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Special Issue "Drug-Protein Interactions and Mechanisms of Action by Structural Modifications Driving Protein Function"
Deadline for manuscript submissions: closed (30 April 2018).
Interests: computational drug design; systems biology of cancer and neurodegenerative diseases; tubulin
Special Issues and Collections in MDPI journals
Special Issue in Cells: Tubulin: Structure, Functions and Roles in Disease
Interests: molecular modeling; computational chemistry; molecular dynamics; molecular dynamics simulation; quantum chemistry; cell mechanics; actin; toll-like receptors; computer aided drug design; microtubule dynamics; Parkinson’s disease; molecular simulation; Alzheimer’s disease; ghrelin receptors; protein–protein interaction; molecular models
Currently, the process of development of a drug molecule is characterized by a huge number of failures, due in large part to inadequate pharmacokinetics, lack of efficacy, toxicity, side effects, etc. In the last few decades molecular modelling has been recognized as a powerful tool helping to shed light on structure-activity relationships, by investigating drug–protein interactions at atomic resolution. Moreover, the availability of thousands of three-dimensional structures of protein offers crucial structural information about key macromolecular drug targets. Starting from drug-target models, the integration of in silico and experimental methods has provided the up-to-date understanding of complex aspects characterizing inter-molecular recognition. For example, flexibility and conformational dynamics of the target is an essential but frequently overlooked aspect in such studies. In fact, receptors may undergo significant local and global structural modifications, following the molecular recognition process, which, subsequently, affects the protein function. Addressing the above-mentioned issues is crucial in evaluating the effect of a binder on the target structure. Computational molecular modelling faces these challenges by employing techniques such as molecular dynamics (MD), which enable quantitative prediction of physical/chemical properties of protein-drug complexes. The emerging enhanced sampling techniques, such as replica exchange MD, metadynamics, simulated annealing and hybrid methods offer improved estimates of the binding free energy by facilitating the system’s escape from conformational traps around local free energy minima. Such computational approaches provide insights into mechanisms of action of drug molecules by exploring both local and non-local effects on protein targets. Hence, they represent a powerful and promising approach aiding in drug discovery and the field of modern medicinal chemistry in general. At present, the research in the area of drug-protein interactions remains an endless source of challenging issues.
This Special Issue will cover latest advances in computational modelling applied to the investigations of physiological and pathological conditions, such as cancer and neurodegenerative diseases. The emphasis will be on: Drug design/screening and molecular docking; classical and enhanced sampling techniques to characterize drug–protein binding, affinity and kinetics; atomistic and coarse-grained approaches to explore local and global effects of drug–protein interactions.
Prof. Dr. Jack A. Tuszynski
Dr. Marco A. Deriu
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 papers will be 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.
- Classical/Enhanced molecular/coarse-grained modelling
- Drug-protein interactions, free-energy, affinity, kinetics
- Drug repurposing, natural compounds, medicinal chemistry
- Neurodegenerative disease, cancer
- Protein conformational changes
- Protein collective motions, modes and Glocal correlations