University of Cape Town: UCT postdoc fellow’s research tackles United Nations’ SDG 3
This is according to Dr Stanley Makumire, a postdoctoral research fellow in the Department of Integrative Biomedical Sciences, based in the Faculty of Health Sciences (FHS) at the University of Cape Town (UCT).
Dr Makumire’s primary career goal is to eliminate or minimise disease progression by specifically targeting proteins using small molecules designed by rational processes. To help him achieve this, his current research makes use of molecular and structural biology tools, and it is funded by the Global Challenges Research Fund – Synchrotron Techniques for African Research and Technology (GCRF START), in collaboration with the FHS.
“I am so motivated by the rapid advancement of biophysics, which we have witnessed in response to the COVID-19 pandemic.”
“Knowledge gained from structural biology has provided insights used to design medicines and vaccines. I am so motivated by the rapid advancement of biophysics, which we have witnessed in response to the COVID-19 pandemic,” he said.
“This has clearly demonstrated the power of today’s visualisation technology and the role of structural biology in vaccine design.”
The background
Makumire’s current research focuses on the enzyme mechanisms of the nitrilase superfamily (amidases and nitrilases), identified as drug targets in tuberculosis. These thiol enzymes are also involved in biosynthesis and post-translational modification in plants, animals and fungi. According to Makumire, these enzymes play a range of roles in cellular processes, and many have found industrial roles in chemical synthesis and environmental protection.
His work places special emphasis on understanding enzymes’ chemistry and thermostability. This process will lead to producing enzymes that are better suited for the industrial environment, with the aim of producing a more diverse range of products including medicines. However, establishing exactly how these enzymes operate has been challenging. While X‑ray crystallographic studies and electron microscopy (experimental sciences used to determine the atomic and molecular structure of proteins) have yielded some excellent clues, he said, the literature contains a multitude of different interpretations.
Dr Stanley Makumire
Dr Stanley Makumire’s research is funded by the Global Challenges Research Fund – Synchrotron Techniques for African Research and Technology, in collaboration with the FHS..
“The biggest problem is that X‑rays cause the active site cysteine (an amino acid which is critical to the enzyme function) to become oxidised; and therefore we cannot effectively image the real active site,” he said.
“Electrons also destroy the active site glutamate (another amino acid essential for the enzyme function), making them invisible in electron microscopy images. The tricks to circumvent these problems, used by various investigators, have introduced artifacts of their own. For the first time, we have finally visualised the intact active site using neutron crystallography – a rare technique made available to us by collaborators in Sweden and France.”
Research goals
Makumire said that the use of the nitrilase superfamily enzymes as biocatalysts (living biological systems that help to speed up chemical reactions) has not yet reached its full industrial potential. Their mechanism of action, the basis of their specificity and their methods for increasing thermostability are not yet well understood.
“Ultimately, my research seeks to elucidate the underlying factors that determine these characteristics, using high-resolution imaging techniques,” said Makumire.
Dr Stanley Makumire
Dr Stanley Makumire’s primary career goal is to eliminate or minimise disease progression by specifically targeting proteins using small molecules designed by rational processes.
He said that currently his most interesting research finding has emerged from the molecular docking and crystallographic data, which demonstrates the “proper positioning” of the amide within the enzyme’s active site. Makumire said he hopes to use the knowledge gained from this research to help address the United Nations’ (UN) third Sustainable Development Goal: good health and well‑being.
Capacity building
Makumire said he remains grateful for the GCRF START grant, without which much of his research would not be possible.
“Thanks to this grant, I’ve been able to collect important X-ray crystallographic data from the Diamond Light Source’s IsPyB platform in the United Kingdom.”
“Thanks to this grant, I’ve been able to collect important X-ray crystallographic data from the Diamond Light Source’s IsPyB platform in the United Kingdom, and have analysed it using their CCP4 software suite,” he said.
Building close relationships with scientist Dr Zoë Fisher, the group head leader of the Deuteration and Macromolecular Crystallisation (DEMAX) platform at the European Spallation Source in Sweden, and Mathew Blakeley, instrument scientist at the Quasi-Laue diffractometer (LADI-III) at the Institut Laue-Langevin (ILL) in France, and drawing on their expertise, have further informed his work.
“Determining the neutron structure of this amidase, in which one can see the hydrogen atoms, will form the basis of proposing a novel mechanism. I’m so excited about all this work and where the results will lead,” he said.