A truly collaborative work – new paper on DsbA

Not one but five CFBD members from our three nodes published a paper on DsbA titled “Identification and characterization of two drug-like fragments that bind to the same cryptic binding pocket of Burkholderia pseudomallei DsbA” in Acta Crystallographica Section D.


Disulfide-bond-forming proteins (Dsbs) play a crucial role in the pathogenicity of many Gram-negative bacteria. Disulfide-bond-forming protein A (DsbA) catalyzes the formation of the disulfide bonds necessary for the activity and stability of multiple substrate proteins, including many virulence factors. Hence, DsbA is an attractive target for the development of new drugs to combat bacterial infections. Here, two fragments, bromophenoxy propanamide (1) and 4-methoxy-N-phenylbenzenesulfonamide (2), were identified that bind to DsbA from the pathogenic bacterium Burkholderia pseudomallei, the causative agent of melioidosis. The crystal structures of oxidized B. pseudomallei DsbA (termed BpsDsbA) co-crystallized with 1 or 2 show that both fragments bind to a hydrophobic pocket that is formed by a change in the side-chain orientation of Tyr110. This conformational change opens a `cryptic’ pocket that is not evident in the apoprotein structure. This binding location was supported by 2D-NMR studies, which identified a chemical shift perturbation of the Tyr110 backbone amide resonance of more than 0.05 p.p.m. upon the addition of 2 mM fragment 1 and of more than 0.04 p.p.m. upon the addition of 1 mM fragment 2. Although binding was detected by both X-ray crystallography and NMR, the binding affinity (Kd) for both fragments was low (above 2 mM), suggesting weak interactions with BpsDsbA. This conclusion is also supported by the crystal structure models, which ascribe partial occupancy to the ligands in the cryptic binding pocket. Small fragments such as 1 and 2 are not expected to have a high energetic binding affinity due to their relatively small surface area and the few functional groups that are available for intermolecular interactions. However, their simplicity makes them ideal for functionalization and optimization. The identification of the binding sites of 1 and 2 to BpsDsbA could provide a starting point for the development of more potent novel antimicrobial compounds that target DsbA and bacterial virulence.

Read the full article here.

First Author paper for PhD student Sarah Müller

Congratulations to PhD student Sarah Müller from Griffith University who published a paper as first author. 

The Glitazone Class of Drugs as Carbonic Anhydrase Inhibitors—A Spin-Off Discovery from Fragment Screening

Most of the drugs we know target the activity of specific proteins that play an important role in the disease being treated. One of the big challenges in the discovery of new drugs is finding molecules that bind specifically to one target and not bind to other proteins too. This is necessary to avoid causing treatment side effects. Hence, drug discovery researchers are always on the lookout for ways to find better lead molecules.
We identified an old drug class called glitazones that target a new protein known as carbonic anhydrase II, an enzyme that helps to maintain pH levels in cells. Carbonic anhydrase comes in many different forms and has been a successful target for drug development for various diseases like glaucoma, heart failure and epilepsy.
The glitazone drugs, such as rosiglitazone, are used to treat Type II diabetes. However, because of the severe side effects caused by the use of glitazones they were taken off the market. Our findings suggest that the unintended targeting of carbonic anhydrase may be one reason for the side effects of these drugs. This shows how important it is to carry out research to fully understand the effect of drugs and can help future researchers in drug discovery.

The paper was published in Molecules in May 2021.

We are hiring – Biomolecular NMR spectroscopist/Structural Biologist

We have a postdoctoral position available for a Biomolecular NMR spectroscopist/Structural Biologist within the ARC Centre for Fragment-Based Design.

The exciting opportunity for a Research Fellow who will be working our Centre. The successful candidate will contribute to research on fragment-based drug design projects with a focus on a range of therapeutic targets across different areas such as infectious disease, cancer and diabetes.

You will have:

  • A PhD in structural biology with related research experience
  • Strong theoretical knowledge of NMR spectroscopy and its application in the analysis of biomolecules
  • Strong practical experimental skills in the characterisation of protein structures from experimental data
  • Prior knowledge and experience in data analytics is desirable
  • Experience with industry will be highly regarded

If you are ready to take the next step in your research career, we look forward to receiving your application.

New paper out by PhD student Karoline Sanches

Congratulations to PhD student Karoline Sanches from Monash University who published a paper as first author. The paper was published in Toxicon in October 2021.

Conformational dynamics in peptide toxins: Implications for receptor interactions and molecular design

Karoline Sanchesa,b,1, Dorothy C.C. Waia,1, Raymond S. Nortona,b
aMedicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
bARC Centre for Fragment-Based Design, Monash University, Parkville, Victoria, 3052, Australia
1These authors contributed equally

Peptide toxins are often potent and selective blockers of ion channels and are therefore of significant interest to the pharmaceutical and biotech industries. For example, an analogue of the sea anemone peptide ShK, which targets the voltage-gated potassium channel Kv1.3, is currently in clinical trials for the treatment of autoimmune disorders. Studying the structure-function relationship and the dynamics of these peptides is pivotal to understanding their binding to receptors, as well as to designing new drugs. In this article, we highlight the important contribution of NMR to characterising peptide toxin dynamics. It is shown that even disulphide-rich peptides display dynamics in various timescales, the characterisation of which through NMR is crucial for understanding their receptor interactions.

CFBD CI receives funding for cystic fibrosis research

CFBD CI Professor Ray Norton has been awarded a grant worth $49,000 from the Monash Health Foundation 65 km Walk for Cystic Fibrosis Research Funding for his project entitled “Validating a potential new target for the treatment of cystic fibrosis”.

Ray’s project seeks to determine whether the protein channel KV1.3 plays a role in airway inflammation in individuals with cystic fibrosis [CF]. Ray and his team will examine broncho-alveolar lavage [BAL] fluid obtained from both young children with CF and adults with CF following lung transplantation.

Previous research has shown that KV1.3 is involved in other inflammatory diseases such as rheumatoid arthritis and inflammatory bowel disease, but it is unknown if it is also important in CF lung disease or rejection in CF lung transplant recipients.

Lung inflammatory cells from BAL fluid will be tested for the presence of the KV1.3 channel. The group will also analyse BAL fluid from adults with CF post lung transplant, who will be having BAL as part of their routine post-transplant care at the Alfred Hospital Lung Transplant Service. We expect to find that KV1.3 is abundantly present in airway inflammatory cells in both patient groups.

If KV1.3 is detected, the next step will be to test whether blocking this channel with HsTX1[R14A], a novel peptide developed at Monash University, reduces inflammation and lung damage in animal models of CF lung disease and chronic rejection.

ARC Discovery Project Success

Congratulations to CFBD CI Professor Sally-Ann Poulsen from Griffith University for being awarded an ARC Discovery Project grant worth $415,495 together with Professor Katherine Andrews (Griffith Institute for Drug Discovery, Sciences). The project Chemical probes to dissect the cell cycle of globally important parasites aims to develop new reagents, called chemical probes, to visualise key biological events in globally important pathogens. The team will use innovative chemistry to modify the building blocks of DNA and provide researchers with essential tools to ‘see’ DNA synthesis in order to study growth and replication of pathogens in combination with microscopy. This project expects to support a major technical advance that will address important gaps in our understanding of many pathogens (e.g. those that cause malaria and tuberculosis), at both the cellular and molecular levels. This should provide significant benefits by enabling researchers worldwide to identify new intervention opportunities that target unique aspects of pathogen biology (with Dr Martin Blume, Robert Koch Institute).

CFBD Deputy Director appointed Acting Theme Leader

Congratulations to CFBD Deputy Director A/Prof Ben Capuano for being appointed as Acting Theme Leader in the Medicinal Chemistry Department at the Monash Insitute of Pharmaceutical Sciences (MIPS).

Ben has taken over the position from Prof Peter Scammells who will now be focusing on his role as Associate Dean, Research, Faculty of Pharmacy & Pharmaceutical Sciences. Within CFBD, Ben leads the Fragment Elaboration theme. He is a synthetic medicinal chemist specialising in GPCRs.

Faculty Research Award for CI Professor Jonathan Baell

Congratulations to CFBD CI Professor Jonathan Baell for being awarded the Faculty Research Award from the Monash Institute of Pharmaceutical Sciences.

Jonathan discovers new medicines for treating diseases with unmet medical needs with a particular focus on cancer and infectious diseases. His track record is hallmarked by high-quality research outcomes in a variety of different areas, as exemplified by a broad and diverse suite of personally driven but widely collaborative patents integrated with subsequent high-quality publications.

With more than 70 granted patents, throughout his career Jonathan has been a driving force in facilitating commercial outcomes from academic research. At any given time, he incubates a variety of enterprising projects to maximise the chances of multiple translational outputs.

He is also the Director of the Australian Translational Medicinal Chemistry Facility (ATMCF), located at MIPS and which works with researchers nationwide in order to translate biomedical research outcomes. The Facility has secured over $7M in funding to enable the de-risking of projects through medicinal chemistry optimisation. In addition to the enterprise embodied in the ATMCF, Jonathan’s own patented KAT6A anticancer drug candidates have catalysed a global focus by Pharma on KATs as druggable targets. This innovative KAT6A work also has underpinned several awards, including Australia’s highest medicinal chemistry award, the Adrien Albert Award for Sustained Excellence in Medicinal Chemistry (2018), the Monash University Research Award for the Faculty of Pharmacy and Pharmacology (2019), the Scientific Achievement Award in Drug Discovery and Development (2020), awarded by the American Society for Pharmacology and Experimental Therapeutics, and in 2021 The Australian Academy of Technology and Engineering (ATSE) Clunies Ross Award for Knowledge Commercialisation.

Grant Success! CFBD CI Professor Joel Mackay to receive NHMRC Ideas Grant

Congratulations to CFBD CI Professor Joel Mackay from Sydney University who received an NHMRC Ideas Grant worth $829, 494.

New approaches to cancer treatment through mRNA display

This project will pioneer the development of a new class of molecules – cyclic peptides – that will block the activity of proteins that regulate gene expression and have been shown to be promising targets for a range of diseases, predominantly cancer. These molecules have the potential to be much more selective and potent than existing molecules and to also open up new directions for cancer therapy by allowing previously intractable molecular targets to be addressed.