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

Deadline for manuscript submissions: closed (20 March 2026) | Viewed by 6958

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Dr. Pavel Rehak

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Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
Interests: nanoscale simulations; computational chemistry; supramolecular self-assembly; drug design; ligand docking; GPCRs
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Dear Colleagues,

Biomolecules play a big role in serving life functions. They are essential in understanding how life functions at the basic molecular level, which can have macroscopic implications. Understanding how they function can help us not only understand disease mechanisms and potential novel therapeutics, but also design new materials and industrial processes that can be more environmentally friendly and efficient. While many experiments can describe and elucidate what we observe on the macroscopic level, it does not explain microscopic phenomena in atomistic or molecular detail. Therefore, molecular dynamics simulations can be a tool to supplement experiments to help us understand and elucidate biochemical reactions, processes, biomolecular properties, and supramolecular assemblies of biomolecules. Starting from quantum calculations and scaling up into hybrid quantum mechanics/molecular mechanics and classical molecular mechanics simulations, we would like to understand biochemical processes and biomaterial properties more adequately at the molecular level. Topics can include but are not limited to photosynthesis, carbohydrates, lipids, combustion, nucleic acids, protein synthesis, metabolite self-assembly, protein folding, metabolite self-assembly, inter-cellular signaling, and intra-celluar signaling.

Dr. Pavel Rehak
Guest Editor

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Keywords

molecular dynamics simulations
biochemical processes
biomaterial properties

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Published Papers (4 papers)

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Research

17 pages, 4203 KB

Open AccessArticle

Temperature-Dependent Active-Site Rearrangements of PETaseSM14: Insights from Molecular Dynamics Simulations

by Ki Hyun Nam

Int. J. Mol. Sci. 2026, 27(6), 2825; https://doi.org/10.3390/ijms27062825 - 20 Mar 2026

Viewed by 451

Abstract

Polyethylene terephthalate (PET) is a synthetic polymer that is widely used in the production of textiles, packaging materials, and beverage bottles. However, its high durability and resistance to abiotic degradation result in serious environmental and health problems. PETase is an enzyme that can depolymerize PET into value-added products, thereby providing an environmentally friendly strategy for PET recycling. PETaseSM14 from a marine sponge, Streptomyces sp. SM14, has a high salt tolerance and thermal stability, thus suggesting its potential for PET degradation applications. However, the substrate recognition mechanism of PETase remains unclear because the catalytic residue is buried within residues that form the substrate-binding cleft. To elucidate the molecular mechanism of PETaseSM14, all-atom molecular dynamics simulations were performed at 300, 320, and 340 K. The results revealed that the overall α/β fold remained stable at all temperatures, whereas temperature-dependent local fluctuations and conformational changes were observed in the substrate-binding cleft and N-terminal region. At 300 and 320 K, positional shifts and conformational changes in Tyr88 exposed the catalytic Ser156 to the solvent, thereby forming a potential substrate-binding cleft. In contrast, at 340 K, which is higher than the melting temperature of PETaseSM14, disruption of the charge-relay system of the catalytic triad occurs through conformational changes in His234. Substantial temperature-dependent conformational and positional changes in the N-terminal region of PETaseSM14 were observed at 320 and 340 K. These results provide mechanistic insight into the temperature-dependent active-site rearrangements and offer rational engineering strategies to enhance the efficiency of PETase for PET biodegradation. Full article

(This article belongs to the Special Issue Molecular Dynamics Simulation of Biomolecules)

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23 pages, 1379 KB

Open AccessArticle

Identification of Enhanced Cyclooxygenase-2 (COX-2) Inhibitors Beyond Curcumin Through Virtual Screening to Target Inflammation-Related Metabolic Complications

by Marakiya T. Moetlediwa, Rudzani Ramashia, Mpatla B. Mangale, Carmen Pheiffer, Babalwa U. Jack, Elliasu Y. Salifu and Pritika Ramharack

Int. J. Mol. Sci. 2026, 27(4), 1624; https://doi.org/10.3390/ijms27041624 - 7 Feb 2026

Viewed by 1333

Abstract

Cyclooxygenase-2 (COX-2) is a key enzyme in inflammatory pathways and serves as a therapeutic target in the treatment of inflammation-related diseases. Curcumin, a bioactive polyphenol from turmeric, has gained scientific attention due to its potent anti-inflammatory properties, largely mediated through COX-2 inhibition. However, the poor solubility and limited bioavailability of Curcumin limit its potential as a therapeutic agent targeting inflammatory diseases. We used an in silico approach to identify Curcumin-like scaffolds as novel COX-2 inhibitors with improved drug-like properties and therapeutic potential. A pharmacophore model derived from the key binding moieties of Curcumin was used to virtually screen the ZINC-22 database, identifying 237 candidate compounds for further evaluation. Molecular docking further prioritized these compounds to 10 candidates with the highest binding affinities. Most hits obeyed Lipinski’s rules, except for ZINC32605424 and ZINC47133707, which exhibited high LogP and molecular weight, respectively. Toxicity screening indicated that ZINC47133693 and ZINC09499196 exhibited high safety profiles, with ZINC15942488 being highly toxic. Furthermore, certain hits such as ZINC32605424 and ZINC15942488 were predicted to be P-glycoprotein substrates and potential inhibitors of cytochrome P450. Molecular dynamics simulations confirmed the stability of COX-2–ligand complexes, with critical interactions observed at conserved residues Tyr323 and Leu320. Binding energy calculations identified ZINC32605424 as the strongest COX-2 binder, mainly stabilized by Van der Waals forces. Overall, compounds such as ZINC32605424, ZINC08644750, ZINC47133693, and ZINC09499196 demonstrated potent COX-2 inhibition. These candidates show strong potential for further preclinical validation in studies investigating inflammation-related metabolic complications. Full article

(This article belongs to the Special Issue Molecular Dynamics Simulation of Biomolecules)

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32 pages, 7937 KB

Open AccessArticle

Structure-Based Identification of Natural Inhibitors Targeting the Gc Glycoprotein of Oropouche Virus: An In Silico Approach

by Carlos Vargas-Echeverría, Oscar Saurith-Coronell, Juan Rodriguez-Macías, Edgar A. Márquez Brazón, José R. Mora, Fabio Fuentes-Gandara, José L. Paz and Franklin Salazar

Int. J. Mol. Sci. 2025, 26(21), 10541; https://doi.org/10.3390/ijms262110541 - 30 Oct 2025

Cited by 1 | Viewed by 1195

Abstract

Oropouche virus (OROV), an emerging orthobunyavirus of increasing public health concern in the Americas, currently lacks approved antiviral therapies. In this study, we employed a structure-based in silico approach to identify natural antiviral scaffolds capable of targeting the Gc glycoprotein, a class II fusion protein essential for host membrane fusion and viral entry. A library of 537 plant-derived compounds was screened against the Gc head domain (PDB ID: 6H3X) through molecular docking and redocking, followed by 100-nanosecond molecular dynamics simulations, MM-PBSA free energy calculations, and ADMET profiling. Curcumin and Berberine emerged as standout candidates. Curcumin demonstrated a balanced profile, with stable binding (−38.14 kcal/mol), low backbone RMSD (1.82 Å), and consistent radius of gyration (Rg ~ 18.8 Å), suggesting strong conformational stability and compactness of the protein–ligand complex. Berberine exhibited the most favorable binding energy (−13.10 kcal/mol) and retained dynamic stability (RMSD 1.86 Å; Rg ~ 19.0 Å), though accompanied by predicted cytotoxicity that may require structural refinement. Both compounds induced reduced residue-level fluctuations (RMSF < 2.5 Å) in functionally critical regions of the Gc protein, consistent with a mechanism of action that involves stabilization of the prefusion conformation and interference with the structural transitions required for viral entry. These findings identify curcumin and berberine as promising scaffolds for anti-OROV drug development and offer a rational foundation for future experimental validation targeting viral fusion mechanisms. Full article

(This article belongs to the Special Issue Molecular Dynamics Simulation of Biomolecules)

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14 pages, 3033 KB

Open AccessArticle

Luminescence Properties of Hoechst 33258 in Polyvinyl Alcohol Films

by Bong Lee, Agnieszka Jablonska, Danh Pham, Rajveer Sagoo, Zygmunt Gryczynski, Trang Thien Pham and Ignacy Gryczynski

Int. J. Mol. Sci. 2025, 26(2), 514; https://doi.org/10.3390/ijms26020514 - 9 Jan 2025

Cited by 3 | Viewed by 2370

Abstract

We report a comprehensive investigation of the photophysical properties of Hoechst 33258 (HOE) embedded in polyvinyl alcohol (PVA) films. HOE displays a bright, highly polarized, blue fluorescence emission centered at 430 nm, indicating effective immobilization within the polymer matrix of PVA. Its fluorescence quantum yield is notably high (~0.74), as determined relative to a quinine sulfate standard. In addition, we observed that HOE-doped PVA films exhibit room temperature phosphorescence (RTP) that remains visible for several seconds after UV excitation ceases. The slightly negative phosphorescence anisotropy implies that the triplet–singlet radiative transition is orthogonal to the singlet–singlet transition governing fluorescence. Notably, we observed that direct triplet-state excitation at longer wavelengths (beyond the primary absorption band) produces highly polarized RTP. We believe this possibility of direct triplet-state excitation opens new avenues for studying RTP in polymer-immobilized molecules. Full article

(This article belongs to the Special Issue Molecular Dynamics Simulation of Biomolecules)

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