Molecular Structure and Simulation in Biological System 3.0

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

Deadline for manuscript submissions: 31 December 2024 | Viewed by 888

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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
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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

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Keywords

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

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Published Papers (1 paper)

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Research

13 pages, 1570 KiB  
Article
In Silico Design of Novel Piperazine-Based mTORC1 Inhibitors Through DFT, QSAR and ADME Investigations
by El Mehdi Karim, Oussama Abchir, Hassan Nour, Ossama Daoui, Souad El Khattabi, Farhan Siddique, M’Hammed El Kouali, Mohammed Talbi, Abdelkbir Errougui and Samir Chtita
Biophysica 2024, 4(4), 517-529; https://doi.org/10.3390/biophysica4040034 - 24 Oct 2024
Viewed by 549
Abstract
Mammalian target of rapamycin complex 1 (mTORC1) is an important and promising alternative biological target for the treatment of different types of cancer including breast, lung and renal cell carcinoma. This study contributed to the development of mathematical models highlighting the quantitative structure-activity [...] Read more.
Mammalian target of rapamycin complex 1 (mTORC1) is an important and promising alternative biological target for the treatment of different types of cancer including breast, lung and renal cell carcinoma. This study contributed to the development of mathematical models highlighting the quantitative structure-activity relationship of a series of piperazine derivatives reported as mTORC1 inhibitors. Various molecular descriptors were calculated using Gaussian 09, Chemsketch, and ChemOffice software. The density funcional theory (DFT) method at the level B3LYP/6-31G+(d, p) was applied to determine the structural, electronic and energetic parameters associated with the studied molecules. The predictive ability of the built models, which is obtained by two methods (MLR and MNLR), showed that the built models are statistically significant. The QSAR modeling results revealed that the six molecular descriptors of lowest unoccupied molecular orbital energy (ELUMO), electrophilicity index (ω), molar refractivity (MR), aqueous solubility (Log S), topological polar surface area (PSA), and refractive index (n) significantly correlated to the biological inhibitory activity of piperazine derivatives. Using QSAR models and in silico pharmacokinetic profiles predictions, five new candidate compounds are selected as potential inhibitors against cancer. Full article
(This article belongs to the Special Issue Molecular Structure and Simulation in Biological System 3.0)
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