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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: closed (20 March 2026) | Viewed by 5972

Special Issue Editor


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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

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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

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Published Papers (3 papers)

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Research

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22 pages, 3576 KB  
Article
Discovery of New Antioxidant Molecules Enhancing the Nrf2-Mediated Pathway: Docking Studies and Biological Evaluation
by Simona De Vita, Elena González-Burgos, Stefania Terracciano, Maria Giovanna Chini, María Pilar Gómez-Serranillos and Giuseppe Bifulco
Int. J. Mol. Sci. 2026, 27(4), 1862; https://doi.org/10.3390/ijms27041862 - 15 Feb 2026
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Abstract
Oxidative stress has been reported to be implicated in the pathogenesis of many neurodegenerative diseases, such as Alzheimer’s and Parkinson’s diseases. Enhancing antioxidant response, through the activation of the transcription factor Nrf2, may represent a potential strategy, based on in vitro models. To [...] Read more.
Oxidative stress has been reported to be implicated in the pathogenesis of many neurodegenerative diseases, such as Alzheimer’s and Parkinson’s diseases. Enhancing antioxidant response, through the activation of the transcription factor Nrf2, may represent a potential strategy, based on in vitro models. To identify scaffolds potentially able to modulate the Nrf2-Keap1 interaction, docking experiments were carried out using a library of commercially available and in-house synthesized molecules. Compounds 14 were selected, and their direct and indirect antioxidant activity was evaluated in an acute oxidative stress model induced by Fenton’s reaction in the human neuroblastoma SH-SY5Y cell line. Results showed that these compounds exerted the most pronounced protective effect under the tested conditions at the following concentrations: 10 μM for 1, 25 μM for 2, 10 μM for 3, and 5 μM for 4. Moreover, these molecules notably decreased intracellular ROS production and lipid peroxidation by-products and increased the GSH/GSSG ratio. Furthermore, these molecules promoted the protein expression of antioxidant enzymes downstream of the Nrf2 transcriptional pathway. Interestingly, compound 3 resulted in being the most active among the four. Full article
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16 pages, 1493 KB  
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 3 | Viewed by 2437
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
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Review

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23 pages, 1938 KB  
Review
Molecular Modeling of the Pathogenetic Mechanisms of Neuropsychiatric Disorders
by Amal Abdurazakov, Dmitrii A. Abashkin, Ekaterina V. Semina, Yulia A. Chaika and Vera E. Golimbet
Int. J. Mol. Sci. 2026, 27(8), 3563; https://doi.org/10.3390/ijms27083563 - 16 Apr 2026
Viewed by 689
Abstract
Neuropsychiatric diseases are characterized by complex molecular underpinnings that remain challenging to fully elucidate. Molecular dynamics (MD) simulations have emerged as a powerful computational tool, providing a crucial bridge between static genetic data and the dynamic functional consequences of molecular alterations. This review [...] Read more.
Neuropsychiatric diseases are characterized by complex molecular underpinnings that remain challenging to fully elucidate. Molecular dynamics (MD) simulations have emerged as a powerful computational tool, providing a crucial bridge between static genetic data and the dynamic functional consequences of molecular alterations. This review offers a comprehensive overview of the application of MD simulations in studying the molecular basis of neuropsychiatric disorders. We highlight key applications, including the assessment of mutation pathogenicity in disease-associated proteins, the influence of post-translational modifications on protein function, folding, misfolding, and aggregation, and the characterization of psychopharmacological drug–target interactions at atomic resolution. Through relevant examples from research on psychiatric and neurodegenerative diseases, we illustrate how these computational methods are implemented to gain mechanistic insights. Importantly, this review traces the historical development of MD simulations in biological applications, critically examines the method’s limitations, and outlines future perspectives for simulating long-timescale physiological processes, large molecular ensembles, and even whole-cell environments. Ultimately, this work highlights MD simulations as a useful and complementary tool for modern neuropsychiatry research, capable of revealing disease mechanisms and guiding the development of novel therapeutic strategies. Full article
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