Rational design of antimiRs targeting miRNA675-5p for glioblastoma multiforme therapy F.Tandaa, I. Gadoa, L. Guidettia, F.E. Agharbaouia, C. Martellib, L. Ottobrinib, C. Pellizzerc, M. Cacciac,d, F. Vasilea, M. Civeraa, A. Lo Dicoc,d, S. Sattina aUniversità degli studi di Milano, Dipartimento di Chimica, Via Golgi 19, Milano bUniversità degli studi di Milano, Dipartimento di Fisiopatologia Medico-Chirurgica e dei Trapianti, Via Francesco Sforza 35, Milano cIstituto di Bioimmagini e Sistemi Complessi (IBSBC)-CNR, Segrate dNBFC, National Biodiversity Future Center, Palermo [email protected] MicroRNAs (miRNAs) are short, endogenous non-coding RNA molecules (19-25 nt) that regulate key cellular processes and are frequently dysregulated in cancer.1,2 Specifically, miRNA675-5p is overexpressed in glioblastoma multiforme (GBM) and promotes hypoxia-mediated angiogenesis.3 The MOONLIT project aims to develop chemically modified antisense oligonucleotides, or antimiRs, to sequester mature miRNA675-5p, thereby reducing its activity and modulating tumorigenesis.4–7 To address the challenges posed by the inherent structural flexibility of miRNAs, we first employed molecular dynamics (MD) simulations to explore the conformational behavior of miRNA675-5p and its natural antimiR, miRNA675-3p, as single strands. We then analyzed their interactions in duplex form, comparing the interaction network of miRNA675-5p/miRNA675-3p with those of two modified systems: a DNA-based miRNA675-3p and a fully complementary DNA strand. Through systematic analysis of the resulting interaction networks, we identified key nucleotide modifications that enhance the stability of the miRNA-antimiR duplex. Building on these insights, we introduced Locked Nucleic Acid (LNA) modifications to further improve resistance to degradation and optimize binding affinity, which required novel parameterization. Computational predictions were validated by NMR spectroscopy, confirming the model’s reliability. These findings provide a rational framework for designing modified antimiRs, driven by computational predictions and experimentally validated, with the aim of enhancing their therapeutic potential. References: [1] A. Ventura, et al., Cell 2009, 136, 586–591. [2] Y. Peng, C. Croce, Sig. Transduct Target Ther. 2016, 1, 15004. [3] V. Costa, et al., Oncotarget 2017, 8, 24292–24302. [4] J. Stenvang, A. Petri, M. Lindow, S. Obad, S. Kauppinen, Silence 2012, 3, 1. [5] K. A. Lennox, M. A. Behlke, Gene Therapy 2011, 18, 1111–1120. [6] S. Obad, et al., Nat Genet 2011, 43, 371–380. [7] A. Lo Dico et al., Theranostics 2016, 6, 1105–1118.
Rational design of antimiRs targeting miRNA675-5p for glioblastoma multiforme therapy / F. Tanda. 42. Convegno Nazionale della Divisione di Chimica Organica (CDCO) : 21-25 settembre Villasimius, Caagliari 2025.
Rational design of antimiRs targeting miRNA675-5p for glioblastoma multiforme therapy
F. Tanda
2025
Abstract
Rational design of antimiRs targeting miRNA675-5p for glioblastoma multiforme therapy F.Tandaa, I. Gadoa, L. Guidettia, F.E. Agharbaouia, C. Martellib, L. Ottobrinib, C. Pellizzerc, M. Cacciac,d, F. Vasilea, M. Civeraa, A. Lo Dicoc,d, S. Sattina aUniversità degli studi di Milano, Dipartimento di Chimica, Via Golgi 19, Milano bUniversità degli studi di Milano, Dipartimento di Fisiopatologia Medico-Chirurgica e dei Trapianti, Via Francesco Sforza 35, Milano cIstituto di Bioimmagini e Sistemi Complessi (IBSBC)-CNR, Segrate dNBFC, National Biodiversity Future Center, Palermo [email protected] MicroRNAs (miRNAs) are short, endogenous non-coding RNA molecules (19-25 nt) that regulate key cellular processes and are frequently dysregulated in cancer.1,2 Specifically, miRNA675-5p is overexpressed in glioblastoma multiforme (GBM) and promotes hypoxia-mediated angiogenesis.3 The MOONLIT project aims to develop chemically modified antisense oligonucleotides, or antimiRs, to sequester mature miRNA675-5p, thereby reducing its activity and modulating tumorigenesis.4–7 To address the challenges posed by the inherent structural flexibility of miRNAs, we first employed molecular dynamics (MD) simulations to explore the conformational behavior of miRNA675-5p and its natural antimiR, miRNA675-3p, as single strands. We then analyzed their interactions in duplex form, comparing the interaction network of miRNA675-5p/miRNA675-3p with those of two modified systems: a DNA-based miRNA675-3p and a fully complementary DNA strand. Through systematic analysis of the resulting interaction networks, we identified key nucleotide modifications that enhance the stability of the miRNA-antimiR duplex. Building on these insights, we introduced Locked Nucleic Acid (LNA) modifications to further improve resistance to degradation and optimize binding affinity, which required novel parameterization. Computational predictions were validated by NMR spectroscopy, confirming the model’s reliability. These findings provide a rational framework for designing modified antimiRs, driven by computational predictions and experimentally validated, with the aim of enhancing their therapeutic potential. References: [1] A. Ventura, et al., Cell 2009, 136, 586–591. [2] Y. Peng, C. Croce, Sig. Transduct Target Ther. 2016, 1, 15004. [3] V. Costa, et al., Oncotarget 2017, 8, 24292–24302. [4] J. Stenvang, A. Petri, M. Lindow, S. Obad, S. Kauppinen, Silence 2012, 3, 1. [5] K. A. Lennox, M. A. Behlke, Gene Therapy 2011, 18, 1111–1120. [6] S. Obad, et al., Nat Genet 2011, 43, 371–380. [7] A. Lo Dico et al., Theranostics 2016, 6, 1105–1118.
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