Evidence map›Paper›PMID 25684450›Full record

ArticleAnalytical biochemistry2015

A [(32)P]NAD(+)-based method to identify and quantitate long residence time enoyl-acyl carrier protein reductase inhibitors.

Weixuan Yu, Carla Neckles, Andrew Chang, Gopal Reddy Bommineni, Lauren Spagnuolo, Zhuo Zhang, Nina Liu, Christina Lai, James Truglio, Peter J Tonge

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Analytical biochemistry, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing 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

6 citing papers in PubMed.

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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

10 authors.

Weixuan YuInstitute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11790, USA.
Carla NecklesInstitute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11790, USA.
Andrew ChangInstitute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11790, USA.
Gopal Reddy BommineniInstitute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11790, USA.
Lauren SpagnuoloInstitute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11790, USA.
Zhuo ZhangInstitute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11790, USA.
Nina LiuInstitute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11790, USA.
Christina LaiGreat Neck South High School, Great Neck, NY 11020, USA.
James TruglioGreat Neck South High School, Great Neck, NY 11020, USA.
Peter J TongeInstitute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11790, USA. Electronic address: peter.tonge@stonybrook.edu.

Funding

Mechanism of Slow Onset Enzyme Inhibition and Translation to Time-Dependent Drug ActivityR01GM102864 · NIGMS · STATE UNIVERSITY NEW YORK STONY BROOK · PI TONGE, PETER J · 2012 to 2021
$2.6M
SBU Chemistry-Biology Interface Training ProgramT32GM092714 · NIGMS · STATE UNIVERSITY NEW YORK STONY BROOK · PI SAMPSON, NICOLE S, TONGE, PETER J · 2010 to 2019
$1.7M
NIGMS NIH HHS GM102864NIGMS NIH HHS R01 GM102864NIGMS NIH HHS T32 GM092714
6 · The paper itself

Abstract

The classical methods for quantifying drug-target residence time (tR) use loss or regain of enzyme activity in progress curve kinetic assays. However, such methods become imprecise at very long residence times, mitigating the use of alternative strategies. Using the NAD(P)H-dependent FabI enoyl-acyl carrier protein (enoyl-ACP) reductase as a model system, we developed a Penefsky column-based method for direct measurement of tR, where the off-rate of the drug was determined with radiolabeled [adenylate-(32)P]NAD(P(+)) cofactor. In total, 23 FabI inhibitors were analyzed, and a mathematical model was used to estimate limits to the tR values of each inhibitor based on percentage drug-target complex recovery following gel filtration. In general, this method showed good agreement with the classical steady-state kinetic methods for compounds with tR values of 10 to 100 min. In addition, we were able to identify seven long tR inhibitors (100-1500 min) and to accurately determine their tR values. The method was then used to measure tR as a function of temperature, an analysis not previously possible using the standard kinetic approach due to decreased NAD(P)H stability at elevated temperatures. In general, a 4-fold difference in tR was observed when the temperature was increased from 25 to 37 °C.

Indexed as

Acyl Carrier ProteinBiochemistryComputer SimulationEnoyl-(Acyl-Carrier-Protein) Reductase (NADH)Enzyme InhibitorsFeasibility StudiesHigh-Throughput Screening AssaysKineticsNADPhosphorus RadioisotopesReproducibility of ResultsTemperatureTime FactorsAcyl Carrier ProteinEnoyl-(Acyl-Carrier-Protein) Reductase (NADH)Enzyme InhibitorsNADPhosphorus RadioisotopesEnoyl ACP reductaseHigh-throughput screeningMethodologyPenefsky columnResidence time (t(R))Steady-state kinetics

Identifiers

PMID25684450
PMCPMC4454744

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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.