ArticleInternational journal of molecular sciences2019
Extensive Reliability Evaluation of Docking-Based Target-Fishing Strategies.
Article in International journal of molecular sciences, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- The Art and Science of Molecular Docking.Annual review of biochemistry · 2024Review
- Target Prediction by Multiple Virtual Screenings: Analyzing the SARS-CoV-2 Phenotypic Screening by the Docking Simulations Submitted to the MEDIATE Initiative.International journal of molecular sciences · 2023Article
- Discovery of Potent Indolyl-Hydrazones as Kinase Inhibitors for Breast Cancer: Synthesis, X-ray Single-Crystal Analysis, and In Vitro and In Vivo Anti-Cancer Activity Evaluation.Pharmaceuticals (Basel, Switzerland) · 2023Article
- Gallic Acid Alkyl Esters: Trypanocidal and Leishmanicidal Activity, and Target Identification via Modeling Studies.Molecules (Basel, Switzerland) · 2022Article
- TAIGET: A small-molecule target identification and annotation web server.Frontiers in pharmacology · 2022Article
- Drug repositioning: A bibliometric analysis.Frontiers in pharmacology · 2022Review
- Recent Advances in In Silico Target Fishing.Molecules (Basel, Switzerland) · 2021Review
- Probabilistic divergence of a template-based modelling methodology from the ideal protocol.Journal of molecular modeling · 2021Article
- Discovery of Novel µ-Opioid Receptor Inverse Agonist from a Combinatorial Library of Tetrapeptides through Structure-Based Virtual Screening.Molecules (Basel, Switzerland) · 2019Article
- Molecular Docking: Shifting Paradigms in Drug Discovery.International journal of molecular sciences · 2019Review
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Authors and funding
6 authors.
Funding
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Abstract
The development of target-fishing approaches, aimed at identifying the possible protein targets of a small molecule, represents a hot topic in medicinal chemistry. A successful target-fishing approach would allow for the elucidation of the mechanism of action of all therapeutically interesting compounds for which the actual target is still unknown. Moreover, target-fishing would be essential for preventing adverse effects of drug candidates, by predicting their potential off-targets, and it would speed up drug repurposing campaigns. However, due to the huge number of possible protein targets that a small-molecule might interact with, experimental target-fishing approaches are out of reach. In silico target-fishing represents a valuable alternative, and examples of receptor-based approaches, exploiting the large number of crystallographic protein structures determined to date, have been reported in the literature. To the best of our knowledge, no proper evaluation of such approaches is, however, reported yet. In the present work, we extensively assessed the reliability of docking-based target-fishing strategies. For this purpose, a set of X-ray structures belonging to different targets was selected, and a dataset of compounds, including 10 experimentally active ligands for each target, was created. A target-fishing benchmark database was then obtained, and used to assess the performance of 13 different docking procedures, in identifying the correct target of the dataset ligands. Moreover, a consensus docking-based target-fishing strategy was developed and evaluated. The analysis highlighted that specific features of the target proteins could affect the reliability of the protocol, which however, proved to represent a valuable tool in the proper applicability domain. Our study represents the first extensive performance assessment of docking-based target-fishing approaches, paving the way for the development of novel efficient receptor-based target fishing strategies.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.