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Virtual Screening in Modern Medicinal Chemistry

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

Deadline for manuscript submissions: closed (30 April 2023) | Viewed by 9690

Special Issue Editor


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Guest Editor
Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genova, Viale Benedetto XV 3, 16132 Genova, Italy
Interests: drug design; homology modeling; molecular docking calculations; virtual screening; 3D-QSAR analyses
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Special Issue Information

Dear Colleagues,

Drug discovery is a time-consuming and expensive process, usually carried out through rational design methods or HTS (high-throughput screening) of large libraries of compounds. This requires appropriate experimental models to evaluate and validate the therapeutic potential of new putative hit compounds and then specific biological assays and clinical trials to evaluate the safety and efficacy profiles of the discovered molecules. Much effort has been focused on rationalizing, speeding up, and lowering the costs of the drug discovery process. In this context, virtual screening (VS) is becoming an increasingly fast and inexpensive approach for identifying and selecting biologically active molecules targeting pharmaceutically relevant proteins. The rapid development of new tools to better understand the structure and function of proteins and their pathophysiological correlations has uncovered new promising targets to be exploited for the design and optimization of novel therapeutic approaches. Virtual screening relying on structure-based strategies opens up opportunities to speed up efforts in the search for novel drugs, addressing new challenges in the modern medicinal chemistry scenario. In addition, virtual screening represents a useful tool for performing effective drug repositioning for existing drugs in the market, with a remarkable reduction in the developmental costs of the whole drug discovery process. This Special Issue will cover all different aspects of virtual screening methodology and applications, leading to hit compounds or to optimized leads based on the structural knowledge of the target, including X-ray crystallography or homology modeling-based structures, or integrated bioinformatics pipelines for fast drug identification.

Dr. Elena Cichero
Guest Editor

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Keywords

  • virtual screening
  • orphan target
  • GPCR
  • bioinformatics
  • drug repositioning

Published Papers (4 papers)

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Research

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21 pages, 2499 KiB  
Article
Small Molecular Drug Screening Based on Clinical Therapeutic Effect
by Cai Zhong, Jiali Ai, Yaxin Yang, Fangyuan Ma and Wei Sun
Molecules 2022, 27(15), 4807; https://doi.org/10.3390/molecules27154807 - 27 Jul 2022
Viewed by 1352
Abstract
Virtual screening can significantly save experimental time and costs for early drug discovery. Drug multi-classification can speed up virtual screening and quickly predict the most likely class for a drug. In this study, 1019 drug molecules with actual therapeutic effects are collected from [...] Read more.
Virtual screening can significantly save experimental time and costs for early drug discovery. Drug multi-classification can speed up virtual screening and quickly predict the most likely class for a drug. In this study, 1019 drug molecules with actual therapeutic effects are collected from multiple databases and documents, and molecular sets are grouped according to therapeutic effect and mechanism of action. Molecular descriptors and molecular fingerprints are obtained through SMILES to quantify molecular structures. After using the Kennard–Stone method to divide the data set, a better combination can be obtained by comparing the combined results of five classification algorithms and a fusion method. Furthermore, for a specific data set, the model with the best performance is used to predict the validation data set. The test set shows that prediction accuracy can reach 0.862 and kappa coefficient can reach 0.808. The highest classification accuracy of the validation set is 0.873. The more reliable molecular set has been found, which could be used to predict potential attributes of unknown drug compounds and even to discover new use for old drugs. We hope this research can provide a reference for virtual screening of multiple classes of drugs at the same time in the future. Full article
(This article belongs to the Special Issue Virtual Screening in Modern Medicinal Chemistry)
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11 pages, 1731 KiB  
Article
Identification of Human Dihydroorotate Dehydrogenase Inhibitor by a Pharmacophore-Based Virtual Screening Study
by Salvatore Galati, Stefano Sainas, Marta Giorgis, Donatella Boschi, Marco L. Lolli, Gabriella Ortore, Giulio Poli and Tiziano Tuccinardi
Molecules 2022, 27(12), 3660; https://doi.org/10.3390/molecules27123660 - 07 Jun 2022
Cited by 4 | Viewed by 2282
Abstract
Human dihydroorotate dehydrogenase (hDHODH) is an enzyme belonging to a flavin mononucleotide (FMN)-dependent family involved in de novo pyrimidine biosynthesis, a key biological pathway for highly proliferating cancer cells and pathogens. In fact, hDHODH proved to be a promising therapeutic target for the [...] Read more.
Human dihydroorotate dehydrogenase (hDHODH) is an enzyme belonging to a flavin mononucleotide (FMN)-dependent family involved in de novo pyrimidine biosynthesis, a key biological pathway for highly proliferating cancer cells and pathogens. In fact, hDHODH proved to be a promising therapeutic target for the treatment of acute myelogenous leukemia, multiple myeloma, and viral and bacterial infections; therefore, the identification of novel hDHODH ligands represents a hot topic in medicinal chemistry. In this work, we reported a virtual screening study for the identification of new promising hDHODH inhibitors. A pharmacophore-based approach combined with a consensus docking analysis and molecular dynamics simulations was applied to screen a large database of commercial compounds. The whole virtual screening protocol allowed for the identification of a novel compound that is endowed with promising inhibitory activity against hDHODH and is structurally different from known ligands. These results validated the reliability of the in silico workflow and provided a valuable starting point for hit-to-lead and future lead optimization studies aimed at the development of new potent hDHODH inhibitors. Full article
(This article belongs to the Special Issue Virtual Screening in Modern Medicinal Chemistry)
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21 pages, 10916 KiB  
Article
Discovery of a New Drug-like Series of OGT Inhibitors by Virtual Screening
by Elena M. Loi, Tihomir Tomašič, Cyril Balsollier, Kevin van Eekelen, Matjaž Weiss, Martina Gobec, Matthew G. Alteen, David J. Vocadlo, Roland J. Pieters and Marko Anderluh
Molecules 2022, 27(6), 1996; https://doi.org/10.3390/molecules27061996 - 19 Mar 2022
Cited by 3 | Viewed by 2721
Abstract
O-GlcNAcylation is an essential post-translational modification installed by the enzyme O-β-N-acetyl-d-glucosaminyl transferase (OGT). Modulating this enzyme would be extremely valuable to better understand its role in the development of serious human pathologies, such as diabetes and cancer. However, the [...] Read more.
O-GlcNAcylation is an essential post-translational modification installed by the enzyme O-β-N-acetyl-d-glucosaminyl transferase (OGT). Modulating this enzyme would be extremely valuable to better understand its role in the development of serious human pathologies, such as diabetes and cancer. However, the limited availability of potent and selective inhibitors hinders the validation of this potential therapeutic target. To explore new chemotypes that target the active site of OGT, we performed virtual screening of a large library of commercially available compounds with drug-like properties. We purchased samples of the most promising virtual hits and used enzyme assays to identify authentic leads. Structure-activity relationships of the best identified OGT inhibitor were explored by generating a small library of derivatives. Our best hit displays a novel uridine mimetic scaffold and inhibited the recombinant enzyme with an IC50 value of 7 µM. The current hit represents an excellent starting point for designing and developing a new set of OGT inhibitors that may prove useful for exploring the biology of OGT. Full article
(This article belongs to the Special Issue Virtual Screening in Modern Medicinal Chemistry)
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Review

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49 pages, 7019 KiB  
Review
Virtual Screening in the Identification of Sirtuins’ Activity Modulators
by Elena Abbotto, Naomi Scarano, Francesco Piacente, Enrico Millo, Elena Cichero and Santina Bruzzone
Molecules 2022, 27(17), 5641; https://doi.org/10.3390/molecules27175641 - 01 Sep 2022
Cited by 10 | Viewed by 2639
Abstract
Sirtuins are NAD+-dependent deac(et)ylases with different subcellular localization. The sirtuins’ family is composed of seven members, named SIRT-1 to SIRT-7. Their substrates include histones and also an increasing number of different proteins. Sirtuins regulate a wide range of different processes, ranging [...] Read more.
Sirtuins are NAD+-dependent deac(et)ylases with different subcellular localization. The sirtuins’ family is composed of seven members, named SIRT-1 to SIRT-7. Their substrates include histones and also an increasing number of different proteins. Sirtuins regulate a wide range of different processes, ranging from transcription to metabolism to genome stability. Thus, their dysregulation has been related to the pathogenesis of different diseases. In this review, we discussed the pharmacological approaches based on sirtuins’ modulators (both inhibitors and activators) that have been attempted in in vitro and/or in in vivo experimental settings, to highlight the therapeutic potential of targeting one/more specific sirtuin isoform(s) in cancer, neurodegenerative disorders and type 2 diabetes. Extensive research has already been performed to identify SIRT-1 and -2 modulators, while compounds targeting the other sirtuins have been less studied so far. Beside sections dedicated to each sirtuin, in the present review we also included sections dedicated to pan-sirtuins’ and to parasitic sirtuins’ modulators. A special focus is dedicated to the sirtuins’ modulators identified by the use of virtual screening. Full article
(This article belongs to the Special Issue Virtual Screening in Modern Medicinal Chemistry)
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