H3D has a dedicated parasitology team to perform blood stage screening for malaria with access to other lifecycle stages through our partnerships. The malaria biology team have developed various enzymatic assays as well as an in vivo mouse model.

See the table below for additional details, including average turnaround time and control(s). For assays where an average turnaround time/control(s) are not available, this indicates that turnaround time is dependent on your unique experimental design and conditions; please book a consultation for an estimated turnaround time or additional information.

Malaria Biology Team, H3D Parasitology Labs at the IDM, UCT (Dec, 2021)

H3D's expertise and experience is especially pronounced in the following Malaria Biology areas:

Phenotypic Screening

The NF54 and K1 strains are two of the most commonly used F. plasmodium strains in labs worldwide and is used by H3D for many Malaria biology assays. Screening in both drug sensitive and resistant strains is available.

  • Plasmodium Single point or dose-response IC50 assays in 96-well plates
    • NF54: Wild-type drug-sensitive strain of P. falciparum
    • K1: Multidrug-resistant strain of P. falciparum
    • 3d7: Chloroquine-sensitive strain of P. falciparum
    • Dd2: Chloroquine-resistant strain of P. falciparum
  • Mutant Resistant Strains (specialized mutants produced in-house)
    • KAF156-Dd2: Lab-generated mutant to in-development antimalarial KAF-156/Ganaplacide used in mechanism of action studies
    • PKG-3d7: Lab-generated mutant containing altered PKG enzyme used for cGMP kinase target studies
    • 048-Dd2: Lab-generated mutant to in-development antimalarial MMV048 used in mechanism of action studies to identify PI4 kinase inhibitors
  • Stage Specificity

The entire malarial life cycle contains 14 stages between the human and mosquito hosts; stage-specific assessment of candidate drug inhibitory effects is necessary to clarify which symptomatic stage or stages a compound has potential for clinically relevant activity in.

  • Parasite Reduction Ratio (PRR) assays

short method (48h drug exposure): 6 weeks

long method (120h drug exposure): 10 week


Fluorescence-activated cell-sorting (FACS)

Target Based Screening

  • PI4K Enzymatic Assay: Phosphatidylinositol 4-kinase
  • PKG Enzymatic Assay: cGMP-dependent protein kinase

In vivo NSG Mouse Model

NSG/SCID studies are a highly specialized and unique set of assays in which new antiplasmodial compounds can be properly evaluated in a live model using human species of malaria. This is accomplished by using SCID (severe combined immunodeficiency) mice that have been infused with human blood, and subsequently can be studied as an experimental model of functional human malaria.

  • NSG/SCID studies
    • NSG in vivo antimalarial efficacy and PK/PD study
    • Dose fractionation study in vivo

Data from these assays can be used for lead optimization and drug candidate evaluation and results from these assays thereby inform key decision making and experimental design of human and/or animal in vivo studies.


Assay Group Assay Specifications
Phenotypic Screening  
Plasmodium single pt or dose response NF54 % inhibition, 96 well plate
Plasmodium single pt or dose response K1 % inhibition, 96 well plate
Plasmodium IC50 NF54
Plasmodium IC50 K1
Plasmodium IC50 3d7
Plasmodium IC50 Dd2
Mutant Resistant Strains  
Plasmodium IC50 KA156-Dd2
Plasmodium IC50 PKG-3d7
Plasmodium IC50 048-Dd2
Stage Specificity  
Parasite Reduction Ratio (PRR) PRR Short Method (48h drug exposure)
Parasite Reduction Ratio (PRR) PRR Long Method (120h drug exposure)
Target Based Screening  
PI4K Enzymatic Assay  
PKG Enzymatic Assay  
In vivo NSG Mouse Model  
NSG/SCID study NSG in vivo antimalarial efficacy and PK/PD study
NSG/SCID study Dose Fractionation Study in vivo
Selected Relevant H3D Authored Publications

Le Manach C, Nchinda AT, Paquet T, Gonzàlez Cabrera D, Younis Y, Han Z, Bashyam S, Zabiulla M, Taylor D, Lawrence N, White KL, Charman SA, Waterson D, Witty MJ, Wittlin S, Botha ME, Nondaba SH, Reader J, Birkholtz LM, Jiménez-Díaz MB, Martínez MS, Ferrer S, Angulo-Barturen I, Meister S, Antonova-Koch Y, Winzeler EA, Street LJ, Chibale K. Identification of a Potential Antimalarial Drug Candidate from a Series of 2-Aminopyrazines by Optimization of Aqueous Solubility and Potency across the Parasite Life Cycle. J Med Chem. 2016 Nov 10;59(21):9890-9905. doi: 10.1021/acs.jmedchem.6b01265. Epub 2016 Oct 26. PMID: 27748596.

Yoo E, Stokes BH, de Jong H, Vanaerschot M, Kumar T, Lawrence N, Njoroge M, Garcia A, Van der Westhuyzen R, Momper JD, Ng CL, Fidock DA, Bogyo M. Defining the Determinants of Specificity of Plasmodium Proteasome Inhibitors. J Am Chem Soc. 2018 Sep 12;140(36):11424-11437. doi: 10.1021/jacs.8b06656. Epub 2018 Aug 29. PMID: 30107725; PMCID: PMC6407133.

Manu Vanaerschot, James M. Murithi, Charisse Flerida A. Pasaje, Sonja Ghidelli-Disse, Louis Dwomoh, Megan Bird, Natasha Spottiswoode, Nimisha Mittal, Lauren B. Arendse, Edward S. Owen, Kathryn J. Wicht, Giulia Siciliano, Markus Bösche, Tomas Yeo, T.R. Santha Kumar, Sachel Mok, Emma F. Carpenter, Marla J. Giddins, Olalla Sanz, Sabine Ottilie, Pietro Alano, Kelly Chibale, Manuel Llinás, Anne-Catrin Uhlemann, Michael Delves, Andrew B. Tobin, Christian Doerig, Elizabeth A. Winzeler, Marcus C.S. Lee, Jacquin C. Niles, David A. Fidock. Inhibition of Resistance-Refractory P. falciparum Kinase PKG Delivers Prophylactic, Blood Stage, and Transmission-Blocking Antiplasmodial Activity. Cell Chemical Biology 2020; 27(7):806-816.e8, ISSN 2451-9456; https://doi.org/10.1016/j.chembiol.2020.04.001.

Murithi JM, Owen ES, Istvan ES, Lee MCS, Ottilie S, Chibale K, Goldberg DE, Winzeler EA, Llinás M, Fidock DA, Vanaerschot M. Combining Stage Specificity and Metabolomic Profiling to Advance Antimalarial Drug Discovery. Cell Chem Biol. 2020 Feb 20;27(2):158-171.e3. doi: 10.1016/j.chembiol.2019.11.009. Epub 2019 Dec 5. PMID: 31813848; PMCID: PMC7031696.

Okombo J, Brunschwig C, Singh K, Dziwornu GA, Barnard L, Njoroge M, Wittlin S, Chibale K. Antimalarial Pyrido[1,2- a]benzimidazole Derivatives with Mannich Base Side Chains: Synthesis, Pharmacological Evaluation, and Reactive Metabolite Trapping Studies. ACS Infect Dis. 2019 Mar 8;5(3):372-384. doi: 10.1021/acsinfecdis.8b00279. Epub 2019 Jan 17. PMID: 30608648.

Sinxadi P, Donini C, Johnstone H, Langdon G, Wiesner L, Allen E, Duparc S, Chalon S, McCarthy JS, Lorch U, Chibale K, Möhrle J, Barnes KI. Safety, Tolerability, Pharmacokinetics, and Antimalarial Activity of the Novel Plasmodium Phosphatidylinositol 4-Kinase Inhibitor MMV390048 in Healthy Volunteers. Antimicrob Agents Chemother. 2020 Mar 24;64(4):e01896-19. doi: 10.1128/AAC.01896-19. PMID: 31932368; PMCID: PMC7179259.

Kandepedu N, Gonzàlez Cabrera D, Eedubilli S, Taylor D, Brunschwig C, Gibhard L, Njoroge M, Lawrence N, Paquet T, Eyermann CJ, Spangenberg T, Basarab GS, Street LJ, Chibale K. Identification, Characterization, and Optimization of 2,8-Disubstituted-1,5-naphthyridines as Novel Plasmodium falciparum Phosphatidylinositol-4-kinase Inhibitors with in Vivo Efficacy in a Humanized Mouse Model of Malaria. J Med Chem. 2018 Jul 12;61(13):5692-5703. doi: 10.1021/acs.jmedchem.8b00648. Epub 2018 Jun 27. PMID: 29889526.

Additional References supporting H3D’s materials & methods:

Makler MT, Ries JM, Williams JA, Bancroft JE, Piper RC, Gibbins BL, Hinrichs DJ. Parasite lactate dehydrogenase as an assay for Plasmodium falciparum drug sensitivity. Am J Trop Med Hyg. 1993 Jun;48(6):739-41. doi: 10.4269/ajtmh.1993.48.739. PMID: 8333566.

Snyder C, Chollet J, Santo-Tomas J, Scheurer C, Wittlin S. In vitro and in vivo interaction of synthetic peroxide RBx11160 (OZ277) with piperaquine in Plasmodium models. Exp Parasitol. 2007 Mar;115(3):296-300. doi: 10.1016/j.exppara.2006.09.016. Epub 2006 Nov 7. PMID: 17087929.