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The Machine Learning, Applications in the Discovery of New Bioactive Molecules, 2nd Edition

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Medicinal Chemistry".

Deadline for manuscript submissions: closed (31 January 2025) | Viewed by 1728

Special Issue Editor


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Guest Editor
Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Faculty of Pharmacy, University of Lisbon, Av. Prof. Gama Pinto, 1649-019 Lisbon, Portugal
Interests: computational medicinal chemistry; design of new drugs; anti-infectious agents; anti-cancer agents; in silico methods; virtual screening; molecular docking; de novo design; homology modelling; pharmacophore modelling; molecular dynamics; Monte Carlo; quantum chemistry
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Special Issue Information

Dear Colleagues,

Various computational approaches support the development of new biologically active substances at all stages. Among them, machine learning (ML) methods are gaining great popularity due to their high prediction power and ability to handle a large amount of data in a relatively short time. ML-based tools not only assist in the search for new ligands with a particular activity profile but also help to predict and optimize physicochemical and pharmacokinetic properties, while avoiding side effects. In addition, ML also takes part in the enumeration of compound libraries, covering desired activity and property profiles via the application of deep learning methods.

The present Special Issue aims to cover all aspects of ML-based tool applications in computer-aided drug design—from ligand-based approaches (in both activity and physicochemical/ADMET property predictions) in structure-based protocols (e.g., for post-processing of docking results) to the generation of new ligands (e.g., with the use of deep learning). Manuscripts presenting methods that are experimentally verified are of particular interest.

Dr. Rita Guedes
Guest Editor

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 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

  • machine learning
  • deep learning
  • computer-aided drug design
  • ligand-based approaches
  • structure-based approaches
  • in silico compound profiling
  • virtual screening
  • ADMET property evaluation

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Published Papers (1 paper)

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Research

17 pages, 1611 KiB  
Article
Sertraline as a Multi-Target Modulator of AChE, COX-2, BACE-1, and GSK-3β: Computational and In Vivo Studies
by Minhajul Arfeen and Vasudevan Mani
Molecules 2024, 29(22), 5354; https://doi.org/10.3390/molecules29225354 - 14 Nov 2024
Cited by 1 | Viewed by 1440
Abstract
Alzheimer’s disease (AD) is a neurodegenerative disorder associated with the dysregulation of several key enzymes, including acetylcholinesterase (AChE), cyclooxygenase-2 (COX-2), glycogen synthase kinase 3β (GSK-3β), β-site amyloid precursor protein cleaving enzyme 1 (BACE-1), and caspase-3. In this study, machine learning algorithms such as [...] Read more.
Alzheimer’s disease (AD) is a neurodegenerative disorder associated with the dysregulation of several key enzymes, including acetylcholinesterase (AChE), cyclooxygenase-2 (COX-2), glycogen synthase kinase 3β (GSK-3β), β-site amyloid precursor protein cleaving enzyme 1 (BACE-1), and caspase-3. In this study, machine learning algorithms such as Random Forest (RF), Gradient Boost (GB), and Extreme Gradient Boost (XGB) were employed to screen US-FDA approved drugs from the ZINC15 database to identify potential dual inhibitors of COX-2 and AChE. The models were trained using molecules obtained from the ChEMBL database, with 5039 molecules for AChE and 3689 molecules for COX-2. Specifically, 1248 and 3791 molecules were classified as active and inactive for AChE, respectively, while 858 and 2831 molecules were classified as active and inactive for COX-2. The three machine learning models achieved prediction accuracies ranging from 92% to 95% for both AChE and COX-2. Virtual screening of US-FDA drugs from the ZINC15 database identified sertraline (SETL) as a potential dual inhibitor of AChE and COX-2. Further docking studies of SETL in the active sites of AChE and COX-2, as well as BACE-1, GSK-3β, and caspase-3, revealed strong binding affinities for all five proteins. In vivo validation was conducted using a lipopolysaccharide (LPS)-induced rat model pretreated with SETL for 30 days. The results demonstrated a significant decrease in the levels of AChE (p < 0.001), BACE-1 (p < 0.01), GSK-3β (p < 0.05), and COX-2 (p < 0.05). Additionally, the downstream effects were evaluated, showing significant decreases in the apoptosis marker caspase-3 (p < 0.05) and the oxidative stress marker malondialdehyde (MDA) (p < 0.001), indicating that SETL is clinically localized in its effectiveness, mitigating both enzymatic activity and the associated pathological changes of cognitive impairment and AD. Full article
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