Summary of Study ST004017
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002514. The data can be accessed directly via it's Project DOI: 10.21228/M8PG32 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST004017 |
| Study Title | Collateral hypersensitivity between ZY19489 and piperaquine neutralizes PfCRT-mediated drug efflux and Plasmodium falciparum resistance |
| Study Summary | Here we interrogated the in vitro metabolic effects of AZ412/ZY19489 using ultra-high performance liquid chromatography mass-spectrometry (UHPLC-MS). The resulting metabolic fingerprints provide information on the parasite biochemical pathways affected by pharmacologic intervention. We interrogate the metabolic effects on the 3D7 and DD2 parasite strain. The metabolic fingerprints provided show that certain biochemical pathways are affected by the drug inhibitory effect. |
| Institute | Pennsylvania State University |
| Last Name | Llinas |
| First Name | Manuel |
| Address | W126 Millenium Science Complex, University Park, PA 16802 |
| manuel@psu.edu | |
| Phone | 814-867-3527 |
| Submit Date | 2025-06-13 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-12-15 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002514 |
| Project DOI: | doi: 10.21228/M8PG32 |
| Project Title: | Collateral hypersensitivity between ZY19489 and piperaquine neutralizes PfCRT-mediated drug efflux and Plasmodium falciparum resistance |
| Project Summary: | This metabolomics dataset supports research into new antimalarials by examining resistance to ZY19489. A N246H mutation in the P. falciparum chloroquine resistance transporter (PfCRT) confers low-grade ZY19489 resistance, reduces parasite fitness, and maintains sensitivity to piperaquine and other 4-aminoquinolines. Metabolomic analyses show that ZY19489 treatment lowers hemoglobin-derived peptide levels and increases pyrimidine intermediates, suggesting effects on hemoglobin degradation and pyrimidine biosynthesis. These findings highlight a resistance marker and support the use of ZY19489-PPQ combination therapy to limit resistance emergence. |
| Institute: | Pennsylvania State University |
| Last Name: | Llinas |
| First Name: | Manuel |
| Address: | W126 Millenium Science Complex, University Park, PA 16802 |
| Email: | manuel@psu.edu |
| Phone: | 814-867-3527 |
Subject:
| Subject ID: | SU004155 |
| Subject Type: | Cultured cells |
| Subject Species: | Plasmodium falciparum |
| Taxonomy ID: | 5833 |
| Genotype Strain: | 3D7, DD2 |
Factors:
Subject type: Cultured cells; Subject species: Plasmodium falciparum (Factor headings shown in green)
| mb_sample_id | local_sample_id | Factor1 | Factor2 | Sample source |
|---|---|---|---|---|
| SA462012 | 3D7_ATQ1 | 10X IC50 | 2.5 hours | MACS purified 3D7 Troph |
| SA462013 | 3D7_ATQ2 | 10X IC50 | 2.5 hours | MACS purified 3D7 Troph |
| SA462014 | 3D7_ATQ3 | 10X IC50 | 2.5 hours | MACS purified 3D7 Troph |
| SA462015 | 3D7_ZY19489_1 | 10X IC50 | 2.5 hours | MACS purified 3D7 Troph |
| SA462016 | 3D7_ZY19489_2 | 10X IC50 | 2.5 hours | MACS purified 3D7 Troph |
| SA462017 | 3D7_ZY19489_3 | 10X IC50 | 2.5 hours | MACS purified 3D7 Troph |
| SA462018 | Dd2_ZY19489_3 | 10X IC50 | 2.5 hours | MACS purified DD2 Troph |
| SA462019 | Dd2_ZY19489_2 | 10X IC50 | 2.5 hours | MACS purified DD2 Troph |
| SA462020 | Dd2_ZY19489_1 | 10X IC50 | 2.5 hours | MACS purified DD2 Troph |
| SA462021 | Dd2_ATQ3 | 10X IC50 | 2.5 hours | MACS purified DD2 Troph |
| SA462022 | Dd2_ATQ2 | 10X IC50 | 2.5 hours | MACS purified DD2 Troph |
| SA462023 | Dd2_ATQ1 | 10X IC50 | 2.5 hours | MACS purified DD2 Troph |
| SA462024 | Sample name | Concentration | Treatment time | Parasite Strain |
| SA462025 | 3D7_ND3 | N/A | N/A | MACS purified 3D7 Troph |
| SA462026 | 3D7_Blank2 | N/A | N/A | MACS purified 3D7 Troph |
| SA462027 | 3D7_ND1 | N/A | N/A | MACS purified 3D7 Troph |
| SA462028 | 3D7_ND2 | N/A | N/A | MACS purified 3D7 Troph |
| SA462029 | 3D7_Blank1 | N/A | N/A | MACS purified 3D7 Troph |
| SA462030 | 3D7_Pool1 | N/A | N/A | MACS purified 3D7 Troph |
| SA462031 | 3D7_Pool2 | N/A | N/A | MACS purified 3D7 Troph |
| SA462032 | 3D7_Pool3 | N/A | N/A | MACS purified 3D7 Troph |
| SA462033 | 3D7_Blank3 | N/A | N/A | MACS purified 3D7 Troph |
| SA462034 | Dd2_ND2 | N/A | N/A | MACS purified DD2 Troph |
| SA462035 | Dd2_ND3 | N/A | N/A | MACS purified DD2 Troph |
| SA462036 | Dd2_Pool1 | N/A | N/A | MACS purified DD2 Troph |
| SA462037 | Dd2_Pool2 | N/A | N/A | MACS purified DD2 Troph |
| SA462038 | Dd2_Pool3 | N/A | N/A | MACS purified DD2 Troph |
| SA462039 | Dd2_Blank1 | N/A | N/A | MACS purified DD2 Troph |
| SA462040 | Dd2_Blank2 | N/A | N/A | MACS purified DD2 Troph |
| SA462041 | Dd2_Blank3 | N/A | N/A | MACS purified DD2 Troph |
| SA462042 | Dd2_ND1 | N/A | N/A | MACS purified DD2 Troph |
| Showing results 1 to 31 of 31 |
Collection:
| Collection ID: | CO004148 |
| Collection Summary: | Cells were isolated by magnetic separation using MACS column. Then cell concentration was determined by hemocytometer and cells were either diluted or concentrated to 1x10^8 cells/ul and put in wells with media before treatment. |
| Sample Type: | Pf infected RBCs |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR004164 |
| Treatment Summary: | Purified Plasmodium falciparum infected red blood cells (iRBCs) were treated with 10xIC50 drug for 2.5 hours. Atovaquone (ATQ) was used as positive control for treatment effect. Compared all treatments to a no drug (ND) negative control for log fold changes. |
| Treatment Compound: | ZY19489 |
Sample Preparation:
| Sampleprep ID: | SP004161 |
| Sampleprep Summary: | A 1xPBS (Phosphate buffered saline) wash was performed to get a cell pellet before 90% Methanol/10% water with aspartate standard was added to the pellet for vortexing and clarification via centrifugation. |
| Processing Method: | Lysis |
| Processing Storage Conditions: | 4℃ |
| Extraction Method: | See: Cobbold SA, Vaughan AM, Lewis IA, Painter HJ, Camargo N, Perlman DH, Fishbaugher M, Healer J, Cowman AF, Kappe SH, Llinás M. Kinetic flux profiling elucidates two independent acetyl-CoA biosynthetic pathways in Plasmodium falciparum. J Biol Chem. 2013 Dec 20;288(51):36338-50. doi: 10.1074/jbc.M113.503557. Epub 2013 Oct 25. PMID: 24163372; PMCID: PMC3868748. |
| Extract Cleanup: | Clarification via centrifugation followed by nitrogen drying |
| Extract Storage: | -80℃ |
| Sample Spiking: | Internal Standard 13C4,15N1-Aspartate used for sample preparation normalizer |
Combined analysis:
| Analysis ID | AN006622 | AN006623 |
|---|---|---|
| Chromatography ID | CH005032 | CH005032 |
| MS ID | MS006321 | MS006322 |
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 |
| Column | Waters XSelect HSS T3 C18 (100 x 2.1 mm, 2.5um) | Waters XSelect HSS T3 C18 (100 x 2.1 mm, 2.5um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Plus Orbitrap |
| Ion Mode | NEGATIVE | NEGATIVE |
| Units | peak area | peak area |
Chromatography:
| Chromatography ID: | CH005032 |
| Chromatography Summary: | Lu W, Clasquin MF, Melamud E, Amador-Noguez D, Caudy AA, Rabinowitz JD. Metabolomic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone orbitrap mass spectrometer. Anal Chem. 2010 Apr 15;82(8):3212-21. doi: 10.1021/ac902837x. PMID: 20349993; PMCID: PMC2863137. Column along with flow gradient adapted for our methods. |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters XSelect HSS T3 C18 (100 x 2.1 mm, 2.5um) |
| Column Temperature: | 30 |
| Flow Gradient: | 0 min, 0% B; 2.5 min, 0% B; 5 min, 20% B;7.5 min, 20% B; 13 min, 55% B; 15.5 min, 95% B; 18.5 min, 95% B; 19 min, 0% B; 25 min, 0% B |
| Flow Rate: | 0.200 mL/minute |
| Solvent A: | 97% Water/3% Methanol; 15 mM Acetic Acid; 10 mM Tributylamine; 2.5 uM Medronic Acid |
| Solvent B: | 100% Methanol |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS006321 |
| Analysis ID: | AN006622 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The software used to process and do manual peak picking of the converted .mzXML files was El-Maven. Manual peak picking was done by choosing peaks that overlapped with standards run on the same instrument to achieve suitable accuracy. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS006322 |
| Analysis ID: | AN006623 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The software used to process and do manual peak picking of the converted .mzXML files was El-Maven. Manual peak picking was done by choosing peaks that overlapped with standards run on the same instrument to achieve suitable accuracy. |
| Ion Mode: | NEGATIVE |
