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Computational insight into the phthalocyanine-DNA binding via docking and molecular dynamics simulations

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dc.contributor.authorMUTLU, ÖZAL
dc.contributor.authorsOzalp, Lalehan; Erdem, Safiye Sag; Yuce-Dursun, Basak; Mutlu, Ozal; Ozbil, Mehmet
dc.date.accessioned2022-03-12T22:25:19Z
dc.date.available2022-03-12T22:25:19Z
dc.date.issued2018
dc.description.abstractPhthalocyanines are considered as good DNA binders, which makes them promising anti-tumor drug leads. The purpose of this study is to investigate the interactions between DNA and quaternary metallophthalocyanine derivatives (Q-MPc) possessing varying metals (M = Zn, Ni, Cu, Fe, Mg and Ca) by molecular docking since there seems to be a lack of information in the literature regarding this issue. In this direction, Autodock Vina and Molegro Virtual Docker programs were employed. Autodock Vina results reveal that each Q-MPc derivative binds to DNA strongly with similar binding energies and almost identical binding modes. They bind to the grooves of DNA by constituting favorable interactions between phosphate groups of DNA and Q-MPcs. Although changing the metal has no significant effect on binding, presence of quaternary amine substituents increases the binding constant K-b by about 2-fold comparing to the core Pc (ZnPc). Contrary to Autodock Vina, the calculated Molegro Virtual Docker binding scores have been more diverse indicating that the scoring function of Molegro is better in differentiating these metals. Despite the fact that Molegro is superior to Autodock Vina in terms of metal characterization, Autodock Vina and Molegro exhibit similar binding sites for the studied metallophthalocyanines. We propose that Q-MPc derivatives designed in this study are promising anti-tumor lead compounds since they tightly bind to DNA with considerably high K-b values. Cationic substituents and presence of metal have both positive effects on DNA binding which is critical for designing DNA-active drugs. Additional calculations employing molecular dynamics (MD) simulations verified the stability of Q-MPc-DNA complexes which remained in contact after 20 ns via attractive interactions mainly between DNA backbone and the Pc metal center.
dc.identifier.doi10.1016/j.compbiolchem.2018.09.009
dc.identifier.eissn1476-928X
dc.identifier.issn1476-9271
dc.identifier.pubmed30245350
dc.identifier.urihttps://hdl.handle.net/11424/234903
dc.identifier.wosWOS:000455858400009
dc.language.isoeng
dc.publisherELSEVIER SCI LTD
dc.relation.ispartofCOMPUTATIONAL BIOLOGY AND CHEMISTRY
dc.rightsinfo:eu-repo/semantics/closedAccess
dc.subjectDocking
dc.subjectBinding affinity
dc.subjectDrug design
dc.subjectMolecular modelling
dc.subjectAutodock Vina
dc.subjectMolegro Virtual Docker
dc.subjectFREE-ENERGY
dc.subjectCATIONIC PHTHALOCYANINES
dc.subjectBASE-PAIRS
dc.subjectCOMPLEXES
dc.subjectHETERODIMERIZATION
dc.subjectOPTIMIZATION
dc.subjectALGORITHM
dc.subjectACCURACY
dc.subjectZINC(II)
dc.titleComputational insight into the phthalocyanine-DNA binding via docking and molecular dynamics simulations
dc.typearticle
dspace.entity.typePublication
local.avesis.ida2b92a3d-815b-4e04-8402-c76824d3f741
local.import.packageSS17
local.indexed.atWOS
local.indexed.atSCOPUS
local.indexed.atPUBMED
local.journal.numberofpages10
local.journal.quartileQ3
oaire.citation.endPage96
oaire.citation.startPage87
oaire.citation.titleCOMPUTATIONAL BIOLOGY AND CHEMISTRY
oaire.citation.volume77
relation.isAuthorOfPublication7a1f8128-8f83-44b5-8eb0-9bc61e75943d
relation.isAuthorOfPublication.latestForDiscovery7a1f8128-8f83-44b5-8eb0-9bc61e75943d

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