Study On The Species Variability Of Succinate Dehydrogenase And The Mechanism Of The Inhibitor Action

Emerging infectious diseases(EIDs)caused by fungi are increasingly recognized as a threat to food security worldwide,and epidemics of plant diseases caused by fungi and fungus-like oomycetes have changed the course of human history.The use of fungicides is the most cost-effective means of plant disease control and plays an important role in agricultural production.Among them,succinate dehydrogenase inhibitors(SDHIs)are one of the important fungicides,and their target succinate dehydrogenase(SDH)is widely present in fungi,oomycetes,mammals,plants and other species.According to the literature research and the group’s preliminary study,the sterilization of SDHIs is currently limited to fungal diseases and has no inhibitory activity against oomycete diseases.The main reasons for this are the variability of SDH in different species and the lack of reported SDH structures in fungi and oomycetes;the lack of information on SDH crystal structure makes the mechanism of SDHIs and pathogenic bacteria still need to be further elucidated.This paper focuses on the species variability of SDH,the structure of SDH of oomycetes and the mechanism of interaction between SDHIs and downy mildew diseases.Based on the above three aspects,this paper firstly collected the web information of SDH based on web crawlers and literature mining,and removed the data redundancy and dirty data based on the known sequence length of four SDH subunits.Based on the collected sequences,we performed a chemoinformatics analysis,which mainly includes:physicochemical property prediction,sequence comparison,Identity calculation and phylogenetic tree construction.The results showed that the C subunit of most species such as fungi,mammals and oomycetes presented hydrophobic,while plants presented hydrophilic.In the phylogenetic tree of C and D subunits,the oomycete branch had a larger difference in tree scale than the rest of the species branches,indicating that it was more differentiated from all the rest of the collected species.Based on the results of the differentiality study,we selected Peronophythora litchii from the oomycetes as target species and used a combination of Modeller and Alphafold2 methods to predict the structure of Peronophythora litchii.Procheck and kinetic simulations showed that the structures obtained by the combination of Alphafold2 and Modeller were more stable and reliable than those obtained by one method alone in SDH structure prediction.The structures obtained using the combination of Alphafold2 and Modeller are stable and more representative of species variability than those obtained using one method alone.Based on the obtained stable and reliable SDH structures of Peronophythora litchii and the series of diclazuril compounds developed by our group(which have been proved to be effective against fungal diseases through activity testing),we used molecular docking,molecular dynamics simulation and MM/PBSA binding energy calculation to investigate the mechanism of action of fungal pathogens and SDHIs.The results showed that the triazinedione ring of diclazuril series compounds is the main efficacy group and that the amide fungicides are unable to act on downy mildew mainly because the cavity structure is somewhat altered,resulting in the carbonyl group of the amide bond unable to form interactions with key amino acid residues.In summary,we explored the interspecies variability based on the SDH sequences of different species and predicted the 3D structures of Lychee fungus pathogens using a protein structure prediction method combining Modeller and Alphafold2 as the target species.We further investigated the mechanism of action of SDHIs of Peronophythora litchii using various methods such as molecular docking on the basis of the constructed structures.The study of SDH species differences and their inhibitor mechanism of action provides some ideas and references for the future expansion of the sterilization of SDHIs and the creation of new drugs.