Target type: molecularfunction
Binding to G-quadruplex DNA structures, in which groups of four guanines adopt a flat, cyclic Hoogsteen hydrogen-bonding arrangement known as a guanine tetrad. The stacking of guanine tetrads results in G-quadruplex DNA structures. G-quadruplex DNA can form under physiological conditions from some G-rich sequences, such as those found in telomeres, immunoglobulin switch regions, gene promoters, fragile X repeats, and the dimerization domain in the human immunodeficiency virus (HIV) genome. [PMID:16142245, PMID:9512530]
G-quadruplex DNA binding refers to the interaction of proteins or small molecules with G-quadruplex structures within DNA. G-quadruplexes are non-canonical DNA structures formed by guanine-rich sequences, characterized by stacked planar G-quartets, where four guanines are linked by Hoogsteen hydrogen bonds. These structures can adopt various topologies, including parallel, antiparallel, and hybrid forms, and are implicated in diverse cellular functions.
The molecular function of G-quadruplex DNA binding involves recognition and interaction of the binding entity with the G-quadruplex structure. This interaction can be driven by various factors, including:
* **Shape complementarity:** The binding entity may possess a shape that fits into the grooves or loops of the G-quadruplex, promoting specific binding.
* **Electrostatic interactions:** Positive charges on the binding entity can interact with the negatively charged phosphate backbone of the G-quadruplex.
* **Hydrogen bonding:** Specific amino acid residues or functional groups on the binding entity can form hydrogen bonds with the guanine bases within the G-quadruplex.
* **Hydrophobic interactions:** Non-polar residues on the binding entity can interact with the hydrophobic core of the G-quadruplex.
* **Stacking interactions:** Aromatic rings on the binding entity can stack onto the G-quartets within the G-quadruplex, contributing to stabilization.
These interactions can influence the stability, conformation, and function of the G-quadruplex, potentially regulating gene expression, telomere maintenance, and other cellular processes. For example, G-quadruplex binding proteins can modulate DNA replication, transcription, and translation by stabilizing or destabilizing G-quadruplex structures.
G-quadruplex DNA binding has significant implications in drug discovery and development. Small molecules that bind to G-quadruplexes have been investigated as potential therapeutics for various diseases, including cancer, neurodegenerative disorders, and infectious diseases. These molecules can target specific G-quadruplex structures involved in disease pathogenesis and exert therapeutic effects by modulating gene expression, inhibiting enzyme activity, or disrupting DNA replication.'
"
Protein | Definition | Taxonomy |
---|---|---|
Werner syndrome ATP-dependent helicase | A bifunctional 3-5 exonuclease/ATP-dependent helicase WRN that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q14191] | Homo sapiens (human) |
Bloom syndrome protein | A RecQ-like DNA helicase BLM that is encoded in the genome of human. [PRO:DNx, UniProtKB:P54132] | Homo sapiens (human) |
Lon protease homolog, mitochondrial | A Lon protease, mitochondrial that is encoded in the genome of human. [PRO:DNx, UniProtKB:P36776] | Homo sapiens (human) |
Nucleoside diphosphate kinase B | A nucleoside diphosphate kinase B that is encoded in the genome of human. [PRO:DAN, UniProtKB:P22392] | Homo sapiens (human) |
Compound | Definition | Classes | Roles |
---|---|---|---|
thymidine 5'-diphosphate | dTDP : A thymidine phosphate having a diphosphate group at the 5'-position. thymidine 5'-diphosphate: see also record for thymidine 3',5'-diphosphate, RN 2863-04-9 | pyrimidine 2'-deoxyribonucleoside 5'-diphosphate; thymidine phosphate | Escherichia coli metabolite; mouse metabolite |
bortezomib | amino acid amide; L-phenylalanine derivative; pyrazines | antineoplastic agent; antiprotozoal drug; protease inhibitor; proteasome inhibitor | |
1-(3,4-dichlorophenyl)-3-(5-pyridin-4-yl-1,3,4-thiadiazol-2-yl)urea | ureas | ||
alvocidib | alvocidib : A synthetic dihydroxyflavone that is 5,7-dihydroxyflavone which is substituted by a 3-hydroxy-1-methylpiperidin-4-yl group at position 8 and by a chlorine at the 2' position (the (-)-3S,4R stereoisomer). A cyclin-dependent kinase 9 (CDK9) inhibitor, it has been studied for the treatment of acute myeloid leukaemia, arthritis and atherosclerotic plaque formation. alvocidib: structure given in first source | dihydroxyflavone; hydroxypiperidine; monochlorobenzenes; tertiary amino compound | antineoplastic agent; antirheumatic drug; apoptosis inducer; EC 2.7.11.22 (cyclin-dependent kinase) inhibitor |
saracatinib | aromatic ether; benzodioxoles; diether; N-methylpiperazine; organochlorine compound; oxanes; quinazolines; secondary amino compound | anticoronaviral agent; antineoplastic agent; apoptosis inducer; autophagy inducer; EC 2.7.10.2 (non-specific protein-tyrosine kinase) inhibitor; radiosensitizing agent | |
vx 702 | VX 702: a p38 MAP kinase inhibitor | phenylpyridine | |
chir-265 | aromatic ether | ||
pf-562,271 | indoles | ||
buparlisib | NVP-BKM120: a pan class I PI3 kinase inhibitor with antineoplastic activity; structure in first source | aminopyridine; aminopyrimidine; morpholines; organofluorine compound | antineoplastic agent; EC 2.7.1.137 (phosphatidylinositol 3-kinase) inhibitor |
pha 848125 | N,1,4,4-tetramethyl-8-((4-(4-methylpiperazin-1-yl)phenyl)amino)-4,5-dihydro-1H-pyrazolo(4,3-h)quinazoline-3-carboxamide: a cyclin dependent kinase inhibitor | ||
gdc 0941 | pictrelisib : A sulfonamide composed of indazole, morpholine, and methylsulfonyl-substituted piperazine rings bound to a thienopyrimidine ring. | indazoles; morpholines; piperazines; sulfonamide; thienopyrimidine | EC 2.7.1.137 (phosphatidylinositol 3-kinase) inhibitor |
cudc 101 | 7-(4-(3-ethynylphenylamino)-7-methoxyquinazolin-6-yloxy)-N-hydroxyheptanamide: a histone deacetylase inhibitor; structure in first source | ||
mln 8237 | MLN 8237: an aurora kinase A inhibitor | benzazepine | |
pci 32765 | ibrutinib : A member of the class of acrylamides that is (3R)-3-[4-amino-3-(4-phenoxyphenyl)pyrazolo[3,4-d]pyrimidin-1-yl]piperidine in which the piperidine nitrogen is replaced by an acryloyl group. A selective and covalent inhibitor of the enzyme Bruton's tyrosine kinase, it is used for treatment of B-cell malignancies. ibrutinib: a Btk protein inhibitor | acrylamides; aromatic amine; aromatic ether; N-acylpiperidine; pyrazolopyrimidine; tertiary carboxamide | antineoplastic agent; EC 2.7.10.2 (non-specific protein-tyrosine kinase) inhibitor |
tak 733 | |||
entrectinib | entrectinib : A member of the class of indazoles that is 1H-indazole substituted by [4-(4-methylpiperazin-1-yl)-2-(tetrahydro-2H-pyran-4-ylamino)benzoyl]amino and 3,5-difluorobenzyl groups at positions 3 and 5, respectively. It is a potent inhibitor of TRKA, TRKB, TRKC, ROS1, and ALK (IC50 values of 0.1 to 1.7 nM), and used for the treatment of NTRK, ROS1 and ALK gene fusion-positive solid tumours. entrectinib: inhibits TRK, ROS1, and ALK receptor tyrosine kinases; structure in first source | benzamides; difluorobenzene; indazoles; N-methylpiperazine; oxanes; secondary amino compound; secondary carboxamide | antibacterial agent; antineoplastic agent; apoptosis inducer; EC 2.7.10.1 (receptor protein-tyrosine kinase) inhibitor |
gsk 2126458 | omipalisib : A member of the class of quinolines that is quinoline which is substituted by pyridazin-4-yl and 5-[(2,4-difluorobenzene-1-sulfonyl)amino]-6-methoxypyridin-3-yl groups at positions 4 and 6, respectively. It is a highly potent inhibitor of PI3K and mTOR developed by GlaxoSmithKline and was previously in human phase 1 clinical trials for the treatment of idiopathic pulmonary fibrosis and solid tumors. omipalisib: inhibitor of mTOR protein | aromatic ether; difluorobenzene; pyridazines; pyridines; quinolines; sulfonamide | anticoronaviral agent; antineoplastic agent; autophagy inducer; EC 2.7.1.137 (phosphatidylinositol 3-kinase) inhibitor; mTOR inhibitor; radiosensitizing agent |
gsk 1363089 | GSK 1363089: a multikinase inhibitor that acts on Met, RON, Axl, and VEGFR; structure in first source | aromatic ether | |
1-[4-fluoro-3-(trifluoromethyl)phenyl]-3-(5-pyridin-4-yl-1,3,4-thiadiazol-2-yl)urea | ureas | ||
osimertinib | osimertinib : A member of the class of aminopyrimidines that is 4-(1-methylindol-3-yl)pyrimidin-2-amine in which one of the amino hydrogens is replaced by a 2-methoxy-4-[2-(dimethylamino)ethyl](methyl)amino-5-acrylamidophenyl group. Used (as the mesylate salt) for treatment of EGFR T790M mutation positive non-small cell lung cancer. osimertinib: an EGFR tyrosine kinase inhibitor | acrylamides; aminopyrimidine; biaryl; indoles; monomethoxybenzene; secondary amino compound; secondary carboxamide; substituted aniline; tertiary amino compound | antineoplastic agent; epidermal growth factor receptor antagonist |