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Latest Advances in Protein-Ligand Interactions

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

Deadline for manuscript submissions: 20 October 2025 | Viewed by 1559

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Special Issue Information

Dear Colleagues,

This Special Issue is titled “Latest Advances in Protein-Ligand Interactions”. It will focus on recent studies aimed at investigating protein–ligand interactions with a special aim to elucidate molecular modes of action, the protein targets of drugs, natural compounds, and the cellular pathways involved. Protein–ligand interactions may affect both protein conformation and biological activity. However, knowledge of their molecular targets, their effects on protein structure, and how they can modulate different cellular pathways and functions is lacking for many bioactive compounds. Studies providing such information are welcomed and will help to elucidate the molecular bases for many drug activities and the development of new drugs. All papers will be fully open access upon publication after peer review.

Prof. Dr. Fabio Altieri
Guest Editor

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Keywords

  • protein–ligand interaction
  • molecular mode of actions
  • target identification
  • drug discovery
  • bioactive agents

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Published Papers (1 paper)

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Research

22 pages, 2861 KiB  
Article
Molecular Determinants for Guanine Binding in GTP-Binding Proteins: A Data Mining and Quantum Chemical Study
by Pawan Bhatta and Xiche Hu
Int. J. Mol. Sci. 2024, 25(22), 12449; https://doi.org/10.3390/ijms252212449 - 20 Nov 2024
Cited by 2 | Viewed by 1181
Abstract
GTP-binding proteins are essential molecular switches that regulate a wide range of cellular processes. Their function relies on the specific recognition and binding of guanine within their binding pockets. This study aims to elucidate the molecular determinants underlying this recognition. A large-scale data [...] Read more.
GTP-binding proteins are essential molecular switches that regulate a wide range of cellular processes. Their function relies on the specific recognition and binding of guanine within their binding pockets. This study aims to elucidate the molecular determinants underlying this recognition. A large-scale data mining of the Protein Data Bank yielded 298 GTP-binding protein complexes, which provided a structural foundation for a systematic analysis of the intermolecular interactions that are responsible for the molecular recognition of guanine in proteins. It was found that multiple modes of non-bonded interactions including hydrogen bonding, cation–π interactions, and π–π stacking interactions are employed by GTP-binding proteins for binding. Subsequently, the strengths of non-bonded interaction energies between guanine and its surrounding protein residues were quantified by means of the double-hybrid DFT method B2PLYP-D3/cc-pVDZ. Hydrogen bonds, particularly those involving the N2 and O6 atoms of guanine, confer specificity to guanine recognition. Cation–π interactions between the guanine ring and basic residues (Lys and Arg) provide significant electrostatic stabilization. π–π stacking interactions with aromatic residues (Phe, Tyr, and Trp) further contribute to the overall binding affinity. This synergistic interplay of multiple interaction modes enables GTP-binding proteins to achieve high specificity and stability in guanine recognition, ultimately underpinning their crucial roles in cellular signaling and regulation. Notably, the NKXD motif, while historically considered crucial for guanine binding in GTP-binding proteins, is not universally required. Our study revealed significant variability in hydrogen bonding patterns, with many proteins lacking the NKXD motif but still effectively binding guanine through alternative arrangements of interacting residues. Full article
(This article belongs to the Special Issue Latest Advances in Protein-Ligand Interactions)
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