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Nucleic Acid Recognition and Pharmaceutical Ligand Design

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Macromolecules".

Deadline for manuscript submissions: 31 December 2024 | Viewed by 1161

Special Issue Editors


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Guest Editor
Laboratory for Biomolecular Interactions and Spectroscopy, Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička 54, 10000 Zagreb, Croatia
Interests: supramolecular chemistry; DNA; RNA; molecular recognition; spectroscopy; heterocyclic chemistry
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Guest Editor
Institute of Organic Chemistry with Centre of Phytochemistry (IOCCP), Bulgarian Academy of Sciences, Sofia, Bulgaria
Interests: synthetic organic chemistry; feterocyclic chemistry; DNA; fluorescence; luminescence; absorption; fluorescence imaging; UV-Visible spectroscopy; spectral analysis; spectroscopy

Special Issue Information

Dear Colleagues,

Nucleic acid recognition plays a crucial role in the design of pharmaceutical ligands, offering a targeted approach to treating a wide array of genetic and infectious diseases. The selective interaction between nucleic acids and synthetic ligands can inhibit the replication of DNA and its transcription to RNA, modulate gene expression, inhibit viral replication, and correct genetic mutations. Recent advancements in structural biology and computational chemistry have illuminated the specific binding mechanisms of nucleic acids, promoting the development of high-affinity, sequence-specific ligands. These ligands, including small molecules, peptides, and antisense oligonucleotides, are engineered to interact with distinct nucleic acid sequences or structures, such as DNA double helices, including DNA:RNA hybrids, triplex and multistranded nucleic acid structures, RNA folds, aptamers, or G-quadruplexes. This specificity is crucial for minimizing off-target effects and enhancing therapeutic efficacy. Moreover, the integration of bioinformatics and high-throughput screening accelerates the identification of promising ligand candidates. However, challenges remain in optimizing the stability, bioavailability, and delivery of these ligands in vivo. Nevertheless, combining innovative design strategies and classical and advanced analytical techniques continues to move the field forward, promising new therapeutic agents for complex genetic and viral pathologies. The synergy of pharmacological ligand design and nucleic acid recognition announces a new era in precise medicine that promises to completely transform the therapeutic options available.

Dr. Marijana Radić Stojković
Dr. Atanas Kurutos
Guest Editors

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Keywords

  • nucleic acid recognition
  • ligand design
  • analytical techniques
  • computational chemistry
  • therapeutics

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Published Papers (1 paper)

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Research

16 pages, 2872 KiB  
Article
Interactions with DNA Models of the Oxaliplatin Analog (cis-1,3-DACH)PtCl2 
by Alessandra Barbanente, Paride Papadia, Anna Maria Di Cosola, Concetta Pacifico, Giovanni Natile, James D. Hoeschele and Nicola Margiotta
Int. J. Mol. Sci. 2024, 25(13), 7392; https://doi.org/10.3390/ijms25137392 - 5 Jul 2024
Viewed by 990
Abstract
It is generally accepted that adjacent guanine residues in DNA are the primary target for platinum antitumor drugs and that differences in the conformations of the Pt-DNA adducts can play a role in their antitumor activity. In this study, we investigated the effect [...] Read more.
It is generally accepted that adjacent guanine residues in DNA are the primary target for platinum antitumor drugs and that differences in the conformations of the Pt-DNA adducts can play a role in their antitumor activity. In this study, we investigated the effect of the carrier ligand cis-1,3-diaminocyclohexane (cis-1,3-DACH) upon formation, stability, and stereochemistry of the (cis-1,3-DACH)PtG2 and (cis-1,3-DACH)Pt(d(GpG)) adducts (G = 9-EthlyGuanine, guanosine, 5′- and 3′-guanosine monophosphate; d(GpG) = deoxyguanosil(3′-5′)deoxyguanosine). A peculiar feature of the cis-1,3-DACH carrier ligand is the steric bulk of the diamine, which is asymmetric with respect to the Pt-coordination plane. The (cis-1,3-DACH)Pt(5′GMP)2 and (cis-1,3-DACH)Pt(3′GMP)2 adducts show preference for the ΛHT and ∆HT conformations, respectively (HT stands for Head-to-Tail). Moreover, the increased intensity of the circular dichroism signals in the cis-1,3-DACH derivatives with respect to the analogous cis-(NH3)2 species could be a consequence of the greater bite angle of the cis-1,3-DACH carrier ligand with respect to cis-(NH3)2. Finally, the (cis-1,3-DACH)Pt(d(GpG)) adduct is present in two isomeric forms, each one giving a pair of H8 resonances linked by a NOE cross peak. The two isomers were formed in comparable amounts and had a dominance of the HH conformer but with some contribution of the ΔHT conformer which is related to the HH conformer by having the 3′-G base flipped with respect to the 5′-G residue. Full article
(This article belongs to the Special Issue Nucleic Acid Recognition and Pharmaceutical Ligand Design)
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