In silico identification of genetic mutations conferring resistance to acetohydroxyacid synthase inhibitors: A case study of Kochia scoparia

Prevalence, spatial structure and evolution of resistance to acetolactate-synthase (ALS) inhibitors and 2,4-D in the major weed Papaver rhoeas (L.) assessed using a massive, country-wide sampling

BACKGROUND

Corn poppy (Papaver rhoeas) is the most damaging broadleaf weed in France. Massively parallel amplicon sequencing was used to investigate the prevalence, mode of evolution and spread of resistance-endowing ALS alleles in 422 populations randomly sampled throughout poppy's range in France. Bioassays were used to detect resistance to the synthetic auxin 2,4-D in 43 of these populations.

RESULTS

A total of 21 100 plants were analysed and 24 mutant ALS alleles carrying an amino-acid substitution involved or potentially involved in resistance were identified. The vast majority (97.6%) of the substitutions occurred at codon Pro197, where all six possible single-nucleotide non-synonymous substitutions plus four double-nucleotide substitutions were identified. Changes observed in the enzymatic properties of the mutant ALS isoforms could not explain the differences in prevalence among the corresponding alleles. Sequence read analysis showed that mutant ALS alleles had multiple, independent evolutionary origins, and could have evolved several times independently within an area of a few kilometres. Finally, 2,4-D resistance was associated with mutant ALS alleles in individual plants in one third of the populations assayed.

CONCLUSION

The intricate geographical mosaic of mutant ALS alleles observed is the likely result of the combination of huge population sizes, multiple independent mutation events and human-mediated spread of resistance. Our work highlights the ability of poppy populations and individual plants to accumulate different ALS alleles and as yet unknown mechanisms conferring resistance to synthetic auxins. This does not bode well for the continued use of chemical herbicides to control poppy. © 2023 Society of Chemical Industry.

Antibiotic resistance lessons for the herbicide resistance crisis

The challenges of resistance to antibiotics and resistance to herbicides have much in common. Antibiotic resistance became a risk in the 1950s, but a concerted global effort to manage it did not begin until after 2000. Widespread herbicide use began during the 1950s and was soon followed by an unabated rise in resistance. Here, we examine what lessons for combatting herbicide resistance could be learnt from the global, coordinated efforts of all stakeholders to avert the antibiotic resistance crisis. © 2021 Society of Chemical Industry.

Recent Developments in Free Energy Calculations for Drug Discovery

The grand challenge in structure-based drug design is achieving accurate prediction of binding free energies. Molecular dynamics (MD) simulations enable modeling of conformational changes critical to the binding process, leading to calculation of thermodynamic quantities involved in estimation of binding affinities. With recent advancements in computing capability and predictive accuracy, MD based virtual screening has progressed from the domain of theoretical attempts to real application in drug development. Approaches including the Molecular Mechanics Poisson Boltzmann Surface Area (MM-PBSA), Linear Interaction Energy (LIE), and alchemical methods have been broadly applied to model molecular recognition for drug discovery and lead optimization. Here we review the varied methodology of these approaches, developments enhancing simulation efficiency and reliability, remaining challenges hindering predictive performance, and applications to problems in the fields of medicine and biochemistry.

Unravelling the effect of two herbicide resistance mutations on acetolactate synthase kinetics and growth traits

Gene mutations conferring herbicide resistance are hypothesized to have negative pleiotropic effects on plant growth and fitness, which may in turn determine the evolutionary dynamics of herbicide resistance alleles. We used the widespread, annual, diploid grass weed Alopecurus aequalis as a model species to investigate the effect of two resistance mutations-the rare Pro-197-Tyr mutation and the most common mutation, Trp-574-Leu-on acetolactate synthase (ALS) functionality and plant growth. We characterized the enzyme kinetics of ALS from two purified A. aequalis populations, each homozygous for the resistance mutation 197-Tyr or 574-Leu, and assessed the pleiotropic effects of these mutations on plant growth. Both mutations reduced sensitivity of ALS to ALS-inhibiting herbicides without significant changes in extractable ALS activity. The 197-Tyr mutation slightly decreased the substrate affinity (corresponding to an increased Km for pyruvate) and maximum reaction velocity (Vmax) of ALS, whereas the 574-Leu mutation significantly increased these kinetics. Significant decrease or increase in plant growth associated, respectively, with the 197-Tyr and 574-Leu resistance mutations was highly correlated with their impact on ALS kinetics, suggesting more likely persistence of the 574-Leu mutation than the 197-Tyr mutation if herbicide application is discontinued.

Molecular Dynamics Simulations Study on the Resistant Mechanism of Insects to Imidacloprid due to Y151-S and R81T Mutations in nAChRs

Imidacloprid (IMI) is the first widely used neonicotinoid insecticide due to its high insecticidal activity and low toxicity. However, as its extensive use in crop protection, many insects are resistant to IMI. One of the main resistance mechanisms of insects to IMI is Y151-S and R81T mutations in nicotinic acetylcholine receptor (nAChR). However, how these two mutations affect the interaction of IMI with nAChR is unknown. Here, to uncover the resistant mechanism of nAChR to IMI due to Y151-S and R81T mutations, molecular dynamics simulations and molecular mechanics/generalized Born surface area (MM-GBSA) calculation, residue interaction network (RIN) analysis were performed. Due that the structure of nAChR is still unkonwn, the crystal structure of lymnaea stagnalis acetylcholine binding protein (Ls-AChBP) was used here to simulate nAChR. Y151 and R81 in nAChR correspond to H145 and Q55 in Ls-AChBP, respectively. The calculated binding free energy indicated that two mutations reduced the binding ability of IMI with Ls-AChBP. Q55T mutation reduced the contribution of several key residues, such as W53, T55, Y113, T144 and C187. As for H145-S mutation, the contribution of W53, Q55 and Y113 residues also decreased. RIN analysis showed that two mutants changed the binding pocket by changing the conformation of residues that interact directly with the mutated residues. The obtained resistance mechanism of IMI will be helpful for the design of potent insecticides.