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Biophysica
Special Issues
Molecular Structure and Simulation in Biological System 2.0
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Molecular Structure and Simulation in Biological System 2.0

A special issue of Biophysica (ISSN 2673-4125).

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 8812

Special Issue Editor

Dr. Paulino Gómez-Puertas

E-Mail Website
Guest Editor
Molecular Modeling Group, Centro de Biologia Molecular Severo Ochoa (CBM, CSIC-UAM). CL Nicolas Cabrera, 1. Campus UAM, 28049 Madrid, Spain
Interests: computational biology; molecular dynamics; rare diseases; antimicrobials; antivirals; cancer
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Structural information at the atomic scale of macromolecules allows a precise understanding of the mechanisms underlying different types of biological system, including intermolecular interactions, intracellular interactions, and so on.

Knowledge of this information, as well as techniques capable of computationally simulating the movement of these macromolecules in their biological system, helps us to rationalize the mechanisms and understand how biological systems work.

This Special Issue welcomes papers using 3D molecular structure and/or virtual modeling techniques in computational biology, alone or in combination with in vitro or in vivo strategies. The aim of these techniques may be the prevention, discovery, characterization or therapy of diseases, including cancers, genetic diseases, or those related to viral or bacterial infections. We also welcome papers addressing 3D screening strategies, the design of new drugs and therapies and any original articles or comprehensive reviews related to molecular structure and simulation in biological system.

Dr. Paulino Gómez-Puertas
Guest Editor

Manuscript Submission Information

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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. Biophysica is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1000 CHF (Swiss Francs). 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

  • macromolecular structure
  • computational biology
  • drug design
  • molecular dynamics
  • virtual modeling

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Published Papers (5 papers)

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Research

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17 pages, 5148 KiB  
Article
Interaction between Vitamins C and E When Scavenging the Superoxide Radical Shown by Hydrodynamic Voltammetry and DFT
by Francesco Caruso, Jens Z. Pedersen, Sandra Incerpi, Stuart Belli, Raiyan Sakib and Miriam Rossi
Biophysica 2024, 4(2), 310-326; https://doi.org/10.3390/biophysica4020022 - 18 Jun 2024
Cited by 2 | Viewed by 1025
Abstract
In this study, we examine the cooperative effect between vitamins C and E that mitigates oxidative stress by using experimental and computational methods. We performed superoxide scavenging experiments on each vitamin individually and their combination using rotating ring–disk electrode voltammetry. The results indicate [...] Read more.
In this study, we examine the cooperative effect between vitamins C and E that mitigates oxidative stress by using experimental and computational methods. We performed superoxide scavenging experiments on each vitamin individually and their combination using rotating ring–disk electrode voltammetry. The results indicate that vitamins E and C together produce more effective scavenging of superoxide as evaluated by a steeper slope in the efficiency graph, −7.2 × 104, compared to that of vitamin E alone, −1.8 × 103, or vitamin C alone, −1.3 × 104. Density Functional Theory calculations agree with our experimental results, and we describe a mechanism for the antioxidant action of individual vitamins E and C, plus the synergistic action when both vitamins interact. This process involves the restoration of vitamin E by vitamin C and includes π-π interactions between superoxide and scavengers. The overall result produces an increase in scavenging superoxide radicals when both vitamins act together. Full article
(This article belongs to the Special Issue Molecular Structure and Simulation in Biological System 2.0)
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21 pages, 3863 KiB  
Article
Constant-pH Simulations of a Coarse-Grained Model of Polyfunctional Weak Charged Biopolymers
by David Naranjo, Pablo M. Blanco, Josep L. Garcés, Sergio Madurga and Francesc Mas
Biophysica 2024, 4(1), 107-127; https://doi.org/10.3390/biophysica4010008 - 28 Feb 2024
Viewed by 999
Abstract
A coarse-grained model of linear polyfunctional weak charged biopolymers was implemented, formed of different proportions of acid-base groups resembling the composition of humic substances. These substances are mainly present in dissolved organic matter in natural water. The influence of electrostatic interactions computing methods, [...] Read more.
A coarse-grained model of linear polyfunctional weak charged biopolymers was implemented, formed of different proportions of acid-base groups resembling the composition of humic substances. These substances are mainly present in dissolved organic matter in natural water. The influence of electrostatic interactions computing methods, factors concerning the structure of the chain, different functional groups, and the ionic strength on polyelectrolytes were studied. Langevin dynamics with constant pH simulations were performed using the ESPResSO package and the Python-based Molecule Builder for ESPResSo (pyMBE) library. The coverage was fitted to a polyfunctional Frumkin isotherm, with a mean-field interaction between charged beads. The composition of the chain affects the charge while ionic strength affects both the charge and the radius of gyration. Additionally, the parameters intrinsic to the polyelectrolyte model were well reproduced by fitting the polyfunctional Frumkin isotherm. In contrast, the non-intrinsic parameters depended on the ionic strength. The method developed and applied to a polyfunctional polypeptide model, that resembles a humic acid, will be very useful for characterizing biopolymers with several acid-base functional groups, where their structure, the composition of the different functional groups, and the determination of the main intrinsic proton binding constants and their proportion are not exactly known. Full article
(This article belongs to the Special Issue Molecular Structure and Simulation in Biological System 2.0)
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17 pages, 4139 KiB  
Article
Screening and Analysis of Potential Inhibitors of SHMT2
by Bojin Chen and John Z. H. Zhang
Biophysica 2023, 3(4), 651-667; https://doi.org/10.3390/biophysica3040044 - 3 Dec 2023
Viewed by 1743
Abstract
Serine hydroxymethyltransferase 2 (SHMT2) has garnered significant attention as a critical catalytic regulator of the serine/glycine pathway in the one-carbon metabolism of cancer cells. Despite its potential as an anti-cancer target, only a limited number of inhibitors have been identified so far. In [...] Read more.
Serine hydroxymethyltransferase 2 (SHMT2) has garnered significant attention as a critical catalytic regulator of the serine/glycine pathway in the one-carbon metabolism of cancer cells. Despite its potential as an anti-cancer target, only a limited number of inhibitors have been identified so far. In this study, we employed seven different scoring functions and skeleton clustering to screen the ChemDiv database for 38 compounds, 20 of which originate from the same skeleton structure. The most significant residues from SHMT2 and chemical groups from the inhibitors were identified using ASGBIE (Alanine Scanning with Generalized Born model and Interaction Entropy), and the binding energy of each residue was quantitatively determined, revealing the essential features of the protein–inhibitor interaction. The two most important contributing residues are TYR105 and TYR106 of the B chain followed by LEU166 and ARG425 of the A chain. The findings will be greatly helpful in developing a thorough comprehension of the binding mechanisms involved in drug–SHMT2 interactions and offer valuable direction for designing more potent inhibitors. Full article
(This article belongs to the Special Issue Molecular Structure and Simulation in Biological System 2.0)
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16 pages, 3065 KiB  
Article
Exploring Quercetin Hydrate’s Potential as an Antiviral Treatment for Oropouche Virus
by Gabriela de Lima Menezes, Marielena Vogel Saivish, Lívia Sacchetto, Gislaine Celestino Dutra da Silva, Igor da Silva Teixeira, Natalia Franco Bueno Mistrão, Maurício Lacerda Nogueira, Jonas Ivan Nobre Oliveira, Katyanna Sales Bezerra, Roosevelt Alves da Silva and Umberto Laino Fulco
Biophysica 2023, 3(3), 485-500; https://doi.org/10.3390/biophysica3030032 - 12 Aug 2023
Viewed by 2292
Abstract
The Oropouche virus is an orthobunyavirus responsible for causing Oropouche fever, a disease that primarily affects thousands of people in South and Central America. Currently, no specific antiviral treatments or vaccines are available against this virus, highlighting the urgent need for safe, affordable, [...] Read more.
The Oropouche virus is an orthobunyavirus responsible for causing Oropouche fever, a disease that primarily affects thousands of people in South and Central America. Currently, no specific antiviral treatments or vaccines are available against this virus, highlighting the urgent need for safe, affordable, and effective therapies. Natural products serve as an important source of bioactive compounds, and there is growing interest in identifying natural bioactive molecules that could be used for treating viral diseases. Quercetin hydrate is a compound classified as a flavonoid, which has garnered scientific attention due to its potential health benefits and its presence in various plant-based foods. In this study, we aim to evaluate the in vitro antiviral activity of quercetin hydrate against the Oropouche virus (OROV). Furthermore, we intend to explore its mode of action through in silico approaches. The cytotoxicity and antiviral activity of the compound were assessed using Vero cells. In addition, in silico studies were also performed through molecular docking, molecular dynamics simulations, Molecular Mechanics Poisson–Boltzmann surface area (MM/PBSA), and quantum-mechanical analysis in order to evaluate the interaction with the Gc protein of OROV. The assay revealed that the compound was highly active against the virus, inhibiting OROV with an EC50 value of 53.5 ± 26.5 µM under post-infection treatment conditions. The present study demonstrates that the compound is a promising antiviral agent; however, the mechanisms of action proposed in this study need to be experimentally verified by future assays. Full article
(This article belongs to the Special Issue Molecular Structure and Simulation in Biological System 2.0)
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Review

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16 pages, 908 KiB  
Review
Bioprinting of Hydrogel-Based Drug Delivery Systems for Nerve Tissue Regeneration
by Eliza Marie Steele, Zacheus L. Carr and Emily Dosmar
Biophysica 2024, 4(1), 58-73; https://doi.org/10.3390/biophysica4010004 - 31 Jan 2024
Viewed by 1945
Abstract
Globally, thousands of people are affected by severe nerve injuries or neurodegenerative disorders. These conditions cannot always be cured because nerve tissue either does not regenerate or does so at a slow rate. Therefore, tissue engineering has emerged as a potential treatment approach. [...] Read more.
Globally, thousands of people are affected by severe nerve injuries or neurodegenerative disorders. These conditions cannot always be cured because nerve tissue either does not regenerate or does so at a slow rate. Therefore, tissue engineering has emerged as a potential treatment approach. This review discusses 3D bioprinting for scaffold manufacturing, highlights the advantages and disadvantages of common bioprinting techniques, describes important considerations for bioinks, biomaterial inks, and scaffolds, and discusses some drug delivery systems. The primary goal of this review is to bring attention to recent advances in nerve tissue engineering and its possible clinical applications in peripheral nerve, spinal cord, and cerebral nerve regeneration. Only studies that use 3D bioprinting or 3D printing to manufacture hydrogel scaffolds and incorporate the sustained release of a drug or growth factor for nerve regeneration are included. This review indicates that 3D printing is a fast and precise scaffold manufacturing technique but requires printing materials with specific properties to be effective in nervous tissue applications. The results indicate that the sustained release of certain drugs and growth factors from scaffolds can significantly improve post-printing cell viability, cell proliferation, adhesion, and differentiation, as well as functional recovery compared with scaffolds alone. However, more in vivo research needs to be conducted before this approach can be used in clinical applications. Full article
(This article belongs to the Special Issue Molecular Structure and Simulation in Biological System 2.0)
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