Summary of Study ST004424
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 PR002795. The data can be accessed directly via it's Project DOI: 10.21228/M8CK2X This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST004424 |
| Study Title | Stereochemistry-Driven Design and Synthesis of Tadalafil Analogues as Antiplasmodial Agents |
| Study Summary | Analogues of tadalafil, an FDA-approved inhibitor of human phosphodiesterase 5 have been reported to block Plasmodium falciparum growth in vitro. In this study, we synthesized 56 new tadalafil analogues with specific stereochemistry; some of the novel analogues showed potent antiplasmodial activity at nanomolar concentrations and high selectivity in vitro. Compound 33 demonstrated the highest potency, with an IC50 of 80 nM against cultured parasites and an IC50 > 20 µM on human HeLa cells, resulting in a selectivity index >250. Most active compounds showed stereospecific activity favoring the cis isomer with a 6R, 12aR configuration. We demonstrate that conformational and spatial orientation play a more critical role than lipophilicity in determining the activity of these compounds. Metabolomic profiling revealed that several tadalafil analogues strongly affect hemoglobin catabolism; yet principal component analysis (PCA) grouped them separately, suggesting subtle differences in their antiplasmodial mechanisms. Further work will be needed to elucidate their precise mode of action, and future structural optimization will be necessary towards development of tadalafil analogues as antimalarial treatments. |
| Institute | Pennsylvania State University |
| Last Name | Rangel |
| First Name | Gabriel |
| Address | 491 Pollock Road, University Park, PA, 16802, USA |
| grangel0955@gmail.com | |
| Phone | 8148673527 |
| Submit Date | 2025-12-01 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-12-29 |
| Release Version | 1 |
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Project:
| Project ID: | PR002795 |
| Project DOI: | doi: 10.21228/M8CK2X |
| Project Title: | Stereochemistry-Driven Design and Synthesis of Tadalafil Analogues as Antiplasmodial Agents |
| Project Summary: | Analogues of tadalafil, an FDA-approved inhibitor of human phosphodiesterase 5 have been reported to block Plasmodium falciparum growth in vitro. In this study, we synthesized 56 new tadalafil analogues with specific stereochemistry; some of the novel analogues showed potent antiplasmodial activity at nanomolar concentrations and high selectivity in vitro. Compound 33 demonstrated the highest potency, with an IC50 of 80 nM against cultured parasites and an IC50 > 20 µM on human HeLa cells, resulting in a selectivity index >250. Most active compounds showed stereospecific activity favoring the cis isomer with a 6R, 12aR configuration. We demonstrate that conformational and spatial orientation play a more critical role than lipophilicity in determining the activity of these compounds. Metabolomic profiling revealed that several tadalafil analogues strongly affect hemoglobin catabolism; yet principal component analysis (PCA) grouped them separately, suggesting subtle differences in their antiplasmodial mechanisms. Further work will be needed to elucidate their precise mode of action, and future structural optimization will be necessary towards development of tadalafil analogues as antimalarial treatments. |
| Institute: | Pennsylvania State University |
| Department: | Biochemistry and Molecular Biology |
| Laboratory: | Manuel Llinás |
| Last Name: | Rangel |
| First Name: | Gabriel |
| Address: | 491 Pollock Road, University Park, PA, 16802, USA |
| Email: | grangel0955@gmail.com |
| Phone: | 8148673527 |
Subject:
| Subject ID: | SU004584 |
| Subject Type: | Cultured cells |
| Subject Species: | Plasmodium falciparum |
| Taxonomy ID: | 5833 |
| Genotype Strain: | 3D7 MR4 |
Factors:
Subject type: Cultured cells; Subject species: Plasmodium falciparum (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Treatment |
|---|---|---|---|
| SA522635 | ATQ-2 | Cultured Plasmodium falciparum 3D7 MR4 | 10nM Atovaquone |
| SA522636 | ATQ-1 | Cultured Plasmodium falciparum 3D7 MR4 | 10nM Atovaquone |
| SA522637 | ATQ-3 | Cultured Plasmodium falciparum 3D7 MR4 | 10nM Atovaquone |
| SA522638 | Cpd16-1 | Cultured Plasmodium falciparum 3D7 MR4 | Compound 16 |
| SA522639 | Cpd16-2 | Cultured Plasmodium falciparum 3D7 MR4 | Compound 16 |
| SA522640 | Cpd16-3 | Cultured Plasmodium falciparum 3D7 MR4 | Compound 16 |
| SA522641 | Cpd19-3 | Cultured Plasmodium falciparum 3D7 MR4 | Compound 19 |
| SA522642 | Cpd19-1 | Cultured Plasmodium falciparum 3D7 MR4 | Compound 19 |
| SA522643 | Cpd19-2 | Cultured Plasmodium falciparum 3D7 MR4 | Compound 19 |
| SA522644 | Cpd33-2 | Cultured Plasmodium falciparum 3D7 MR4 | Compound 33 |
| SA522645 | Cpd33-3 | Cultured Plasmodium falciparum 3D7 MR4 | Compound 33 |
| SA522646 | Cpd33-1 | Cultured Plasmodium falciparum 3D7 MR4 | Compound 33 |
| SA522647 | Cpd35-1 | Cultured Plasmodium falciparum 3D7 MR4 | Compound 35 |
| SA522648 | Cpd35-2 | Cultured Plasmodium falciparum 3D7 MR4 | Compound 35 |
| SA522649 | Cpd35-3 | Cultured Plasmodium falciparum 3D7 MR4 | Compound 35 |
| SA522650 | Cpd4-3 | Cultured Plasmodium falciparum 3D7 MR4 | Compound 4 |
| SA522651 | Cpd4-2 | Cultured Plasmodium falciparum 3D7 MR4 | Compound 4 |
| SA522652 | Cpd4-1 | Cultured Plasmodium falciparum 3D7 MR4 | Compound 4 |
| SA522653 | DMSO-1 | Cultured Plasmodium falciparum 3D7 MR4 | DMSO |
| SA522654 | DMSO-2 | Cultured Plasmodium falciparum 3D7 MR4 | DMSO |
| SA522655 | DMSO-3 | Cultured Plasmodium falciparum 3D7 MR4 | DMSO |
| SA522656 | QC-1 | Cultured Plasmodium falciparum 3D7 MR4 | Pooled Quality Control |
| SA522657 | QC-2 | Cultured Plasmodium falciparum 3D7 MR4 | Pooled Quality Control |
| SA522658 | QC-3 | Cultured Plasmodium falciparum 3D7 MR4 | Pooled Quality Control |
| SA522659 | QC-4 | Cultured Plasmodium falciparum 3D7 MR4 | Pooled Quality Control |
| Showing results 1 to 25 of 25 |
Collection:
| Collection ID: | CO004577 |
| Collection Summary: | Each sample represents metabolites extracted from 1E8 Plasmodium falciparum infected human red blood cells (iRBCs). After treatment, the iRBCs were washed with cold PBS and metabolites were extracted using a 90% methanol solution. This solution was evaporated under nitrogen gas flow, resuspended in water plus chlorpropamide as an internal control, and run on the ThermoFisher Exactive Plus. |
| Sample Type: | Plasmodium cells |
Treatment:
| Treatment ID: | TR004593 |
| Treatment Summary: | Heparin synchronized (6-hour window) P. falciparum 3D7 parasites were grown to approximately 24 hours post-invasion, and infected red blood cells (iRBCs) were purified using magnet activated cell sorting (MACS). Purified iRBCs were then counted and plated at ~1X10^6 cells per technical replicate and allowed to recover in standard incubation conditions for 1.5 hours. After recovery, drug treatment was added at 10 X IC50 and incubated for 2.5 hours before washing and extraction of metabolites. |
Sample Preparation:
| Sampleprep ID: | SP004590 |
| Sampleprep Summary: | Parasites were pelleted (500 g, 4°C, 1 min) and washed in 1 mL ice cold PBS. Then metabolites were extracted from the pellet with 1 ml ice cold 90% methanol, vortexed 30 seconds, and centrifuged for 10 min at maximum speed (16000 x g) at 4°C. Samples were treated identically and swiftly to ensure reproducible results. The methanol supernatants were stored at -70°C until further processing could be done, when they were transferred to fresh 1.5 mL tubes, dried down completely under nitrogen gas flow, and the metabolite residues stored at -70°C. |
| Processing Storage Conditions: | On ice |
| Extraction Method: | 90% methanol |
| Extract Storage: | -80℃ |
Combined analysis:
| Analysis ID | AN007401 |
|---|---|
| Chromatography ID | CH005607 |
| MS ID | MS007093 |
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Thermo Dionex Ultimate 3000 |
| Column | Waters XSelect HSS T3 Column XP (100 x 2.1 mm, 2.5 µm) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Exactive Plus Orbitrap |
| Ion Mode | NEGATIVE |
| Units | blank-subtracted peak area |
Chromatography:
| Chromatography ID: | CH005607 |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters XSelect HSS T3 Column XP (100 x 2.1 mm, 2.5 µm) |
| Column Temperature: | 30°C |
| Flow Gradient: | 0-5.0 min: 100% A, 0% B; 5.0-13.0 min: 80% A, 20% B; 13.0-15.0 min: 45% A, 55% B; 15.0-17.5 min: 35% A, 65% B; 17.5-21.0 min: 5% A, 95% B; 21.0-25 min: 100% A, 0% B |
| Flow Rate: | 0.200 mL/min |
| Internal Standard: | chlorpropamide 1 µM |
| Solvent A: | 97% water/3% methanol; 15 mM acetic acid; 10 mM tributylamine; 2.5 µM medronic acid |
| Solvent B: | 100% Methanol |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS007093 |
| Analysis ID: | AN007401 |
| Instrument Name: | Thermo Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | .raw files were converted to .mzML files using MSConvert software of the ProteoWizard software package. The .mzML files were processed using EL MAVEN software for peak picking, alignment, and annotation. |
| Ion Mode: | NEGATIVE |
| Mass Accuracy: | 10 ppm |
| Resolution Setting: | 140,000 at m/z 200 |
| Scanning Range: | 85-1000 m/z |
