanding the binding process between ligands and G-quadruplex is essential for a discovery of selective ligands with high binding affinity to G-quadruplex. In the present work, binding mechanisms of 4-quinazolinones to c-KIT G-quadruplex were investigated theoretically by means of molecular dynamics (MD) simulations. To explore the binding affinity of ligands, binding free energy calculations were performed using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method. We demonstrate that the key interactions in G-quadruplex-ligand complexes are π-π stacking and hydrogen bond interactions. However, neither of these two interactions alone determines the stability of the G-quadruplex-ligand complexes; rather, it is the result of an intricate interplay between the two. To further examine the nature of the binding, a free energy decomposition analysis at residue level was carried out. The results clearly demonstrate the crucial roles of two hot spot residues (DG4 and DG8) for the binding of ligands to c-KIT G-quadruplex, and highlight the importance of the planar aromatic moiety of ligands in G-quadruplex stabilization via π-π stacking interactions. Our study can assist in the design of new derivatives of 4-quinazolinone with high binding affinity for c-KIT G-quadruplex.
Collapse
Affiliation(s)
| | - Alex H de Vries
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Shirin Faraji
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.
| |
Collapse
|
5
|
Głuszyńska A, Juskowiak B, Kuta-Siejkowska M, Hoffmann M, Haider S. Carbazole ligands as c-myc G-quadruplex binders. Int J Biol Macromol 2018; 114:479-490. [DOI: 10.1016/j.ijbiomac.2018.03.135] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 03/16/2018] [Accepted: 03/21/2018] [Indexed: 10/24/2022]
|
6
|
Głuszyńska A, Juskowiak B, Kuta-Siejkowska M, Hoffmann M, Haider S. Carbazole Derivatives' Binding to c-KIT G-Quadruplex DNA. Molecules 2018; 23:E1134. [PMID: 29747481 PMCID: PMC6099540 DOI: 10.3390/molecules23051134] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 04/25/2018] [Accepted: 05/07/2018] [Indexed: 11/17/2022] Open
Abstract
The binding affinities of three carbazole derivatives to the intramolecular G-quadruplex (GQ) DNA formed by the sequence 5′-AGGGAGGGCGCTGGGAGGAGGG-3′, derived from the c-KIT 1 oncogene region, were investigated. All carbazole cationic ligands that differed in the substituents on the nitrogen atom were able to stabilize G-quadruplex, as demonstrated using UV-Vis, fluorescence and CD spectroscopic techniques as well as molecular modeling. The spectrophotometric titration results showed spectral features characteristic of these ligands-bathochromic shifts and initial hypochromicity followed by hyperchromicity at higher GQ concentrations. All free carbazole ligands exhibited modest fluorescent properties, but after binding to the DNA the fluorescence intensity increased significantly. The binding affinities of carbazole ligands to the c-KIT 1 DNA were comparable showing values in the order of 10⁵ M−1. Molecular modeling highlights the differences in interactions between each particular ligand and studied G-quadruplex, which potentially influenced binding strength. Obtained results relevant that all three investigated ligands have stabilization properties on studied G-quadruplex.
Collapse
Affiliation(s)
- Agata Głuszyńska
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska Street 89b, 61-614 Poznań, Poland.
| | - Bernard Juskowiak
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska Street 89b, 61-614 Poznań, Poland.
| | - Martyna Kuta-Siejkowska
- Laboratory of Quantum Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska Street 89b, 61-614 Poznań, Poland.
| | - Marcin Hoffmann
- Laboratory of Quantum Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska Street 89b, 61-614 Poznań, Poland.
| | - Shozeb Haider
- School of Pharmacy, University College London, London WC1N 1AX, UK.
| |
Collapse
|
7
|
Tojo Y, Urushibara K, Yamamoto S, Mori H, Masu H, Kudo M, Hirano T, Azumaya I, Kagechika H, Tanatani A. Conformational Properties of Aromatic Oligoamides Bearing Pyrrole Rings. J Org Chem 2018; 83:4606-4617. [DOI: 10.1021/acs.joc.8b00349] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yukiko Tojo
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Ko Urushibara
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Sawori Yamamoto
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Hirotoshi Mori
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Hyuma Masu
- Center for Analytical Instrumentation, Chiba University, Yayoi-cho, Chiba-shi, Chiba 263-8522, Japan
| | - Mayumi Kudo
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Tomoya Hirano
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Isao Azumaya
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Hiroyuki Kagechika
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Aya Tanatani
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| |
Collapse
|
8
|
Kumar R, Gaurav A, Pal S, Kumar KR, Sridhar B, Tewari AK. Reverse Intramolecular Stacking in o-Xylene Bridge Symmetrical Dimers of 2-Thiopyridine Derivative: Assessment of the Conformational Stability. ChemistrySelect 2017. [DOI: 10.1002/slct.201700269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ranjeet Kumar
- Department of Chemistry (Centre of Advanced Studies); Institute of Science; Banaras Hindu University; Varanasi 221005 India
| | - Archana Gaurav
- Department of Chemistry (Centre of Advanced Studies); Institute of Science; Banaras Hindu University; Varanasi 221005 India
| | - Shiv Pal
- Indian Institute of Science Education and Research, Pune; Dr. Homi Bhabha Road, Pashan Pune 411008 India
| | - Krishnan R. Kumar
- Laboratory of X-ray Crystallography; Indian Institute of Chemical Technology; Hyderabad 500 607 India
| | - Balasubramanian Sridhar
- Laboratory of X-ray Crystallography; Indian Institute of Chemical Technology; Hyderabad 500 607 India
| | - Ashish K. Tewari
- Department of Chemistry (Centre of Advanced Studies); Institute of Science; Banaras Hindu University; Varanasi 221005 India
| |
Collapse
|
9
|
Guerrini G, Ciciani G, Ciattini S, Crocetti L, Daniele S, Martini C, Melani F, Vergelli C, Giovannoni MP. Pyrazolo[1,5-a]quinazoline scaffold as 5-deaza analogue of pyrazolo[5,1-c][1,2,4]benzotriazine system: synthesis of new derivatives, biological activity on GABAA receptor subtype and molecular dynamic study. J Enzyme Inhib Med Chem 2015; 31:195-204. [DOI: 10.3109/14756366.2015.1014475] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Gabriella Guerrini
- Dipartimento NEUROFARBA, Sezione Farmaceutica e Nutraceutica, Università degli Studi di Firenze, Firenze, Italy,
| | - Giovanna Ciciani
- Dipartimento NEUROFARBA, Sezione Farmaceutica e Nutraceutica, Università degli Studi di Firenze, Firenze, Italy,
| | - Samuele Ciattini
- Dipartimento di Chimica, Centro di Cristallografia, Università degli Studi di Firenze, Firenze, Italy, and
| | - Letizia Crocetti
- Dipartimento NEUROFARBA, Sezione Farmaceutica e Nutraceutica, Università degli Studi di Firenze, Firenze, Italy,
| | - Simona Daniele
- Dipartimento di Farmacia, Università degli Studi di Pisa, Pisa, Italy
| | - Claudia Martini
- Dipartimento di Farmacia, Università degli Studi di Pisa, Pisa, Italy
| | - Fabrizio Melani
- Dipartimento NEUROFARBA, Sezione Farmaceutica e Nutraceutica, Università degli Studi di Firenze, Firenze, Italy,
| | - Claudia Vergelli
- Dipartimento NEUROFARBA, Sezione Farmaceutica e Nutraceutica, Università degli Studi di Firenze, Firenze, Italy,
| | - Maria Paola Giovannoni
- Dipartimento NEUROFARBA, Sezione Farmaceutica e Nutraceutica, Università degli Studi di Firenze, Firenze, Italy,
| |
Collapse
|
10
|
Moghaddam KG, Hashemianzadeh SM. The effect of amino substituents on the interactions of quinazolone derivatives with c-KIT G-quadruplex: insight from molecular dynamics simulation study for rational design of ligands. RSC Adv 2015. [DOI: 10.1039/c5ra13615f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Our study provides insight into the effect of different substituents on the G-quadruplex–ligand interactions which helps us rational ligand design.
Collapse
Affiliation(s)
- Kiana Gholamjani Moghaddam
- Molecular Simulation Research Laboratory
- Department of Chemistry
- Iran University of Science & Technology
- Tehran
- Iran
| | - Seyed Majid Hashemianzadeh
- Molecular Simulation Research Laboratory
- Department of Chemistry
- Iran University of Science & Technology
- Tehran
- Iran
| |
Collapse
|
11
|
Liu ZQ, Zhuo ST, Tan JH, Ou TM, Li D, Gu LQ, Huang ZS. Facile syntheses of disubstituted bis(vinylquinolinium)benzene derivatives as G-quadruplex DNA binders. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.04.045] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|