Evidence map›Paper›PMID 36142566›Full record

ArticleInternational journal of molecular sciences2022

Machine Learning-Based Virtual Screening for the Identification of Cdk5 Inhibitors.

Miriana Di Stefano, Salvatore Galati, Gabriella Ortore, Isabella Caligiuri, Flavio Rizzolio, Costanza Ceni, Simone Bertini, Giulia Bononi, Carlotta Granchi, Marco Macchia and 2 more

Open access · goldAbstract read
In one paragraph

Article in International journal of molecular sciences, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.

0numbers the graph read from it
0cells of the map it votes in
20citing papers in PubMed
4.4field-weighted citation impact, top 5% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

20 citing papers in PubMed, 31 citations in OpenAlex.

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  14. VenomPred 2.0: A NovelJournal of chemical information and modeling · 2024
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors at 4 institutions in 1 country.

Miriana Di StefanoDepartment of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy.ORCID 0000-0001-6727-5816
Salvatore GalatiDepartment of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy.ORCID 0000-0002-1959-5839
Gabriella OrtoreDepartment of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy.
Isabella CaligiuriPathology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy.
Flavio RizzolioPathology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy.ORCID 0000-0002-3400-4363
Costanza CeniDepartment of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy.
Simone BertiniDepartment of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy.ORCID 0000-0001-8832-8075
Giulia BononiDepartment of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy.
Carlotta GranchiDepartment of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy.ORCID 0000-0002-5849-0722
Marco MacchiaDepartment of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy.
Giulio PoliDepartment of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy.
Tiziano TuccinardiDepartment of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy.ORCID 0000-0002-6205-4069
University of Pisa · ITUniversity of Siena · ITCa' Foscari University of Venice · ITCentro di Riferimento Oncologico · IT

Funding

Tuscany Region Bando Ricerca Salute 2018, DEM-AGING
6 · The paper itself

Abstract

Cyclin-dependent kinase 5 (Cdk5) is an atypical proline-directed serine/threonine protein kinase well-characterized for its role in the central nervous system rather than in the cell cycle. Indeed, its dysregulation has been strongly implicated in the progression of synaptic dysfunction and neurodegenerative diseases, such as Alzheimer's disease (AD) and Parkinson's disease (PD), and also in the development and progression of a variety of cancers. For this reason, Cdk5 is considered as a promising target for drug design, and the discovery of novel small-molecule Cdk5 inhibitors is of great interest in the medicinal chemistry field. In this context, we employed a machine learning-based virtual screening protocol with subsequent molecular docking, molecular dynamics simulations and binding free energy evaluations. Our virtual screening studies resulted in the identification of two novel Cdk5 inhibitors, highlighting an experimental hit rate of 50% and thus validating the reliability of the in silico workflow. Both identified ligands, compounds

Indexed as

Cyclin-Dependent Kinase 5Cyclin-Dependent Kinase Inhibitor ProteinsLigandsMachine LearningMolecular Docking SimulationProlineReproducibility of ResultsSerineThreonineCyclin-Dependent Kinase 5Cyclin-Dependent Kinase Inhibitor ProteinsLigandsProlineSerineThreonineCDK5kinasemachine learningvirtual screening

Identifiers

PMID36142566
PMCPMC9502400
OpenAlexW4296002892

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

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.