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Background
[edit]The identification of structures with a high guanine association became apparent in the early 1960’s, through the identification of gel-like substances associated with guanines.[1] More specifically, this research detailed the four-stranded DNA structures with a high association of guanines, which was later identified in eukaryotic telomeric regions of DNA in the 1980’s.[2] The importance of discovering G-quadruplex structure was best hypothesized by the statement, “If G-quadruplexes form so readily in vitro, Nature will have found a way of using them in vivo” - Aaron Klug, Nobel Prize Winner in Chemistry (1982). With the abundance of G-quadruplexes in vivo, these structures hold a biologically relevant role through interactions with the promoter regions of oncogenes and the telomeric regions of DNA strands. Current research consists of identifying the biological function of these G-Quadruplex structures for specific oncogenes and discovering effective therapeutic treatments for cancer based on interactions with G-Quadruplexes.
Cancer
[edit]Telomeres
[edit]G-quadruplex forming sequences are prevalent in eukaryotic cells especially in telomeres, 5` untranslated strands, and translocation hot spots. G-quadruplexes can inhibit normal cell function and in healthy cells are easily and readily unwound by helicase. However, in cancer cells that have mutated helicase these complexes cannot be unwound and leads to potential damage of the cell. This causes replication of damaged and cancerous cells. For therapeutic advances, stabilizing the G-quadruplexes of cancerous cells can inhibit cell growth and replication leading to the cells death.[3]
Promoter Regions
[edit]Along with the association of G-quadruplexes in telomeric regions of DNA, G-quadruplex structures have been identified in various human proto-oncogene promoter regions. The structures most present in the promoter regions of these oncogenes tend to be parallel-stranded G-quadruplex DNA structures.[4] Some of these oncogenes include c-KIT, PDGF-A, c-Myc and VEGF, showing the importance of this secondary structure in cancer growth and development. While the formation of G-quadruplex structure vary to some extent for the different promoter regions of oncogenes, the consistent stabilization of these structures have been found in cancer development.[5] Current therapeutic research actively focuses on targeting this stabilization of G-quadruplex structures to arrest unregulated cell growth and division.
![](http://upload.wikimedia.org/wikipedia/commons/thumb/c/cb/C-Myc_binding_interaction_with_Potassium_Ligand_through_PYMOL.png/220px-C-Myc_binding_interaction_with_Potassium_Ligand_through_PYMOL.png)
One particular gene region, the c-myc pathway, plays an integral role in the regulation of a protein product, c-Myc. With this product, the c-Myc protein functions in the processes of apoptosis and cell growth or development and as a transcriptional control on human telomerase reverse transcriptase. This specific pathway has exhibited the formation of a parallel-stranded G-quadruplex structure, with a consistent pattern of a repeating motif across various oncogene promoter regions.[6][7]
![](http://upload.wikimedia.org/wikipedia/commons/thumb/6/61/VEGF-Quad2.png/220px-VEGF-Quad2.png)
Another gene pathway deals with the VEGF gene, Vascular Endothelial Growth Factor, which remains involved in the process of angiogenesis or the formation of new blood vessels. The formation of an intramolecular G-quadruplex structure has been shown through studies on the polypurine tract of the promoter region of the VEGF gene. Through recent research on the role of G-quadruplex function in vivo, the stabilization of G-quadruplex structures was shown to regulate VEGF gene transcription, with inhibition of transcription factors in this pathway. The intramolecular G-quadruplex structures are formed mostly through the abundant guanine sequence in the promoter region of this specific pathway.[8]
Hypoxia inducible factor 1ɑ, HIF-1ɑ, remains involved in cancer signaling through its binding to Hypoxia Response Element, HRE, in the presence of hypoxia to begin the process of angiogenesis. Through recent research into this specific gene pathway, the polypurine and polypyrimidine region allows for the transcription of this specific gene and the formation of an intramolecular G-quadruplex structure. However, more research is necessary to determine whether the the formation of G-quadruplex regulates the expression of this gene in the positive and negative manner.[9]
The c-kit oncogene deals with a pathway that encodes an RTK, which was shown to have elevated expression levels in certain types of cancer. The rich guanine sequence of this promoter region has shown the ability to form a variety of quadruplexes. Current research on this pathway is focusing on discovering the biological function of this specific quadruplex formation on the c-kit pathway, while this quadruplex sequence has been noticed in various species.[10]
The RET oncogene functions in the transcription of kinase which has been abundant in certain types of cancer. The guanine rich sequence in the promoter region for this pathway exudes a necessity for baseline transcription of this receptor tyrosine kinase. In certain types of cancers, the RET protein has shown increased expression levels. The research on this pathway suggested the formation of a G-quadruplex in the promoter region and an applicable target for therapeutic treatments.[11]
Another oncogene pathway involving PDGF-A, platelet-derived growth factor, involves the process of wound healing and function as mitogenic growth factors for cells. High levels of expression of PDGF have been associated with increased cell growth and cancer. The presence of a guanine-rich sequence in the promoter region of PDGF-A has exhibited the ability to form intramolecular parallel G-quadruplex structures and remains suggested to play a role in transcriptional regulation of PDGF-A. However, research has also identified the presence of G-quadruplex structures within this region due to the interaction of TMPyP4 with this promoter sequence.[12]
Therapeutics
[edit]Telomeres are generally made up of G-quadruplexes and remain important targets for therapeutic research and discoveries.These complexes have a high affinity for porphyrin rings which makes them effective anticancer agents. However TMPyP4 has been limited for used due to its non-selectivity toward cancer cell telomeres and normal double stranded DNA (dsDNA). To address this issue analog of TMPyP4 was synthesized known as 5Me which targets only G quadruplex DNA which inhibits cancer growth more effectively than TMPyP4.[13]
Ligand design and development remains an important field of research into therapeutic reagents due to the abundance of G-quadruplexes and their multiple conformational differences. One type of ligand involving a Quindoline derivative, SYUIQ-05, utilizes the stabilization of G-quadruplexes in promoter regions to inhibit the production of both the c-Myc protein product and the human telomerase reverse transcriptase (hTERT). This main pathway of targeting this region results in the lack of telomerase elongation, leading to arrested cell development. Further research remains necessary for the discovery of a single gene target, to minimize unwanted reactivity with more efficient antitumor activity.[14]
Ligand-Binding
[edit]The binding of ligands to G-quadruplexes is vital for anti-cancer pursuits because G-quadruplexes are found typically at translocation hot spots. MM41, a ligand that binds selectively for a quadruplex on the BCL-2 promoter, is shaped with a central core and 4 side chains branching sterically out. The shape of the ligand is vital because it closely matches the quadruplex which has stacked quartets and the loops of nucleic acids holding it together. When bound, MM41’s central chromophore is situated on top of the 3’ terminal G-quartet and the side chains of the ligand associate to the loops of the quadruplex. The quartet and the chromophore are bound with a π-π bond while the side chains and loops are not bound but are in close proximity. What makes this binding strong is the fluidity in the position of the loops to better associate with the ligand side chains.[15]
When designing ligands to be bound to quadruplexes it is important to note that the best binding is done in parallel with the ligand and quadruplex. It’s been found that ligands with smaller side chains bind better to the quadruplex because smaller ligands have more concentrated electron density. Also, the hydrogen bonds of ligands with smaller side chains are shorter and therefore stronger. The side chains and the loops of the quadruplexes are mobile and due to this are able to associate strongly when in the proper conformations.[16]
- ^ Gellert, M.; Lipsett, M. N.; Davies, D. R. (1962-12-15). "Helix formation by guanylic acid". Proceedings of the National Academy of Sciences of the United States of America. 48: 2013–2018. ISSN 0027-8424. PMC 221115. PMID 13947099.
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: CS1 maint: PMC format (link) - ^ Henderson, Eric; Hardin, Charles C.; Walk, Steven K.; Tinoco, Ignacio; Blackburn, Elizabeth H. (1987-12). "Telomeric DNA oligonucleotides form novel intramolecular structures containing guanine·guanine base pairs". Cell. 51 (6): 899–908. doi:10.1016/0092-8674(87)90577-0. ISSN 0092-8674.
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(help) - ^ Neidle, Stephen (2016-02-16). "Quadruplex Nucleic Acids as Novel Therapeutic Targets". Journal of Medicinal Chemistry. 59 (13): 5987–6011. doi:10.1021/acs.jmedchem.5b01835. ISSN 0022-2623.
- ^ Chen, Yuwei; Yang, Danzhou (2012-9). "Sequence, stability, and structure of G-quadruplexes and their interactions with drugs". Current Protocols in Nucleic Acid Chemistry. Chapter 17: Unit17.5. doi:10.1002/0471142700.nc1705s50. ISSN 1934-9289. PMC 3463244. PMID 22956454.
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(help)CS1 maint: PMC format (link) - ^ Brooks, Tracy A.; Kendrick, Samantha; Hurley, Laurence (2010-9). "Making sense of G-quadruplex and i-motif functions in oncogene promoters". The FEBS journal. 277 (17): 3459–3469. doi:10.1111/j.1742-4658.2010.07759.x. ISSN 1742-4658. PMC 2971675. PMID 20670278.
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(help)CS1 maint: PMC format (link) - ^ Chen, Yuwei; Yang, Danzhou (2012-09), "Sequence, Stability, and Structure of G-Quadruplexes and Their Interactions with Drugs", Current Protocols in Nucleic Acid Chemistry, John Wiley & Sons, Inc., pp. 17.5.1–17.5.17, doi:10.1002/0471142700.nc1705s50, ISBN 0471142700, PMC 3463244, PMID 22956454, retrieved 2018-11-19
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(help)CS1 maint: PMC format (link) - ^ Ou, Tian-Miao; Lin, Jing; Lu, Yu-Jing; Hou, Jin-Qiang; Tan, Jia-Heng; Chen, Shu-Han; Li, Zeng; Li, Yan-Ping; Li, Ding (2011-08-25). "Inhibition of cell proliferation by quindoline derivative (SYUIQ-05) through its preferential interaction with c-myc promoter G-quadruplex". Journal of Medicinal Chemistry. 54 (16): 5671–5679. doi:10.1021/jm200062u. ISSN 1520-4804. PMID 21774525.
- ^ Sun, D. (2005-10-12). "Facilitation of a structural transition in the polypurine/polypyrimidine tract within the proximal promoter region of the human VEGF gene by the presence of potassium and G-quadruplex-interactive agents". Nucleic Acids Research. 33 (18): 6070–6080. doi:10.1093/nar/gki917. ISSN 0305-1048. PMC 1266068. PMID 16239639.
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: CS1 maint: PMC format (link) - ^ De Armond, Richard; Wood, Stacey; Sun, Daekyu; Hurley, Laurence H.; Ebbinghaus, Scot W. (2005-12). "Evidence for the Presence of a Guanine Quadruplex Forming Region within a Polypurine Tract of the Hypoxia Inducible Factor 1α Promoter†". Biochemistry. 44 (49): 16341–16350. doi:10.1021/bi051618u. ISSN 0006-2960.
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(help) - ^ Fernando, Himesh; Reszka, Anthony P.; Huppert, Julian; Ladame, Sylvain; Rankin, Sarah; Venkitaraman, Ashok R.; Neidle, Stephen; Balasubramanian, Shankar (2006-06). "A Conserved Quadruplex Motif Located in a Transcription Activation Site of the Human c-kit Oncogene". Biochemistry. 45 (25): 7854–7860. doi:10.1021/bi0601510. ISSN 0006-2960. PMC 2195898. PMID 16784237.
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(help)CS1 maint: PMC format (link) - ^ Guo, Kexiao; Pourpak, Alan; Beetz-Rogers, Kara; Gokhale, Vijay; Sun, Daekyu; Hurley, Laurence H. (2007-08). "Formation of Pseudosymmetrical G-Quadruplex and i-Motif Structures in the Proximal Promoter Region of theRETOncogene". Journal of the American Chemical Society. 129 (33): 10220–10228. doi:10.1021/ja072185g. ISSN 0002-7863. PMC 2566970. PMID 17672459.
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(help)CS1 maint: PMC format (link) - ^ Qin, Y.; Rezler, E. M.; Gokhale, V.; Sun, D.; Hurley, L. H. (2007-11-26). "Characterization of the G-quadruplexes in the duplex nuclease hypersensitive element of the PDGF-A promoter and modulation of PDGF-A promoter activity by TMPyP4". Nucleic Acids Research. 35 (22): 7698–7713. doi:10.1093/nar/gkm538. ISSN 0305-1048. PMC 2190695. PMID 17984069.
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: CS1 maint: PMC format (link) - ^ Chilakamarthi, Ushasri; Koteshwar, Devulapally; Jinka, Sudhakar; Vamsi Krishna, Narra; Sridharan, Kathyayani; Nagesh, Narayana; Giribabu, Lingamallu (2018-11-09). "Novel Amphiphilic G-Quadruplex Binding Synthetic Derivative of TMPyP4 and Its Effect on Cancer Cell Proliferation and Apoptosis Induction". Biochemistry. doi:10.1021/acs.biochem.8b00843. ISSN 1520-4995. PMID 30369235.
- ^ Ou, Tian-Miao; Lin, Jing; Lu, Yu-Jing; Hou, Jin-Qiang; Tan, Jia-Heng; Chen, Shu-Han; Li, Zeng; Li, Yan-Ping; Li, Ding (2011-08-25). "Inhibition of cell proliferation by quindoline derivative (SYUIQ-05) through its preferential interaction with c-myc promoter G-quadruplex". Journal of Medicinal Chemistry. 54 (16): 5671–5679. doi:10.1021/jm200062u. ISSN 1520-4804. PMID 21774525.
- ^ Ohnmacht, Stephan A.; Marchetti, Chiara; Gunaratnam, Mekala; Besser, Rachael J.; Haider, Shozeb M.; Di Vita, Gloria; Lowe, Helen L.; Mellinas-Gomez, Maria; Diocou, Seckou (2015-06-16). "A G-quadruplex-binding compound showing anti-tumour activity in an in vivo model for pancreatic cancer". Scientific Reports. 5: 11385. doi:10.1038/srep11385. ISSN 2045-2322. PMC 4468576. PMID 26077929.
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: CS1 maint: PMC format (link) - ^ Collie, Gavin W.; Promontorio, Rossella; Hampel, Sonja M.; Micco, Marialuisa; Neidle, Stephen; Parkinson, Gary N. (2012-01-31). "Structural Basis for Telomeric G-Quadruplex Targeting by Naphthalene Diimide Ligands". Journal of the American Chemical Society. 134 (5): 2723–2731. doi:10.1021/ja2102423. ISSN 0002-7863.