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Kircheva N, Dobrev S, Petkova V, Bakalova S, Kaneti J, Angelova S. Theoretical Assessment of the Ligand/Metal/Quadruplex Recognition in the Non-Canonical Nucleic Acids Structures. Molecules 2023; 28:6109. [PMID: 37630360 PMCID: PMC10459790 DOI: 10.3390/molecules28166109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Quadruplexes (GQs), peculiar DNA/RNA motifs concentrated in specific genomic regions, play a vital role in biological processes including telomere stability and, hence, represent promising targets for anticancer therapy. GQs are formed by folding guanine-rich sequences into square planar G-tetrads which stack onto one another. Metal cations, most often potassium, further stabilize the architecture by coordinating the lone electron pairs of the O atoms. The presence of additional nucleic acid bases, however, has been recently observed experimentally and contributes substantially to the structural heterogeneity of quadruplexes. Therefore, it is of paramount significance to understand the factors governing the underlying complex processes in these structures. The current study employs DFT calculations to model the interactions between metal cations (K+, Na+, Sr2+) and diverse tetrads composed of a guanine layer in combination with a guanine (G)-, adenine (A)-, cytosine (C)-, thymine (T)-, or uracil (U)-based tetrad layer. Moreover, the addition of 4-(3,4-dihydroisoquinolin-2-yl)-2-(quinolin-2-yl)quinazoline to the modeled quadruplexes as a possible mechanism of its well-exerted antitumor effect is assessed. The calculations imply that the metal cation competition and ligand complexation are influenced by the balance between electronic and implicit/explicit solvation effects, the composition of the tetrad layers, as well as by the solvent exposure to the surrounding environment expressed in terms of different dielectric constant values. The provided results significantly enhance our understanding of quadruplex diversity, ligand recognition, and the underlying mechanisms of stabilization at an atomic level.
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Affiliation(s)
- Nikoleta Kircheva
- Institute of Optical Materials and Technologies “Acad. J. Malinowski”, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (N.K.); (S.D.); (V.P.)
| | - Stefan Dobrev
- Institute of Optical Materials and Technologies “Acad. J. Malinowski”, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (N.K.); (S.D.); (V.P.)
| | - Vladislava Petkova
- Institute of Optical Materials and Technologies “Acad. J. Malinowski”, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (N.K.); (S.D.); (V.P.)
| | - Snezhana Bakalova
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (S.B.); (J.K.)
| | - Jose Kaneti
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (S.B.); (J.K.)
| | - Silvia Angelova
- Institute of Optical Materials and Technologies “Acad. J. Malinowski”, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (N.K.); (S.D.); (V.P.)
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Kaneti J, Kurteva V, Georgieva M, Krasteva N, Miloshev G, Tabakova N, Petkova Z, Bakalova SM. Small Heterocyclic Ligands as Anticancer Agents: QSAR with a Model G-Quadruplex. Molecules 2022; 27:7577. [PMID: 36364401 PMCID: PMC9655707 DOI: 10.3390/molecules27217577] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/28/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
G-quadruplexes (GQs) have become valid targets for anticancer studies in recent decades due to their multifaceted biological function. Herewith, we aim to quantify interactions of potential heterocyclic ligands (Ls) with model GQs. For seven 4-aminoquinazolines and three 2-heteroaryl perimidines, seven of this ten-membered group so far unknown, we use routine quantum chemical modeling. As shown in the literature, a preferred mode of interaction of heterocycles with cellular structures is stacking to exposable faces of G-quadruplexes. To exploit the energy of this interaction as a molecular descriptor and achieve the necessary chemical precision, we use state of the art large-scale density functional theory (DFT) calculations of stacked heterocycles to a GQ. Actually, the GQ has been simplified for the computation by stripping it off all pentose phosphate residues into a naked model of stacked guanine quartets. The described model thus becomes computable. The obtained heterocyclic ligand GQ.L stacking energies, that is, their GQ affinities, are the necessary ligand descriptors. Using the ligand biological inhibitory activities (IC50) on a human malignant melanoma A375 cell line, we obtain a good linear relationship between computed ligand stacking affinities to GQ, and experimental log (IC50) values. Based on the latter relationship, we discuss a putative mechanism of anticancer activity of heterocyclic ligands via stacking interactions with GQs and thereby controlling cell regulatory activity. This mechanism may tentatively be applied to other condensed five- and six-membered small heterocycles as well.
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Luparello C, Cruciata I, Joerger AC, Ocasio CA, Jones R, Tareque RK, Bagley MC, Spencer J, Walker M, Austin C, Ferrara T, D′Oca P, Bellina R, Branni R, Caradonna F. Genotoxicity and Epigenotoxicity of Carbazole-Derived Molecules on MCF-7 Breast Cancer Cells. Int J Mol Sci 2021; 22:ijms22073410. [PMID: 33810274 PMCID: PMC8038095 DOI: 10.3390/ijms22073410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/01/2022] Open
Abstract
The carbazole compounds PK9320 (1-(9-ethyl-7-(furan-2-yl)-9H-carbazol-3-yl)-N-methylmethanamine) and PK9323 (1-(9-ethyl-7-(thiazol-4-yl)-9H-carbazol-3-yl)-N-methylmethanamine), second-generation analogues of PK083 (1-(9-ethyl-9H-carbazol-3-yl)-N-methylmethanamine), restore p53 signaling in Y220C p53-mutated cancer cells by binding to a mutation-induced surface crevice and acting as molecular chaperones. In the present paper, these three molecules have been tested for mutant p53-independent genotoxic and epigenomic effects on wild-type p53 MCF-7 breast adenocarcinoma cells, employing a combination of Western blot for phospho-γH2AX histone, Comet assay and methylation-sensitive arbitrarily primed PCR to analyze their intrinsic DNA damage-inducing and DNA methylation-changing abilities. We demonstrate that small modifications in the substitution patterns of carbazoles can have profound effects on their intrinsic genotoxic and epigenetic properties, with PK9320 and PK9323 being eligible candidates as “anticancer compounds” and “anticancer epi-compounds” and PK083 a “damage-corrective” compound on human breast adenocarcinoma cells. Such different properties may be exploited for their use as anticancer agents and chemical probes.
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Affiliation(s)
- Claudio Luparello
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Viale delle Scienze, Edificio 16, 90128 Palermo, Italy; (I.C.); (T.F.); (P.D.); (R.B.); (R.B.)
- Correspondence: (C.L.); (J.S.); (F.C.)
| | - Ilenia Cruciata
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Viale delle Scienze, Edificio 16, 90128 Palermo, Italy; (I.C.); (T.F.); (P.D.); (R.B.); (R.B.)
| | - Andreas C. Joerger
- Institute of Pharmaceutical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany;
- Buchmann Institute for Molecular Life Sciences, Structural Genomics Consortium (SGC), 60438 Frankfurt am Main, Germany
| | - Cory A. Ocasio
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, UK; (C.A.O.); (R.J.); (R.K.T.); (M.C.B.)
| | - Rhiannon Jones
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, UK; (C.A.O.); (R.J.); (R.K.T.); (M.C.B.)
| | - Raysa Khan Tareque
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, UK; (C.A.O.); (R.J.); (R.K.T.); (M.C.B.)
| | - Mark C. Bagley
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, UK; (C.A.O.); (R.J.); (R.K.T.); (M.C.B.)
| | - John Spencer
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, UK; (C.A.O.); (R.J.); (R.K.T.); (M.C.B.)
- Correspondence: (C.L.); (J.S.); (F.C.)
| | - Martin Walker
- Eurofins Integrated Discovery UK Ltd., Fyfield Business & Research Park, Fyfield Road, Ongar, Essex CM5 0GS, UK; (M.W.); (C.A.)
| | - Carol Austin
- Eurofins Integrated Discovery UK Ltd., Fyfield Business & Research Park, Fyfield Road, Ongar, Essex CM5 0GS, UK; (M.W.); (C.A.)
| | - Tiziana Ferrara
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Viale delle Scienze, Edificio 16, 90128 Palermo, Italy; (I.C.); (T.F.); (P.D.); (R.B.); (R.B.)
| | - Pietro D′Oca
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Viale delle Scienze, Edificio 16, 90128 Palermo, Italy; (I.C.); (T.F.); (P.D.); (R.B.); (R.B.)
| | - Rossella Bellina
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Viale delle Scienze, Edificio 16, 90128 Palermo, Italy; (I.C.); (T.F.); (P.D.); (R.B.); (R.B.)
| | - Rossella Branni
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Viale delle Scienze, Edificio 16, 90128 Palermo, Italy; (I.C.); (T.F.); (P.D.); (R.B.); (R.B.)
| | - Fabio Caradonna
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Viale delle Scienze, Edificio 16, 90128 Palermo, Italy; (I.C.); (T.F.); (P.D.); (R.B.); (R.B.)
- Correspondence: (C.L.); (J.S.); (F.C.)
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