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Falanga AP, Lupia A, Tripodi L, Morgillo CM, Moraca F, Roviello GN, Catalanotti B, Amato J, Pastore L, Cerullo V, D'Errico S, Piccialli G, Oliviero G, Borbone N. Exploring the DNA 2-PNA heterotriplex formation in targeting the Bcl-2 gene promoter: A structural insight by physico-chemical and microsecond-scale MD investigation. Heliyon 2024; 10:e24599. [PMID: 38317891 PMCID: PMC10839560 DOI: 10.1016/j.heliyon.2024.e24599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 02/07/2024] Open
Abstract
Peptide Nucleic Acids (PNAs) represent a promising tool for gene modulation in anticancer treatment. The uncharged peptidyl backbone and the resistance to chemical and enzymatic degradation make PNAs highly advantageous to form stable hybrid complexes with complementary DNA and RNA strands, providing higher stability than the corresponding natural analogues. Our and other groups' research has successfully shown that tailored PNA sequences can effectively downregulate the expression of human oncogenes using antigene, antisense, or anti-miRNA approaches. Specifically, we identified a seven bases-long PNA sequence, complementary to the longer loop of the main G-quadruplex structure formed by the bcl2midG4 promoter sequence, capable of downregulating the expression of the antiapoptotic Bcl-2 protein and enhancing the anticancer activity of an oncolytic adenovirus. Here, we extended the length of the PNA probe with the aim of including the double-stranded Bcl-2 promoter among the targets of the PNA probe. Our investigation primarily focused on the structural aspects of the resulting DNA2-PNA heterotriplex that were determined by employing conventional and accelerated microsecond-scale molecular dynamics simulations and chemical-physical analysis. Additionally, we conducted preliminary biological experiments using cytotoxicity assays on human A549 and MDA-MB-436 adenocarcinoma cell lines, employing the oncolytic adenovirus delivery strategy.
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Affiliation(s)
- Andrea P. Falanga
- Dipartimento di Farmacia, Università Degli Studi di Napoli Federico II, Naples, 80131, Italy
| | - Antonio Lupia
- Dipartimento di Farmacia, Università Degli Studi di Napoli Federico II, Naples, 80131, Italy
| | - Lorella Tripodi
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli Federico II, Naples, 80131, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore S.c.a.r.l., Naples, 80145, Italy
| | - Carmine M. Morgillo
- Dipartimento di Farmacia, Università Degli Studi di Napoli Federico II, Naples, 80131, Italy
| | - Federica Moraca
- Dipartimento di Farmacia, Università Degli Studi di Napoli Federico II, Naples, 80131, Italy
| | - Giovanni N. Roviello
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale Delle Ricerche, Naples, 80131, Italy
| | - Bruno Catalanotti
- Dipartimento di Farmacia, Università Degli Studi di Napoli Federico II, Naples, 80131, Italy
| | - Jussara Amato
- Dipartimento di Farmacia, Università Degli Studi di Napoli Federico II, Naples, 80131, Italy
| | - Lucio Pastore
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli Federico II, Naples, 80131, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore S.c.a.r.l., Naples, 80145, Italy
| | - Vincenzo Cerullo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli Federico II, Naples, 80131, Italy
- ImmunoViroTherapy Lab (IVT), Drug Research Program (DRP), Faculty of Pharmacy, University of Helsinki, 00100, Helsinki, Finland
| | - Stefano D'Errico
- Dipartimento di Farmacia, Università Degli Studi di Napoli Federico II, Naples, 80131, Italy
| | - Gennaro Piccialli
- Dipartimento di Farmacia, Università Degli Studi di Napoli Federico II, Naples, 80131, Italy
| | - Giorgia Oliviero
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli Federico II, Naples, 80131, Italy
| | - Nicola Borbone
- Dipartimento di Farmacia, Università Degli Studi di Napoli Federico II, Naples, 80131, Italy
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