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Advances in Molecular Dynamics Simulation of Chemical and Biomedical Systems

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: 20 October 2024 | Viewed by 1123

Special Issue Editors


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Guest Editor
Coimbra Chemistry Centre, Institute of Molecular Sciences (IMS), Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
Interests: computational chemistry; bio-inspired systems; molecular dynamics; Monte Carlo simulations; modelling
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
Coimbra Chemistry Centre, Institute of Molecular Sciences (IMS), Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
Interests: computational chemistry; molecular dynamics; modelling; machine learning; artificial intelligence
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
1. Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
2. Coimbra Chemistry Centre, Institute of Molecular Sciences (IMS), Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
Interests: nanotechnology; drug permeation enhancement; transdermal and oral drug delivery; brain targeting
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Molecular Dynamics Simulation (MD) has emerged as a key tool in the study of chemical and biomedical systems, fostering a new era of understanding and innovation. This special issue focuses on the remarkable progress and impact of MD simulations within these domains. Advances in MD simulations have revolutionized our comprehension of molecular-level processes in chemical and biomedical systems. These simulations have enabled researchers to unravel complex molecular interactions, predict protein structures, investigate drug binding mechanisms, and explore the behaviour of biomolecules in unprecedented detail. MD simulations have played a key role in the design of new drugs, in the development of materials for biomedicine, and the understanding of fundamental biological processes.

This special issue seeks to foster collaboration and knowledge exchange among researchers working at the intersection of molecular dynamics simulations and chemical and biomedical sciences. We invite you to submit your manuscripts, fostering a deeper understanding of molecular processes, by presenting novel MD simulation studies addressing critical questions in chemical and biomedical research, demonstrating significant insights into molecular mechanisms, validation of experimental data, or the discovery of new phenomena.

The manuscripts should focus on the development and improvement of MD simulation techniques tailored for chemical and biomedical applications, or present innovative algorithms, software tools, or hardware enhancements that enhance the accuracy and efficiency of MD simulations.

Articles highlighting the integration of MD simulations with other experimental and computational techniques, such as cryo-electron microscopy, X-ray crystallography, or quantum mechanics, are also encouraged. These contributions should demonstrate how MD simulations can complement and expand the scope of research in diverse scientific domains.

Comprehensive reviews summarizing the current state of the art in MD simulations applied to chemical and biomedical systems, are also desired. These articles should provide a synthesis of key findings, challenges, methodological advancements, opportunities and future directions, as well as the potential societal impact of MD simulations, serving as valuable references for other researchers.

Dr. Sandra Nunes
Dr. Tânia Cova
Dr. Carla Vitorino
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

  • molecular dynamics simulation
  • chemical and biomedical systems
  • molecular-level processes
  • protein structures
  • drug binding mechanisms
  • biomolecular behavior
  • drug design
  • biomedicine materials

Published Papers (2 papers)

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Research

18 pages, 5122 KiB  
Article
Impact of Phosphorylation at Various Sites on the Active Pocket of Human Ferrochelatase: Insights from Molecular Dynamics Simulations
by Mingshan Guo, Yuhong Lin, Chibuike David Obi, Peng Zhao, Harry A. Dailey, Amy E. Medlock and Yong Shen
Int. J. Mol. Sci. 2024, 25(12), 6360; https://doi.org/10.3390/ijms25126360 - 8 Jun 2024
Viewed by 191
Abstract
Ferrochelatase (FECH) is the terminal enzyme in human heme biosynthesis, catalyzing the insertion of ferrous iron into protoporphyrin IX (PPIX) to form protoheme IX (Heme). Phosphorylation increases the activity of FECH, and it has been confirmed that the activity of FECH phosphorylated at [...] Read more.
Ferrochelatase (FECH) is the terminal enzyme in human heme biosynthesis, catalyzing the insertion of ferrous iron into protoporphyrin IX (PPIX) to form protoheme IX (Heme). Phosphorylation increases the activity of FECH, and it has been confirmed that the activity of FECH phosphorylated at T116 increases. However, it remains unclear whether the T116 site and other potential phosphorylation modification sites collaboratively regulate the activity of FECH. In this study, we identified a new phosphorylation site, T218, and explored the allosteric effects of unphosphorylated (UP), PT116, PT218, and PT116 + PT218 states on FECH in the presence and absence of substrates (PPIX and Heme) using molecular dynamics (MD) simulations. Binding free energies were evaluated with the MM/PBSA method. Our findings indicate that the PT116 + PT218 state exhibits the lowest binding free energy with PPIX, suggesting the strongest binding affinity. Additionally, this state showed a higher binding free energy with Heme compared to UP, which facilitates Heme release. Moreover, employing multiple analysis methods, including free energy landscape (FEL), principal component analysis (PCA), dynamic cross-correlation matrix (DCCM), and hydrogen bond interaction analysis, we demonstrated that phosphorylation significantly affects the dynamic behavior and binding patterns of substrates to FECH. Insights from this study provide valuable theoretical guidance for treating conditions related to disrupted heme metabolism, such as various porphyrias and iron-related disorders. Full article
15 pages, 6487 KiB  
Article
Unveiling Therapeutic Potential: Targeting Fusobacterium nucleatum’s Lipopolysaccharide Biosynthesis for Endodontic Infections—An In Silico Screening Study
by Nezar Boreak, Ethar Awad Alrajab, Rayan Ali Nahari, Loay Ebrahim Najmi, Muhannad Ali Masmali, Atiah Abdulrahman Ghawi, Mohammed M. Al Moaleem, Majed Yahya Alhazmi and Abdulrahman Abdullah Maqbul
Int. J. Mol. Sci. 2024, 25(8), 4239; https://doi.org/10.3390/ijms25084239 - 11 Apr 2024
Viewed by 629
Abstract
Complex microbial communities have been reported to be involved in endodontic infections. The microorganisms invade the dental pulp leading to pulpitis and initiating pulp inflammation. Fusobacterium nucleatum is a dominant bacterium implicated in both primary and secondary endodontic infections. Drugs targeting the molecular [...] Read more.
Complex microbial communities have been reported to be involved in endodontic infections. The microorganisms invade the dental pulp leading to pulpitis and initiating pulp inflammation. Fusobacterium nucleatum is a dominant bacterium implicated in both primary and secondary endodontic infections. Drugs targeting the molecular machinery of F. nucleatum will minimize pulp infection. LpxA and LpxD are early acyltransferases involved in the formation of lipid A, a major component of bacterial membranes. The identification of leads which exhibit preference towards successive enzymes in a single pathway can also prevent the development of bacterial resistance. A stringent screening strategy utilizing physicochemical and pharmacokinetic parameters along with a virtual screening approach identified two compounds, Lomefloxacin and Enoxacin, with good binding affinity towards the early acyltransferases LpxA and LpxD. Lomefloxacin and Enoxacin, members of the fluoroquinolone antibiotic class, exhibit wide-ranging activity against diverse bacterial strains. Nevertheless, their effectiveness in the context of endodontic treatment requires further investigation. This study explored the potential of Lomefloxacin and Enoxacin to manage endodontic infections via computational analysis. Moreover, the compounds identified herein serve as a foundation for devising novel combinatorial libraries with enhanced efficacy for endodontic therapeutic strategies. Full article
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