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Structure, Energy, and Dynamics of Molecular Interactions—2nd Edition
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Structure, Energy, and Dynamics of Molecular Interactions—2nd Edition

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

Deadline for manuscript submissions: closed (20 December 2024) | Viewed by 3907

Special Issue Editors

Dr. Csaba Hetényi

E-Mail Website1 Website2
Guest Editor
Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
Interests: proteins; molecular structure; thermodynamics; drug design; chemoinformatics
Special Issues, Collections and Topics in MDPI journals
Dr. Uko Maran

E-Mail Website
Guest Editor
Institute of Chemistry, University of Tartu, Ravila 14A, 50411 Tartu, Estonia
Interests: theoretical and computer chemistry; malaria drug development
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The organization of matter is based on intra- and intermolecular interactions. Understanding the structure and thermodynamics of molecular interactions is therefore key to answering to the challenges of drug design and the development of new materials with unusual properties. Whereas molecular interactions occur in such distant challenges of living nature and lifeless industrial plants, the same physicochemical laws apply to both situations. The present Special Issue aims to demonstrate the diversity of research focusing on the solution of important issues in understanding molecular interactions via experimental measurements and/or theoretical calculations. Contributions are welcome from all fields of method development, theory, and applications. The Special Issue covers both living nature and inorganic materials. Studies connecting the dynamics of molecular interactions to natural phenomena are of particular interest.

Dr. Csaba Hetényi
Dr. Uko Maran
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • binding
  • conformation
  • affinity
  • complex
  • energy
  • structure
  • isothermal titration calorimetry
  • crystallography
  • molecular mechanics
  • quantum chemistry
  • quantitative structure–activity relationship
  • reaction kinetics
  • inhibitor
  • substrate
  • target
  • ligand
  • receptor
  • surface
  • interface

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Published Papers (2 papers)

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17 pages, 21153 KiB  
Article
The Role of Vimentin Peptide Citrullination in the Structure and Dynamics of HLA-DRB1 Rheumatoid Arthritis Risk-Associated Alleles
by Cinthia C. Alves, Jaila Lewis, Dinler A. Antunes and Eduardo A. Donadi
Int. J. Mol. Sci. 2025, 26(1), 34; https://doi.org/10.3390/ijms26010034 - 24 Dec 2024
Cited by 1 | Viewed by 1439
Abstract
Citrullination, a post-translational modification (PTM), plays a critical role in rheumatoid arthritis (RA) by triggering immune responses to citrullinated self-antigens. Some HLA-DRB1 genes encode molecules with the shared epitope (QKRAA/QRRAA) sequence in the peptide-binding groove which preferentially presents citrulline-modified peptides, like vimentin, that [...] Read more.
Citrullination, a post-translational modification (PTM), plays a critical role in rheumatoid arthritis (RA) by triggering immune responses to citrullinated self-antigens. Some HLA-DRB1 genes encode molecules with the shared epitope (QKRAA/QRRAA) sequence in the peptide-binding groove which preferentially presents citrulline-modified peptides, like vimentin, that intensifies the immune response in RA. In this study, we used computational approaches to evaluate intermolecular interactions between vimentin peptide-ligands (with/without PTM) and HLA-DRB1 alleles associated with a significantly increased risk for RA development. Crystal structures for HLA-DRB1*04:01, *04:04, and *04:05 bound to citrullinated peptides (PDB ID: 4MCY, 4MD5, 6BIR) were retrieved from the Protein Data Bank and non-citrullinated 3D structures were generated by mutating citrulline to arginine. The pHLA complexes were submitted to four rounds (50 ns each) of molecular dynamic simulations (MD) with Gromacs v.2022. Our results show that citrulline strengthens the interaction between vimentin and the HLA-DRB1 molecules, therefore impacting both the peptide affinity to the HLAs and pHLA stability; it also induces more intermolecular hydrogen bond formation during MD in the pHLA. Citrulline prevents repulsion between amino acid 71β and the P4-residue of native vimentin. Thus, vimentin citrullination seems to affect pHLA binding and dynamics, which may influence RA-related immune responses. Full article
(This article belongs to the Special Issue Structure, Energy, and Dynamics of Molecular Interactions—2nd Edition)
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18 pages, 1404 KiB  
Article
Data-Driven Modelling of Substituted Pyrimidine and Uracil-Based Derivatives Validated with Newly Synthesized and Antiproliferative Evaluated Compounds
by Selma Zukić, Amar Osmanović, Anja Harej Hrkać, Sandra Kraljević Pavelić, Selma Špirtović-Halilović, Elma Veljović, Sunčica Roca, Snežana Trifunović, Davorka Završnik and Uko Maran
Int. J. Mol. Sci. 2024, 25(17), 9390; https://doi.org/10.3390/ijms25179390 - 29 Aug 2024
Cited by 2 | Viewed by 1490
Abstract
The pyrimidine heterocycle plays an important role in anticancer research. In particular, the pyrimidine derivative families of uracil show promise as structural scaffolds relevant to cervical cancer. This group of chemicals lacks data-driven machine learning quantitative structure-activity relationships (QSARs) that allow for generalization [...] Read more.
The pyrimidine heterocycle plays an important role in anticancer research. In particular, the pyrimidine derivative families of uracil show promise as structural scaffolds relevant to cervical cancer. This group of chemicals lacks data-driven machine learning quantitative structure-activity relationships (QSARs) that allow for generalization and predictive capabilities in the search for new active compounds. To achieve this, a dataset of pyrimidine and uracil compounds from ChEMBL were collected and curated. A workflow was developed for data-driven machine learning QSAR using an intuitive dataset design and forwards selection of molecular descriptors. The model was thoroughly externally validated against available data. Blind validation was also performed by synthesis and antiproliferative evaluation of new synthesized uracil-based and pyrimidine derivatives. The most active compound among new synthesized derivatives, 2,4,5-trisubstituted pyrimidine was predicted with the QSAR model with differences of 0.02 compared to experimentally tested activity. Full article
(This article belongs to the Special Issue Structure, Energy, and Dynamics of Molecular Interactions—2nd Edition)
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