Michaela Prothiwa TT. asst. research professor

Research Michaela Prothiwa

Research team

Expertise

As a dedicated scientist with deep expertise in chemical proteomics, I lead a research group at the forefront of exploring host-pathogen interactions. Just three years after obtaining my PhD, I established this group, demonstrating my commitment and rapid progression in the field. Our work aims to decode how pathogens evade immune defenses, facilitating their virulence and resistance to antibiotics. Through an interdisciplinary toolkit encompassing methods from organic chemistry, proteomics, microbiology and cell biology, we strive to discover new molecular mechanisms and develop innovative therapeutic strategies. Core Expertise: Chemical Proteomics My career began with a highly successful research project at the Harvard University, where I developed peptide-hormone analogues to address diabetes, resulting in a notable first-author publication in the Journal of the American Chemical Society (JACS). This work laid the foundation for my expertise in peptide synthesis and chemical biology. During my PhD, I specialized in creating covalent probes to investigate the activity of virulence-related enzymes in pathogens, integrating chemical proteomics techniques to uncover novel molecular mechanisms. My postdoctoral research at KU Leuven further expanded my skill set, focusing on peptide-based chemical probes for profiling human proteases in complex samples. Interdisciplinary Research: Beyond my focus on chemical proteomics, I possess a broad skill set in biochemical and biological techniques. My research encompasses a range of methods from organic chemistry, biochemistry and microbiology to cell biology, demonstrating my ability to integrate diverse approaches for comprehensive studies. My group's current research revolves around three core projects: 1) Bacterial Proteases: We are developing chemical strategies to understand the role of these enzymes in infections better. 2) Microbial Virulence Factors: Our aim is to innovate chemical proteomic methods to identify bacterial components critical for virulence. 3) In Vivo Imaging Tools: We are pioneering the creation of chemical tools for visualizing bacterial enzymes in live models, enhancing our insight into host-pathogen interactions. In summary, my career is distinguished by a pioneering spirit in chemical proteomics, underscored by the early establishment of my research group. This initiative reflects my commitment to advancing our understanding of infectious diseases and contributing to the development of new therapeutic interventions.

(Chemo)proteomic approaches for discovery of bacterial cathepsin inhibitors. 01/01/2025 - 31/12/2028

Abstract

This proposal describes novel methods to study how bacteria manipulate a certain group of enzymes called cathepsins. These enzyme play a crucial role in macrophages, which are immune cells that can engulf and eliminate harmful bacteria. Unfortunately, some bacteria use proteins to inactivate cathepsins and, as result, evade the immune system's defense. Our goal is to identify these bacterial proteins that can alter cathepsins. To achieve this, we will develop a broadly applicable screening platform that uses activity-based protein profiling (ABPP) to detect bacterial proteins that inhibit cathepsins. We will also use a technique called cross-linking mass spectrometry (XL-MS) to figure out in which way they interact. Lastly, we will use a new method called TurboID to map the interactions between bacterial proteins and cathepsins in living cells. This research is important because once we decipher the interactions between cathepsins and bacterial proteins, another exciting opportunity arises: the future development of novel drugs to treat infections.

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  • Research Project

Development of chemical tools for deciphering the virulent roles of Streptococcus pneumoniae HtrA protease. 01/10/2024 - 30/09/2027

Abstract

Streptococcus pneumoniae (SP) is a leading cause of community-acquired pneumonia, with a concerning rise in drug-resistant strains. Central to its virulence is the high-temperature requirement A protease (HtrA), which plays a dual role as a chaperone and protease. HtrA is pivotal in SP's pathological processes, offering an innovative target for antibacterial strategies. Yet, the exact role of HtrA during infection remains elusive, posing challenges for drug development. This project aims to elucidate SP-HtrA's protease function during the infection process. We plan to develop activity-based probes (ABPs) for detecting and localizing active SP-HtrA proteases, alongside cyclic peptides as specific, irreversible inhibitors. These tools and inhibitors will contain a specific peptide scaffold, tailored to SP-HtrA's active site through advanced techniques, including positional scanning combinatorial libraries and phage display, ensuring specificity and avoiding interference with human HtrAs. We will demonstrate the power of these ABPs and inhibitors in both in vitro and in vivo infection models by offering proteomic insights into the activity status of SP-HtrA within an infection context. Overall, this project will provide a novel strategy to examine SP-HtrA protease activity during infection, which goes beyond the capabilities of conventional expression profiling technologies.

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  • Research Project

A 400 MHz Nuclear Magnetic Resonance (NMR) spectrometer. 01/05/2024 - 30/04/2028

Abstract

Nuclear Magnetic Resonance (NMR) is a spectroscopic technique that provides unique insight into the chemical structure and conformational dynamics of molecules. It is indispensable for medicinal and organic chemistry, for natural products research and for all related domains drawing on organic chemistry. For all publications in these fields, journals demand that research data are extensively supported by NMR-analysis: if NMR data are not or only partially delivered, research cannot be accepted for publication. This is because NMR spectroscopy is a sui generis methodology for which no generally applicable alternatives exist. There are currently only two operating NMRs left at UAntwerpen (both 400 MHz): one in the Medicinal Chemistry research group (UAMC) and one in the Organic Synthesis group (ORSY). In both groups, a large number of externally and internationally funded projects entirely rely on these very intensively used machines. Loss or temporary drop-out of a remaining instrument would have ruinous consequences on research. The available spectrometer at UAMC will be 15 years old in 2024 and at the end of its expected life-time. We therefore would like to replace the UAMC NMR. Spectrometers working at 400 MHz are the literature standard for most medicinal, organic and natural products applications and are expected to remain so for the next two decades. This application also fits in a long-term strategy to ensure that NMR-dependent research remains possible at UAntwerp.

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  • Research Project

Development of photoactive affinity probes for profiling of Streptococcus pneumoniae IgA1 protease 01/01/2024 - 31/12/2024

Abstract

The project aims to develop the first chemical probes for the IgA1 protease (IgA1P) of Streptococcus pneumoniae (S. pneumoniae), a key virulence factor in bacterial pathogenesis. This enzyme plays a crucial role in evading the host immune response by cleaving the IgA1 antibody. S. pneumoniae is a significant cause of bacterial pneumonia and meningitis, posing a global health challenge. The IgA1P of S. pneumoniae specifically targets the IgA1 antibody in the human immune system, cleaving it and thereby helping the bacteria evade immune detection and response. Specifically, the project will involve designing, synthesizing, and testing various probes to enable activity-based profiling of the S. pneumoniae Iga1P. Successful probes of the IgA1 protease could pave the way for new therapeutic strategies against Streptococcus pneumoniae infections. The project aims to contribute valuable insights into the enzyme's mechanism and potential for drug targeting. This research is critical in the context of increasing antibiotic resistance and the need for novel therapeutic strategies against bacterial pathogens. The development of specific inhibitors against bacterial virulence factors like IgA1 protease represents a promising approach in antimicrobial therapy.

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  • Research Project

Versatile chemical tools for profiling IgA1 protease activity in neisserial infections. 01/10/2023 - 30/09/2027

Abstract

This PhD project aims to investigate the virulent roles of IgA1 proteases during infections with pathogenic Neisseria species. Immunoglobulin A1 (IgA1) is a major antibody class that provides the first line of defense on mucosal surfaces. However, some pathogenic bacteria such as Neisseria gonorrhoeae and Neisseria meningitidis secrete IgA1 proteases to evade the immune response, and their specific impact on bacterial virulence remains unclear. Therefore, this PhD project aims to investigate the effect of neisserial IgA1 proteases on virulence. Specifically, we will develop a set of reagents for highly sensitive and selective detection of IgA1 proteases. To achieve the desired outcomes, this PhD project is outlined in three specific aims: (I) synthesizing highly sensitive peptide substrates as potential diagnostic tools, (II) developing activity-based chemical probes for in vivo monitoring of protease activity, and (III) exploring cyclic peptides containing a diphenyl phosphonate warhead as irreversible inhibitors. The successful execution of the project will provide valuable insights into the pathogenesis of neisserial infections and contribute to the development of novel anti-infective drugs and diagnostic tools. Given the emergence of high-level resistance strains of N. gonorrhoeae and the lack of rapid diagnostic tests for N. meningitidis, the project's outcomes can be a great asset to biomedical research on IgA1 proteases.

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  • Research Project

Chemical strategies to understand microbiota-immune interactions in infectious diseases 01/01/2023 - 31/12/2027

Abstract

My research group focuses on understanding the complex interactions between pathogens and the human immune system during the infection process. We use a combination of organic chemistry, natural product identification, proteomics, and biology to study how microbial factors such as pathogenic enzymes, toxic proteins, and small molecule metabolites enable pathogens to evade the immune system and contribute to virulence and antibiotic resistance. Our goal is to uncover the unknown molecular mechanisms of these interactions, in order to develop new antibiotics or alternative treatment strategies.

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  • Research Project

Modulation of cathepsin activity by pathogenic bacteria. 01/01/2023 - 31/12/2026

Abstract

We will investigate how some harmful bacteria can evade the immune system and cause infections. Our focus is on how these bacteria manipulate enzymes called cathepsins, which immune cells use to fight off infections. Some bacteria can evade the immune system by manipulating these enzymes, making the infection worse. Our goal is to understand how they do it and find new ways to treat infections. To do this, we will use special chemical tools called "activity-based probes" that detect and highlight cathepsins. We will isolate these enzymes from immune cells and create chemical probes that specifically target them. By using these probes, we will identify the microbial molecules that can stop the cathepsins working. Finally, we will pinpoint the exact molecules interacting with the cathepsins using analytical techniques. Armed with this knowledge, we can develop new treatments that target these molecules and stop bacteria from causing harm.

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  • Research Project