Evidence map›Paper›PMID 27564465›Full record

ArticleBiochemistry2016

Dynamic Structure and Inhibition of a Malaria Drug Target: Geranylgeranyl Diphosphate Synthase.

Clarisse G Ricci, Yi-Liang Liu, Yonghui Zhang, Yang Wang, Wei Zhu, Eric Oldfield, J Andrew McCammon

Open access · greenAbstract read
In one paragraph

Article in Biochemistry, 2016. 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
1.0field-weighted citation impact, top 21% 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

4 citing papers in PubMed, 9 citations in OpenAlex.

  1. MalDA, Accelerating Malaria Drug Discovery.Trends in parasitology · 2021
    Review
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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

7 authors at 2 institutions in 1 country.

Clarisse G RicciDepartment of Pharmacology and Department of Chemistry & Biochemistry, University of California at San Diego , La Jolla, California 92093, United States.
Yi-Liang LiuDepartment of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States.
Yonghui ZhangDepartment of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States.
Yang WangDepartment of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States.
Wei ZhuDepartment of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States.
Eric OldfieldDepartment of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States.
J Andrew McCammonDepartment of Pharmacology and Department of Chemistry & Biochemistry, University of California at San Diego , La Jolla, California 92093, United States.
University of Illinois Urbana-Champaign · USUniversity of California, San Diego · US

Funding

National Biomedical Computation Resource - Competitive Revision SupplementP41GM103426 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI AMARO, ROMMIE E · 2012 to 2019
$14.0M
THEORY OF BIOMOLECULAR DIFFUSIONR01GM031749 · NIGMS · UNIVERSITY OF HOUSTON · PI HUBER, GARY ALEXANDER, MCCAMMON, JAMES ANDREW · 1985 to 2022
$7.8M
Structure, Function and Inhibition of [4Fe-4S] ProteinsR01GM065307 · NIGMS · UNIVERSITY OF ILLINOIS URBANA-CHAMPAIGN · PI OLDFIELD, ERIC · 2002 to 2017
$5.4M
Next generation bisphosphonates for chemo- and immuno-therapyR01CA158191 · NCI · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · PI OLDFIELD, ERIC · 2011 to 2015
$1.6M
Howard Hughes Medical InstituteNCI NIH HHS R01 CA158191NIGMS NIH HHS P41 GM103426NIGMS NIH HHS R01 GM031749NIGMS NIH HHS R01 GM065307
6 · The paper itself

Abstract

We report a molecular dynamics investigation of the structure, function, and inhibition of geranylgeranyl diphosphate synthase (GGPPS), a potential drug target, from the malaria parasite Plasmodium vivax. We discovered several GGPPS inhibitors, benzoic acids, and determined their structures crystallographically. We then used molecular dynamics simulations to investigate the dynamics of three such inhibitors and two bisphosphonate inhibitors, zoledronate and a lipophilic analogue of zoledronate, as well as the enzyme's product, GGPP. We were able to identify the main motions that govern substrate binding and product release as well as the molecular features required for GGPPS inhibition by both classes of inhibitor. The results are of broad general interest because they represent the first detailed investigation of the mechanism of action, and inhibition, of an important antimalarial drug target, geranylgeranyl diphosphate synthase, and may help guide the development of other, novel inhibitors as new drug leads.

Indexed as

AntimalarialsBinding SitesCrystallography, X-RayEnzyme InhibitorsFarnesyltranstransferaseMolecular Dynamics SimulationPlasmodium vivaxPrincipal Component AnalysisThermodynamicsAntimalarialsEnzyme InhibitorsFarnesyltranstransferase

Identifiers

PMID27564465
PMCPMC5319852
OpenAlexW2510963512

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.