Evidence map›Paper›PMID 38727192›Full record

ArticleJournal of chemical information and modeling2024

Machine Learning Models Identify Inhibitors of New Delhi Metallo-β-lactamase.

Zishuo Cheng, Mahesh Aitha, Caitlyn A Thomas, Aidan Sturgill, Mitch Fairweather, Amy Hu, Christopher R Bethel, Dann D Rivera, Patricia Dranchak, Pei W Thomas and 14 more

Abstract read
In one paragraph

Article in Journal of chemical information and modeling, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
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

4 citing papers in PubMed.

  1. Review
  2. Review
  3. Review
  4. Review
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

24 authors.

Zishuo ChengDepartment of Chemistry and Biochemistry, Miami University, Oxford ,Ohio 45056, United States.
Mahesh AithaDivision of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville ,Maryland 20850, United States.
Caitlyn A ThomasDepartment of Chemistry and Biochemistry, Miami University, Oxford ,Ohio 45056, United States.
Aidan SturgillDepartment of Chemistry and Biochemistry, Miami University, Oxford ,Ohio 45056, United States.
Mitch FairweatherDepartment of Chemistry and Biochemistry, Miami University, Oxford ,Ohio 45056, United States.
Amy HuDepartment of Chemistry and Biochemistry, Miami University, Oxford ,Ohio 45056, United States.
Christopher R BethelResearch Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland ,Ohio 44106, United States.
Dann D RiveraDivision of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin ,Texas 78712, United States.
Patricia DranchakDivision of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville ,Maryland 20850, United States.
Pei W ThomasDivision of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin ,Texas 78712, United States.
Han LiDepartment of Chemistry and Biochemistry, Miami University, Oxford ,Ohio 45056, United States.
Qi FengDepartment of Chemistry and Biochemistry, Miami University, Oxford ,Ohio 45056, United States.
Kaicheng TaoDepartment of Chemistry and Biochemistry, Miami University, Oxford ,Ohio 45056, United States.
Minshuai SongDepartment of Chemistry and Biochemistry, Miami University, Oxford ,Ohio 45056, United States.
Na SunDepartment of Chemistry and Biochemistry, Miami University, Oxford ,Ohio 45056, United States.
Shuo WangDepartment of Chemistry and Biochemistry, Miami University, Oxford ,Ohio 45056, United States.
Surendra Bikram SilwalDepartment of Chemistry and Biochemistry, Miami University, Oxford ,Ohio 45056, United States.ORCID 0009-0002-8540-8349
Richard C PageDepartment of Chemistry and Biochemistry, Miami University, Oxford ,Ohio 45056, United States.ORCID 0000-0002-3006-3171
Walt FastDivision of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin ,Texas 78712, United States.ORCID 0000-0001-7567-2213
Robert A BonomoResearch Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland ,Ohio 44106, United States.ORCID 0000-0002-3299-894X
Maria WeeseDepartment of Chemistry and Biochemistry, Miami University, Oxford ,Ohio 45056, United States.
Waldyn MartinezDepartment of Chemistry and Biochemistry, Miami University, Oxford ,Ohio 45056, United States.
James IngleseDivision of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville ,Maryland 20850, United States.ORCID 0000-0002-7332-5717
Michael W CrowderDepartment of Chemistry and Biochemistry, Miami University, Oxford ,Ohio 45056, United States.ORCID 0000-0002-3138-0283

Funding

Target-based Assays and Screening Strategies for Chemical Probe and Therapeutic Lead DiscoveryZIATR000053 · NCATS · NATIONAL CENTER FOR ADVANCING TRANSLATIONAL SCIENCES · PI INGLESE, JAMES · 2015 to 2025
$4.5M
Triage mechanisms for directing protein refolding and degradationR35GM128595 · NIGMS · MIAMI UNIVERSITY OXFORD · PI Richard C Page · 2018 to 2026
$2.8M
Institutional Clinical and Translational Science AwardKL2TR000053 · NCATS · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI CRONSTEIN, BRUCE NEIL · 2012 to 2014
$899k
Machine Learning Approach for finding novel metallo-b-lactamase inhibitorsR15GM134454 · NIGMS · MIAMI UNIVERSITY OXFORD · PI CROWDER, MICHAEL W · 2019 to 2022
$867k
The Continuing Challenge of Carbapenemases in K. pneumoniae: KPC-2 & NDM-1I01BX001974 · VA · LOUIS STOKES CLEVELAND VA MEDICAL CENTER · PI BONOMO, ROBERT A. · 2013 to 2024
–
BLRD VA I01 BX001974Intramural NIH HHS ZIA TR000053NCATS NIH HHS KL2 TR000053NIGMS NIH HHS R15 GM134454NIGMS NIH HHS R35 GM128595
6 · The paper itself

Abstract

The worldwide spread of the metallo-β-lactamases (MBL), especially New Delhi metallo-β-lactamase-1 (NDM-1), is threatening the efficacy of β-lactams, which are the most potent and prescribed class of antibiotics in the clinic. Currently, FDA-approved MBL inhibitors are lacking in the clinic even though many strategies have been used in inhibitor development, including quantitative high-throughput screening (qHTS), fragment-based drug discovery (FBDD), and molecular docking. Herein, a machine learning-based prediction tool is described, which was generated using results from HTS of a large chemical library and previously published inhibition data. The prediction tool was then used for virtual screening of the NIH Genesis library, which was subsequently screened using qHTS. A novel MBL inhibitor was identified and shown to lower minimum inhibitory concentrations (MICs) of Meropenem for a panel of

Indexed as

beta-Lactamase Inhibitorsbeta-LactamasesMachine LearningMicrobial Sensitivity TestsMolecular Docking SimulationEscherichia coliHigh-Throughput Screening AssaysKlebsiella pneumoniaebeta-Lactamase Inhibitorsbeta-lactamase NDM-1beta-Lactamases

Identifiers

PMID38727192
PMCPMC11129921

What OpenQuestion holds

Textmetadata
LicenceTDM
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.