Pyrethroids in an AlphaFold2 Model of the Insect Sodium Channel

The major component of Heteractis magnifica sea anemone venom, RpIII, exhibits strong subtype selectivity for insects over mammalian voltage-gated sodium channels

Voltage-gated sodium channels (NaV) are molecular targets for the development of drugs for the treatment of diseases such as epilepsy, neuropathic pain, long QT syndrome, etc., as well as for insecticides. Therefore, the search for novel selective NaV channel ligands is relevant. Using amplicon deep sequencing of tentacle cDNA libraries from sea anemones Heteractis magnifica, 36 transcripts related to RpIII neurotoxin, a NaV channel modulators, were revealed. The recombinant RpIII was moderately toxic for mice (LD50 0.030 ± 0.004 mg/kg) but did not demonstrate any activity towards NaV in human SH-SY5Y cells. The toxin inhibited inactivation of heterologously expressed mammalian, insect, and arachnid NaV channels with higher specificity to insect channels. Cockroach (Blattella germanica) sodium channel BgNaV1 (EC50 of 2.4 ± 0.2 nM) and yellow fever mosquito (Aedes aegypti) channel AaNaV1 (EC50 of 1.5 ± 0.3 nM) were the most sensitive to RpIII, while mammals NaV had EC50 values above 100 nM except mNaV1.6 (EC50 of 43.8 ± 3.6 nM). The low nanomolar RpIII affinity to insect AaNaV1 may be explained by the extensive intermolecular contacts found by docking study. According to the predicted data, the toxin lands on the ion channel between voltage-sensing domain IV and pore domain I, also known as toxin site 3, followed by stabilizing the channels in the open state what was measured at electrophysiological experiments.

Alanine to glycine substitution in the PyR2 confers sodium channel resistance to Type I pyrethroids

BACKGROUND

Aedes aegypti is a primary urban vector of dengue, yellow fever, Zika and chikungunya worldwide. Pyrethroid insecticides are the most effective insecticides for controlling Ae. aegypti. However, pyrethroid resistance has developed due to the long-term overuse of the insecticides, and many knockdown resistance (kdr) mutations have been identified in the resistant populations. A1007G, an alanine to glycine substitution, was found in resistant Ae. aegypti from Vietnam and Malaysia, which has always co-existed with F1534C and V1016G. However, the role of A1007G in pyrethroid resistance and the linkage of A1007G and F1534C or V1016G remain unknown.

RESULTS

In this study, we examined the effects of mutations on the sodium channel gating properties and pyrethroid sensitivity in Xenopus oocytes. We found mutations A1007G, A1007G + F1534C and A1007G + V1016G + F1534C shifted the voltage dependence of activation in the depolarizing direction. Mutations A1007G + F1534C and A1007G + V1016G + F1534C shifted the voltage dependence of inactivation in the depolarizing direction. Both mutations A1007G and F1534C reduced the channel sensitivity to two Type I pyrethroids, permethrin and bifenthrin, and synergistic effects were observed between mutations A1007G and F1534C. However, none of the mutations, A1007G, F1534C and A1007G + F1534C affected the channel sensitivity to two Type II pyrethroids, deltamethrin and cypermethrin. Furthermore, triple mutations A1007G + V1016G + F1534C significantly reduced the channel sensitivity to both Type I and Type II pyrethroids.

CONCLUSION

We identified A1007G had a distinct effect on sodium channel sensitivity to Type I, but not to Type II pyrethroids, also A1007G exhibited synergistic effects with F1534C to Type I pyrethroids, which will provide a fundamental insight into the distinct molecular interactions between insect sodium channel and Type I or Type II pyrethroids. © 2024 Society of Chemical Industry.

Capsaicin preferentially inhibits slow-inactivation sodium currents in insects

Capsaicin, a pungent ingredient found in chili peppers, exhibits various pharmacological activities including inhibiting voltage-gated sodium channels (VGSCs) in mammals, suppressing sodium currents. Although capsaicin shows insecticidal activity, its underlying mechanism of action on insect VGSCs remains unclear. Here, we evaluated the effects of capsaicin on insect nerve cords and VGSCs using neurophysiological techniques. Capsaicin injection immediately induced paralysis in American cockroaches (Periplaneta americana). Extracellular recordings of their nerve cords revealed that capsaicin inhibited the allethrin-induced excitation of nerve cord activity. Furthermore, in Xenopus oocytes expressing VGSCs of German cockroaches (Blattella germanica), capsaicin inhibited the steady-state activation of VGSCs, with an IC50 value of 130.6 μM. Capsaicin significantly shifted the half-inactivation potential of the inactivation curve of insect VGSCs in a slow-inactivated state from -44.61 to -48.92 mV. Although the state dependency of sodium current inhibition by capsaicin remains unknown, based on its effective concentration, capsaicin may preferentially inhibit sodium currents by acting on insect VGSCs in a slow-inactivated state. This unique profile may serve as a foundation for the creation of novel insecticides based on capsaicin properties.

Discovery of novel acetylcholinesterase inhibitors through AI-powered structure prediction and high-performance computing-enhanced virtual screening

Virtual screening (VS) methodologies have become key in the drug discovery process but are also applicable to other fields including catalysis, material design, and, more recently, insecticide solutions. Indeed, the search for effective pest control agents is a critical industrial objective, driven by the need to meet stringent regulations and address public health concerns. Cockroaches, known vectors of numerous diseases, represent a major challenge due to the toxicity of existing control measures to humans. In this article, we leverage an Artificial Intelligence (AI)-based screening of the Drug Bank (DB) database to identify novel acetylcholinesterase (AChE) inhibitors, a previously uncharacterized target in the American cockroach (Periplaneta americana). Our AI-based VS pipeline starts with the deep-learning-based AlphaFold to predict the previously unknown 3D structure of AChE based on its amino acid sequence. This first step enables the subsequent ligand-receptor VS of potential inhibitors, the development of which is performed using a consensus VS protocol based on two different tools: Glide, an industry-leading solution, and METADOCK 2, a metaheuristic-based tool that takes advantage of GPU acceleration. The proposed VS pipeline is further refined through rescoring to pinpoint the most promising biocide compounds against cockroaches. We show the search space explored by different metaheuristics generated by METADOCK 2 and how this search is more exhaustive, but complementary, than the one offered by Glide. Finally, we applied Molecular Mechanics Generalized Born Surface Area (MMGBSA) to list the most promising compounds to inhibit the AChE enzyme.

Genomic assessment of targets implicated in Rhipicephalus microplus acaricide resistance

Globally, the prevalence of Rhipicephalus microplus resistance to various acaricides has increased, and there is a need for the identification of molecular markers that can predict phenotypic resistance. These markers could serve as alternatives to the larval packet test (LPT), enabling rapid and accurate monitoring of resistance in these ticks against multiple acaricides. However, many of the historically identified markers are present in isolates from specific countries and their role in acaricide resistance remains unclear. This study aimed to assess these mutations by sequencing genomic regions encoding proteins historically associated with acaricide target site insensitivity and increased acaricide detoxification and comparing resistant and susceptible isolates from eight different countries. Employing a novel multiplex PCR setup developed during the study, the coding regions of 11 acaricide-resistant targets were amplified and sequenced across 37 R. microplus isolates from different locations. The identified mutations, both previously reported and novel, were compared between acaricide-susceptible and acaricide-resistant isolates, phenotypically characterized using the larval packet test or larval immersion test across five acaricide classes. Genotypes were then correlated with available phenotypes, and protein modelling of novel nonsynonymous mutations was conducted to assess their potential impact on acaricide resistance. Previously reported resistance-associated mutations were detected, some of which were present in both resistant and susceptible isolates. Novel mutations emerged from the 11 targets, but distinctions between susceptible and resistant isolates were not evident, except for the prevalent kdr mutation in synthetic pyrethroid-resistant isolates. The quest for predictive molecular markers for monitoring acaricide resistance remains challenging. Nevertheless, by utilizing a representative group of isolates, we determined that several historical mutations were present in both resistant and susceptible isolates. Additionally, the study provides valuable genetic data on acaricide-resistant and susceptible isolates from different geographical regions, focusing on genomic regions implicated in resistance. This baseline data offers a critical foundation for further research and the identification of more reliable molecular markers.

A unique mechanism of transfluthrin action revealed by mapping its binding sites in the mosquito sodium channel

Pyrethroid insecticides exert their toxic action by prolonging the opening of insect voltage-gated sodium channels, resulting in the characteristic tail current during membrane repolarization in voltage clamp experiments. Permethrin (PMT) and deltamethrin (DMT), representative type I and type II pyrethroids, respectively, are predicted to bind to two lipid-exposed pyrethroid receptor sites, PyR1 and PyR2, at the lipid-exposed interfaces of repeats II/III and I/II, respectively. Transfluthrin (TF), a volatile type I pyrethroid and mosquito repellent, has received increased attention in the global combat of vector-borne human diseases. However, the electrophysiological and molecular bases of TF action on insect sodium channels remain unexplored. In this study we discovered that, unlike DMT and PMT, TF barely induces the characteristic tail current of the Aedes aegypti mosquito sodium channel (AaNav1-1) expressed in Xenopus oocytes. Instead, TF induces a unique persistent current. We docked TF into the AlphaFold2 model of AaNav1-1 and found that the tetrafluorophenyl ring of TF binds to alpha helices S5, P1, and S6, but not to the linker helices S4-S5 within either PyR1 or PyR2. In agreement with the model, functional examination of 15 AaNav1-1 mutants demonstrated that substitutions of DMT/PMT-sensing residues in helices S5, P1, and S6, but not in the linker-helices S4-S5, altered channel sensitivity to TF. These results revealed the unique action of TF on channel gating and suggest a distinct subtype of type I pyrethroids with a previously uncharacterized pattern of interactions with residues at the dual pyrethroid receptor sites.

Unravelling impacts of the insecticide deltamethrin on neuronal sodium channels in honey bees: Molecular insights and behavioural outcomes

The current risk assessment framework for insecticides suffers from certain shortcomings in adequately addressing the effects of low doses on off-target species. To remedy this gap, a combination of behavioural assays and in vitro cellular approaches are required to refine the precision of toxicity assessment. The domestic honey bee has long been standing as an emblematic pollinator in ecotoxicology, and once more, it provides us with a practical testing model for this purpose. First, newly emerged bees (D1) were found more vulnerable than 6 days-old bees (D6) to deltamethrin, a widely used α-cyano-3-phenoxybenzyle pyrethroid. In D1 bees, the range of doses inducing mortality was shifted towards lower values (∼2-fold) with a correspondingly lower LD50 (11 ng/bee). Moreover, at low doses that do not induce mortality in laboratory conditions, the locomotor behaviour of D1 bees was more impacted than in D6 bees. This was evidenced by an increase in immobility time and a decrease in locomotor performance across all tested doses for D1 bees (0.75, 1.5 and 3 ng/bee) during automated 21 h-long observations. Behavioural disorders are linked to deltamethrin's disruption of voltage-gated sodium channels (NaVs) functions, as quantified in cultured neuronal cells. In the presence of deltamethrin, patch-clamp experiments revealed a concentration- and a use-dependent slowing of NaV kinetics. Channel's deactivation is slowed by three orders of magnitude at 10 μM deltamethrin. Two additional phenoxybenzyle pyrethroids, including the commonly used cypermethrin, elicited quantitatively similar effects on NaV kinetics. The integration of in vitro cellular assays and behavioural assays may facilitate a deeper understanding and prediction of insecticides toxicity.

Monitoring of pyrethroid resistance in Aedes aegypti: first report of double and triple kdr mutations in Buenos Aires Province

BACKGROUND

Dengue is an emerging disease in Argentina due to the colonization of Aedes aegypti, the mosquito vector. Buenos Aires Province is the biggest and most populated district in Argentina, suffering dengue outbreaks of growing magnitude. During epidemic periods, pyrethroid insecticides are used in this country to control adult mosquitoes. Pyrethroid resistance in dengue vectors has been reported worldwide, making it necessary to implement resistance management strategies. The voltage-gated sodium channel is the target site of pyrethroids. Mutations in the gene encoding this protein, called kdr mutations, are usually the molecular cause of pyrethroid resistance in insects. In Ae. aegypti from the Americas, three kdr substitutions were described: V410L, V1016I, and F1534C. The diagnostic of kdr mutations is recommended for the early detection of pyrethroid resistance as well as the consequent planning of evidence-based control policies.

METHODS

We distributed ovitraps across 16 localities in Buenos Aires Province, collecting 22,123 eggs. A total of 522 mosquitoes were genotyped in positions 1016 and 1534 of voltage-gated channel using multiplex high-resolution melting and/or TaqMan probe methods. A subset of 449 samples was also genotyped by a singleplex high-resolution melting method developed ad hoc and/or Sanger sequencing.

RESULTS

We have documented, for the first time to our knowledge in the central region of Argentina, the presence of the 1016Ikdr + 1534Ckdr allele. Additionally, our study reports the first identification of the V410L mutation in central Argentina. These results underscore a growing trend of pyrethroid resistance in Ae. aegypti, fueled by the widespread use of these insecticides.

CONCLUSIONS

We detected 1016Ikdr + 1534Ckdr and 410Lkdr mutations in central Argentina for the first time and improved the processivity and accuracy of kdr genotyping methods. The results are both a tool for resistance monitoring and a sign of alarm to direct efforts towards finding sustainable methods for vector control to complement or replace pyrethroids. Joint efforts between academia and authorities to develop and implement public policies for vector control are a productive way to transfer scientific results for their application in public health.

Functional Characterization of Double Mutations T929I/K1774N in the Voltage-Gated Sodium Channel of Megalurothrips usitatus (Bagnall) Related to Pyrethroid Resistance

Megalurothrips usitatus (Bagnall), the main pest on legume vegetables, is controlled by pyrethroids in the field. Field strains of M. usitatus resistant to pyrethroids were collected from three areas in Hainan Province (Haikou, Ledong, and Sanya City), and two mutations, T929I and K1774N, were detected in the voltage-gated sodium channel. In this study, the sodium channel in M. usitatus was first subcloned and successfully expressed in Xenopus oocytes. The single mutation (T929I or K1774N) and double mutation (T929I/K1774N) shifted the voltage dependence of activation in the hyperpolarization direction. The three mutants all reduced the amplitude of tail currents induced by type I (permethrin and bifenthrin) and type II (deltamethrin and λ-cyhalothrin) pyrethroids. Homology modeling analysis of these two mutations shows that they may change the local hydrophobicity and positive charge of the sodium channel. Our data can be used to reveal the causes of the resistance of M. usitatus to pyrethroids and provide guidance for the comprehensive control of M. usitatus in the future.

Pesticides: An alarming detrimental to health and environment

Pesticides are chemical substances of natural or synthetic origin that are used to eradicate pests and insects. These are indispensable in the agricultural processes for better crop production. Pesticide use aims to promote crop yield and protect the crops from diseases and damage. Pesticides must be handled carefully and disposed of appropriately because they are dangerous to people and other species by default. Environmental pollution occurs when pesticide contamination spreads away from the intended plants. Older pesticides such as lindane and dichlorodiphenyltrichloroethane (DDT) may remain in water and soil for a longer time. These accumulate in various parts of the food chain and cause damage to the ecosystem. Biological techniques in the management of pest control such as importation, augmentation, and conservation, and the accompanying procedures are more efficient, less expensive, and ecologically sound than other ways. This review mainly focuses on the consequences on the targeted and non-targeted organisms including the health and well-being of humans by the use of pesticides and their toxicity. The side effects that occur when a pesticide's LD50 exceeds the accepted limit through oral or skin penetration due to their binding to various receptors such as estrogen receptors, GABA, EGFR, and others. These pesticide classes include carbamates, pyrethroids, organochlorides, organophosphorus, and others. The current study seeks to highlight the urgent requirement for a novel agricultural concept that includes a major reduction in the use of chemical pesticides.

Leucine to tryptophane substitution in the pore helix IIP1 confer sodium channel resistance to pyrethroids and DDT

Aedes aegypti is responsible for transmitting a variety of arboviral infectious diseases such as dengue and chikungunya. Insecticides, particularly pyrethroids, are used widely for mosquito control. However, intensive used of pyrethroids has led to the selection of kdr mutations on sodium channels. L982W, locating in the PyR1 (Pyrethroid receptor site 1), was first reported in Ae. aegypti populations collected from Vietnam. Recently, the high frequency of L982W was detected in pyrethroid-resistant populations of Vietnam and Cambodia, and also concomitant mutations L982W + F1534C was detected in both countries. However, the role of L982W in pyrethroid resistance remains unclear. In this study, we examined the effects of L982W on gating properties and pyrethroid sensitivity in Xenopus oocytes. We found that mutations L982W and L982W + F1534C shifted the voltage dependence of activation in the depolarizing direction, however, neither mutations altered the voltage dependence of inactivation. L982W significantly reduced channel sensitivity to Type I pyrethroids, permethrin and bifenthrin, and Type II pyrethroids, deltamethrin and cypermethrin. No enhancement was observed when synergized with F1534C. In addition, L982W and L982W + F1534C mutations reduced the channel sensitivity to DDT. Our results illustrate the molecular basis of resistance mediates by L982W mutation, which will be helpful to understand the interacions of pyrethroids or DDT with sodium channels and develop molecular markers for monitoring pest resistance to pyrethroids and DDT.

First report on knockdown resistance mutations in wild populations of Aedes aegypti from Argentina determined by a novel multiplex high-resolution melting polymerase chain reaction method

BACKGROUND

The mosquito Aedes aegypti is an urban vector of dengue and other arboviruses. During epidemics of these viruses, pyrethroid insecticides are used for the control of adult mosquitoes. The worldwide resistance of Ae. aegypti to these insecticides is a cause of failure of vector control campaigns. The primary target of pyrethroids is the voltage-gated sodium channel. Point mutations in the gene coding for this channel, called knockdown resistance (kdr) mutations, are associated with pyrethroid resistance. Two kdr mutations, V1016I and F1534C, have increased in frequency in natural populations of Ae. aegypti in the Americas during the last decade. Their association with pyrethroid resistance has been largely demonstrated in field populations throughout the Americas, and in in vitro assays. Diagnostics for kdr polymorphism allow early detection of the spread of insecticide resistance, which is critical for timely decisions on vector management. Given the importance of resistance management, high-throughput methods for kdr genotyping are valuable tools as they can be used for resistance monitoring programs. These methods should be cost-effective, to allow regional-scale surveys. Despite the extensive presence of Ae. aegypti and incidence of dengue in Argentina, the presence, abundance, and distribution of kdr mutations in populations of this mosquito have yet to be reported for the country.

METHODS

Aedes aegypti samples were collected as immature stages or adults from Buenos Aires Metropolitan Area and northern localities of Tartagal (Salta Province) and Calilegua (Jujuy Province). Immature stages were maintained in the laboratory until they developed into adults. A high-resolution melting assay, based on an analysis of melting temperatures, was developed for the simultaneous genotyping of V1016I and F1534C kdr mutations. We used this method to infer the presence and frequencies of kdr alleles in 11 wild populations from Argentina.

RESULTS

We demonstrated the presence of kdr mutations in Ae. aegypti in Argentina in regions where this species is under different selection pressures due to the use of pyrethroids. The populations under analysis are located in geographically distant regions of the species' distribution in Argentina: the northern provinces of Salta and Jujuy and the Buenos Aires Metropolitan Area. Higher frequencies of resistant-associated alleles were detected in the northern region. We report a multiplex high-throughput assay based on a high-resolution melting polymerase chain reaction method for the simultaneous genotyping of V1016I and F1534C kdr mutations. This assay was shown to be cost-effective, and thus provides an interesting molecular tool for kdr genotyping in A. aegypti control campaigns.

CONCLUSIONS

We report, to the best of our knowledge for the first time, the presence of kdr mutations in populations of Ae. aegypti from geographically distant locations of Argentina that differ with respect to their epidemiological situation and history of mosquito control. We have developed a high-throughput method for the genotyping of kdr mutations in Ae. aegypti from the Americas. Given its affordability and short running time, this method can be used in control campaigns to monitor the presence and spread of kdr alleles. The information provided here is relevant for the rational design of control strategies in the context of integrated vector management.

Transfluthrin enhances odorant receptor-mediated spatial repellency in Aedes aegypti

Mosquito-borne diseases are an increasing global health challenge and vector-based interventions remain the most important methods for reducing the public health burden of most mosquito-borne diseases. Transfluthrin, a volatile pyrethroid insecticide, is used widely and effectively as an insecticide and as a repellent. In a recent study, we showed that at very low concentrations transfluthrin repels Aedes aegypti mosquitoes in a hand-in-cage assay without detectable stimulation of antennal olfactory responses. Furthermore, activation of sodium channels by transfluthrin enhances repellency by DEET, which has been reported to repel mosquitoes via odorant receptor (Or)-dependent and Or-independent mechanisms. However, whether activation of sodium channels by transfluthrin can serve as a general mechanism for synergizing the activities of other repellents remain unknown. In this study, we found that, in hand-in-cage assay, transfluthrin enhanced repellency by geranyl acetate and (E)-β-farnesene, which activate AaOr31. Such enhancement was not observed in AaOr31-knockout mosquitoes and dampened in a pyrethroid-resistant strain carrying two sodium channel mutations, which reduce the action of transfluthrin on sodium channels. In addition, transfluthrin also enhanced repellency by (-)-borneol, (±)-citronellal, camphor, and eucalyptol, which activate Or-mediated repellency. Our study has uncovered the ability of transfluthrin to enhance the repellency to a variety of mosquito repellents, beyond DEET, and provided experimental support for the emerging paradigm of synergistic interactions between repellency mediated by sodium channel activation and Or activation. These findings have potential implications in the development of more effective mosquito repellent mixtures.

AlphaFold2 and its applications in the fields of biology and medicine

AlphaFold2 (AF2) is an artificial intelligence (AI) system developed by DeepMind that can predict three-dimensional (3D) structures of proteins from amino acid sequences with atomic-level accuracy. Protein structure prediction is one of the most challenging problems in computational biology and chemistry, and has puzzled scientists for 50 years. The advent of AF2 presents an unprecedented progress in protein structure prediction and has attracted much attention. Subsequent release of structures of more than 200 million proteins predicted by AF2 further aroused great enthusiasm in the science community, especially in the fields of biology and medicine. AF2 is thought to have a significant impact on structural biology and research areas that need protein structure information, such as drug discovery, protein design, prediction of protein function, et al. Though the time is not long since AF2 was developed, there are already quite a few application studies of AF2 in the fields of biology and medicine, with many of them having preliminarily proved the potential of AF2. To better understand AF2 and promote its applications, we will in this article summarize the principle and system architecture of AF2 as well as the recipe of its success, and particularly focus on reviewing its applications in the fields of biology and medicine. Limitations of current AF2 prediction will also be discussed.

Detection of ryanodine receptor G4911E and I4754M mutation sites and analysis of binding modes of diamide insecticides with RyR on Galeruca daurica (Coleoptera: Chrysomelidae)

In recent years, the leaf beetle Galeruca daurica has broken out in the northern grasslands of Inner Mongolia, its management still mainly depends on chemical control using traditional insecticides or with novel action. The study was aim to identify mutation locus associated with resistance to diamide insecticides in field population of G. daurica, to provide a reference for rational selection of insecticides and to avoid the rapid resistance development to diamide insecticides. We cloned the full length of the ryanodine receptor gene of G. daurica (GdRyR), constructed 3D model and transmembrane regions by homologous modeling based on deduced amino acid sequence. Two potential mutation loci (Gly4911Glu and Ile4754Met) and allelic mutation frequencies were detected in individuals of G. daurica. In addition, their binding patterns to two diamide insecticides (chlorantraniliprole, cyantraniliprole) were analyzed separately using a molecular docking method. The full-length cDNA sequence of GdRyR (GenBank accession number: OP828593) was obtained by splicing and assembling, which is 15,399 bp in length and encodes 5,133 amino acids. The amino acid similarity of GdRyR with that of other Coleopteran insects were 86.70%-91.33%, which possessed the typical structural characteristics. An individual resistance allelic mutation frequency test on fifty field leaf beetles has identified 12% and 32% heterozygous individuals at two potential mutation loci Gly4911Glu and Ile4754Met, respectively. The affinity of the I4754M mutant model of GdRyR for chlorantraniliprole and cyantraniliprole was not significantly different from that of the wild type, and all had non-covalent interactions such as hydrogen bonding, hydrophobic interactions and π-cation interactions. However, the G4911E mutant model showed reduced affinity and reduced mode of action with two diamide insecticides, thus affecting the binding stability of the ryanodine receptor to the diamide insecticides. In conclusion, the G4911E mutation in GdRyR may be a potential mechanism for the development of resistance to diamide insecticides on G. daurica and should be a key concern for resistance risk assessment and reasonable applications of diamide insecticides for control in future. Moreover, this study could provide a reference for ryanodine receptor structure-based insecticides design.