ijms-logo

Journal Browser

Journal Browser

Advances in Computational Biology: Molecular Dynamics Simulation of Biomolecules

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 August 2025 | Viewed by 2825

Special Issue Editor


E-Mail Website
Guest Editor

Special Issue Information

Dear Colleagues,

The simulation of important processes in biomedicine and biotechnology using computational methods has become a well-established field in recent years. We can simulate motions associated with the function of key macromolecules in cellular processes. Using molecular dynamics systems, we can study the effect of a mutation that causes a rare disease or a carcinogenic process on the structure and/or function of a macromolecule. We can also design molecules with the ability to act as antimicrobial, antiviral or anticancer agents. All these processes, as well as the methodology that makes them possible, are welcome in this Special Issue of IJMS.

Dr. Paulino Gómez-Puertas
Guest Editor

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

  • computational biology
  • molecular dynamics
  • molecular simulation of rare diseases
  • computational design of antimicrobials
  • computational design of antivirals
  • molecular simulation of cancer-related processes
  • computational design of anti-cancer molecules
  • molecular simulation of biotechnology processes

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (1 paper)

Order results
Result details
Select all
Export citation of selected articles as:

Research

16 pages, 1493 KiB  
Article
In Silico Design of miniACE2 Decoys with In Vitro Enhanced Neutralization Activity against SARS-CoV-2, Encompassing Omicron Subvariants
by Jenny Andrea Arévalo-Romero, Gina López-Cantillo, Sara Moreno-Jiménez, Íñigo Marcos-Alcalde, David Ros-Pardo, Bernardo Armando Camacho, Paulino Gómez-Puertas and Cesar A. Ramírez-Segura
Int. J. Mol. Sci. 2024, 25(19), 10802; https://doi.org/10.3390/ijms251910802 - 8 Oct 2024
Cited by 2 | Viewed by 1457
Abstract
The COVID-19 pandemic has overwhelmed healthcare systems and triggered global economic downturns. While vaccines have reduced the lethality rate of SARS-CoV-2 to 0.9% as of October 2024, the continuous evolution of variants remains a significant public health challenge. Next-generation medical therapies offer hope [...] Read more.
The COVID-19 pandemic has overwhelmed healthcare systems and triggered global economic downturns. While vaccines have reduced the lethality rate of SARS-CoV-2 to 0.9% as of October 2024, the continuous evolution of variants remains a significant public health challenge. Next-generation medical therapies offer hope in addressing this threat, especially for immunocompromised individuals who experience prolonged infections and severe illnesses, contributing to viral evolution. These cases increase the risk of new variants emerging. This study explores miniACE2 decoys as a novel strategy to counteract SARS-CoV-2 variants. Using in silico design and molecular dynamics, blocking proteins (BPs) were developed with stronger binding affinity for the receptor-binding domain of multiple variants than naturally soluble human ACE2. The BPs were expressed in E. coli and tested in vitro, showing promising neutralizing effects. Notably, miniACE2 BP9 exhibited an average IC50 of 4.9 µg/mL across several variants, including the Wuhan strain, Mu, Omicron BA.1, and BA.2 This low IC50 demonstrates the potent neutralizing ability of BP9, indicating its efficacy at low concentrations.Based on these findings, BP9 has emerged as a promising therapeutic candidate for combating SARS-CoV-2 and its evolving variants, thereby positioning it as a potential emergency biopharmaceutical. Full article
Show Figures

Figure 1

Back to TopTop