Structural Biology and Biochemistry (SBB) Theme Seminar

Title:  Complete CryoEM Data Processing on Bunya HPC Cloud Desktops

Speaker: Dr Farrah Blades

Abstract: As cryoEM data sets grow and the price of GPUs continue to increase, it is time we decrease our reliance on data processing workstations and move into cloud based visual desktops. This talk introduces the new Bunya on-demand desktop which is both visual and can push big processing jobs onto the supercomputer, without having to login to visual nodes or write scripts. The Bunya on-demand desktop will feature Relion, ModelAngelo, Coot, ChimeraX, PyMol, IMOD, EMAN and more; all in one space. This work is a continually evolving project with the Research Computing Center (RCC) at UQ, community feedback and suggestions are always welcomed.

Bio: Farrah Blades has been a post doctoral research fellow at the IMB within the Hankamer group since 2021. Farrah’s main post doctoral project is around elucidating the structure of the photosystem II supercomplex and its light harvesting antennae while optimising CryoEM data processing pipelines at UQ. Farrah was awarded her PhD in 2021 from the Florey Institute at the University of Melbourne, her contributions to science during this time include; identifying the role of the tyrosine kinase receptor, Tyro3, in myelin thickness and Tyro3's novel role in retinal formation. Farrah undertook Honors in Biochemistry, working towards establishing two novel mouse models of multiple sclerosis and testing nanobody therapeutics.

Title: Discovery and characterization of new KARI inhibitors showing both anti-tb and herbicidal activity

Speaker:  Xin Lin

Abstract: Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mt) infection, remains a significant global health concern with increasing cases and limited treatment options. The success of using the first enzyme in the BCAA pathway, AHAS, as a target for commercial herbicides, has encouraged the exploration of other enzymes in this pathway as potential targets for the development of antimicrobial drugs or herbicides. This study focuses on inhibitors aiming at the second enzyme in this pathway, KARI. A compound that our group discovered in 2020 and its 19 derivatives were designed, synthesized, and characterized.

Results indicate that the most potent derivative, JK-5-114, is a special inhibitor of both class I and class II KARI, with Ki values in the low nM range against MtKARI and CjKARI and in the low µM range against riceKARI. This derivative has a 25-fold stronger inhibition against MtKARI compared to the original compound, NSC116565. Remarkably, kinetic assays reveal the unique inhibition mode of JK-5-114, suggesting its competition not only for the substrate AL but also for the co-factor, NADPH. Two co-crystallized protein structures, SaKARI.Mg2+.JK-5-114 and SaKARI.Mg2+.JK-5-115, confirm the competition between JK-5-114 and NADPH. Additionally, the comparison between these two structures explains how JK-5-114 competes with NADPH.

Multiple compounds demonstrate reasonable anti-TB or herbicidal activities. These compounds show inhibitory activity against MtH37Rv growth, with the MIC in the low µM range. The study establishes a strong correlation between Ki values and MIC, reinforcing KARI as the primary target. The best compound, JK-5-114, exhibits a synergistic effect with an AHAS inhibitor, FS, offering potential for more effective TB treatment strategies. On the other hand, the derivative 1a exhibits 100% herbicidal activity at 1500 g/ha in a plant assay. This is the first time that a KARI inhibitor shows herbicidal activity comparable to commercial herbicides targeting AHAS.

Bio:  Xin Lin is a PhD candidate supervised by Prof. Luke Guddat at SCMB, UQ. He began his PhD project in molecular biology and biochemistry in 2020. His research focuses on enzymes from the Branched-Chain Amino Acids (BCAA) biosynthesis pathway. Specifically, he is interested in the mechanisms and applications of the first enzyme (AHAS) and the second enzyme (KARI) from this pathway. Currently, he has submitted his PhD thesis and is continuing his research in the Guddat lab with the aim of verifying the possibility of using AHAS and KARI as potential targets for antibiotics and antifungal drugs.