Taki, A.C., Wang, T., Nguyen, N.N., Ang, C.-S., Leeming, M.G., Nie, S., Byrne, J.J., Young, N.D., Zheng, Y., Ma, G., Korhonen, P.K., Koehler, A.V., Williamson, N.A., Hofmann., A., Chang, B.C.H., Häberli, C., Keiser, J., Jabbar, A., Sleebs, B.E., Gasser, R.B. (2022) Front. Pharmacol. 13, 1014804

Parasitic roundworms (nematodes) cause destructive diseases, and immense suffering in humans and other animals around the world. The control of these parasites relies heavily on anthelmintic therapy, but treatment failures and resistance to these drugs are widespread. As efforts to develop vaccines against parasitic nematodes have been largely unsuccessful, there is an increased focus on discovering new anthelmintic entities to combat drug resistant worms. Here, we employed thermal proteome profiling (TPP) to explore hit pharmacology and to support optimisation of a hit compound (UMW-868), identified in a high-throughput whole-worm, phenotypic screen. Using advanced structural prediction and docking tools, we inferred an entirely novel, parasite-specific target (HCO_011565) of this anthelmintic small molecule in the highly pathogenic, blood-feeding barber’s pole worm, and in other socioeconomically important parasitic nematodes. The “hit-to-target” workflow constructed here provides a unique prospect of accelerating the simultaneous discovery of novel anthelmintics and associated parasite-specific targets.

Zheng, Y., Ma, G., Wang, T., Hofmann, A., Song, J., Gasser, R.B., Young, N.D. (2022) Int. J. Parasitol. 52, 581-590

The ubiquitin-mediated pathway has been comprehensively explored in the free-living nematode Caenorhabditis elegans, but very little is known about this pathway in parasitic nematodes. Here, we inferred the ubiquitination pathway for an economically significant and pathogenic nematode – Haemonchus contortus – using abundant resources available for C. elegans. We identified 215 genes encoding ubiquitin (Ub; n = 3 genes), ubiquitin-activating enzyme (E1; one), -conjugating enzymes (E2s; 21), ligases (E3s; 157) and deubiquitinating enzymes (DUBs; 33). With reference to C. elegans, Ub, E1 and E2 were relatively conserved in sequence and structure, and E3s and DUBs were divergent, likely reflecting functional and biological uniqueness in H. contortus. Most genes encoding ubiquitination pathway components exhibit high transcription in the egg compared with other stages, indicating marked protein homeostasis in this early developmental stage. The ubiquitination pathway model constructed for H. contortus provides a foundation to explore the ubiquitin-proteasome system, crosstalk between autophagy and the proteasome system, and the parasite-host interactions. Selected E3 and DUB proteins which are very divergent in sequence and structure from host homologues or entirely unique to H. contortus and related parasitic nematodes may represent possible anthelmintic targets.

Seo, P.-W., Hofmann, A., Kim, J.-H., Hwangbo, S.-A., Kim, J.-H., Kim, J.-W., Huynh, T.Y.L., Choy, H.E., Kim, S.-J., Lee, J., Lee, J.-O., Jin, K.S., Park, S.-Y., Kim, J.-S. (2022) Int. J. Biol. Macromol. 208, 381-389

Type I restriction-modification enzymes are oligomeric proteins composed of methylation (M), DNA sequence-recognition (S), and restriction (R) subunits. The different bipartite DNA sequences of 2-4 consecutive bases are recognized by two discerned target recognition domains (TRDs) located at the two-helix bundle of the two conserved regions (CRs). Two M-subunits and a single S-subunit form an oligomeric protein that functions as a methyltransferase (M2S1 MTase). Here, we present the crystal structure of the intact MTase from Vibrio vulnificus YJ016 in complex with the DNA-mimicking Ocr protein and the S-adenosyl-L-homocysteine (SAH). This MTase includes the M-domain with a helix tail (M-tail helix) and the S_1/2-domain of a TRD and a CR α-helix. The Ocr binds to the cleft of the TRD surface and SAH is located in the pocket within the M-domain. The solution- and negative-staining electron microscopy-based reconstructed (M₁S_1/2)₂ structure reveals a symmetric (S_1/2)₂ assembly using two CR-helices and two M-tail helices as a pivot, which is plausible for recognizing two DNA regions of same sequence. The conformational flexibility of the minimal M₁S_1/2 MTase dimer indicates a particular state resembling the structure of M₂S₁ MTases.

Korhonen, P., Kinkar, L., Young, N.D., Cai, H., Lightowlers, M.W., Gauci1, C., Jabbar, A., Chang, B.C.H., Wang, T., Hofmann, A., Koehler, A.V., Li, J., Li, J., Qiangba, G., Xie, J., Wang, D., Yin, J., Jenkins, D.J., Saarma, U., Laurimäe, T., Rostami-Nejad, M., Andresiuk, V., Irshadullah, M., Mirhendi, H., Sharbatkhori, M., Ponce Gordo, F., Simsek, S., Casulli, A., Zait, H., Luiz de la Rue, M., Romig, T., Wassermann, M., Atoyan, H.A., Aghayan, S.A., Hasmik, G., Yang, B., Gasser, R.B. (2022) Commun. Biol. 5, 199

Cystic echinococcosis is a socioeconomically important parasitic disease caused by the larval stage of the canid tapeworm Echinococcus granulosus, afflicting millions of humans and animals worldwide. The development of a vaccine (called EG95) has been the most significant translational advance in the fight against this disease in animals. However, almost nothing is known about the genomic organisation/location of the family of genes encoding EG95 and related molecules, the extent of their conservation or their functions. The lack of a complete reference genome for E. granulosusE. granulosus, and the development of improved tools for the diagnosis and chemotherapy of cystic echinococcosis of humans.

Campos, T.L., Korhonen, P.K., Hofmann, A., Gasser, R.B., Young, N.D. (2022) Biotechnol. Advances 54, 107822

The availability of high-quality genomes and advances in functional genomics have enabled large-scale studies of essential genes in model eukaryotes, including the ‘elegant worm’ (Caenorhabditis elegans; Nematoda) and the ‘vinegar fly’ (Drosophila melanogaster; Arthropoda). However, this is not the case for other, much less-studied organisms, such as socioeconomically important parasites, for which functional genomic platforms usually do not exist. Thus, there is a need to develop innovative techniques or approaches for the prediction, identification and investigation of essential genes. A key approach that could enable the prediction of such genes is machine learning (ML). Here, we undertake an historical review of experimental and computational approaches employed for the characterisation of essential genes in eukaryotes, with a particular focus on model ecdysozoans (C. elegans and D. melanogaster), and discuss the possible applicability of ML-approaches to organisms such as socioeco­nomically important parasites. We highlight some recent results showing that high-performance ML, combined with feature engineering, allows a reliable prediction of essential genes from extensive, publicly available ‘omic data sets, with major potential to prioritise such genes (with statistical confidence) for subsequent functional genomic validation. These findings could ‘open the door’ to fundamental and applied research areas. Evidence of some commonality in the essential gene-complement between these two organisms indicates that an ML–engineering approach could find broader applicability to ecdysozoans such as parasitic nematodes or arthro­pods, provided that suitably large and informative data sets become/are available for proper feature engineering, and for the robust training and validation of algorithms. This area warrants detailed exploration to, for example, facilitate the identification and characterisation of essential molecules as novel targets for drugs and vaccines against parasitic diseases. This focus is particularly important, given the substantial impact that such diseases have worldwide, and the current challenges associated with their prevention and control and with drug resis­tance in parasite populations.