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Study of Protein–Ligand Interactions by 2D and 3D Techniques
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Study of Protein–Ligand Interactions by 2D and 3D Techniques

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

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 3055

Special Issue Editors

Dr. Ádám Juhász

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Guest Editor
Interdisciplinary Excellence Center, Department of Physical Chemistry and Materials Science, University of Szeged, Rerrich B. Sqr. 1, 6720 Szeged, Hungary
Interests: surface plasmon resonance; study of protein–ligand interactions via 2D and 3D techniques; protein- and polysaccharide-based colloidal drug carriers; surfactants
Special Issues, Collections and Topics in MDPI journals
Dr. Edit Csapó

E-Mail Website
Guest Editor
MTA-SZTE Lendület “Momentum” Noble Metal Nanostructures Research Group, University of Szeged, Rerrich B. Sqr. 1, H-6720 Szeged, Hungary
Interests: plasmonic mono- and bimetallic nanoparticles; fluorescent gold-based nanostructures; serum protein- and polymer-based colloidal drug delivery systems
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Protein–ligand interactions form the basis of molecular recognition and have an essential role in many scientific areas. In addition to protein–ligand interactions, protein–peptide and protein–protein interactions represent other classes of predominant protein-related interactions and are involved in numerous cellular processes, such as immune response and signal transduction. Moreover, proteins and peptides have become attractive drug and drug carrier candidates. Thus, the biomimetic modeling and characterization of biomolecular interactions is a popular topic in today’s pharmaceutical- and nanomedicine-motivated research. Furthermore, the quantitative data produced by these studies contribute to the knowledge of essential physiological processes at the molecular level. Thus, data from quasi-two-dimensional (2D) sensors such as surface plasmon resonance (SPR) spectroscopy or quartz crystal microbalance (QCM) techniques and typical bulk/solution-phase (3D) methods such as fluorescence spectroscopy, isothermal titration calorimetry (ITC) or circular dichroism (CD) spectroscopy, which complement and support each other, provide important kinetic, thermodynamic and indirect structural information.

This Special Issue of the International Journal of Molecular Sciences aims to publish original high-quality research papers covering the most recent advances as well as comprehensive reviews addressing state-of-the-art topics in the field of biomimetic modeling and the physicochemical characterization of protein–ligand-type interactions (e.g., among small molecules, peptides, proteins and nano-objects with molecular-like behavior such as clusters and quantum dots) using 2D sensors and traditional solution-phase (3D) methods.

Topics of interest include, but are not limited to the following:

  • Design and development of novel quasi-2D and 3D biomimetic sensors.
  • Presentation of original signal/data evaluation methods for biomimetic sensors.
  • Application of 2D and 3D biomimetic sensors in the design and development of drug carriers.
  • Kinetic and/or thermodynamic protein–ligand, protein–protein and protein–peptide interactions.
  • Kinetic and/or thermodynamic protein–metal nanocluster, protein–quantum dot interactions.

I would like to gratefully acknowledge in advance the authors and reviewers who chose to participate in this Special Issue, whose work will contribute to the further development of research on colloidal drug delivery systems.

Dr. Ádám Juhász
Dr. Edit Csapó
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.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • biomimetic sensors
  • proteine-drug interaction
  • proteine-proteine ineteaction
  • proteine-peptide ineteaction
  • proteine-nanocluster ineteaction
  • proteine-quantum dot ineteaction

Published Papers (2 papers)

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Research

11 pages, 2686 KiB  
Article
Thermodynamic Characterization of the Interaction of Biofunctionalized Gold Nanoclusters with Serum Albumin Using Two- and Three-Dimensional Methods
by Ádám Juhász, Gyöngyi Gombár, Egon F. Várkonyi, Marek Wojnicki, Ditta Ungor and Edit Csapó
Int. J. Mol. Sci. 2023, 24(23), 16760; https://doi.org/10.3390/ijms242316760 - 25 Nov 2023
Cited by 1 | Viewed by 1340
Abstract
Fluorescent gold nanoclusters have been successfully used as fluorescent markers for imaging of cells and tissues, and their potential role in drug delivery monitoring is coming to the fore. In addition, the development of biosensors using structure-tunable fluorescent nanoclusters is also a prominent [...] Read more.
Fluorescent gold nanoclusters have been successfully used as fluorescent markers for imaging of cells and tissues, and their potential role in drug delivery monitoring is coming to the fore. In addition, the development of biosensors using structure-tunable fluorescent nanoclusters is also a prominent research field. In the case of these sensor applications, the typical goal is the selective identification of, e.g., metal ions, small molecules having neuroactive or antioxidant effects, or proteins. During these application-oriented developments, in general, there is not enough time to systematically examine the interaction between nanoclusters and relevant biomolecules/proteins from a thermodynamic viewpoint. In this way, the primary motivation of this article is to carry out a series of tests to partially fill this scientific gap. Besides the well-known fluorescent probes, the mentioned interactions were investigated using such unique measurement methods as surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC). These two-dimensional (at the solid/liquid interface) and three-dimensional (in the bulk phase) measuring techniques provide a unique opportunity for the thermodynamic characterization of the interaction between different gold nanoclusters containing various surface functionalizing ligands and bovine serum albumin (BSA). Full article
(This article belongs to the Special Issue Study of Protein–Ligand Interactions by 2D and 3D Techniques)
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27 pages, 12377 KiB  
Article
Leveraging the Fragment Molecular Orbital Method to Explore the PLK1 Kinase Binding Site and Polo-Box Domain for Potent Small-Molecule Drug Design
by Haiyan Jin, Jongwan Kim, Onju Lee, Hyein Kim and Kyoung Tai No
Int. J. Mol. Sci. 2023, 24(21), 15639; https://doi.org/10.3390/ijms242115639 - 27 Oct 2023
Viewed by 1309
Abstract
Polo-like kinase 1 (PLK1) plays a pivotal role in cell division regulation and emerges as a promising therapeutic target for cancer treatment. Consequently, the development of small-molecule inhibitors targeting PLK1 has become a focal point in contemporary research. The adenosine triphosphate (ATP)-binding site [...] Read more.
Polo-like kinase 1 (PLK1) plays a pivotal role in cell division regulation and emerges as a promising therapeutic target for cancer treatment. Consequently, the development of small-molecule inhibitors targeting PLK1 has become a focal point in contemporary research. The adenosine triphosphate (ATP)-binding site and the polo-box domain in PLK1 present crucial interaction sites for these inhibitors, aiming to disrupt the protein’s function. However, designing potent and selective small-molecule inhibitors can be challenging, requiring a deep understanding of protein–ligand interaction mechanisms at these binding sites. In this context, our study leverages the fragment molecular orbital (FMO) method to explore these site-specific interactions in depth. Using the FMO approach, we used the FMO method to elucidate the molecular mechanisms of small-molecule drugs binding to these sites to design PLK1 inhibitors that are both potent and selective. Our investigation further entailed a comparative analysis of various PLK1 inhibitors, each characterized by distinct structural attributes, helping us gain a better understanding of the relationship between molecular structure and biological activity. The FMO method was particularly effective in identifying key binding features and predicting binding modes for small-molecule ligands. Our research also highlighted specific “hot spot” residues that played a critical role in the selective and robust binding of PLK1. These findings provide valuable insights that can be used to design new and effective PLK1 inhibitors, which can have significant implications for developing anticancer therapeutics. Full article
(This article belongs to the Special Issue Study of Protein–Ligand Interactions by 2D and 3D Techniques)
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