Research

Natural products have long been regarded as ‘nature’s medicine chest’ providing a rich source of lead compounds as invaluable platforms for developing front-line drugs. Our research focuses on making and modifying naturally occurring bioactive compounds that have been isolated from plants, animal tissue, microbes or marine and soil organisms, which are rare or hard to isolate in abundance. These compounds provide rich and diverse chemical structures that challenge the synthetic chemist to develop new flexible synthetic methodology for their construction. The preparation of synthetic analogues of the natural compound may improve the biological activity and provide an understanding of the mechanism of action of the naturally occurring compound.

 

Our research group also comprises a national peptide, peptidomimetic and glycopeptide chemistry facility that occupies a world-class laboratory in the Institute for Innovation in Biotechnology. The peptide synthesis laboratory supports growth in the burgeoning area of peptide therapeutics that is growing at twice the rate of small molecule therapeutics by engaging with the local biotech community to develop viable drug candidates based on peptide leads. An example is the development of NNZ-2566 for Neuren Pharmaceuticals that is currently in Phase IIb clinical trials for traumatic brain injury and was successful in phase II clinical trials for Rett Syndrome and has been given the name trofinetide by the WHO.

 

Our laboratory has also been licensed by medsafe for the GMP manufacture of peptides for the clinical trial of melanoma vaccines (MELVAC trial).  The synthesis of natural product peptides containing unnatural amino acids, depsipeptides, cyclic peptides and natural proteins that exhibit potent antimicrobial activity, is one theme in our peptide chemistry laboratory. Analogues of the natural peptides are then synthesised to either simplify or stabilise the molecule with the aim of producing a more potent analogue. The ability to combine contemporary organic reactions such as cross-metathesis, “peptide stapling”, click chemistry, thiol-ene chemistry and the preparation of unnatural amino-acid building blocks with modern solid phase synthesis methods provides a powerful peptidomimetic platform to combat the problem of increasing resistance to existing antibiotics.  The peptide chemistry group also synthesizes peptide-based hydrogels with applications in bionanotechnology and regenerative medicine.

 

The following is a representative list of our research projects. Many of our research projects are not listed and we encourage you to contact us should you have further query.

 

 

 

 

Natural Product Synthesis: Asymmetric Synthesis of Spiroketals

With Dr Dan Furkert

Synthesis of spiroketals and spiroketal-containing natural products is a longstanding interest of our group. These molecular scaffolds, consisting of two (or sometimes even three) rings joined at a quaternary carbon with two bonds to oxygen, are found in a wide range of natural products that demonstrate interesting bioactivity. Some examples of our current and previous targets are shown (spiroketals highlighted in grey).

This research area offers a great opportunity to apply your organic chemistry background to natural product synthesis, building on our group’s particular expertise in spiroketals. Projects will based on stereoselective multistep organic synthesis, aiming to successfully prepare structures found in recently-isolated natural products. There will be a chance to learn a wide variety of classic and state-of-the-art chemistry techniques for asymmetric synthesis including catalysis, pericyclic reactions, aldol reactions and organometallic additions.

Drug Discovery: New Antibiotics Based on Novel Aminoacid Components

With Dr Dan Furkert

Growing incidence of antimicrobial resistance to clinically used antibiotic drugs is an immediate global health concern, as recently highlighted by the World Health Organisation (WHO), US and NZ governments. Due to the low numbers of new pharma drug candidates currently entering the development pipeline, academia and small biotech firms have an important role to play in generating novel compounds to address the resistance problem. Teixobactin, a complex antimicrobial peptide recently isolated from a culture of soil bacteria, demonstrates not only extremely potent activity against clinically-relevant resistant strains of MRSA, vancomycin-resistant Enterococci (VRE), M. tuberculosis (Mtb) and C. difficile, but crucially a very low incidence of acquired resistance.

The rare aminoacid enduracididine (End) is critical to the activity of teixobactin, but has proven surprisingly challenging to synthesise. Work on this project offers the chance to learn important synthesis skills in a drug discovery context, on a problem of genuine global relevance. The development of a robust and efficient route to End itself and the preparation of new active analogues to support medicinal chemistry studies will be the initial project goals, with the eventual aim of identification and synthesis of new antimicrobial peptide drug candidates, in collaboration with the group’s SBS-based peptide unit.

New Chemical Reactions: Synthetic Applications of Vinyl Azide and Vinyl Amides

With Dr Dan Furkert

The discovery and development of new reactions offers opportunities to improve synthetic routes to important materials, readily and selectively access previously challenging structures and improve our fundamental understanding of chemical processes. Recently, our group uncovered an unexpected reaction to form alpha,beta-unsaturated vinyl amides directly from esters. Our investigations revealed that the reaction likely involves an unusual [3+2] cylcloaddition of an ester or aldehyde enolate, with in situ generated vinyl azide, a little-used reagent with an intriguing history dating back to original work in 1910.

We are keenly pursuing the possibilities opened up by this new reactivity; for rapid access to previously hard-to-access vinyl amides (versatile synthetic intermediates and useful industrial polymer feedstocks) and synthesis based on them; to explore the mechanistic basis of their reactivity through experiment and calculation (e.g. transition state TS1); and finally to assess the potential of vinyl azide itself in organic synthesis. This project offers an unusual and fast-moving chance to discover new areas of chemistry, while expanding your synthesis and lateral thinking skills.

Total Synthesis and Medicinal Chemistry: Spirocyclic Imine Natural Products

With Dan Furkert

Shellfish toxins produced by dinoflagellates in during algal blooms such as portimine and gymnodimine are a significant risk to human health – but also provide a stern challenge for existing synthetic methods, and inspirational leads for medicinal chemistry and drug development.  Portimine  exhibits promising selective anti-cancer activity and apoptosis induction, and gymnodimine is an extremely selective ligand for the nicotinic acetylcholine receptors important in nerve signal transduction. Our group has a strong ongoing interest in the total synthesis of these complex and highly bioactive molecules, and revealing their potential use in medicinal chemistry through structure-activity studies.

Working in this area will give new students a superb opportunity to be involved in the exciting challenge of natural product synthesis, and gain an insight into the tactics and techniques of complex organic chemistry. Projects currently available in this specific area include; stereoselective assembly of key spirocyclic imine natural product fragments, development of new methods to prepare challenging chemical structures, and determination of structure-activity relationships in partnership with our biochemistry collaborators.

Asymmetric Synthesis of Benzannulated Spiroketals: Towards Novel Telomerase Inhibitors

With Dr Dan Furkert

Telomerase inhibitors are of much current interest as a selective approach for the control of human cancer. The rubromycins (inset) are a unique class of antibiotics produced from a strain of Streptomyces that have been shown to inhibit human telomerase. We have previously completed the synthesis of rubromycin, and are currently interested in novel catalytic methods for asymmetric synthesis of this unusual class of compound, that possess a single chiral centre at the spiroketal position.

We will investigate the asymmetric synthesis of benzannulated spiroketals using chiral Lewis acid catalysis, using a new route to prepare the necessary cyclisation substrates only recently identified in our group. In addition to probing the properties and stereochemistry of the compound class, we aim to develop new practical synthetic routes in order to assess the biological activity of chiral lead structures based on rubromycin.

This project offers the chance to work towards the development of new methods for chiral catalysis, based on the benzannulated spiroketal scaffold, as well as excellent general organic synthetic training.

Total Synthesis and Structural Elucidation of Callyspongiolide

With Dr Dan Furkert

Callyspongiolide is a 14-membered macrolide isolated in 2013 from an Indonesian marine sponge of the genus Callyspongia Sponges of this genus are known to produce a diverse variety of bioactive secondary metabolites, including polyketides, polyacetylenes, alkaloids and cyclic peptides, but to date, callyspongiolide is the only reported macrolide. Callyspongiolide was found to exhibit potent cytotoxicity against a range of cell lines (L5178Y mouse lymphoma IC50 320 nM, human Jurkat J16 T lymphocytes 70 nM, Ramos B lymphocytes 60 nM). Interestingly, addition of a caspase inhibitor (QVD-OPh) did not attenuate the activity of callyspongiolide, suggesting that it promotes cell death through a caspase independent mechanism.

The relative configuration of the C5, 7, 9 and 12 chiral centres was determined using a combination of 1D NMR proton coupling constants and transannular correlations in the 2D ROESY spectrum. Due to the extremely hindered nature of the secondary alcohol at C21, however, it did not prove possible to prepare any Mosher ester derivatives. As a result, the absolute stereochemistry of callyspongiolide, and the configuration at C21, has not been assigned to date. The C14-19 yn-diene side chain linking the macrolide and bromoaryl domains is unprecedented in macrolide natural products reported to date, although known polyacetylenic algal metabolites are legion.

Total synthesis of the callyspongiolide will enable the complete structural elucidation of the natural product to be completed and permit convenient access to the key sub-structures for SAR investigation of the important biological activity observed. This project will give an excellent introduction into the world of asymmetric synthesis, for those interested in the challenge of natural products and decoding their structure-activity relationships as pharmaceutical lead compounds.

Drug Discovery: Towards New Therapeutics for Mycobacterium tuberculosis (TB)

With Associate Professor Shaun Lott, Dr Jodie Johnston and Dr Dan Furkert

Tuberculosis (TB) currently affects tens of millions globally and imposes a significant economic and health burden, especially in developing countries. The menaquinone (vitamin K) biosynthetic pathway offers a new drug development target, as control of menaquinone levels can affect the survival of the causative bacterium Mycobacterium tuberculosis in hypoxic environments. (+)‑Isochorismate is the substrate for the first committed step in menaquinone biosynthesis, catalysed by the enzyme MenD.

We will investigate the MenD-catalysed reaction of isochorismate, and its potential as a druggable target in TB. The study will draw together complementary expertise in asymmetric synthesis and compound library preparation for SAR study (SCS), alongside structural biology and enzyme kinetics (SBS). This project will provide an excellent introduction into the process of drug design in an academic context, with opportunities to work with specialists in related disciplines, in an effort to validate the menaquinone pathway as a potential target for new anti-TB treatments.

Molecular Basis of Cannabinoid CB1 Receptor Binding for Modulation of CNS Cell Signalling Pathways

With Associate Professor Prof Michelle Glass and Dr Dan Furkert

Cannabinoid CB1 and dopamine D2 receptor signalling pathways are central to central nervous system (CNS) function and are implicated in neurobehavioural disorders. Evidence suggests that multi-receptor complexes involving the CB1 G-protein coupled receptor (GPCR), presently not well understood, play an important pharmacological role. Current work in our group focuses on development of new ligands to target the CB1-D2 receptor complex, for investigation of cell signalling pathways and as lead compounds for new specific therapeutic agents for CNS disorders.

This research project will further explore the detailed nature of ligand binding to the CB1 receptor and resultant effects in downstream cell signalling pathways. The work will involve synthesis of a series of novel CB1 ligands, using chemistry that has been developed in our labs at SCS. These will then be investigated for receptor binding affinity, functional activity and signalling behaviour in the Glass lab in Pharmacology (FMHS). The project would suit a student interested in the application of organic synthesis to the investigation of biological systems, ideally (but not necessarily) with some background in biological sciences or medicinal chemistry. Most of the time will be spent doing organic synthesis, but there will most likely be some opportunity to gain experience in pharmacology and the use of in silico molecular modelling.

TLR2 Activation: Modulating the Activity of Lipopeptide Constructs

With Dr Geoff Williams and Professor Rod Dunbar (SBS)

Toll-like receptor 2 (TLR2) is a highly conserved membrane pattern recognition receptor that has evolved to recognize Lipoprotein motifs expressed by foreign pathogens. On binding of an agonist motif the receptor is activated and, after internalisation of the foreign agent, then modulates the production of signalling factors that up-regulate an effective immune response to that pathogen.

It has been shown that activation of TLR2 can be attained with S-(2,3-bispalmitoyloxypropyl)Cysteine-based (Pam2-Cys and Pam-1-Cys) lipid motifs present in the cell wall of Gram-positive bacteria. Thus, by creating a construct in which this lipid is linked to a suitable peptide epitope, the TLR2 receptor can be recruited into producing a highly targeted immune response that can then be directed against cancerous cells within a host.

The linker portion of the lipid-peptide construct epitope has conventionally been Ser-Lys-Lys-Lys-Lys but it is still not clear to what extent TLR2 activation is governed by this sequence. The project aims to investigate this question by exchanging the key Serine residue by other amino acids – both natural and unnatural – to gauge the effect on receptor activation and through this to better modulate the immunogenic response.

The relative activity of the library of analogues thus generated will be evaluated in the HEK-blue™ cell assay.

The skills necessary to carry this project out will include some organic synthesis and modern solid-phase peptide synthesis and purification.

Synthesis of Pseudoxylallemycins, Antimicrobial Cyclic Tetrapeptides

With Dr Harveen Kaur and Dr Dan Furkert

Multidrug antibiotic resistance poses an increasingly urgent threat to human health. Amongst antibiotic resistant species, Gram-negative bacteria in particular have become resistant to almost all available treatments. Whilst a number of antibiotics are currently being developed to target Gram-positive infections, only few are in progress for Gram-negative infections.

Recently, a family of four cyclic tetrapeptides, namely pseudoxylallemycins A-D, isolated from the termite-associated fungus Pseudoxylaria sp. X802 were found to exhibit Gram-negative antimicrobial activity (MICs of 12.5-25.0 μg/mL), cytotoxicity (HeLa cells, CC50 10.3-49.5 μg/mL) and antiproliferative activity (HUVEC cells, GI50 4.3-33.8 μg/mL; K-562 cells, GI50 4.2-42.8 μg/mL).

Pseudoxylallemycins B-D contain unique allene moieties (highlighted in blue), which rarely occur in natural products. Using a combination of organic and peptide chemistry, this project aims to synthesise the natural products pseudoxylallemycins A-D and structurally related analogues, which will then be evaluated for antimicrobial activity in collaboration with Professor Greg Cook (Uni of Otago).

Chemical Synthesis Of a Conotoxin Derived from the Venom of Cone Snails

With Dr Paul Harris

Cone snails have evolved a venomous harpoon able to paralyse prey with an arsenal of toxic compounds, such as conotoxins, which show great promise in the treatment of conditions such as pain and neuromuscular disorders. κA-conotoxins are a major component of the venom of several species of fish-hunting cone snail, but as a class of compounds have been less well studied due to their molecular complexity and post-translational modifications.

CcTx is a 30 residue glycopeptide that contains an intricate serine-linked pentasaccaride, 3 intramolecular disulphide bonds, several hydroxylated proline residues and a C-terminal alpha helix spanning residues 23Ser-27Thr.  The unique pentasaccaride moiety, which contains several rare and unnatural L-sugars, probably plays a key role in its bioactivity.

Using chemical synthesis techniques this project will embark on a total synthesis of CcTx using glycosylation and peptide chemistry to assemble from individual amino acids, the fully functional molecule. Candidates will become well versed in the modern methods of glycopeptide chemistry including exposure to advanced biophysical techniques such as HPLC and mass spectrometry.

Chemical Synthesis of Prostate Cancer Cell Growth Inhibitors Leucinostatins

With Dr Iman Kavianinia

Leucinostatins are naturally occurring peptides which were isolated from Penicillium lilacinum almost 40 years ago. Twenty-four different structures have been described in the leucinostatin family, with leucinostatins A and B significantly suppressing prostate cancer growth in a coculture system in which prostate stromal cells stimulated the growth of DU-145 human prostate cancer cells through insulin-like growth factor-I.

In order to execute the total synthesis of leucinostatins A and B, synthesis of the seven unnatural amino acid building blocks namely: (2S)-N,N-dimethylpropane-1,2-diamine (DMPD), (S)-N-methylpropane-1,2-diamine (MPD), beta-hydroxyleucine (beta-HyLeu), 4-methyl-L-proline (MePro), (4S,2E)-4-methylhex-2-enoic acid (MeHA), (2S,4S,6S)-AHMOD  and (2S,4S,6R)-AHMOD is required. Site-specific individual incorporation of a (2S,4S,6S)-AHMOD  or (2S,4S,6R)-AHMOD  residue into the peptide framework of leucinostatin is also required to determine the absolute configuration at C-6 in the AHMOD residue.

Solid-phase peptide synthesis (SPPS) techniques will be used for peptide elongation to avoid tedious purification of the intermediates, thus expediting the assembly of the target nonapeptide.

This research project aims to establish a comprehensive structure–activity relationship of leucinostatins A and B in order to search for analogues with improved anti-tumor properties.

Synthesis of New Generation Lipopeptide-based Antibiotics

With Dr Paul Harris

Antibiotic resistance has been recognised by the WHO as one of the greatest threats to humanity and infectious diseases rank as the second most common cause of death worldwide. This is further compounded by the observation that development of new structural classes of antibiotics has all but ceased in the past 40 years.

An emerging subset of peptide based antibiotics e.g. daptomycin are cyclic peptides containing a lipid or fatty acid.   They have been shown to be clinically relevant and are used as the “last line of defence” against otherwise untreatable bacterial infections.  The challenge remains, however, to efficiently produce new antibiotics based on a cyclic peptide scaffold incorporating the crucial lipid motif.

Using our newly devised method of installing a lipid onto a peptide (a thiol-ene reaction), this projects aims to exploit and develop this chemistry to generate a chemical library of peptide based antibiotics, which will undergo biological testing against the most antibiotic resistant strains of bacteria.

Successful candidates will be using organic synthesis techniques and modern methods of solid phase peptide synthesis.

Synthesis of the Novel Macrocyclic Peptide, Streptide

With Dr Paul Harris

Quorum sensing is a system of intercellular communication by which some species of pathogenic bacteria coordinate the regulation of gene expression and production of virulence factors in order to have maximum impact on their environment. As a result, quorum sensing has significant implications in the pathogenicity of disease-causing bacteria. Understanding the transcription products involved in quorum sensing systems provides insight into the regulation of these systems and may help identify potential biological targets for the development of novel antibiotic compounds that inhibit quorum sensing.

Streptococcal bacteria use peptide signals as a means of intraspecies communication. These peptides can contain unusual post-translational modifications, providing opportunities for expanding our understanding of nature’s chemical and biosynthetic repertoires. Streptide is a novel macrocyclic peptide produced by Streptococcus thermophilus, a non-pathogenic streptococcal model strain that is used in the fermentation of dairy products. Although it does not express the virulence factors of its pathogenic relatives (which include Streptococcus mitis, Streptococcus pyogenes and Streptococcus pneumoniae), it does harbour a new, recently identified quorum sensing system common to many streptococci, including pathogenic strains.

Streptide contains an unprecedented tryptophan-lysine cross-link (C-7 to beta) in the macrocycle.  In combination with solid phase peptide synthesis, C-H activation will be used to install the tryptophan-lysine cross-link and synthesise the unnatural amino acid (blue) required to complete an initial total synthesis of streptide.

A successful synthesis will allow evaluation of the biological activity of streptide and will provide the basis for future syntheses of related cross-link-containing macrocyclic peptides.

Development of Antimicrobial Peptides in the Fight Against Bacterial Resistance

With Dr Paul Harris

The emergence and spread of multi-drug-resistant bacteria is becoming a great threat to the health of humankind. The rate of bacteria developing resistance to both frontline and ‘last line of defence’ antibiotics is currently greater than the introduction of new compounds into clinical practice. This poses a severe problem as simple routine medical procedures will become life threatening as any resulting bacterial infection will not be easily and effectively treated.

Naturally-occurring antimicrobial peptides (AMPs) are the tools by which many living organisms employ to defend themselves against bacterial attack. These unique compounds therefore show great potential as new source of antibiotics.

The ascidian metabolite and mannopeptimycin have been show to possess antimicrobial activity and contain the rare cyclic amino acid enduracididine (highlighted in blue).

This project will involve two aspects of modern synthetic chemistry. Firstly, an organic synthesis of enduracididine and secondly, solid phase peptide chemistry to incorporate End into synthetic polypeptides.  A successful synthesis of enduracididine will not only allow access to the above antimicrobial peptides and therefore the development of more potent analogues though SAR studies, but provide the basis for investigation of other peptides containing this intriguing amino acid e.g. teixobactin.

Synthesis of Amylin Mimics (Pramlitide) as a Treatment for Diabetes

With Professor Deborah Hay (SBS) and Dr Paul Harris

Diabetes Mellitus (DM) is a vast worldwide medical problem. The associated medical complications lead to heart disease, stroke, renal failure, premature blindness, amputation and significant mortality rates.

Existing therapies revolve around maintaining glucose at an appropriate level by administration of pramlitide, a 37 amino acid residue polypeptide a structurally related but non-toxic analogue of Amylin. However, pramlitide therapy suffers from several shortcomings such as low bio-availability and a half-life of just 48 mins thus necessitating a challenging 3 times daily injection.

Lipidation of polypeptides or glycosylation of polypeptides is known to increase both circulatory half-life and bio-availability whilst maintaining biological effects.  Using click chemistry or thiol-ene chemistry, this research project aims to install lipids or sugars in a chemoselective manner on specific amino acid residues thereby synthesising modified pramlitide molecules that will be submitted to both biological evaluation (Prof. Debbie Hay, SBS) and estimation of half-life in the body by enzymatic hydrolysis. 

Successful candidates will employ organic synthesis techniques to access suitable glycosylated amino acids, solid phase peptide synthesis to prepare polypeptides and be exposed to biological testing techniques.

The Impact of AGEs in Alzheimer’s Disease

With Dr Harveen Kaur

Alzheimer’s disease (AD) is a complex neurodegenerative disorder that results in progressive cognitive impairment, loss of memory and changes in behaviour. In 2011, 34 million people worldwide were diagnosed with AD, and it is estimated that this figure will triple by 2050 due to an increasing ageing population. Despite vast research spanning more than a century, current treatments for AD are still limited to modest symptomatic relief and the precise causes of AD remain largely unknown.

Recently, new evidence has suggested that beta-amyloid (A-beta) peptides (a hallmark of AD) that have been irreversibly modified by sugar derivatives known as advanced glycation end products (AGEs) are more pathogenic than A-beta itself. However, the A-beta-AGE peptides used in these studies were prepared by the non-specific incubation of A-beta in glucose; this results in the formation of a complex mixture of A-beta-AGE peptides. Thus, the precise impact of individual AGEs on the biophysical properties of A-beta remains to be evaluated.

This project aims to prepare a small library of Aβ-AGE peptides, which will then undergo biological testing by Associate Professor Nigel Birch (SBS) and Professor Michael Dragunow (FMHS). Successful candidates will employ organic synthesis techniques to prepare AGE building blocks followed by incorporation of the AGE building blocks into the A-beta peptide using solid phase peptide synthesis.