Antimalarial drug resistance: linking Plasmodium falciparum parasite biology to the clinic

Repurposing antimalarials: pyrimethamine exhibits superior in vitro activity to metronidazole against Gardnerella while sparing Lactobacillus

BACKGROUND

Bacterial vaginosis (BV) is associated with significant reproductive health risks and high recurrence rates after standard antibiotic treatment. Sulfadoxine/pyrimethamine, an antimalarial drug, demonstrated unexpected clearance of BV in clinical trials, suggesting potential antimicrobial effects. Drug repurposing, which leverages existing drugs for new therapeutic applications, offers a promising approach to address the challenges of antimicrobial resistance and high recurrence rates in BV.

OBJECTIVE

To determine the in vitro activity of sulfadoxine/pyrimethamine and its components, sulfadoxine and pyrimethamine, on key species associated with BV.

METHODS

Minimum inhibitory concentration (MIC) and minimum bactericidal concentration were determined for sulfadoxine/pyrimethamine (20:1 ratio), sulfadoxine, pyrimethamine, and standard-of-care antibiotics, metronidazole and clindamycin, against BV-associated species (Gardnerella spp., Fannyhessea vaginae, Prevotella bivia) and Lactobacillus crispatus (vaginal health marker). Gardnerella biofilms were also exposed to sulfadoxine/pyrimethamine, pyrimethamine, or metronidazole, and biofilm biomass and biofilm cells culturability were assessed.

RESULTS

Sulfadoxine had no effect, while pyrimethamine inhibited all Gardnerella strains with MIC values ranging from 0.125 to 4 mg/L, lower than MICs observed for metronidazole (2-128 mg/L). Pyrimethamine also outperformed metronidazole in inhibiting biofilm mass accumulation and reducing biofilm culturable cells in 3/4 Gardnerella strains. Sulfadoxine/pyrimethamine presented lower MICs than metronidazole for 5/8 Gardnerella strains. Sulfadoxine, pyrimethamine, and sulfadoxine/pyrimethamine showed no activity against other BV-associated species or L. crispatus.

CONCLUSIONS

These findings suggest that pyrimethamine (and sulfadoxine/pyrimethamine) could be promising alternative or adjuvant therapies for BV, warranting further clinical trials.

The fast-evolving FIKK kinase family of Plasmodium falciparum can be inhibited by a single compound

Of 250 Plasmodium species, 6 infect humans, with P. falciparum causing over 95% of 600,000 annual malaria-related deaths. Its pathology arises from host cell remodelling driven by over 400 exported parasite proteins, including the FIKK kinase family. About one million years ago, a bird-infecting Plasmodium species crossed into great apes and a single non-exported FIKK kinase gained an export element. This led to a rapid expansion into 15-21 atypical, exported Ser/Thr effector kinases. Here, using genomic and proteomic analyses, we demonstrate FIKK differentiation via changes in subcellular localization, expression timing and substrate motifs, which supports an individual important role in host-pathogen interactions. Structural data and AlphaFold2 predictions reveal fast-evolving loops in the kinase domain that probably enabled rapid functional diversification for substrate preferences. One FIKK evolved exclusive tyrosine phosphorylation, previously thought absent in Plasmodium. Despite divergence of substrate preferences, the atypical ATP binding pocket is conserved and we identified a single compound that inhibits all FIKKs. A pan-specific inhibitor could reduce resistance development and improve malaria control strategies.

The ATM Kinase Inhibitor AZD0156 Is a Potent Inhibitor of Plasmodium Phosphatidylinositol 4-Kinase (PI4Kβ) and Is an Attractive Candidate for Medicinal Chemistry Optimization Against Malaria

New compounds targeting human malaria parasites are critical for effective malaria control and elimination. Here, we pursued the imidazoquinolinone AZD0156 (MMV1580483), a human ataxia-telangiectasia mutated (ATM) kinase inhibitor that completed Phase I clinical trials as an anticancer agent. We validated its in vitro activity against the two main forms of the Plasmodium falciparum parasite in the human host, viz. the asexual blood (symptomatic) stage and sexual gametocyte (transmission) stage. Resistance selection, cross-resistance, biochemical, and conditional knockdown studies revealed that AZD0156 inhibits P. falciparum phosphatidylinositol 4-kinase type III beta (PfPI4Kβ), a clinically-validated target for the treatment of malaria. Metabolic perturbations, fixed-ratio isobolograms, killing kinetics and morphological evaluation correlated AZD0156 inhibition with other known PI4Kβ inhibitors. The compound showed favorable in vivo pharmacokinetic properties and 81% antimalarial efficacy (4 × 50 mg kg-1) in a P. berghei mouse malaria infection model. Importantly, a cleaner biochemical profile was measured against human kinases (MAP4K4, MINK1) implicated in embryofoetal developmental toxicity associated with the PfPI4Kβ inhibitor MMV390048. This improved kinase selectivity profile and structural differentiation from other PI4Kβ inhibitors, together with its multistage antiplasmodial activity and favorable pharmacokinetic properties, makes AZD0156 an attractive candidate for target-based drug repositioning against malaria via a medicinal chemistry optimization approach.

Potential and pitfalls of using identity-by-descent for malaria genomic surveillance

The ability to genotype malaria parasites on an epidemiological scale is crucial for genomic surveillance as it aids in understanding malaria transmission dynamics and parasite demography changes in response to antimalarial interventions. Identity-by-descent (IBD)-based methods have demonstrated potential in various aspects of malaria genomic surveillance. However, there is a need for validation of existing approaches and development of new techniques to address challenges posed by the parasites' unique evolutionary dynamics and complex biological characteristics, which differ markedly from organisms like humans. This review examines current IBD use cases, identifies limitations of IBD-based methods, and explores promising future directions to enhance malaria genomic surveillance.

Marine Guanidine Alkaloids Inhibit Malaria Parasites Development in In Vitro, In Vivo and Ex Vivo Assays

Malaria is a disease caused by pathogenic protozoa Plasmodium spp., with a significant global impact on human health. Increasing resistance of P. falciparum strains to drugs treating malaria highlights the urgent need for the discovery of new antimalarial candidates. Batzelladines are marine guanidine alkaloids that exhibit potent antiparasitic activity. Herein, results of the parasitological profiling assessment of batzelladines F and L are reported. Both compounds exhibited potent antiplasmodial activity, moderate cytotoxicity, and suitable selectivity indexes. Batzelladines F and L are fast-acting P. falciparum inhibitors, with a pronounced inhibitory activity against resistant strains and laboratory-adapted clinical isolates of P. falciparum. Batzelladines F and L also demonstrated ex vivo activity against clinical isolates of P. falciparum and P. vivax, and batzelladine F showed in vivo antimalarial activity in a P. berghei malaria model. The results reported constitute a robust rationale for the development of guanidine alkaloid derivatives as lead candidates for malaria treatment.

Biogenesis of Cytochromes c and c1 in the Electron Transport Chain of Malaria Parasites

Plasmodium malaria parasites retain an essential mitochondrional electron transport chain (ETC) that is critical for growth within humans and mosquitoes and is a key antimalarial drug target. ETC function requires cytochromes c and c1, which are unusual among heme proteins due to their covalent binding to heme via conserved CXXCH sequence motifs. Heme attachment to these proteins in most eukaryotes requires the mitochondrial enzyme holocytochrome c synthase (HCCS) that binds heme and the apo cytochrome to facilitate the biogenesis of the mature cytochrome c or c1. Although humans encode a single bifunctional HCCS that attaches heme to both proteins, Plasmodium parasites are like yeast and encode two separate HCCS homologues thought to be specific for heme attachment to cyt c (HCCS) or cyt c1 (HCC1S). To test the function and specificity of Plasmodium falciparum HCCS and HCC1S, we used CRISPR/Cas9 to tag both genes for conditional expression. HCC1S knockdown selectively impaired cyt c1 biogenesis and caused lethal ETC dysfunction that was not reversed by the overexpression of HCCS. Knockdown of HCCS caused a more modest growth defect but strongly sensitized parasites to mitochondrial depolarization by proguanil, revealing key defects in ETC function. These results and prior heterologous studies in Escherichia coli of cyt c hemylation by P. falciparum HCCS and HCC1S strongly suggest that both homologues are essential for mitochondrial ETC function and have distinct specificities for the biogenesis of cyt c and c1, respectively, in parasites. This study lays a foundation to develop novel strategies to selectively block ETC function in malaria parasites.

Temporal Patterns of Haplotypic and Allelic Diversity Reflect the Changing Selection Landscape of the Malaria Parasite Plasmodium falciparum

The malaria parasite Plasmodium falciparum regularly confronts orchestrated changes in frontline drug treatment that drastically alter its selection landscape. When this has occurred, the parasite has successfully adapted to new drugs through novel resistance mutations. These novel mutations, however, emerge in a genetic background already shaped by prior drug selection. In some instances, selection imposed by different drugs targets the same loci in either synergistic or antagonistic ways, which may leave genomic signatures that are hard to attribute to a specific agent. Here, we use two approaches for detecting sequential bouts of drug adaptation: haplotype-based selection testing and temporal changes in allele frequencies. Using a set of longitudinal samples from French Guiana, we determine that since the official introduction of artemisinin combination therapy in 2007 there have been rapid hard selective sweeps at both known and novel loci. At four high-profile genes with demonstrated involvement in drug resistance (pfcrt, pfmdr1, pfaat1, and pfgch1), we see selection signals both before and after drug regime change; however, selection favored different haplotypes in the two time periods. Similarly, allele frequency analysis identified coding variants whose frequency trajectory changed signs under the new drug pressure. These selected alleles were enriched for genes implicated in artemisinin or partner-drug resistance in other global populations. Overall, these results suggest that drug resistance in P. falciparum is governed by known alleles of large effect along with a polygenic architecture of potentially more subtle variants, any of which can experience fitness reversals under distinct drug regimes.

Aminoquinoline-Pyrimidine-Based Alkyl-Piperazine Tethered Hybrids: Synthesis, Antiplasmodial Activity, and Mechanistic Studies

Though great progress has been made to eliminate malaria globally, effective and inexpensive strategies to design new antimalarials are still required due to the problem of drug resistance to the currently used antimalarials. Herein, in continuation of our efforts to improve the therapeutic efficacy of 4-aminoquinoline-pyrimidine (4-AQ-Py) based molecular hybrids, a series of 4-AQ-Py hybrids linked through diamine-piperazine (flexible and rigid) linkers was synthesized and assessed for in vitro antiplasmodial activity. In the in vitro assay, these hybrids exhibited excellent potency and selectivity index against both the chloroquine (CQ)-sensitive (D6) and CQ-resistant (W2) strains of Plasmodium falciparum. Compound 7i was found to be the most potent (5-fold more active than CQ) against the D6 strain, while compound 7e displayed the most potency (53-fold more potent than CQ) against the W2 strain. Furthermore, nine compounds (7d, 7f-i, 7l, and 7o-q) showed better antiplasmodial activity than the reference drug artemisinin (ART) against the D6 strain, and compared to ART, seven compounds (7d-e, 7i-k, and 7p-q) demonstrated better activity against the W2 strain. All the synthesized hybrids were found noncytotoxic against the mammalian VERO cell lines. Two potent compounds, 7e and 7i, were evaluated for their in vivo antiplasmodial activity against P. berghei-infected mouse models. Additionally, one of the best active compounds, 7i, was tested for heme binding, and docking studies were conducted with Pf-DHFR to determine the primary mechanism of action of these hybrids.

Synthesis and SAR Studies of Acyl-Thiourea Platinum(II) Complexes Yield Analogs with Dual-Stage Antiplasmodium Activity

Mixed-ligand platinum(II) complexes incorporating bipyridine and acyl-thiourea ligands were synthesized and evaluated for their in vitro growth inhibitory activity against the human malaria parasite Plasmodium falciparum (Pf). The substituents at four distinct sites were varied to identify structure-activity relationships for this series. Most complexes displayed potent PfNF54 activity with IC50 values in the nanomolar range and favorable cytotoxicity profiles. Five complexes (C1, C11, C12, C15, and C17) exhibited activity against both the asexual blood and sexual (gametocyte) stage parasites, with another complex (C8) exhibiting activity against late-stage gametocytes only. In addition, the complexes showed comparable ABS potency against the PfK1 multidrug-resistant strain. The pharmacokinetic parameters of one analog (C6), which displayed good solubility and mouse microsomal metabolic stability, were measured. This work demonstrates the potential of acyl-thiourea platinum(II) complexes as selective, multistage-active antiplasmodium compounds as part of the search for new antimalarial agents.

Genome-wide scanning for genetic markers associated with anti-malarial drugs sensitivity of Plasmodium falciparum isolates from the China-Myanmar border region

BACKGROUND

Understanding the emergence and spread of anti-malarial resistance, particularly to artemisinin and its partner drugs, is essential for eradicating malaria in worldwide. To identify genetic markers associated with susceptibility to common anti-malarial drugs, the in vitro sensitivities of anti-malarial drugs were evaluated, and a genome-wide association study of Plasmodium falciparum susceptibility in vitro to multiple anti-malarial drugs was conducted.

METHODS

Genomic DNA from 34 samples of P. falciparum collected between 2007 and 2010 in the Nabang-Lazan Valley along the China-Myanmar border was extracted and subjected to whole-genome sequencing. The standard SYBR Green I-based fluorescence assay and RSA assay were used to evaluated the in vitro sensitivities of anti-malarial drugs. Plink v1.90 was used to investigate the associations of genome-wide SNP with in vitro sensitivities to anti-malarial drugs.

RESULTS

The proportion of isolates showed reduced-susceptible to CQ,SP,QN,PPQ and PND were 88.24%,92.59%,8.82%,8.82%,5.88%, respectively. 93.54% of isolates showed high level of the IC50 values of CQ have a pfcrt CIETS mutations. The isolates with pfdhfr IRNI, NRNL and IRNL mutations showed high SP IC50 values. SNPs on pfhsp90 and pfevp1 showed significant association with IC50 values of CQ. Of particular interest is the significant association found between a locus on chromosome 13 and the sensitivity to dihydroartemisinin. This locus is situated within the gene encoding the inner membrane complex protein 1F (IMC1F),which has been found to be associated with the kelch13 compartment in schizont stages of P. falciparum.

CONCLUSIONS

Multiple genetic markers correlating with anti-malarial drug susceptibility were identified in the study, which provide a reference for further investigations into the association between oxidative stress-mediated activity and anti-malarial drugs susceptibility.

Harnessing engineered symbionts to combat concurrent malaria and arboviruses transmission

Concurrent malaria and arbovirus infections pose significant public health challenges in tropical and subtropical regions, demanding innovative control strategies. Here, we describe a strategy that employs multifunctional engineered symbiotic bacteria to suppress concurrent transmission of malaria parasites, dengue, and Zika viruses by various vector mosquitoes. The symbiotic bacterium Serratia AS1, which efficiently spreads through Anopheles and Aedes populations, is engineered to simultaneously produce anti-Plasmodium and anti-arbovirus effector proteins controlled by a selected blood-induced promoter. Laboratory and outdoor field-cage studies show that the multifunctional engineered symbiotic strains effectively inhibit Plasmodium infection in Anopheles mosquitoes and arbovirus infection in Aedes mosquitoes. Our findings provide the foundation for the use of engineered symbiotic bacteria as a powerful tool to combat the concurrent transmission of malaria and arbovirus diseases.

Unravelling the mode of action of the Tres Cantos Antimalarial Set (TCAMS): investigating the mechanism of potent antimalarial compounds potentially targeting the human serotonin receptor

BACKGROUND

Despite the strides made in recent decades, the resistance observed in existing antimalarial drugs, and the intricate life cycle of the Plasmodium parasite underscore the pressing need to develop novel and effective therapeutic interventions. This article provides a comprehensive evaluation of the outcomes stemming from screening a library comprising 48 compounds (TCAMS) against Plasmodium falciparum.

METHODS

This study focused on characterizing the IC50 values of compounds from the Tres Cantos Antimalarial Set (TCAMS) library via a double-labelling method of P. falciparum parasites with SYBR Green-I and MitoTracker Deep Red, which were evaluated via flow cytometry. Evaluation of the cytotoxicity of the best candidates in human embryonic kidney (HEK293) cells, chemoinformatic analysis, and exploration of the effects of the compounds on the action of serotonin and melatonin in the erythrocytic life cycle of the parasite.

RESULTS

IC50 characterization confirmed that 93.75% of the compounds tested exhibited antimalarial activity at concentrations below 2 micromolar (µM), with 5 compounds showing IC50 values below 50 nM (nM) (15.21 ± 5.97 nM to 45.82 ± 5.11 nM). Furthermore, 12 compounds presented IC50 values between 50 and 100 nM (57.43 ± 12.25 nM to 100.6 ± 22.89 nM), highlighting their potent in vitro efficacy against P. falciparum. Cytotoxicity evaluation in HEK293 cells revealed that 12 from 17 compounds did not significantly reduce cell viability. Cheminformatics analysis clustered the compounds based on structural and physicochemical similarities, revealing distinct structural patterns. Exploration of hypothetical targets from the TCAMS library identified 27 compounds with potential targets, 15 specifically targeted serotonergic receptors. Subsequent serotonin and melatonin treatment experiments indicated that certain compounds could inhibit both effects on parasitaemia, suggesting a complex interaction with signaling in P. falciparum.

CONCLUSIONS

This study identifies promising antimalarial candidates with low IC50 values and highlights the significance of targeting serotonin receptors in the development of potential antimalarial drugs.

Heterogeneous constraint and adaptation across the malaria parasite life cycle

Evolutionary forces vary across genomes, creating disparities in how traits evolve. In organisms with complex life cycles, it is unclear how intrinsic differences among discrete life stages impact evolution. We looked for life history-driven changes in patterns of adaptation in Plasmodium falciparum, a malaria-causing parasite with a multi-stage life cycle. Categorizing genes based on their expression in different life stages, we compared patterns of between- and within-species polymorphism across stages by estimating nonsynonymous to synonymous substitution rate ratios (dN/dS) and mean pairwise nucleotide diversity ( π NS/ π S). Considering these alongside estimates of Tajima's D, fixation probability, adaptive divergence proportion and rate, and F ST , we looked for changes in the drift-selection balance in life stages subject to transmission bottlenecks and changes in ploidy. We observed signals of reduced selection efficacy in genes exclusively expressed in sporozoites, the parasite form transmitted from mosquitoes to humans and often targeted by vaccines and monoclonal antibodies. We discuss implications for how parasites evolve to resist therapeutics and consider functional, molecular, and population genetic factors that could contribute to these patterns.

Emerging nanotechnology-driven drug delivery solutions for malaria: Addressing drug resistance and improving therapeutic success

Malaria remains the fifth deadliest parasitic infection worldwide, despite significant advancements in technology. A major challenge in combating this disease lies in the growing resistance of malaria parasites to antimalarial drugs and insect vectors to insecticides. The emerging inefficacy of artemisinin-based combination therapies (ACTs) further exacerbates the issue. Additionally, the absence of a highly effective malaria vaccine continues to be a significant obstacle. The complex biology of the malaria parasite and the multifaceted nature of the disease contribute to these challenges. Recent advancements in nanotechnology offer promising solutions in malaria treatment, providing benefits such as improved drug stability, sustained release, and targeted delivery to specific cells. Encapsulation technology, in particular, addresses critical limitations like poor solubility, low bioavailability, and frequent dosing requirements. Thus, this review explores innovative strategies to combat malaria, focusing on nanotechnology-based antimalarial formulations and their evaluation in vitro and in vivo. Moreover, the study highlights the SAR of potent antimalarial compounds, molecular markers linked with drug resistance, ACTs, advocates for eco-friendly approaches, nanotechnology-driven vaccines, and new antimalarial agents with their specific targets.

Substrate and inhibitor specificity of Plasmodium nucleoside transporters ENT1 orthologs

Malaria caused by Plasmodium infection poses a serious hazard to human health. Plasmodium falciparum equilibrative nucleoside transporter 1 (PfENT1), which mediates nucleoside uptake, is essential for the growth and proliferation of Plasmodium parasites, suggesting that PfENT1 is a potential antimalarial target. The promising compound GSK4 effectively inhibits the transport activity of PfENT1, thereby restraining the growth of Plasmodium parasites. However, it still needs to be clarified whether Plasmodium ENT1 orthologs have different selectivities for nucleosides and inhibitors. Here, we systematically compared the nucleoside selectivity of Plasmodium ENT1 orthologs from P. falciparum (PfENT1), Plasmodium berghei (PbENT1), and Plasmodium vivax (PvENT1), revealing that Plasmodium ENT1 orthologs present a distinct nucleoside recognition pattern. In addition, GSK4 robustly binds to PfENT1 and PvENT1 from two human-hosted Plasmodium parasites but has a weakened binding affinity for PbENT1 from mouse-hosted Plasmodium parasites. We further structurally optimized the inhibitor and generated three GSK4 analogs. One of the GSK4 analogs presented a slightly increased binding affinity for PfENT1. This optimization represents a promising advancement for antimalarial drug development, providing a novel foundation for future endeavors in antimalarial drug design.

Efficacy and Safety of Antimalarial as Repurposing Drug for COVID-19 Following Retraction of Chloroquine and Hydroxychloroquine

Various repurposing drugs have been tested for their efficacy on coronavirus disease 2019 (COVID-19), including antimalarial drugs. During the pandemic, Chloroquine (CQ) and Hydroxychloroquine (HCQ) demonstrated good potential against COVID-19, but further studies showed both drugs had side effects that were more dangerous than the efficacy. This made World Health Organization (WHO) ban the usage for COVID-19 patients. In this context, there is a need to explore other antimalarial drugs as potential therapies for COVID-19. This study provides a descriptive synthesis of clinical trials evaluating antimalarial drugs for COVID-19 treatment conducted after the withdrawal of CQ and HCQ. The method was a literature study using the keywords "antimalarial", "COVID-19", "SARS-CoV-2", "clinical trial", and "randomized controlled trial" on the MEDLINE, Scopus, and Cochrane databases. Inclusion criteria were published clinical trials with randomized controlled trials (RCTs) on the efficacy and safety of single antimalarial drugs for COVID-19, published in English and excluding combination therapies. The results showed 3 antimalarial drugs, namely Quinine Sulfate (QS), Atovaquone (AQ), and Artemisinin-Piperaquine (AP), had gone through clinical trial to assess efficacy and safety against COVID-19 patients. Out of the 3 drugs, only AP showed significant results in the primary outcome, which was the time required to reach undetectable levels of SARS-CoV-2. Furthermore, the intervention group took 10.6 days, and the control group took 19.3 days (p=0.001). Based on this review, AP showed significant potential as a therapy in the fight against COVID-19.

Exploring the Utility of Cell-Penetrating Peptides as Vehicles for the Delivery of Distinct Antimalarial Drug Cargoes

The devastating impact of malaria includes significant mortality and illness worldwide. Increasing resistance of the causative parasite, Plasmodium, to existing antimalarial drugs underscores a need for additional compounds with distinct modes of action in the therapeutic development pipeline. Here we showcase peptide-drug conjugates (PDCs) as an attractive compound class, in which therapeutic or lead antimalarials are chemically conjugated to cell-penetrating peptides. This approach aims to enhance selective uptake into Plasmodium-infected red blood cells and impart additional cytotoxic actions on the intraerythrocytic parasite, thereby enabling targeted drug delivery and dual modes of action. We describe the development of PDCs featuring four compounds with antimalarial activity-primaquine, artesunate, tafenoquine and methotrexate-conjugated to three cell-penetrating peptide scaffolds with varied antiplasmodial activity, including active and inactive analogues of platelet factor 4 derived internalization peptide (PDIP), and a cyclic polyarginine peptide. Development of this diverse set of PDCs featured distinct and adaptable conjugation strategies, to produce conjugates with in vitro antiplasmodial activities ranging from low nanomolar to low micromolar potencies according to the drug cargo and bioactivity of the partner peptide. Overall, this study establishes a strategic and methodological framework for the further development of dual mode of action peptide-drug antimalarial therapeutics.

Low prevalence of copy number variation in pfmdr1 and pfpm2 in Plasmodium falciparum isolates from southern Angola

BACKGROUND

Malaria is the parasitic disease with the highest global morbidity and mortality. According to estimates from the World Health Organization (WHO), there were around 249 million cases in 2022, with 3.4% occurring in Angola. The emergence and spread of drug-resistant Plasmodium falciparum have compromised anti-malarial efficacy and threatens malaria elimination campaigns using artemisinin-based combination therapy (ACT). Increased copy number (CNV) of the P. falciparum gene plasmepsin 2 (pfpm2) have been reported to confer parasite tolerance to piperaquine (PPQ) and the multidrug resistance-1 (pfmdr1), resistance to mefloquine (MEF) and decreased susceptibility to lumefantrine (LUM). PPQ, MEF and LUM are ACT partner drugs. Therefore, CNV detection is a useful tool to track ACT resistance risk. The potential for future treatment failure of artemisinin-based combinations (that include PPQ, LUM and AMQ), due to parasite resistance in the region, emphasizes the need for continued molecular surveillance.

METHODS

One hundred and nine clinically derived samples were collected at Hospital Central Dr. António Agostinho Neto (HCL) in Lubango, Angola. qPCR targeting the small-subunit 18S rRNA gene was used to confirm P. falciparum infection. Copy number estimates were determined using a SYBR green-based quantitative PCR assay.

RESULTS

Overall, this study revealed a low number of resistance CNVs present in the parasite population at Lubango, for the genes pfmdr1 and pfpm2. Of the 102 samples successfully analysed for pfpm2 10 (9.8%) carried increased CNV and 9/101 (8.9%) carried increased CNV of pfmdr1.

CONCLUSIONS

This study provides, for the first time, evidence for the presence of CNVs in the pfpm2 and pfmdr1 genes in P. falciparum isolates from southern Angola.

Drug Interaction Studies of Cabamiquine:Ganaplacide Combination against Hepatic Plasmodium berghei

New antimalarial combination therapies with novel modes of action are required to counter the emergence and spread of Plasmodium drug resistance against existing therapeutics. Here, we present a study to evaluate the preventive activity of a combination of clinical antimalarial drug candidates, cabamiquine and ganaplacide, that have multistage activity against the liver and blood stages of Plasmodium infection. Cabamiquine (DDD107498, M5717) inhibits parasite protein synthesis, and ganaplacide (KAF156) inhibits protein trafficking, blocks the establishment of new permeation pathways, and causes endoplasmic reticulum expansion. The pharmacodynamic parameters of a combination of the two compounds were assessed employing a pharmacometrics approach in conjunction with in vitro-in silico checkerboard analysis. The in vitro study was performed on a previously established 3D infection platform based on human hepatic cell lines that sustain infection by rodent P. berghei parasites. The in vivo efficacy of this drug combination was assessed against the liver stage of the P. berghei. Our results show that the combination of both drugs at the tested concentrations does not interfere with the drugs respective mode of action or affect hepatocyte cell viability. The drug combination was fully effective in preventing the appearance of blood stage parasites when a systemic plasma Cav0-24/EC50 ratio >2 for ganaplacide and >5 for cabamiquine was achieved. These findings demonstrate that chemoprevention using a combination of cabamiquine and ganaplacide has the potential to target the asymptomatic liver stage of Plasmodium infection and prevent the development of parasitemia.

Plasmodium falciparum transcription factor AP2-06B is mutated at high frequency in Southeast Asia but does not associate with drug resistance

Introduction

A continuing challenge for malaria control is the ability of Plasmodium falciparum to develop resistance to antimalarial drugs. Members within the Plasmodium transcription factor family AP2 regulate the growth and development of the parasite, and are also thought to be involved in unclear aspects of drug resistance. Here we screened for single nucleotide polymorphisms (SNPs) within the AP2 family and identified 6 non-synonymous mutations within AP2-06B (PF3D7_0613800), with allele frequencies greater than 0.05. One mutation, K3124R, was located in a PfAP2-06B AP2 domain.

Methods

To investigate transcriptional regulation by PfAP2-06B, ChIP-seq assays were performed on 3D7/PfAP2-06B-GFP schizonts using antibodies against GFP. The DNA sequences of the artemisinin-resistant CWX and the quinoline-resistant strains PfDd2 and Pf7G8 were analyzed for the genetic diversity of AP2-06B, compared with the Pf3D7 strain as a reference sequence. To determine whether AP2-06B can alter the expression of pfk13 and pfcrt, as well as cause artemisinin and quinoline resistance in Plasmodium, we generated both a K3124R mutation and conditional knockdown of AP2-06B in Pf3D7 using CRISPR/Cas9-mediated genome editing.

Results

ChIP-Seq analysis showed that AP2-06B can bind to the loci of the Plasmodium genes pfk13 and pfcrt. The AP2-06B K3124R mutation was also found in the artemisinin-resistant parasite strain CWX and the chloroquine-resistant strains Dd2 and 7G8. Contrary to expectation, Pf3D7 Plasmodium lines modified by either K3124R mutation of AP2-06B or conditional knockdown of AP2-06B did not have altered sensitivity to artemisinin or quinolines by modulating pfk13 or pfcrt expression.

Discussion

AP2-06B was predicted to be associated with artemisinin and quinoline resistance, but no change in resistance was observed after mutation or conditional knockdown. Given the multigenic nature of resistance, it might be difficult to recreate a resistance phenotype. In conclusion, whether AP2-06B regulates the development of artemisinin or quinoline resistance remains to be studied.

The Ivermectin Related Compound Moxidectin Can Target Apicomplexan Importin α and Limit Growth of Malarial Parasites

Signal-dependent transport into and out of the nucleus mediated by members of the importin (IMP) superfamily is crucial for eukaryotic function, with inhibitors targeting IMPα being of key interest as anti-infectious agents, including against the apicomplexan Plasmodium species and Toxoplasma gondii, causative agents of malaria and toxoplasmosis, respectively. We recently showed that the FDA-approved macrocyclic lactone ivermectin, as well as several other different small molecule inhibitors, can specifically bind to and inhibit P. falciparum and T. gondii IMPα functions, as well as limit parasite growth. Here we focus on the FDA-approved antiparasitic moxidectin, a structural analogue of ivermectin, for its IMPα-targeting and anti-apicomplexan properties for the first time. We use circular dichroism and intrinsic tryptophan fluorescence measurements to show that moxidectin can bind directly to apicomplexan IMPαs, thereby inhibiting their key binding functions at low μM concentrations, as well as possessing anti-parasitic activity against P. falciparum in culture. The results imply a class effect in terms of IMPα's ability to be targeted by macrocyclic lactone compounds. Importantly, in the face of rising global emergence of resistance to approved anti-parasitic agents, the findings highlight the potential of moxidectin and possibly other macrocyclic lactone compounds as antimalarial agents.

Rational engineering of an antimalarial peptide with enhanced proteolytic stability and preserved parasite invasion inhibitory activity

We describe rational chemical engineering to enhance the proteolytic stability of a chimeric peptide using a combination of unique strategies that involve the incorporation of a series of d-amino acids into the parent l-peptide sequence and restricting the conformational freedom of the peptide by covalent stitching. We hypothesize that replacing a stretch of sequence of an unstructured peptide motif with d-amino acids would increase its proteolytic stability without significantly affecting its affinity to the target protein. Also, considering the Cβ-Cβ distances, replacing an appropriate pair of residues with cysteine to form an additional disulfide bond in the molecule would provide additional stability to the engineered peptide. To verify this hypothesis, we have implemented these strategies to a previously reported peptidic inhibitor RR, against P. falciparum invasion into red blood cells (RBCs) and designed two novel heterochiral chimeric peptides, RR-I and RR-II. We have demonstrated that these peptides exhibit remarkable inhibitory activity with dramatically enhanced proteolytic stability. Finally, we have designed a cyclic analog, RR-III, to enhance the stability of the peptide against endopeptidases. The RR-III peptide exhibits the same inhibitory activity as RR-II while demonstrating impressive resistance to enzymatic degradation and prolonged stability in human plasma. These developments hold promise for a new generation of peptide-based therapeutics, showcasing the potential of residue selection for tailored modifications, as demonstrated in this work.

Current Trends in Nanotechnology-Based Drug Delivery Systems for the Diagnosis and Treatment of Malaria: A Review

Malaria is still a major endemic disease transmitted in humans via Plasmodium-infected mosquitoes. The eradication of malarial parasites and the control measures have been rigorously and extensively deployed by local and international health organizations. Malaria's recurrence is a result of the failure to entirely eradicate it. The drawbacks related to malarial chemotherapy, non-specific targeting, multiple drug resistance, requirement of high doses, intolerable toxicity, indefinable complexity of Plasmodium's life cycle, and advent of drug-resistant strains of P. falciparum are the causes of the ineffective eradication measures. With the emergence of nanotechnology and its application in various industrial domains, the rising interest in the medical field, especially in epidemiology, has skyrocketed. The applications of nanosized carriers have sparked special attention, aiming towards minimizing the overall side effects caused due to drug therapy and avoiding bioavailability. The applications of concepts of nanobiotechnology to both vector control and patient therapy can also be one of the approaches. The current study focuses on the use of hybrid drugs as next-generation antimalarial drugs because they involve fewer drug adverse effects. The paper encompasses the numerous nanosized delivery-based systems that have been found to be effective among higher animal models, especially in treating malarial prophylaxis. This paper delivers a detailed review of diagnostic techniques, various nanotechnology approaches, the application of nanocarriers, and the underlying mechanisms for the management of malaria, thereby providing insights and the direction in which the current trends are imparted from the innovative and technological perspective.

Identification of new inhibitors of Plasmodium falciparum hypoxanthine-guanine-xanthine Phosphoribosyltransferase (HG(X)PRT): An outlook towards the treatment of malaria

Plasmodium, a protozoan parasite responsible for causing malaria relies on the purine salvage pathway to synthesize purine as they are incapable of synthesizing them de novo. This pathway is crucial for the survival of the parasite and hence enzymes of this pathway can serve as antimalarial drug targets. One of the enzymes of this pathway is hypoxanthine guanine (xanthine) phosphoribosyltransferase [HG(X)PRT] that serves as novel target, potentially less prone to existing resistance mechanisms seen with the use of traditional antimalarial drugs. HGXPRT inhibition disrupts the parasite's ability to synthesize nucleotides, essential for its growth and replication. In this regard, the current study was designed to identify the inhibitors of HGXPRT enzyme. For this purpose, the enzyme was produced through recombinant technology and purified with 10 mg/ L yield. Followed this, UV-based enzyme inhibition assay was optimized and >200 fully characterized compounds were evaluated for their HGXPRT inhibitory activity. Out of them fourteen compounds 1-14 showed significant to weak inhibition of HGXPRT enzyme with IC50 values in the range of 15.7 to 229.6 μM, as compared to the standard inhibitor i.e. 9-deazaguanine (IC50 = 12 ± 1.0 μM). In- silico and biophysical studies were further performed on active compounds to get structural insights into enzyme-inhibitor complex at the atomic level. Docking studies predicted that these inhibitors accommodate the purine binding site of enzyme and interacted with critical residues such as Asp148, Phe197, and Val198. Biophysical studies showed that these identified inhibitors interacted with HGXPRT enzyme in a non-ambiguous manner. Furthermore, these inhibitors were found to be non-cytotoxic against human fibroblast cell line (BJ). Hence, this study identified 14 hits that could lead to further research towards anti-malarial drug design and development.

The Plasmodium falciparum NCR1 transporter is an antimalarial target that exports cholesterol from the parasite's plasma membrane

Malaria, a devastating parasitic infection, is the leading cause of death in many developing countries. Unfortunately, the most deadliest causative agent of malaria, Plasmodium falciparum, has developed resistance to nearly all currently available antimalarial drugs. The P. falciparum Niemann-Pick type C1-related (PfNCR1) transporter has been identified as a druggable target, but its structure and detailed molecular mechanism are not yet available. Here, we present three structures of PfNCR1 with and without the functional inhibitor MMV009108 at resolutions between 2.98 and 3.81 Å using single-particle cryo-electron microscopy (cryo-EM), suggesting that PfNCR1 binds cholesterol and forms a cholesterol transport tunnel to modulate the composition of the parasite plasma membrane. Cholesterol efflux assays show that PfNCR1 is an exporter capable of extruding cholesterol from the membrane. Additionally, the inhibition mechanism of MMV009108 appears to be due to a direct blockage of PfNCR1, preventing this transporter from shuttling cholesterol.

Design, synthesis and therapeutic evaluation of novel antimalarial derivatives based on the clinical antitumor candidate drug Quisinostat

In previous studies, we identified the clinical antitumor drug candidate Quisinostat is a potent Plasmodium falciparum histone deacetylase (PfHDAC) inhibitor with significant activity against drug-resistant malaria but with severe toxicity. To delve deeper into its antimalarial potential, herein we designed and synthesized 36 novel analogues of Quisinostat and systematically evaluated their antimalarial activities and cytotoxicity. Among them, compounds 33 and 37 could effectively eliminate both wild-type and multidrug resistant P. falciparum parasites along with significantly attenuated cytotoxicity, and their metabolic properties were also notably improved. Western blot analysis showed that 33 and 37 upregulated Plasmodium histone acetylation, suggesting that they exerted antimalarial effects through inhibition of PfHDAC like Quisinostat. Furthermore, compounds 33 and 37 also displayed significant antimalarial therapeutic effect and improved animal safety in rodent malaria model. Collectively, 33 and 37 were structurally novel PfHDAC inhibitors and promising antimalarial lead compounds for the next generation of antimalarial drug research.

Auto QSAR-based active learning docking for hit identification of potential inhibitors of Plasmodium falciparum Hsp90 as antimalarial agents

Malaria which is mainly caused by Plasmodium falciparum parasite remains a devastating public health concern, necessitating the need to develop new antimalarial agents. P. falciparum heat shock protein 90 (Hsp90), is indispensable for parasite survival and a promising drug target. Inhibitors targeting the ATP-binding pocket of the N-terminal domain have anti-Plasmodium effects. We proposed a de novo active learning (AL) driven method in tandem with docking to predict inhibitors with unique scaffolds and preferential selectivity towards PfHsp90. Reference compounds, predicted to bind PfHsp90 at the ATP-binding pocket and possessing anti-Plasmodium activities, were used to generate 10,000 unique derivatives and to build the Auto-quantitative structures activity relationships (QSAR) models. Glide docking was performed to predict the docking scores of the derivatives and > 15,000 compounds obtained from the ChEMBL database. Re-iterative training and testing of the models was performed until the optimum Kennel-based Partial Least Square (KPLS) regression model with a regression coefficient R2 = 0.75 for the training set and squared correlation prediction Q2 = 0.62 for the test set reached convergence. Rescoring using induced fit docking and molecular dynamics simulations enabled us to prioritize 15 ATP/ADP-like design ideas for purchase. The compounds exerted moderate activity towards P. falciparum NF54 strain with IC50 values of ≤ 6μM and displayed moderate to weak affinity towards PfHsp90 (KD range: 13.5-19.9μM) comparable to the reported affinity of ADP. The most potent compound was FTN-T5 (PfN54 IC50:1.44μM; HepG2/CHO cells SI≥ 29) which bound to PfHsp90 with moderate affinity (KD:7.7μM), providing a starting point for optimization efforts. Our work demonstrates the great utility of AL for the rapid identification of novel molecules for drug discovery (i.e., hit identification). The potency of FTN-T5 will be critical for designing species-selective inhibitors towards developing more efficient agents against malaria.

Malaria treatment for prevention: a modelling study of the impact of routine case management on malaria prevalence and burden

BACKGROUND

Testing and treating symptomatic malaria cases is crucial for case management, but it may also prevent future illness by reducing mean infection duration. Measuring the impact of effective treatment on burden and transmission via field studies or routine surveillance systems is difficult and potentially unethical. This project uses mathematical modeling to explore how increasing treatment of symptomatic cases impacts malaria prevalence and incidence.

METHODS

Leveraging the OpenMalaria stochastic agent-based transmission model, we first simulated an array of transmission intensities with baseline effective treatment coverages of 28%, 44%, and 54% incorporated to reflect the 2023 coverage distribution across Africa, as estimated by the Malaria Atlas Project. We assessed the impact of increasing coverage to as high as 60%, the highest 2023 estimate on the continent. Subsequently, we performed simulations resembling the specific subnational endemicities of Kenya, Mozambique, and Benin, using the Malaria Atlas Project estimates of intervention coverages to reproduce historical subnational prevalence. We estimated the impact of increasing effective treatment coverage in these example settings in terms of prevalence reduction and clinical cases averted in children under 5 years old and the total population.

RESULTS

The most significant prevalence reduction - up to 50% - was observed in young children from lower transmission settings (prevalence below 0.2), alongside a 35% reduction in incidence, when increasing effective treatment from 28% to 60%. A nonlinear relationship between baseline transmission intensity and the impact of treatment was observed. Increasing effective treatment coverage to 60% reduced the risk in high-risk areas (prevalence in children under 5 years old > 0.3), affecting 39% of young children in Benin and 20% in Mozambique previously living in those areas. In Kenya where most of the population lives in areas with prevalence below 0.15, and case management is fairly high (53.9%), 0.39% of children were estimated to transition to lower-risk areas.

CONCLUSIONS

Improving case management directly reduces the burden of illness, but these results suggest it also reduces transmission, especially for young children. With vector control interventions, enhancing case management can be an important tool for reducing transmission intensity over time.

A virus associated with the zoonotic pathogen Plasmodium knowlesi causing human malaria is a member of a diverse and unclassified viral taxon

The Apicomplexa are a phylum of single-celled eukaryotes that can infect humans and include the mosquito-borne parasite Plasmodium, the cause of malaria. Viruses that infect non-Plasmodium spp. disease-causing protozoa affect the pathogen life cycle and disease outcomes. However, only one RNA virus (Matryoshka RNA virus 1) has been identified in Plasmodium, and none have been identified in zoonotic Plasmodium species. The rapid expansion of the known RNA virosphere via metagenomic sequencing suggests that this dearth is due to the divergent nature of RNA viruses that infect protozoa. We leveraged newly uncovered data sets to explore the virome of human-infecting Plasmodium species collected in Sabah, east (Borneo) Malaysia. From this, we identified a highly divergent RNA virus in two human-infecting P. knowlesi isolates that is related to the unclassified group 'ormycoviruses'. By characterizing 15 additional ormycoviruses identified in the transcriptomes of arthropods, we show that this group of viruses exhibits a complex ecology as noninfecting passengers at the arthropod-mammal interface. With the addition of viral diversity discovered using the artificial intelligence-based analysis of metagenomic data, we also demonstrate that the ormycoviruses are part of a diverse and unclassified viral taxon. This is the first observation of an RNA virus in a zoonotic Plasmodium species. By linking small-scale experimental data to advances in large-scale virus discovery, we characterize the diversity and confirm the putative genomic architecture of an unclassified viral taxon. This approach can be used to further explore the virome of disease-causing Apicomplexa and better understand how protozoa-infecting viruses may affect parasite fitness, pathobiology, and treatment outcomes.

Biogenesis of cytochromes c and c 1 in the electron transport chain of malaria parasites

Plasmodium malaria parasites retain an essential mitochondrional electron transport chain (ETC) that is critical for growth within humans and mosquitoes and a key antimalarial drug target. ETC function requires cytochromes c and c 1 that are unusual among heme proteins due to their covalent binding to heme via conserved CXXCH sequence motifs. Heme attachment to these proteins in most eukaryotes requires the mitochondrial enzyme holocytochrome c synthase (HCCS) that binds heme and the apo cytochrome to facilitate biogenesis of the mature cytochrome c or c 1. Although humans encode a single bifunctional HCCS that attaches heme to both proteins, Plasmodium parasites are like yeast and encode two separate HCCS homologs thought to be specific for heme attachment to cyt c (HCCS) or cyt c 1 (HCC1S). To test the function and specificity of P. falciparum HCCS and HCC1S, we used CRISPR/Cas9 to tag both genes for conditional expression. HCC1S knockdown selectively impaired cyt c 1 biogenesis and caused lethal ETC dysfunction that was not reversed by over-expression of HCCS. Knockdown of HCCS caused a more modest growth defect but strongly sensitized parasites to mitochondrial depolarization by proguanil, revealing key defects in ETC function. These results and prior heterologous studies in E. coli of cyt c hemylation by P. falciparum HCCS and HCC1S strongly suggest that both homologs are essential for mitochondrial ETC function and have distinct specificities for biogenesis of cyt c and c 1, respectively, in parasites. This study lays a foundation to develop novel strategies to selectively block ETC function in malaria parasites.

A novel 4-aminoquinoline chemotype with multistage antimalarial activity and lack of cross-resistance with PfCRT and PfMDR1 mutants

Artemisinin-based combination therapy (ACT) is the mainstay of effective treatment of Plasmodium falciparum malaria. However, the long-term utility of ACTs is imperiled by widespread partial artemisinin resistance in Southeast Asia and its recent emergence in parts of East Africa. This underscores the need to identify chemotypes with new modes of action (MoAs) to circumvent resistance to ACTs. In this study, we characterized the asexual blood stage antiplasmodial activity and resistance mechanisms of LDT-623, a 4-aminoquinoline (4-AQ). We also detected LDT-623 activity against multiple stages (liver schizonts, stage IV-V gametocytes, and ookinetes) of Plasmodium's life cycle, a feature unlike other 4-AQs such as chloroquine (CQ) and piperaquine (PPQ). Using heme fractionation profiling and drug uptake studies in PfCRT-containing proteoliposomes, we observed inhibition of hemozoin formation and PfCRT-mediated transport, which constitute characteristic features of 4-AQs' MoA. We also found minimal cross-resistance to LDT-623 in a panel of mutant pfcrt or pfmdr1 lines, but not the PfCRT F145I mutant that is highly resistant to PPQ resistance yet is very unfit. No P. falciparum parasites were recovered in an in vitro resistance selection study, suggesting a high barrier for resistance to emerge. Finally, a competitive growth assay comprising >50 barcoded parasite lines with mutated resistance mediators or major drug targets found no evidence of cross-resistance. Our findings support further exploration of this promising 4-AQ.

Leveraging the Aggregated Protein Dye YAT2150 for Malaria Chemotherapy

Background/Objectives: YAT2150 is a first-in-class antiplasmodial compound that has been recently proposed as a new interesting drug for malaria therapy. Methods/Results: The fluorescence of YAT2150 rapidly increases upon its entry into Plasmodium, a property that can be of use for the design of highly sensitive diagnostic approaches. YAT2150 blocks the in vitro development of the ookinete stage of Plasmodium and, when added to an infected blood meal, inhibits oocyst formation in the mosquito. Thus, the compound could possibly contribute to future transmission-blocking antimalarial strategies. Cell influx/efflux studies in Caco-2 cells suggest that YAT2150 is internalized by endocytosis and also through the OATP2B1 transporter, whereas its main export route would be via OSTα. YAT2150 has an overall favorable drug metabolism and pharmacokinetics profile, and its moderate cytotoxicity can be significantly reduced upon encapsulation in immunoliposomes, which leads to a dramatic increase in the drug selectivity index to values close to 1000. Although YAT2150 binds amyloid-forming peptides, its in vitro fluorescence emission is stronger upon association with peptides that form amorphous aggregates, suggesting that regions enriched in unstructured proteins are the preferential binding sites of the drug inside Plasmodium cells. The reduction of protein aggregation in the parasite after YAT2150 treatment, which has been suggested to be directly related to the drug's mode of action, is also observed following treatment with quinoline antimalarials like chloroquine and primaquine. Conclusions: Altogether, the data presented here indicate that YAT2150 can represent the spearhead of a new family of compounds for malaria diagnosis and therapy due to its presumed novel mode of action based on the interaction with functional protein aggregates in the pathogen.

A virus associated with the zoonotic pathogen Plasmodium knowlesi causing human malaria is a member of a diverse and unclassified viral taxon

Apicomplexa are single-celled eukaryotes that can infect humans and include the mosquito-borne parasite Plasmodium, the cause of malaria. Increasing rates of drug resistance in human-only Plasmodium species are reducing the efficacy of control efforts and antimalarial treatments. There are also rising cases of P. knowlesi, the only zoonotic Plasmodium species that causes severe disease and death in humans. Thus, there is a need to develop additional innovative strategies to combat malaria. Viruses that infect non-Plasmodium spp. Disease-causing protozoa have been shown to affect pathogen life cycle and disease outcomes. However, only one virus (Matryoshka RNA virus 1) has been identified in Plasmodium, and none have been identified in zoonotic Plasmodium species. The rapid expansion of the known RNA virosphere using structure- and artificial intelligence-based methods suggests that this dearth is due to the divergent nature of RNA viruses that infect protozoa. We leveraged these newly uncovered data sets to explore the virome of human-infecting Plasmodium species collected in Sabah, east (Borneo) Malaysia. We identified a highly divergent RNA virus in two human-infecting P. knowlesi isolates that is related to the unclassified group 'ormycoviruses'. By characterising fifteen additional ormycoviruses identified in the transcriptomes of arthropods we show that this group of viruses exhibits a complex ecology at the arthropod-mammal interface. Through the application of artificial intelligence methods, we then demonstrate that the ormycoviruses are part of a diverse and unclassified viral taxon. This is the first observation of an RNA virus in a zoonotic Plasmodium species. By linking small-scale experimental data to large-scale virus discovery advances, we characterise the diversity and genomic architecture of an unclassified viral taxon. This approach should be used to further explore the virome of disease-causing Apicomplexa and better understand how protozoa-infecting viruses may affect parasite fitness, pathobiology, and treatment outcomes.

Establishment and evaluation of a qPCR method for the detection of pfmdr1 mutations in Plasmodium falciparum, the causal agent of fatal malaria

Drug resistance surveillance is a major integral part of malaria control programs. Molecular methods play a pivotal role in drug resistance detection and related molecular research. This study aimed to develop a rapid and accurate detection method for drug resistance of Plasmodium falciparum (P. falciparum). A quantitative real-time PCR (qPCR) assay has been developed that identifies the mutation at locus A256T in the P.falciparum multi-drug resistance(pfmdr1) gene producing amino acid change at position 86. The results of 198 samples detected by qPCR were consistent with nested PCR and sequencing, giving an accuracy of 94.3%. The sensitivity, specificity, positive and negative predictive value of qPCR were 85.7%, 97.6%, 90.0% and 96.4%, respectively. The results of qPCR are basically consistent with the nested PCR, which is expected to replace the nested PCR as a new molecular biological method for drug resistance detection, providing reliable technical support for global malaria prevention and control.

Current Status of Malaria Control and Elimination in Africa: Epidemiology, Diagnosis, Treatment, Progress and Challenges

The African continent carries the greatest malaria burden in the world. Falciparum malaria especially has long been the leading cause of death in Africa. Climate, economic factors, geographical location, human intervention and unstable security are factors influencing malaria transmission. Due to repeated infections and early interventions, the proportion of clinically atypical malaria or asymptomatic plasmodium carriers has increased significantly, which easily lead to misdiagnosis and missed diagnosis. African countries have made certain progress in malaria control and elimination, including rapid diagnosis of malaria, promotion of mosquito nets and insecticides, intermittent prophylactic treatment in high-risk groups, artemisinin based combination therapies, and the development of vaccines. Between 2000 and 2022, there has been a 40% decrease in malaria incidence and a 60% reduction in mortality rate in the WHO African Region. However, many challenges are emerging in the fight against malaria in Africa, such as climate change, poverty, substandard health services and coverage, increased outdoor transmission and the emergence of new vectors, and the growing threat of resistance to antimalarial drugs and insecticides. Joint prevention and treatment, identifying molecular determinants of resistance, new drug development, expanding seasonal malaria chemo-prevention intervention population, and promoting the vaccination of RTS, S/AS01 and R21/Matrix-M may help to solve the dilemma. China's experience in eliminating malaria is conducive to Africa's malaria prevention and control, and China-Africa cooperation needs to be constantly deepened and advanced. Our review aims to help the global public develop a comprehensive understanding of malaria in Africa, thereby contributing to malaria control and elimination.

The emergence of artemisinin partial resistance in Africa: how do we respond?

Malaria remains one of the most important infectious diseases in the world, with the greatest burden in sub-Saharan Africa, primarily from Plasmodium falciparum infection. The treatment and control of malaria is challenged by resistance to most available drugs, but partial resistance to artemisinins (ART-R), the most important class for the treatment of malaria, was until recently confined to southeast Asia. This situation has changed, with the emergence of ART-R in multiple countries in eastern Africa. ART-R is mediated primarily by single point mutations in the P falciparum kelch13 protein, with several mutations present in African parasites that are now validated resistance mediators based on clinical and laboratory criteria. Major priorities at present are the expansion of genomic surveillance for ART-R mutations across the continent, more frequent testing of the efficacies of artemisinin-based regimens against uncomplicated and severe malaria in trials, more regular assessment of ex-vivo antimalarial drug susceptibilities, consideration of changes in treatment policy to deter the spread of ART-R, and accelerated development of new antimalarial regimens to overcome the impacts of ART-R. The emergence of ART-R in Africa is an urgent concern, and it is essential that we increase efforts to characterise its spread and mitigate its impact.

National genomic profiling of Plasmodium falciparum antimalarial resistance in Zambian children participating in the 2018 Malaria Indicator Survey

The emergence of antimalarial drug resistance is a major threat to malaria control and elimination. Using whole genome sequencing of 282 P. falciparum samples collected during the 2018 Zambia National Malaria Indicator Survey, we determined the prevalence and spatial distribution of known and candidate antimalarial drug resistance mutations. High levels of genotypic resistance were found across Zambia to pyrimethamine, with over 94% (n=266) of samples having the Pfdhfr triple mutant (N51I, C59R, and S108N), and sulfadoxine, with over 84% (n=238) having the Pfdhps double mutant (A437G and K540E). In northern Zambia, 5.3% (n=15) of samples also harbored the Pfdhps A581G mutation. Although 29 mutations were identified in Pfkelch13, these mutations were present at low frequency (<2.5%), and only three were WHO-validated artemisinin partial resistance mutations: P441L (n=1, 0.35%), V568M (n=2, 0.7%) and R622T (n=1, 0.35%). Notably, 91 (32%) of samples carried the E431K mutation in the Pfatpase6 gene, which is associated with artemisinin resistance. No specimens carried any known mutations associated with chloroquine resistance in the Pfcrt gene (codons 72-76). P. falciparum strains circulating in Zambia were highly resistant to sulfadoxine and pyrimethamine but remained susceptible to chloroquine and artemisinin. Despite this encouraging finding, early genetic signs of developing artemisinin resistance highlight the urgent need for continued vigilance and expanded routine genomic surveillance to monitor these changes.

Novel molecular inhibitor design for Plasmodium falciparum Lactate dehydrogenase enzyme using machine learning generated library of diverse compounds

Generative machine learning models offer a novel strategy for chemogenomics and de novo drug design, allowing researchers to streamline their exploration of the chemical space and concentrate on specific regions of interest. In cases with limited inhibitor data available for the target of interest, de novo drug design plays a crucial role. In this study, we utilized a package called 'mollib,' trained on ChEMBL data containing approximately 365,000 bioactive molecules. By leveraging transfer learning techniques with this package, we generated a series of compounds, starting from five initial compounds, which are potential Plasmodium falciparum (Pf) Lactate dehydrogenase inhibitors. The resulting compounds exhibit structural diversity and hold promise as potential novel Pf Lactate dehydrogenase inhibitors.

Exploring the relationship between Plasmodium falciparum genetic diversity and antimalarial drugs resistance markers in a malaria-endemic region of Burkina Faso

Introduction

the diversity of Plasmodium falciparum genotypes affects the dynamics of malaria transmission and is thought to be one of the factors hampering malaria control efforts. This study aimed to investigate the relationship between Plasmodium falciparum genetic diversity and chloroquine and sulfadoxine-pyrimethamine resistance markers in malaria endemic areas of Burkina Faso.

Methods

in a cross-sectional study, populations residing in Nouna health district were randomly recruited. Blood samples were used for microscopic malaria diagnosis, and genetic polymorphism alleles of msp1 and msp2 genotyping by nested PCR. Restricted fragment length polymorphism analysis was used to identify antimalarial resistance markers. Logistic regression analysis explored the association between msp1/msp2 alleles and antimalarial drug resistance markers. ANOVA was used to explore the association between the mean complexity of infection (mCOI) and prevalence of resistance markers.

Results

the overall prevalence of Plasmodium falciparum infection was 27.1%. The proportions of K1, MAD20, RO33, FC27, 3D7 individuals with mutations in the pfcrt76T gene were 4.3%, 6.9%, 7.0%, 6.8% and 7.1% respectively. Those with mutations in pfmdr1 were 2.7%, 2%, 2.3%, 6.8% and 7.1%. No significant associations were detected between msp1/msp2 alleles and chloroquine or sulfadoxine-pyrimethamine resistance markers. However, the mean complexity of infection (mCOI) was significantly higher in individuals with the pfcrt76T mutation.

Conclusion

overall, this study showed that the genetic diversity of Plasmodium falciparum does not significantly affect the presence of antimalarial drug resistance genes. The competition between different strains (polyclonality) of the parasite within the host was probably unfavorable for mutant strains.

A Plasmodium falciparum genetic cross reveals the contributions of pfcrt and plasmepsin II/III to piperaquine drug resistance

Piperaquine (PPQ) is widely used in combination with dihydroartemisinin as a first-line treatment against malaria. Multiple genetic drivers of PPQ resistance have been reported, including mutations in the Plasmodium falciparum chloroquine resistance transporter (pfcrt) and increased copies of plasmepsin II/III (pm2/3). We generated a cross between a Cambodia-derived multidrug-resistant KEL1/PLA1 lineage isolate (KH004) and a drug-susceptible Malawian parasite (Mal31). Mal31 harbors a wild-type (3D7-like) pfcrt allele and a single copy of pm2/3, while KH004 has a chloroquine-resistant (Dd2-like) pfcrt allele with an additional G367C substitution and multiple copies of pm2/3. We recovered 104 unique recombinant parasites and examined a targeted set of progeny representing all possible combinations of variants at pfcrt and pm2/3. We performed a detailed analysis of competitive fitness and a range of PPQ susceptibility phenotypes with these progenies, including PPQ survival assay, area under the dose response curve, and a limited point IC50. We find that inheritance of the KH004 pfcrt allele is required for reduced PPQ sensitivity, whereas copy number variation in pm2/3 further decreases susceptibility but does not confer resistance in the absence of additional mutations in pfcrt. A deep investigation of genotype-phenotype relationships demonstrates that progeny clones from experimental crosses can be used to understand the relative contributions of pfcrt, pm2/3, and parasite genetic background to a range of PPQ-related traits. Additionally, we find that the resistance phenotype associated with parasites inheriting the G367C substitution in pfcrt is consistent with previously validated PPQ resistance mutations in this transporter.IMPORTANCEResistance to piperaquine, used in combination with dihydroartemisinin, has emerged in Cambodia and threatens to spread to other malaria-endemic regions. Understanding the causal mutations of drug resistance and their impact on parasite fitness is critical for surveillance and intervention and can also reveal new avenues to limiting the evolution and spread of drug resistance. An experimental genetic cross is a powerful tool for pinpointing the genetic determinants of key drug resistance and fitness phenotypes and has the distinct advantage of quantifying the effects of naturally evolved genetic variation. Our study was strengthened since the full range of copies of KH004 pm2/3 was inherited among the progeny clones, allowing us to directly test the role of the pm2/3 copy number on resistance-related phenotypes in the context of a unique pfcrt allele. Our multigene model suggests an important role for both loci in the evolution of this multidrug-resistant parasite lineage.

Novel hydrazone compounds with broad-spectrum antiplasmodial activity and synergistic interactions with antimalarial drugs

The development of novel antiplasmodial compounds with broad-spectrum activity against different stages of Plasmodium parasites is crucial to prevent malaria disease and parasite transmission. This study evaluated the antiplasmodial activity of seven novel hydrazone compounds (referred to as CB compounds: CB-27, CB-41, CB-50, CB-53, CB-58, CB-59, and CB-61) against multiple stages of Plasmodium parasites. All CB compounds inhibited blood stage proliferation of drug-resistant or sensitive strains of Plasmodium falciparum in the low micromolar to nanomolar range. Interestingly, CB-41 exhibited prophylactic activity against hypnozoites and liver schizonts in Plasmodium cynomolgi, a primate model for Plasmodium vivax. Four CB compounds (CB-27, CB-41, CB-53, and CB-61) inhibited P. falciparum oocyst formation in mosquitoes, and five CB compounds (CB-27, CB-41, CB-53, CB-58, and CB-61) hindered the in vitro development of Plasmodium berghei ookinetes. The CB compounds did not inhibit the activation of P. berghei female and male gametocytes in vitro. Isobologram assays demonstrated synergistic interactions between CB-61 and the FDA-approved antimalarial drugs, clindamycin and halofantrine. Testing of six CB compounds showed no inhibition of Plasmodium glutathione S-transferase as a putative target and no cytotoxicity in HepG2 liver cells. CB compounds are promising candidates for further development as antimalarial drugs against multidrug-resistant parasites, which could also prevent malaria transmission.

Combating antimicrobial resistance in malaria, HIV and tuberculosis

Antimicrobial resistance poses a significant threat to the sustainability of effective treatments against the three most prevalent infectious diseases: malaria, human immunodeficiency virus (HIV) infection and tuberculosis. Therefore, there is an urgent need to develop novel drugs and treatment protocols capable of reducing the emergence of resistance and combating it when it does occur. In this Review, we present an overview of the status and underlying molecular mechanisms of drug resistance in these three diseases. We also discuss current strategies to address resistance during the research and development of next-generation therapies. These strategies vary depending on the infectious agent and the array of resistance mechanisms involved. Furthermore, we explore the potential for cross-fertilization of knowledge and technology among these diseases to create innovative approaches for minimizing drug resistance and advancing the discovery and development of new anti-infective treatments. In conclusion, we advocate for the implementation of well-defined strategies to effectively mitigate and manage resistance in all interventions against infectious diseases.

Emergence, transmission dynamics and mechanisms of artemisinin partial resistance in malaria parasites in Africa

Malaria, mostly due to Plasmodium falciparum infection in Africa, remains one of the most important infectious diseases in the world. Standard treatment for uncomplicated P. falciparum malaria is artemisinin-based combination therapy (ACT), which includes a rapid-acting artemisinin derivative plus a longer-acting partner drug, and standard therapy for severe P. falciparum malaria is intravenous artesunate. The efficacy of artemisinins and ACT has been threatened by the emergence of artemisinin partial resistance in Southeast Asia, mediated principally by mutations in the P. falciparum Kelch 13 (K13) protein. High ACT treatment failure rates have occurred when resistance to partner drugs is also seen. Recently, artemisinin partial resistance has emerged in Rwanda, Uganda and the Horn of Africa, with independent emergences of different K13 mutants in each region. In this Review, we summarize our current knowledge of artemisinin partial resistance and focus on the emergence of resistance in Africa, including its epidemiology, transmission dynamics and mechanisms. At present, the clinical impact of emerging resistance in Africa is unclear and most available evidence suggests that the efficacies of leading ACTs remain excellent, but there is an urgent need to better appreciate the extent of the problem and its consequences for the treatment and control of malaria.

Structural variety and pharmacological potential of naphthylisoquinoline alkaloids

Naphthylisoquinoline alkaloids are a fascinating class of natural biaryl compounds. They show characteristic mono- and dimeric scaffolds, with chiral axes and stereogenic centers. Since the appearance of the last comprehensive overview on these secondary plant metabolites in this series in 1995, the number of discovered representatives has tremendously increased to more than 280 examples known today. Many novel-type compounds have meanwhile been discovered, among them naphthylisoquinoline-related follow-up products like e.g., the first seco-type (i.e., ring-opened) and ring-contracted analogues. As highlighted in this review, the knowledge on the broad structural chemodiversity of naphthylisoquinoline alkaloids has been decisively driven forward by extensive phytochemical studies on the metabolite pattern of Ancistrocladus abbreviatus from Coastal West Africa, which is a particularly "creative" plant. These investigations furnished a considerable number of more than 80-mostly new-natural products from this single species, with promising antiplasmodial activities and with pronounced cytotoxic effects against human leukemia, pancreatic, cervical, and breast cancer cells. Another unique feature of naphthylisoquinoline alkaloids is their unprecedented biosynthetic origin from polyketidic precursors and not, as usual for isoquinoline alkaloids, from aromatic amino acids-a striking example of biosynthetic convergence in nature. Furthermore, remarkable botanical results are presented on the natural producers of naphthylisoquinoline alkaloids, the paleotropical Dioncophyllaceae and Ancistrocladaceae lianas, including first investigations on the chemoecological role of these plant metabolites and their storage and accumulation in particular plant organs.

Design, synthesis and Anti-Plasmodial activity of Mortiamide-Lugdunin conjugates

In this study, two linear and corresponding cyclic heptapeptide versions of mortiamide A-lugdunin hybrids were designed and synthesized by integrating an anti-malarial peptide epitope derived from Mortiamide A, combined with four residues known for their membrane interactions. Using this synthetic strategy, the sequence of mortiamide A was partly re-engineered with an epitope sequence of lugdunin along with an amino acid replacement using all-L and D/L configurations. Importantly, the re-engineered cyclic mortiamides with all-L (3) and D/L (4) configurations exhibited promising anti-malarial activities against the P. falciparum drug-sensitive TM4/8 strain with half-maximal inhibitory concentration (IC50) values of 6.2 ± 0.5 and 4.8 ± 0.1 μM, respectively. Additionally, they exhibited anti-malarial activities against the P. falciparum multidrug-resistant V1/S strain with IC50 values of 5.0 ± 2.6 and 3.7 ± 0.7 μM, respectively. Interestingly, a linear re-engineered mortiamide with D/L configuration (2) exhibited promising anti-malarial activities, surpassing those of the re-engineered cyclic mortiamides (3 and 4), against both the P. falciparum sensitive TM4/8 and multidrug-resistant V1/S strains with IC50 values of 3.6 ± 0.5 and 2.8 ± 0.7 μM (IC50 of Mortiamide A = 7.85 ± 0.97, 5.31 ± 0.24 μM against 3D7 and Dd2 strains) without any cytotoxicity at >100 µM. The presence of D/L forms in a linear structure significantly impacted the anti-malarial activity against both the P. falciparum sensitive TM4/8 strain and the multidrug-resistant V1/S strain.

Strong positive selection biases identity-by-descent-based inferences of recent demography and population structure in Plasmodium falciparum

Malaria genomic surveillance often estimates parasite genetic relatedness using metrics such as Identity-By-Decent (IBD), yet strong positive selection stemming from antimalarial drug resistance or other interventions may bias IBD-based estimates. In this study, we use simulations, a true IBD inference algorithm, and empirical data sets from different malaria transmission settings to investigate the extent of this bias and explore potential correction strategies. We analyze whole genome sequence data generated from 640 new and 3089 publicly available Plasmodium falciparum clinical isolates. We demonstrate that positive selection distorts IBD distributions, leading to underestimated effective population size and blurred population structure. Additionally, we discover that the removal of IBD peak regions partially restores the accuracy of IBD-based inferences, with this effect contingent on the population's background genetic relatedness and extent of inbreeding. Consequently, we advocate for selection correction for parasite populations undergoing strong, recent positive selection, particularly in high malaria transmission settings.

Trends of Plasmodium falciparum molecular markers associated with resistance to artemisinins and reduced susceptibility to lumefantrine in Mainland Tanzania from 2016 to 2021

BACKGROUND

Therapeutic efficacy studies (TESs) and detection of molecular markers of drug resistance are recommended by the World Health Organization (WHO) to monitor the efficacy of artemisinin-based combination therapy (ACT). This study assessed the trends of molecular markers of artemisinin resistance and/or reduced susceptibility to lumefantrine using samples collected in TES conducted in Mainland Tanzania from 2016 to 2021.

METHODS

A total of 2,015 samples were collected during TES of artemether-lumefantrine at eight sentinel sites (in Kigoma, Mbeya, Morogoro, Mtwara, Mwanza, Pwani, Tabora, and Tanga regions) between 2016 and 2021. Photo-induced electron transfer polymerase chain reaction (PET-PCR) was used to confirm presence of malaria parasites before capillary sequencing, which targeted two genes: Plasmodium falciparum kelch 13 propeller domain (k13) and P. falciparum multidrug resistance 1 (pfmdr1).

RESULTS

Sequencing success was ≥ 87.8%, and 1,724/1,769 (97.5%) k13 wild-type samples were detected. Thirty-seven (2.1%) samples had synonymous mutations and only eight (0.4%) had non-synonymous mutations in the k13 gene; seven of these were not validated by the WHO as molecular markers of resistance. One sample from Morogoro in 2020 had a k13 R622I mutation, which is a validated marker of artemisinin partial resistance. For pfmdr1, all except two samples carried N86 (wild-type), while mutations at Y184F increased from 33.9% in 2016 to about 60.5% in 2021, and only four samples (0.2%) had D1246Y mutations. pfmdr1 haplotypes were reported in 1,711 samples, with 985 (57.6%) NYD, 720 (42.1%) NFD, and six (0.4%) carrying minor haplotypes (three with NYY, 0.2%; YFD in two, 0.1%; and NFY in one sample, 0.1%). Between 2016 and 2021, NYD decreased from 66.1% to 45.2%, while NFD increased from 38.5% to 54.7%.

CONCLUSION

This is the first report of the R622I (k13 validated mutation) in Tanzania. N86 and D1246 were nearly fixed, while increases in Y184F mutations and NFD haplotype were observed between 2016 and 2021. Despite the reports of artemisinin partial resistance in Rwanda and Uganda, this study did not report any other validated mutations in these study sites in Tanzania apart from R622I suggesting that intensified surveillance is urgently needed to monitor trends of drug resistance markers and their impact on the performance of ACT.

Role of seasonal importation and genetic drift on selection for drug-resistant genotypes of Plasmodium falciparum in high-transmission settings

Historically Plasmodium falciparum has followed a pattern of drug resistance first appearing in low-transmission settings before spreading to high-transmission settings. Several features of low-transmission regions are hypothesized as explanations: higher chance of symptoms and treatment seeking, better treatment access, less within-host competition among clones and lower rates of recombination. Here, we test whether importation of drug-resistant parasites is more likely to lead to successful emergence and establishment in low-transmission or high-transmission periods of the same epidemiological setting, using a spatial, individual-based stochastic model of malaria and drug-resistance evolution calibrated for Burkina Faso. Upon controlling for the timing of importation of drug-resistant genotypes and examination of key model variables, we found that drug-resistant genotypes imported during the low-transmission season were (i) more susceptible to stochastic extinction due to the action of genetic drift, and (ii) more likely to lead to establishment of drug resistance when parasites are able to survive early stochastic loss due to drift. This implies that rare importation events are more likely to lead to establishment if they occur during a high-transmission season, but that constant importation (e.g. neighbouring countries with high levels of resistance) may produce a greater risk during low-transmission periods.

Antigenic strain diversity predicts different biogeographic patterns of maintenance and decline of antimalarial drug resistance

The establishment and spread of antimalarial drug resistance vary drastically across different biogeographic regions. Though most infections occur in sub-Saharan Africa, resistant strains often emerge in low-transmission regions. Existing models on resistance evolution lack consensus on the relationship between transmission intensity and drug resistance, possibly due to overlooking the feedback between antigenic diversity, host immunity, and selection for resistance. To address this, we developed a novel compartmental model that tracks sensitive and resistant parasite strains, as well as the host dynamics of generalized and antigen-specific immunity. Our results show a negative correlation between parasite prevalence and resistance frequency, regardless of resistance cost or efficacy. Validation using chloroquine-resistant marker data supports this trend. Post discontinuation of drugs, resistance remains high in low-diversity, low-transmission regions, while it steadily decreases in high-diversity, high-transmission regions. Our study underscores the critical role of malaria strain diversity in the biogeographic patterns of resistance evolution.

Mutation in the 26S proteasome regulatory subunit rpn2 gene in Plasmodium falciparum confers resistance to artemisinin

Introduction

Malaria parasites increasingly develop resistance to all drugs available in the market, hampering the goal of reducing malaria burden.

Methods

Herein, we evaluated the impact of a single-nucleotide variant, E738K, present in the 26S proteasome regulatory subunit rpn2 gene, identified in Plasmodium chabaudi resistant parasites. Plasmids carrying a functional rpn2 interspecies chimeric gene with 5' recombination region from P. falciparum and 3' from P. chabaudi were constructed and transfected into Dd2 P. falciparum parasites.

Results and discussion

The 738K variant parasite line presented increased parasite survival when subjected to dihydroartemisinin (DHA), as well as increased chymotrypsin-like activity and decreased accumulation of polyubiquitinated proteins. We thus conclude that the ubiquitin-proteasome pathway, including the 738K variant, play an important role in parasite response to DHA, being the first report of a mutation in a potential DHA drug target enhancing parasite survival and contributing to a significant advance in the understanding the biology of artemisinin resistance.