Imperial College London

Professor Jake Baum

Faculty of Natural SciencesDepartment of Life Sciences

Professor of Cell Biology and Infectious Diseases
 
 
 
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Contact

 

+44 (0)20 7594 5420jake.baum Website

 
 
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Location

 

609Sir Alexander Fleming BuildingSouth Kensington Campus

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Summary

 

Publications

Publication Type
Year
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132 results found

Blight J, Sala K, Atcheson E, Kramer H, El-Turabi A, Coelho Real E, Dahalan F, Bettenbourt P, Dickinson-Craig E, Alves E, Salman A, Janse C, Ashcroft F, Hill A, Reyes-Sandoval A, Blagborough A, Baum Jet al., 2021, Dissection-independent production of a Plasmodium sporozoites from whole mosquitoes, Life Science Alliance, ISSN: 2575-1077

Journal article

Real E, Howick VM, Dahalan FA, Witmer K, Cudini J, Andradi-Brown C, Blight J, Davidson MS, Dogga SK, Reid AJ, Baum J, Lawniczak MKNet al., 2021, A single-cell atlas of Plasmodium falciparum transmission through the mosquito., Nat Commun, Vol: 12

Malaria parasites have a complex life cycle featuring diverse developmental strategies, each uniquely adapted to navigate specific host environments. Here we use single-cell transcriptomics to illuminate gene usage across the transmission cycle of the most virulent agent of human malaria - Plasmodium falciparum. We reveal developmental trajectories associated with the colonization of the mosquito midgut and salivary glands and elucidate the transcriptional signatures of each transmissible stage. Additionally, we identify both conserved and non-conserved gene usage between human and rodent parasites, which point to both essential mechanisms in malaria transmission and species-specific adaptations potentially linked to host tropism. Together, the data presented here, which are made freely available via an interactive website, provide a fine-grained atlas that enables intensive investigation of the P. falciparum transcriptional journey. As well as providing insights into gene function across the transmission cycle, the atlas opens the door for identification of drug and vaccine targets to stop malaria transmission and thereby prevent disease.

Journal article

Haase S, miller D, Cherkaoui D, Jordan S, Gulbis J, Baum Jet al., 2021, Identification and characterisation of a phospholipid scramblase in the malaria parasite Plasmodium falciparum, Molecular and Biochemical Parasitology, Vol: 243, Pages: 1-15, ISSN: 0166-6851

Recent studies highlight the emerging role of lipids as important messengers in malaria parasite biology. In an attempt to identify interacting proteins and regulators of these dynamic and versatile molecules, we hypothesised the involvement of phospholipid translocases and their substrates in the infection of the host erythrocyte by the malaria parasite Plasmodium spp. Here, using a data base searching approach of the Plasmodium Genomics Resources (www.plasmodb.org), we have identified a putative phospholipid (PL) scramblase in P. falciparum (PfPLSCR) that is conserved across the genus and in closely related unicellular algae. By reconstituting recombinant PfPLSCR into liposomes, we demonstrate metal ion dependent PL translocase activity and substrate preference, confirming PfPLSCR as a bona fide scramblase. We show that PfPLSCR is expressed during asexual and sexual parasite development, localising to different membranous compartments of the parasite throughout the intra-erythrocytic life cycle. Two different gene knockout approaches, however, suggest that PfPLSCR is not essential for erythrocyte invasion and asexual parasite development, pointing towards a possible role in other stages of the parasite life cycle.

Journal article

Okaniwa M, Shibata A, Ochida A, Akao Y, White KL, Shackleford DM, Duffy S, Lucantoni L, Dey S, Striepen J, Yeo T, Mok S, Aguiar ACC, Sturm A, Crespo B, Sanz LM, Churchyard A, Baum J, Pereira DB, Guido RVC, Dechering KJ, Wittlin S, Uhlemann A-C, Fidock DA, Niles JC, Avery VM, Charman SA, Laleu Bet al., 2021, Repositioning and characterization of 1-(Pyridin-4-yl)pyrrolidin-2-one derivatives as plasmodium cytoplasmic prolyl-tRNA synthetase inhibitors., ACS Infectious Diseases, ISSN: 2373-8227

Prolyl-tRNA synthetase (PRS) is a clinically validated antimalarial target. Screening of a set of PRS ATP-site binders, initially designed for human indications, led to identification of 1-(pyridin-4-yl)pyrrolidin-2-one derivatives representing a novel antimalarial scaffold. Evidence designates cytoplasmic PRS as the drug target. The frontrunner 1 and its active enantiomer 1- S exhibited low-double-digit nanomolar activity against resistant Plasmodium falciparum (Pf) laboratory strains and development of liver schizonts. No cross-resistance with strains resistant to other known antimalarials was noted. In addition, a similar level of growth inhibition was observed against clinical field isolates of Pf and P. vivax. The slow killing profile and the relative high propensity to develop resistance in vitro (minimum inoculum resistance of 8 × 105 parasites at a selection pressure of 3 × IC50) constitute unfavorable features for treatment of malaria. However, potent blood stage and antischizontal activity are compelling for causal prophylaxis which does not require fast onset of action. Achieving sufficient on-target selectivity appears to be particularly challenging and should be the primary focus during the next steps of optimization of this chemical series. Encouraging preliminary off-target profile and oral efficacy in a humanized murine model of Pf malaria allowed us to conclude that 1-(pyridin-4-yl)pyrrolidin-2-one derivatives represent a promising starting point for the identification of novel antimalarial prophylactic agents that selectively target Plasmodium PRS.

Journal article

Lawong A, Gahalawat S, Okombo J, Striepen J, Yeo T, Mok S, Deni I, Bridgford JL, Niederstrasser H, Zhou A, Posner B, Wittlin S, Gamo FJ, Crespo B, Churchyard A, Baum J, Mittal N, Winzeler E, Laleu B, Palmer MJ, Charman SA, Fidock DA, Ready JM, Phillips MAet al., 2021, Novel antimalarial tetrazoles and amides active against the hemoglobin degradation pathway in plasmodium falciparum., Journal of Medicinal Chemistry, Vol: 64, Pages: 2739-2761, ISSN: 0022-2623

Malaria control programs continue to be threatened by drug resistance. To identify new antimalarials, we conducted a phenotypic screen and identified a novel tetrazole-based series that shows fast-kill kinetics and a relatively low propensity to develop high-level resistance. Preliminary structure-activity relationships were established including identification of a subseries of related amides with antiplasmodial activity. Assaying parasites with resistance to antimalarials led us to test whether the series had a similar mechanism of action to chloroquine (CQ). Treatment of synchronized Plasmodium falciparum parasites with active analogues revealed a pattern of intracellular inhibition of hemozoin (Hz) formation reminiscent of CQ's action. Drug selections yielded only modest resistance that was associated with amplification of the multidrug resistance gene 1 (pfmdr1). Thus, we have identified a novel chemical series that targets the historically druggable heme polymerization pathway and that can form the basis of future optimization efforts to develop a new malaria treatment.

Journal article

Varghese S, Rahmani R, Drew DR, Beeson JG, Baum J, Smith BJ, Baell Jet al., 2021, Structure activity studies of truncated latrunculin analogues with anti-malarial activity, ChemMedChem, Vol: 16, Pages: 679-693, ISSN: 0014-827X

Malarial parasites employ actin dynamics for motility, and any disruption to these dynamics renders the parasites unable to effectively establish infection. Therefore, actin presents a potential target for malarial drug discovery, and naturally occurring actin inhibitors such as latrunculins are a promising starting point. However, the limited availability of the natural product and the laborious route for synthesis of latrunculins have hindered their potential development as drug candidates. In this regard, we recently described novel truncated latrunculins, with superior actin binding potency and selectivity towards P. falciparum actin than the canonical latrunculin B. In this paper, we further explore the truncated latrunculin core to summarize the SAR for inhibition of malaria motility. This study helps further understand the binding pattern of these analogues in order to develop them as drug candidates for malaria.

Journal article

Robert-Paganin J, Moussaoui D, Robblee JP, Auguin D, Blake TCA, Krementsova E, Baum J, Trybus KM, Houdusse Aet al., 2021, Deciphering the Function and the Regulation of Plasmodium falciparum Myosin A, Publisher: CELL PRESS, Pages: 344A-344A, ISSN: 0006-3495

Conference paper

Benns HJ, Storch M, Falco J, Fisher FR, Alves E, Wincott CJ, Baum J, Baldwin GS, Weerapana E, Tate EW, Child MAet al., 2021, Prioritization of antimicrobial targets by CRISPR-based oligo recombineering

<jats:title>Summary</jats:title><jats:p>Nucleophilic amino acids are important in covalent drug development yet underutilized as antimicrobial targets. Over recent years, several chemoproteomic technologies have been developed to mine chemically-accessible residues via their intrinsic reactivity toward electrophilic probes. However, these approaches cannot discern which reactive sites contribute to protein function and should therefore be prioritized for drug discovery. To address this, we have developed a CRISPR-based Oligo Recombineering (CORe) platform to systematically prioritize reactive amino acids according to their contribution to protein function. Our approach directly couples protein sequence and function with biological fitness. Here, we profile the reactivity of &gt;1,000 cysteines on ~700 proteins in the eukaryotic pathogen <jats:italic>Toxoplasma gondii</jats:italic> and prioritize functional sites using CORe. We competitively compared the fitness effect of 370 codon switches at 74 cysteines and identify functional sites in a diverse range of proteins. In our proof of concept, CORe performed &gt;800 times faster than a standard genetic workflow. Reactive cysteines decorating the ribosome were found to be critical for parasite growth, with subsequent target-based screening validating the apicomplexan translation machinery as a target for covalent ligand development. CORe is system-agnostic, and supports expedient identification, functional prioritization, and rational targeting of reactive sites in a wide range of organisms and diseases.</jats:p>

Journal article

Miguel-Blanco C, Murithi JM, Benavente ED, Angrisano F, Sala KA, van Schalkwyk DA, Vanaerschot M, Schwach F, Fuchter MJ, Billker O, Sutherland CJ, Campino SG, Clark TG, Blagborough AM, Fidock DA, Herreros E, Gamo FJ, Baum J, Delves MJet al., 2021, The antimalarial efficacy and mechanism of resistance of the novel chemotype DDD01034957, Scientific Reports, Vol: 11, ISSN: 2045-2322

New antimalarial therapeutics are needed to ensure that malaria cases continue to be driven down, as both emerging parasite resistance to frontline chemotherapies and mosquito resistance to current insecticides threaten control programmes. Plasmodium, the apicomplexan parasite responsible for malaria, causes disease pathology through repeated cycles of invasion and replication within host erythrocytes (the asexual cycle). Antimalarial drugs primarily target this cycle, seeking to reduce parasite burden within the host as fast as possible and to supress recrudescence for as long as possible. Intense phenotypic drug screening efforts have identified a number of promising new antimalarial molecules. Particularly important is the identification of compounds with new modes of action within the parasite to combat existing drug resistance and suitable for formulation of efficacious combination therapies. Here we detail the antimalarial properties of DDD01034957-a novel antimalarial molecule which is fast-acting and potent against drug resistant strains in vitro, shows activity in vivo, and possesses a resistance mechanism linked to the membrane transporter PfABCI3. These data support further medicinal chemistry lead-optimization of DDD01034957 as a novel antimalarial chemical class and provide new insights to further reduce in vivo metabolic clearance.

Journal article

Witmer K, Dahalan F, Delves M, Yahiya S, Watson O, Straschil U, Chiwcharoen D, Sorboon B, Pukrittayakamee S, Pearson R, Howick V, Lawniczak M, White N, Dondorp A, Okell L, Chotivanich K, Ruecker A, Baum Jet al., 2021, Transmission of artemisinin-resistant malaria parasites to mosquitoes under antimalarial drug pressure, Antimicrobial Agents and Chemotherapy, Vol: 65, Pages: 1-17, ISSN: 0066-4804

Resistance to artemisinin-based combination therapy (ACT) in the Plasmodium falciparum parasite is threatening to reverse recent gains in reducing global deaths from malaria. Whilst resistance manifests as delayed parasite clearance in patients the phenotype can only spread geographically via the sexual stages and mosquito transmission. In addition to their asexual killing properties, artemisinin and its derivatives sterilise sexual male gametocytes. Whether resistant parasites overcome this sterilising effect has not, however, been fully tested. Here, we analysed P. falciparum clinical isolates from the Greater Mekong Subregion, each demonstrating delayed clinical clearance and known resistance-associated polymorphisms in Kelch13 (PfK13var). As well as demonstrating reduced asexual sensitivity to drug, certain PfK13var isolates demonstrated a marked reduction in sensitivity to artemisinin in an in vitro male gamete formation assay. Importantly, this same reduction in sensitivity was observed when the most resistant isolate was tested directly in mosquito feeds. These results indicate that, under artemisinin drug pressure, whilst sensitive parasites are blocked, resistant parasites continue transmission. This selective advantage for resistance transmission could favour acquisition of additional host-specificity or polymorphisms affecting partner drug sensitivity in mixed infections. Favoured resistance transmission under ACT coverage could have profound implications for the spread of multidrug resistant malaria beyond Southeast Asia.

Journal article

Qian WW, Xia C, Venugopalan S, Narayanaswamy A, Dimon M, Ashdown GW, Baum J, Peng J, Ando DMet al., 2020, Batch equalization with a generative adversarial network, Bioinformatics, Vol: 36, Pages: I875-I883, ISSN: 1367-4803

MotivationAdvances in automation and imaging have made it possible to capture a large image dataset that spans multiple experimental batches of data. However, accurate biological comparison across the batches is challenged by batch-to-batch variation (i.e. batch effect) due to uncontrollable experimental noise (e.g. varying stain intensity or cell density). Previous approaches to minimize the batch effect have commonly focused on normalizing the low-dimensional image measurements such as an embedding generated by a neural network. However, normalization of the embedding could suffer from over-correction and alter true biological features (e.g. cell size) due to our limited ability to interpret the effect of the normalization on the embedding space. Although techniques like flat-field correction can be applied to normalize the image values directly, they are limited transformations that handle only simple artifacts due to batch effect.ResultsWe present a neural network-based batch equalization method that can transfer images from one batch to another while preserving the biological phenotype. The equalization method is trained as a generative adversarial network (GAN), using the StarGAN architecture that has shown considerable ability in style transfer. After incorporating new objectives that disentangle batch effect from biological features, we show that the equalized images have less batch information and preserve the biological information. We also demonstrate that the same model training parameters can generalize to two dramatically different types of cells, indicating this approach could be broadly applicable.Availability and implementationhttps://github.com/tensorflow/gan/tree/master/tensorflow_gan/examples/starganSupplementary informationSupplementary data are available at Bioinformatics online.

Journal article

Blake T, Haase S, Baum J, 2020, Actomyosin forces and the energetics of red blood cell invasion by the malaria parasite Plasmodium falciparum, PLoS Pathogens, Vol: 16, ISSN: 1553-7366

All symptoms of malaria disease are associated with the asexual blood stages of development, involving cycles of red blood cell (RBC) invasion and egress by the Plasmodium spp. merozoite. Merozoite invasion is rapid and is actively powered by a parasite actomyosin motor. The current accepted model for actomyosin force generation envisages arrays of parasite myosins, pushing against short actin filaments connected to the external milieu that drive the merozoite forwards into the RBC. In Plasmodium falciparum, the most virulent human malaria species, Myosin A (PfMyoA) is critical for parasite replication. However, the precise function of PfMyoA in invasion, its regulation, the role of other myosins and overall energetics of invasion remain unclear. Here, we developed a conditional mutagenesis strategy combined with live video microscopy to probe PfMyoA function and that of the auxiliary motor PfMyoB in invasion. By imaging conditional mutants with increasing defects in force production, based on disruption to a key PfMyoA phospho-regulation site, the absence of the PfMyoA essential light chain, or complete motor absence, we define three distinct stages of incomplete RBC invasion. These three defects reveal three energetic barriers to successful entry: RBC deformation (pre-entry), mid-invasion initiation, and completion of internalisation, each requiring an active parasite motor. In defining distinct energetic barriers to invasion, these data illuminate the mechanical challenges faced in this remarkable process of protozoan parasitism, highlighting distinct myosin functions and identifying potential targets for preventing malaria pathogenesis.

Journal article

Eagon S, Hammill JT, Sigal M, Ahn KJ, Tryhorn JE, Koch G, Belanger B, Chaplan CA, Loop L, Kashtanova AS, Yniguez K, Lazaro H, Wilkinson SP, Rice AL, Falade MO, Takahashi R, Kim K, Cheung A, DiBernardo C, Kimball JJ, Winzeler EA, Eribez K, Mittal N, Gamo F-J, Crespo B, Churchyard A, Garcia-Barbazan I, Baum J, Anderson MO, Laleu B, Guy RKet al., 2020, Synthesis and Structure-Activity Relationship of Dual-Stage Antimalarial Pyrazolo[3,4-b]pyridines, JOURNAL OF MEDICINAL CHEMISTRY, Vol: 63, Pages: 11902-11919, ISSN: 0022-2623

Journal article

Moussaoui D, Robblee JP, Auguin D, Krementsova EB, Haase S, Blake TCA, Baum J, Robert-Paganin J, Trybus KM, Houdusse Aet al., 2020, Full-length Plasmodium falciparum myosin A and essential light chain PfELC structures provide new anti-malarial targets, ELIFE, Vol: 9, ISSN: 2050-084X

Journal article

Real E, Howick VM, Dahalan F, Witmer K, Cudini J, Andradi-Brown C, Blight J, Davidson MS, Dogga SK, Reid AJ, Baum J, Lawniczak MKNet al., 2020, A single-cell atlas of Plasmodium falciparum transmission through the mosquito

<jats:title>Abstract</jats:title><jats:p>Malaria parasites have a complex life cycle featuring diverse developmental strategies, each uniquely adapted to navigate specific host environments. Here we use single-cell transcriptomics to illuminate gene usage across the transmission cycle of the most virulent agent of human malaria – <jats:italic>Plasmodium falciparum</jats:italic>. We reveal developmental trajectories associated with the colonisation of the mosquito midgut and salivary glands and elucidate the transcriptional signatures of each transmissible stage. Additionally, we identify both conserved and nonconserved gene usage between human and rodent parasites, which point to both essential mechanisms in malaria transmission and species-specific adaptations potentially linked to host tropism. Together, the data presented here, which are made freely available via an interactive website, establish the most complete atlas of the <jats:italic>P. falciparum</jats:italic> transcriptional journey to date.</jats:p><jats:sec><jats:title>One sentence summary</jats:title><jats:p>Single-cell transcriptomics of <jats:italic>P. falciparum</jats:italic> transmission stages highlights developmental trajectories and gene usage.</jats:p></jats:sec>

Journal article

Ashdown G, Gaboriau D, Baum J, 2020, A machine learning approach to define antimalarial drug action from heterogeneous cell-based screens, Science Advances, Vol: 6, ISSN: 2375-2548

Drug resistance threatens the effective prevention and treatment of an ever-increasing range ofhuman infections. This highlights an urgent need for new and improved drugs with novelmechanisms of action to avoid cross-resistance. Current cell-based drug screens are,however, restricted to binary live/dead readouts with no provision for mechanism of actionprediction. Machine learning methods are increasingly being used to improve informationextraction from imaging data. Such methods, however, work poorly with heterogeneouscellular phenotypes and generally require time-consuming human-led training. We havedeveloped a semi-supervised machine learning approach, combining human- and machinelabelled training data from mixed human malaria parasite cultures. Designed for highthroughput and high-resolution screening, our semi-supervised approach is robust to naturalparasite morphological heterogeneity and correctly orders parasite developmental stages. Ourapproach also reproducibly detects and clusters drug-induced morphological outliers bymechanism of action, demonstrating the potential power of machine learning for acceleratingcell-based drug discovery.

Journal article

Wang X, Wilkinson MD, Lin X, Ren R, Willison KR, Ivanov AP, Baum J, Edel JBet al., 2020, Correction: Single-molecule nanopore sensing of actin dynamics and drug binding, Chemical Science, Vol: 11, Pages: 8036-8038, ISSN: 2041-6520

Correction for ‘Single-molecule nanopore sensing of actin dynamics and drug binding’ by Xiaoyi Wang et al., Chem. Sci., 2020, 11, 970–979, DOI: 10.1039/C9SC05710B.

Journal article

Baum J, Pasvol G, Carter R, 2020, From 1950s malaria to COVID-19, NATURE, Vol: 582, Pages: 488-488, ISSN: 0028-0836

Journal article

Blight J, Sala KA, Atcheson E, Kramer H, El-Turabi A, Real E, Dahalan FA, Bettencourt P, Dickinson E, Alves E, Salman AM, Janse CJ, Ashcroft F, Hill AVS, Reyes-Sandoval A, Blagborough AM, Baum Jet al., 2020, Dissection-independent production of a protective whole-sporozoite malaria vaccine

<jats:title>Abstract</jats:title><jats:p>Complete protection against human malaria challenge has been achieved using infected mosquitoes as the delivery route for immunization with <jats:italic>Plasmodium</jats:italic> parasites. Strategies seeking to replicate this efficacy with either a manufactured whole-parasite or subunit vaccine, however, have shown only limited success. A major roadblock to whole parasite vaccine progress and understanding of the human infective sporozoite form in general, is reliance on manual dissection for parasite isolation from infected mosquitoes. We report here the development of a four-step process based on whole mosquito homogenization, slurry and density-gradient filtration, combined with free-flow electrophoresis that is able to rapidly produce a pure, aseptic sporozoite inoculum from hundreds of mosquitoes. Murine <jats:italic>P. berghei</jats:italic> or human-infective <jats:italic>P. falciparum</jats:italic> sporozoites produced in this way are 2-3-fold more infective with <jats:italic>in vitro</jats:italic> hepatocytes and can confer sterile protection when immunized intravenously with subsequent challenge using a mouse malaria model. Critically, we can also demonstrate for the first time 60-70% protection when the same parasites are administered via intramuscular (i.m.) route. In developing a process amenable to industrialisation and demonstrating efficacy by i.m. route these data represent a major advancement in capacity to produce a whole parasite malaria vaccine at scale.</jats:p><jats:sec><jats:title>One-Sentence Summary</jats:title><jats:p>A four-step process for isolating pure infective malaria parasite sporozoites at scale from homogenized whole mosquitoes, independent of manual dissection, is able to produce a whole parasite vaccine inoculum that confers sterilizing protection.</jats:p></jats:sec>

Journal article

Saunders CN, Cota E, Baum J, Tate EWet al., 2020, Peptide probes for Plasmodium falciparum MyoA tail interacting protein (MTIP): exploring the druggability of the malaria parasite motor complex, ACS Chemical Biology, Vol: 15, Pages: 1313-1320, ISSN: 1554-8929

Malaria remains an endemic tropical disease, and the emergence of Plasmodium falciparum parasites resistant to current front-line medicines means that new therapeutic targets are required. The Plasmodium glideosome is a multiprotein complex thought to be essential for efficient host red blood cell invasion. At its core is a myosin motor, Myosin A (MyoA), which provides most of the force required for parasite invasion. Here, we report the design and development of improved peptide-based probes for the anchor point of MyoA, the P. falciparum MyoA tail interacting protein (PfMTIP). These probes combine low nanomolar binding affinity with significantly enhanced cell penetration and demonstrable competitive target engagement with native PfMTIP through a combination of Western blot and chemical proteomics. These results provide new insights into the potential druggability of the MTIP/MyoA interaction and a basis for the future design of inhibitors.

Journal article

Llora-Batlle O, Michel-Todo L, Witmer K, Toda H, Fernandez-Becerra C, Baum J, Cortes Aet al., 2020, Conditional expression of PfAP2-G for controlled massive sexual conversion in Plasmodium falciparum, SCIENCE ADVANCES, Vol: 6, ISSN: 2375-2548

Journal article

Wilkinson MD, Lai H-E, Freemont PS, Baum Jet al., 2020, A biosynthetic platform for antimalarial drug discovery, Antimicrobial Agents and Chemotherapy, Vol: 64, Pages: 1-9, ISSN: 0066-4804

Advances in synthetic biology have enabled production of a variety of compounds using bacteria as a vehicle for complex compound biosynthesis. Violacein, a naturally occurring indole pigment with antibiotic properties, can be biosynthetically engineered in Escherichia coli expressing its non-native synthesis pathway. To explore whether this synthetic biosynthesis platform could be used for drug discovery, here we have screened bacterially-derived violacein against the main causative agent of human malaria, Plasmodium falciparum. We show the antiparasitic activity of bacterially-derived violacein against the P. falciparum 3D7 laboratory reference strain as well as drug-sensitive and resistant patient isolates, confirming the potential utility of this drug as an antimalarial. We then screen a biosynthetic series of violacein derivatives against P. falciparum growth. The demonstrated varied activity of each derivative against asexual parasite growth points to potential for further development of violacein as an antimalarial. Towards defining its mode of action, we show that biosynthetic violacein affects the parasite actin cytoskeleton, resulting in an accumulation of actin signal that is independent of actin polymerization. This activity points to a target that modulates actin behaviour in the cell either in terms of its regulation or its folding. More broadly, our data show that bacterial synthetic biosynthesis could become a suitable platform for antimalarial drug discovery with potential applications in future high-throughput drug screening with otherwise chemically-intractable natural products.

Journal article

Rueda-Zubiaurre A, Yahiya S, Fischer O, Hu X, Saunders C, Sharma S, Straschil U, Shen J, Tate EW, Delves M, Baum J, Barnard A, Fuchter MJet al., 2020, Structure-activity relationship studies of a novel class of transmission blocking antimalarials targeting male gametes., Journal of Medicinal Chemistry, Vol: 63, Pages: 2240-2262, ISSN: 0022-2623

Malaria is still a leading cause of mortality among children in the developing world, and despite the immense progress made in reducing the global burden, further efforts are needed if eradication is to be achieved. In this context, targeting transmission is widely recognized as a necessary intervention towards that goal. After carrying out a screen to discover new transmission-blocking agents, herein we report our medicinal chemistry efforts to study the potential of the most robust hit, DDD01035881, as a male-gamete targeted compound. We reveal key structural features for the activity of this series and identify analogues with greater potency and improved metabolic stability. We believe this study lays the groundwork for further development of this series as a transmission blocking agent.

Journal article

Witmer K, Dahalan FA, Delves MJ, Yahiya S, Watson OJ, Straschil U, Chiwcharoen D, Sornboon B, Pukrittayakamee S, Pearson RD, Howick VM, Lawniczak MKN, White NJ, Dondorp AM, Okell LC, Ruecker A, Chotivanich K, Baum Jet al., 2020, Artemisinin-resistant malaria parasites show enhanced transmission to mosquitoes under drug pressure

<jats:title>ABSTRACT</jats:title><jats:p>Resistance to artemisinin combination therapy (ACT) in the <jats:italic>Plasmodium falciparum</jats:italic> parasite is threatening to reverse recent gains in reducing global deaths from malaria. Whilst resistance manifests as delayed asexual parasite clearance in patients following ACT treatment, the phenotype can only spread geographically via the sexual cycle and subsequent transmission through the mosquito. Artemisinin and its derivatives (such as dihydroartemisinin, DHA) as well as killing the asexual parasite form are known to sterilize male, sexual-stage gametes from activation. Whether resistant parasites overcome this artemisinin-dependent sterilizing effect has not, however, been fully tested. Here, we analysed five <jats:italic>P. falciparum</jats:italic> clinical isolates from the Greater Mekong Subregion, each of which demonstrated delayed clinical clearance and carried known resistance-associated polymorphisms in the <jats:italic>Kelch13</jats:italic> gene (PfK13<jats:sup>var</jats:sup>). As well as demonstrating reduced sensitivity to artemisinin-derivates in <jats:italic>in vitro</jats:italic> asexual growth assays, certain PfK13<jats:sup>var</jats:sup> isolates also demonstrated a marked reduction in sensitivity to these drugs in an <jats:italic>in vitro</jats:italic> male gamete activation assay compared to a sensitive control. Importantly, the same reduction in sensitivity to DHA was observed when the most resistant isolate was assayed by standard membrane feeding assays using <jats:italic>Anopheles stephensi</jats:italic> mosquitoes. These results indicate that ACT use can favour resistant over sensitive parasite transmission. A selective advantage for resistant parasite transmission could also favour acquisition of further polymorphisms, such as mosquito host-specificity or antimalarial partne

Journal article

Wang X, Wilkinson MD, Lin X, Ren R, Willison KR, Ivanov A, Baum J, Edel Jet al., 2020, Single-molecule nanopore sensing of actin dynamics and drug binding, Chemical Science, Vol: 11, Pages: 970-979, ISSN: 2041-6520

Actin is a key protein in the dynamic processes within the eukaryotic cell. To date, methods exploring the molecular state of actin are limited to insights gained from structural approaches, providing a snapshot of protein folding, or methods that require chemical modifications compromising actin monomer thermostability. Nanopore sensing permits label-free investigation of native proteins and is ideally suited to study proteins such as actin that require specialised buffers and cofactors. Using nanopores, we determined the state of actin at the macromolecular level (filamentous or globular) and in its monomeric form bound to inhibitors. We revealed urea-dependent and voltage-dependent transitional states and observed unfolding process within which sub-populations of transient actin oligomers are visible. We detected, in real-time, filament-growth, and drug-binding at the single-molecule level demonstrating the promise of nanopores sensing for in-depth understanding of protein folding landscapes and for drug discovery.

Journal article

Warszawski S, Dekel E, Campeotto J, Marshall J, Wright K, Lyth O, Knop N, Regev-Rudzki N, Baum J, Draper S, Higgins M, Fleishman Set al., 2020, Design of a basigin-mimicking inhibitor targeting the malaria invasion protein RH5, Proteins: Structure, Function, and Bioinformatics, Vol: 88, Pages: 187-195, ISSN: 0887-3585

Many human pathogens use host cell-surface receptors to attach and invade cells. Often, thehost-pathogen interaction affinity is low, presenting opportunities to block invasion using asoluble, high-affinity mimic of the host protein. The Plasmodium falciparum reticulocyte-bindingprotein homolog 5 (RH5) provides an exciting candidate for mimicry: it is highly conserved andits moderate affinity binding to the human receptor basigin (KD≥1 μM) is an essential step inerythrocyte invasion by this malaria parasite. We used deep mutational scanning of a solublefragment of human basigin to systematically characterize point mutations that enhance basiginaffinity for RH5 and then used Rosetta to design a variant within the sequence space ofaffinity-enhancing mutations. The resulting seven-mutation design exhibited 2,500-fold higheraffinity (KD<1 nM) for RH5 with a very slow binding off rate (0.23 h-1) and reduced the effectivePlasmodium growth-inhibitory concentration by at least tenfold compared to human basigin. Thedesign provides a favorable starting point for engineering on-rate improvements that are likelyto be essential to reach therapeutically effective growth inhibition. Designed mimics may providetherapeutic advantages over antibodies, since the mimics bind to essential surfaces on the targetpathogen proteins, reducing the likelihood for the emergence of escape mutants

Journal article

Ashdown GW, Dimon M, Fan M, TerĂ¡n FS-R, Witmer K, Gaboriau DCA, Armstrong Z, Hazard J, Ando DM, Baum Jet al., 2019, A machine learning approach to define antimalarial drug action from heterogeneous cell-based screens, Publisher: Cold Spring Harbor Laboratory

<jats:title>Abstract</jats:title><jats:p>Drug resistance threatens the effective prevention and treatment of an ever-increasing range of human infections. This highlights an urgent need for new and improved drugs with novel mechanisms of action to avoid cross-resistance. Current cell-based drug screens are, however, restricted to binary live/dead readouts with no provision for mechanism of action prediction. Machine learning methods are increasingly being used to improve information extraction from imaging data. Such methods, however, work poorly with heterogeneous cellular phenotypes and generally require time-consuming human-led training. We have developed a semi-supervised machine learning approach, combining human- and machine-labelled training data from mixed human malaria parasite cultures. Designed for high-throughput and high-resolution screening, our semi-supervised approach is robust to natural parasite morphological heterogeneity and correctly orders parasite developmental stages. Our approach also reproducibly detects and clusters drug-induced morphological outliers by mechanism of action, demonstrating the potential power of machine learning for accelerating cell-based drug discovery.</jats:p><jats:sec><jats:title>One Sentence Summary</jats:title><jats:p>A machine learning approach to classifying normal and aberrant cell morphology from plate-based imaging of mixed malaria parasite cultures, facilitating clustering of drugs by mechanism of action.</jats:p></jats:sec>

Working paper

Del Rosario M, Periz J, Pavlou G, Lyth O, Latorre-Barragan F, Das S, Pall GS, Stortz JF, Lemgruber L, Whitelaw JA, Baum J, Tardieux I, Meissner Met al., 2019, Apicomplexan F-actin is required for efficient nuclear entry during host cell invasion, EMBO REPORTS, Vol: 20, ISSN: 1469-221X

Journal article

Malpartida-Cardenas K, Miscourides N, Rodriguez-Manzano J, Yu L-S, Moser N, Baum J, Georgiou Pet al., 2019, Quantitative and rapid Plasmodium falciparum malaria diagnosis and artemisinin-resistance detection using a CMOS Lab-on-Chip platform, Biosensors and Bioelectronics, Vol: 145, ISSN: 0956-5663

Early and accurate diagnosis of malaria and drug-resistance is essential to effective disease management. Available rapid malaria diagnostic tests present limitations in analytical sensitivity, drug-resistance testing and/or quantification. Conversely, diagnostic methods based on nucleic acid amplification stepped forwards owing to their high sensitivity, specificity and robustness. Nevertheless, these methods commonly rely on optical measurements and complex instrumentation which limit their applicability in resource-poor, point-of-care settings. This paper reports the specific, quantitative and fully-electronic detection of Plasmodium falciparum, the predominant malaria-causing parasite worldwide, using a Lab-on-Chip platform developed in-house. Furthermore, we demonstrate on-chip detection of C580Y, the most prevalent single-nucleotide polymorphism associated to artemisinin-resistant malaria. Real-time non-optical DNA sensing is facilitated using Ion-Sensitive Field-Effect Transistors, fabricated in unmodified complementary metal-oxide-semiconductor (CMOS) technology, coupled with loop-mediated isothermal amplification. This work holds significant potential for the development of a fully portable and quantitative malaria diagnostic that can be used as a rapid point-of-care test.

Journal article

Eden Primary C, Straschil U, Witmer K, Delves M, Marks S, Baum Jet al., 2019, Screen of traditional soup broths with reported antipyretic activity towards the discovery of potential antimalarials, Archives of Disease in Childhood, Vol: 104, Pages: 1138-1142, ISSN: 0003-9888

Objective The global impact of artemisinin-based combination therapies on malaria-associated mortality and their origins in ancient Chinese medicine has heightened interest in the natural discovery of future antimalarials.Methods A double-blind study to identify potential ingredients with antimalarial activity from traditional remedies with reported antipyretic properties. Recipes of clear broths, passed down by tradition in families of diverse ethnic origin, were sourced by school children. Broths were then tested for their ability to arrest malaria parasite asexual growth or sexual stage development in vitro. Clear broth extract was incubated with in vitro cultures of Plasmodium falciparum asexual or mature sexual stage cultures and assayed for parasite viability after 72 hours.Results Of the 56 broths tested, 5 were found to give >50% in vitro growth inhibition against P. falciparum asexual blood stages, with 2 having comparable inhibition to that seen with dihydroartemisinin, a leading antimalarial. Four other broths were found to have >50% transmission blocking activity, preventing male parasite sexual stage development. After unblinding, two active broths were found to be from siblings from different classes, who had brought in the same vegetarian soup, demonstrating assay robustness.Conclusions This screening approach succeeded in finding broths with activity against malaria parasite in vitro growth, arising from complex vegetable and/or meat-based broths. This represented a successful child education exercise, in teaching about the interface between natural remedies, traditional medicine and evidence-based drug discovery.

Journal article

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