We apply chemistry principles and techniques to the discovery and development of compounds to tackle disease.
Our group has a diverse array of projects on offer, from the targeted drug delivery of anticancer agents, to the development of epigenetic modifiers for treatment of lymphomas and leukemias, to the discovery of drugs for neglected diseases, diabetes, to novel antimalarials, novel treatments of tuberculosis, and finally, novel antibiotics aimed to debilitate "superbugs". This array of projects is made possible through high level collaborations across multiple Universities and Medical Research Institutes both nationally and internationally that have been established over the last 5 years in the Baell lab at MIPS. These medicinal chemistry-centric projects can be tailored to both Honours level and PhD level research and are designed to have highly publishable outcomes.
In summary, our laboratories are new and very well-equipped, and all projects are designed to not only have sub-projects suitable for Honours projects, but set up with biological collaborators to allow for high impact outcomes. Some projects have significantly more focus on molecular modelling, or drug delivery, than medicinal chemistry, as suits the particular student.
The dopamine D2 receptor (D2R) is a Family A G protein-coupled receptor (GPCR) and therapeutic target for Parkinson’s disease and schizophrenia. Irreversible inhibitors inherently form covalent bonds with chemical substrates and have therefore been extensively utilized for structural studies of proteins to elucidate potential binding domains. We aim to synthesize a series of irreversible derivatives of the bitopic ligand SB269652 (the first identified drug-like negative allosteric modulator of the dopamine D2 receptor) as pharmacological tools to probe the structural basis of D2R orthosteric and allosteric binding pockets, and corresponding modulation and signalling mechanisms. These compounds will utilize established functional group protocols for such studies including a photoactivatable aryl azide group for photolabeling and an aryl isothiocyanate for direct conjugation to the protein.
The synthetic approach that will be used to prepare these irreversible derivatives of SB269652 is based on converting the key primary aromatic amine of the SB269652 derivative to a bioconjugatable isothiocyanate or a photoactivatable azide. We envision irreversible ligands of this nature as extremely valuable tools for ‘locking’ the dopamine D2 receptor into a specific conformation, which may allow the crystallization of this elusive receptor and thereby produce invaluable structural information to enhance drug discovery programs to address the aforementioned disease states.
The dopamine D2 receptor (D2R) is a validated target for the treatment of neuropsychiatric disorders such as schizophrenia. To date, drug discovery efforts have focused on targeting the D2R orthosteric binding site, which cause significant side-effects. The proposed new class of allosteric drugs will act to ‘tune’ the activity of dopamine at the D2R.
Currently there is somewhat limited and shallow structure-activity relationship (SAR) data associated with SB269652, indicating scope for further structural interrogation. We will therefore undertake a further study to identify novel, improved negative allosteric modulators for the D2R, based on our developed azaindole analogue ‘lead’ structures with enhanced affinity and varying degrees of negative cooperativity with dopamine and other orthosteric ligands. Through modifications to the ‘tail’ of the scaffold, we aim to identify additional key molecular features that are responsible for changes in functional affinity and negative allosteric cooperativity, thereby further enhancing our understanding of the nature of this allosteric mechanism at the D2R.
We will test the ability of our novel allosteric ligands to modulate DR function. We will use analytical methods to quantify their modulatory effects on the binding affinity and efficacy of orthosteric ligands.
Novel calcium-sensing receptor positive allosteric modulators for the study of biased receptor conformations
The calcium-sensing receptor (CaSR) is a class C GPCR expressed widely in tissues of the body. Its primary role is to detect subtle changes in the concentration of extracellular calcium ions (Ca2+) to maintain Ca2+ homeostasis primarily via regulation of parathyroid hormone (PTH) secretion from the parathyroid glands. However, the CaSR mediates many additional physiological processes by responding to several “biased” allosteric ligands – i.e. ligands that bind to sites distinct from the endogenous agonist binding site and stabilise “biased” receptor signalling states (conformations) that couple to discrete subsets of signalling pathways at the exclusion of others. How this is achieved, however, is not understood.
The current project thus seeks to develop chemical tools and methods that may favour the formation of biased CaSR conformations in recombinant and native cells and to combine chemical and structural techniques to understand biased CaSR conformations. This will be achieved with the following specific aims:
1. To develop covalent (irreversible) and reversible tagged biased CaSR positive allosteric modulators (PAMs) to stabilise biased receptor conformations.
2. To quantify PAM probe binding affinity, cooperativity and selectivity.
3. To evaluate PAM-mediated biased agonism at the CaSR. As a proof-of-concept, the biased CaSR PAMs, AC265347 & cinacalcet, will be used to develop the necessary tools (Scheme 1) required to address the project aims.
The calcium-sensing receptor (CaSR) is a Class C G protein coupled receptor (GPCR). Its primary role is to negatively regulate parathyroid hormone release in response to subtle increases in extracellular calcium (Ca2+) concentrations. Allosteric modulation of the CaSR is an important therapeutic strategy in the treatment of hyperparathyroidism and is a putative approach to treating osteoporosis and calcium handling disorders. However, CaSR drug development has been hindered by an underappreciation of key pharmacological properties that govern allosteric modulation:
1. modulator affinity for the receptor;
2. the magnitude to which modulators alter CaSR responsiveness to Ca2+ (known as cooperativity);
3. the ability of modulators to directly activate (or inhibit) CaSR signalling (known as efficacy); and
4. the capacity of the modulator to deferentially activate or modulate distinct signalling pathways to the exclusion of others (called biased agonism or biased modulation).
The current project therefore seeks to:
1. undertake a medicinal chemistry approach on a truncated structural variant of the clinical candidate ATF936, to generate a library of novel 'drug-like' CaSR modulators for a detailed SAR analysis;
2. characterise the library of novel CaSR modulators using cell based assays and analytical pharmacology to evaluate SAR effects on CaSR modulator affinity, cooperativity, efficacy and bias.
Chemical synthesis & pharmacological evaluation of novel calcium-sensing receptor (CaSR) negative allosteric modulators (NAMs) for idiopathic pulmonary fibrosis (IPF)
Idiopathic pulmonary fibrosis (IPF), a subtype of interstitial lung disease, causes lung-scarring, leading to cough, breathlessness and death, with a median survival of 3 years after diagnosis. Two approved pharmaceutical treatments (pirfenidone and nintedanib) slow IPF progression and extend patient survival by ~2.5 years, but do not halt or reverse IPF. Further, pirfenidone and nintedanib do not always lessen IPF-related symptoms such as breathlessness, and some patients do not respond or cease medication due to adverse gastrointestinal side effects. Novel IPF drugs with distinct mechanisms of action are needed.
The calcium-sensing receptor (CaSR) is a novel drug target for IPF. Expression of the CaSR and its polyamine agonists is upregulated in IPF and other lung diseases. Targeted fibroblast and smooth muscle cell casr gene ablation protects mice from spontaneous age-related lung fibrosis. Similarly, a CaSR negative allosteric modulator (NAM) reduced pro-fibrotic responses of human lung fibroblasts to TGF1Beta, a pro-fibrotic cytokine that upregulates CaSR expression in these cells. NAMs bind to sites topographically distinct from the endogenous (orthosteric) agonist binding site and inhibit agonist-mediated CaSR signalling.
In an ex vivo model of pulmonary fibrosis for screening novel anti-fibrotic drugs, we have discovered a biased CaSR NAM that is anti-fibrotic. Biased NAMs inhibit only a subset of the available intracellular signalling pathways coupled to a receptor at the exclusion of others, enabling greater specificity for inhibiting disease-relevant pathways while avoiding pathways that link to adverse effects. This project will seek to undertake a medicinal chemistry campaign to pharmacologically evaluate a suite of novel drug-like CaSR small molecule NAMs that can be further developed to mediate anti-fibrotic activity.
Small molecule inhibitors of MAP4K4 as a potential therapy for the treatment of Motor Neurone Disease (MND)
Motor Neurone Disease (MND) is a condition involving the progressive degeneration of nerve cells in muscles, degrading the ability of skeletal muscle control while inevitably leading to death within 3-5 years of onset. No cure is known to date with current treatments being insufficient to slow disease progression. Recent studies have identified a new enzyme target, MAP4K4, linking the protein to the disease state as a therapeutic target. We aim to screen and develop novel hit small-molecule inhibitors of MAP4K4 to explore their potential as a therapy for MND.
Lipid-based drug formulations are complex mixtures of components containing the active agent and other components such as oils, fatty acid esters and surfactant polymers. Once the formulation reaches the gastrointestinal (GI) tract, it is diluted and comes into contact with bile, digestive enzymes which can modify formulations components, and other GI tract contents. The result is a complex mixture that is difficult to study using experimental methods. Molecular dynamics (MD) simulation is a powerful computational technique to investigate the behaviour of complex mixtures on the molecular scale.
This project will use molecular dynamics simulations to investigate the structure of drug formulations and how formulations behave within the GI tract. We believe that MD simulations will become an essential tool for drug formulators in the future. Techniques Used: Molecular Dynamics and High Performance Computing.
References: 1.Warren, D. B.; King, D.; Benameur, H.; Pouton, C. W.; Chalmers, D.K. Glyceride lipid formulations: molecular dynamics modeling of phase behavior during dispersion and molecular interactions between drugs and excipients. Pharmaceutical Research 2013, . 2.King, D. T.; Warren, D. B.; Pouton, C. W.; Chalmers, D. K. Usingmolecular dynamics to study liquid phase behavior: Simulations of the ternary sodium laurate/sodium oleate/water system. Langmuir 2011, 27, 11381.
Nanostructures are one of the new frontiers in chemical science, having wide potential applications in medicine, research and industry as molecular sensors, scaffolds, carriers or molecular machines. A key feature of these applications is a requirement for materials with well-defined geometries that can that can be precisely functionalised with auxiliary chemical features such as chromophores, antibodies or drugs. In addition, complex chemical behaviour such as chemical sensing or targeted drug delivery necessitates nanostructures with complex architectures.
This project aims to design, synthesise and characterise complex nanostructures built from cyclic peptides with alternating D and L amino acids. These peptides assemble through a strong hydrogen bonding network to create tubular structures. Such D/L cyclopeptides (CPs) are versatile building blocks for nanostructures but, to date, the physicochemical factors that control nanostructure formation in these materials have not been explored, and the potential for construction of complex, heterogeneous nanostructures has not been exploited. Techniques used include molecular dynamics, solid phase peptide synthesis and analytical methods such as NMR and X-ray crystallography.
Reference 1. Chapman, R.; Danial, M.; Koh, M. L.; Jolliffe, K. A.; Perrier, S. Design and properties of functional nanotubes from the self-assembly of cyclic peptide templates. Chem Soc Rev 2012, 41 (18), 6023-41.
G protein-coupled receptors (GPCRs) are important pharmaceutical targets that are estimated to be the target for between 30 and 50% of current pharmaceuticals. Although the general features of ligand binding to GPCRs are relatively well understood, much remains to be discovered about the precise mechanism of action of the proteins and the pathways of ligand binding. This project will use molecular dynamics simulation running on high-performance computers combined with advanced modelling methods, such as the use of Markov State models, to investigate the binding of drugs to GPCRs and the dynamic behaviour of the proteins themselves. The information obtained through these studies will advance our understanding of GPCR function and inform GPCR drug design.
Molecular Dynamics, High Performance Computing, Markov Models
1.Thomas, T.; Fang, Y.; Yuriev, E.; Chalmers, D. K. Ligand Binding Pathways of Clozapine and Haloperidol in the Dopamine D-2 and D-3 Receptors. J Chem Inf Model 2016, 56 (2), 308-321.
2.Thomas, T.; McLean, K. C.; McRobb, F. M.; Manallack, D. T.; Chalmers, D. K.; Yuriev, E. Homology Modeling of Human Muscarinic Acetylcholine Receptors. J Chem Inf Model 2014, 54, 243−253.
3.Pande, V. S.; Beauchamp, K.; Bowman, G. R. Everything you wanted to know about Markov State Models but were afraid to ask. Methods 2010, 52 (1), 99-105.
The extraordinary and unsustainable cost of new medications is a direct effect of high attrition rates in drug discovery (>99%). This failure rate is an inherent feature of contemporary target-led approaches to drug discovery that rely upon a hypothetical small-molecule / biomolecule (target) interaction. This hypothesis is only testable after extensive and expensive compound screening and medicinal chemistry optimisation for the purposes of undertaking proof-of-concept (PoC) studies, initially in cells and then in animal models (see box). The success rate of these preclinical PoC studies is < 10% and of these successes < 5% succeed in human clinical trials.
Our group is focused on addressing this using the emerging paradigm of phenotypic drug discovery (PDD)
1. PDD has lower discovery costs and is giving higher success rates than target-led approaches
2. A key bottle-neck to PDD is gaining suitable access to the most effective chemotypes for phenotypic screening.
Our work is directed at addressing this by developing efficient synthetic access to privileged multi-stereocentre containing chemotypes including natural products and natural product-like scaffolds (eg 1-3) and to biased libraries that exhibit high preference for specific biochemical pathways implicated in disease (eg 4). This approach is proving very productive with recent PDD successes from our labs including two successful clinical candidates (cancer and anxiety), and emerging therapies for autoimmune disease and cancer.
Nearly every disease involves aberrant DNA transcription and is driven by the disease-associated activation of transcription factors (TFs) that control the transcription of certain genes. Conventionally, these have been regarded as undruggable by small molecules due to the high-affinity nature of their protein-DNA interactions. To date, only very large molecules have been successfully employed in displacing/blocking TF-DNA interactions. The size of these molecules renders them unsuitable as drugs due to poor bioavailability, cell entry and solubility. In this project we seek to design novel small molecules that have a high affinity for specific TF-DNA interfaces and that disrupt their function, halting the disease process. Since displacement of the TF from the DNA is unnecessary, much smaller molecules can perform this role, opening up the possibility of developing them into orally bioavailable drug therapies. This project focuses on developing a drug discovery platform directed to the discovery of novel TF-DNA interfacial inhibitors.
The development of new drug candidates requires versatile, sensitive pharmacological tools for ligand binding and compound screening. The incorporation of a fluorophore into chemical molecules of interest makes fluorescent probes suitable tools for a range of applications. Fluorescent probes have been established as valuable tools in drug discovery, for instance for studying protein targets and the identification of novel hits from screening libraries. However, a major limitation of current probes is the level of chemical modification required to induce fluorescence. The incorporation of fluorophores generally results in a substantial change in chemical structure, molecular size and physiochemical properties in comparison to the parent compound. This is particularly profound for small non-peptide based hits, including those designed to pass the blood–brain barrier. As a result, they may not able to interact with the target or are poorly representative of how the parent compound interacts with the target, and additionally are often less active and drug-like. Therefore, this project focuses on the development of small drug-like fluorescent fluorophores, which will allow for more accurate modelling of the mechanism of action of the parent compound, and opening up the possibility of using such probes for in vivo applications.
More recently, there has been an increasing interest in the degradation of proteins as a means to down-regulate disease related protein function. Proteolysis-targeting chimeric molecules (PROTACs) are an emerging technique for targeted protein degradation. Although, this technology is getting much attention due to its potential for therapeutic intervention, it is still at its infancy stage and much remains to be learned, particularly regarding its potential for GPCR pharmacology. Here, we will focus on the development of novel PROTACs targeting therapeutically relevant proteins for the treatment of cancers.
In recent years, super-resolution microscopy has revolutionised the study of biological and synthetic nanostructures by breaking the diffraction limit, and allowing visualisation of cells and materials on the molecular scale. While this Nobel Prize-winning technology demonstrates great potential for biomedical researchers wishing to unravel molecular-level interactions, the quantitative information obtainable and the progress in this field, are greatly limited by the small number and poor photophysical properties of existing fluorophores. An often-cited quote from Nobel Prize winner, Eric Betzig, who in his work on super-resolution microscopy constantly needed to “beg chemists for better probes”, further emphasises the need for new fluorescent probes with improved properties. In this project you will be working towards the design and synthesis of molecular sensors with super-resolution properties. With the use of cutting-edge super-resolution microscopy techniques, you will be applying the developed sensors towards visualising biological events and processes below the diffraction limit of light.
Sensors play an integral part in monitoring our health, wellbeing and safety. Chemical sensors are an important subclass that use recognition elements and signalling features to detect and quantify important molecules. One of the most powerful chemical-focused sensory tool is our olfactory system smell. A “chemical nose” sensor is broadly defined as an array-based system that uses synthetic molecules and/or materials to mimic the mammalian olfactory system. This project involves the development of array-based sensing technologies that allow us to unravel subtle differences in the microenvironment of amyloids and understand how these differences translate to molecular, structural and physiological interactions of functional and pathogenic amyloids. The developed sensor arrays will be applied in cerebrospinal fluid samples and brain tissue homogenates from mouse-models of Alzheimer's and Parkinson's disease.
Molecules on the plasma membrane control the extent and type of conversations a cell has with its environment, and how the information is internalised and processed. This begins with the lateral separation of plasma membrane-lipids into two phases - liquid-ordered (Lo) and liquid-disordered (Ld) lipid domains. These domains are crucial for endosomal sorting of proteins, signal transduction, immune responses and membrane trafficking. Disturbances in such highly-regulated processes are observed in many diseases including muscular dystrophy, diabetes, and hypertension, and neurodegenerative diseases such as Alzheimer’s and Parkinson’s disease. Due to the lack of sensors for lipid domains, membrane lipid-sorting has only been studied using fluorescently-labelled lipid analogues which exhibit different membrane behaviour compared to unlabelled ones. Therefore, these investigations have not been very successful.
This project aims at the design and development of molecular rotors that exhibit a change in their fluorescence properties, depending on the polarity and viscosity of their environment. Fluorescence microscopy and image analysis thereafter will provide a thorough understanding of the physiological role of lipid domains and their segregation, and facilitate the reliable diagnosis of physiological and pathological changes in cells.
Protein misfolding and aggregation are hallmarks of many neurodegenerative diseases. In Alzheimer’s disease (AD) and frontotemporal lobar degeneration (FTLD), the amyloid-beta, tau and TDP-43 proteins can be found assembled in amyloid fibrils, paired helical filaments or other aggregates where the morphology is less defined. A key question in this field is the nature of the differences between globular and fibrillar aggregates of these proteins. Standard optical techniques are limited by optical diffraction, examine ensemble behaviour and provide no insight into the structural details governing protein aggregation and its impact on other cellular factors. Therefore, an ability to visualise the molecular-level organisation, structure and distribution of proteins in these proteinopathies is central to gaining deeper understanding of the mechanisms underlying the associated neurodegeneration. This project involves the design and development of new amyloid-specific fluorescent probes with photophysical properties suitable for super-resolution imaging. The developed probes will then be applied to image the nano-scale organisation and distribution of aggregated proteins.
Voltage-gated potassium channel inhibitors from sea anemones have high value as potential therapeutics for a wide range of autoimmune diseases, including diabetes, arthritis and psoriasis. More broadly, sea anemone venoms are a natural source of ion channel modulators, but much of the structural and functional diversity of these venoms remains unexplored. We have recently used transcriptome sequencing and proteomics to identify and validate the presence of putative ion channel blockers in the endemic Australian anemone Oulactis sp., and efforts are currently underway to describe their chemical diversity. This project will evaluate the structural and functional diversity of bioactive peptides found in the proteomes of Oulactis sp and other species of Australian anemones.
The student will gain experience in
1) synthetic and/or recombinant techniques for the production of these peptides;
2) high-resolution structural determination by NMR spectroscopy, and
3) functional characterization in a variety of pharmacological and cellular assays together with local collaborators.
Toxins described at the functional level will shed light on the biological role of these molecules in sea anemones and potentially expand the scope of therapeutic candidates from Australian sea anemones.
Super macrophages: new drugs that up-regulate nitric oxide and enhance killing of tuberculosis and other bacteria
Our group has developed the first inhibitors of the nitric oxide-regulating protein family known as SPSB. These inhibitors cause increased NO levels in macrophages and improve macrophage killing of bacteria, including M. tuberculosis. Tuberculosis is a devastating disease that infects one third of the world’s population. Tuberculosis is resistant to all known antibiotics and until now there has been no effective treatment for sufferers of this disease. We are currently developing a range of SPSB inhibitors that include cyclic peptides and small molecules. This project will involve a synthetic component but may, depending on the student’s interests, include some computational modeling or chemical biology such as synthetic membrane permeability assays and surface plasmon resonance experiments.
We are also developing a new polymer-based drug delivery system that selectively delivers our new inhibitors to macrophages. This arm of the project involves synthesis of fluorescent molecular tools for cell targeting and controlled endosomal release. This work will involve the analysis of fluorescent constructs in macrophages using live fluorescence imaging. An Honours student embarking on this project can expect to acquire a good grounding in peptide chemistry and small molecule chemistry as well as an understanding of the drug discovery process and the dynamics of an interdisciplinary research group.
Lipid-activated protein kinase C epsilon (PKCε) plays an important role in insulin resistance and β-cell failure in Type2 Diabetes (T2D). Deletion or inhibition of PKCε improves β-cell function in genetic models of T2D and is therefore an excellent target for the development of novel therapeutics for T2D. Inhibitors of PKCε offer an alternative strategy for improving insulin availability in diabetic patients. The high degree of conservation of the catalytic site within the PKC family and among different kinases poses a serious hurdle for the development of PKCε isozyme specific inhibitors. An effective approach to selectively target PKCε activity is to prevent the interaction of PKCε with its adaptor protein, RACK2, which translocates PKCε from the cytosol to various sub-cellular sites. The N-terminal regulatory C2 domain of PKCε is critical for its interaction with RACK2, and peptides derived from the RACK-binding site of C2 domain have been shown to be selective inhibitors of RACK2/ PKCε interaction. Targeting this protein-protein interaction site with small molecules would facilitate the development of novel PKCε inhibitors with improved selectivity and pharmacokinetic properties. We have performed an NMR-based fragment screen to identify small molecules that bind to the C2 domain of PKCε. Several hits were identified in the primary screen, indicating that this protein-protein interaction site is druggable.
This project will validate the hits identified from the primary screen using various biophysical techniques (like SPR, ITC and NMR) and further elaborate the fragment hits into high-affinity ligands using medicinal chemistry optimisation.
Spirocyclic scaffolds are favourable in a medicinal chemistry setting as they offer enhanced three-dimensionality that can increase potency, selectivity and lead to an improved pharmacokinetic profile. This project aims to explore the use of a combination of transition metal-catalysis and visible-light irradiation to access unique reactive intermediates and harness their reactivity in new synthetic transformations. The new chemical processes are expected to deliver increased economy, efficiency and precision in the synthesis of spirocyclic sp3-rich molecules that are of immense value in pharmaceutical chemistry yet remain challenging to prepare with existing technologies.
Building on our groups recent work exploring the reactivity of nucleophilic carbene intermediates generated via the visible-light irradiation of acyl silanes, this project aims to explore the development of new acyl silane reagents that can be used as tunable frameworks for photoaffinity labelling (PAL) in chemical biology settings. This project will explore the application of these new photochemical probes to deliver an enhanced understanding of how certain molecules behave in a cellular environment, delivering key insights that can be used to develop new medicines with increased binding selectivity, improved safety profiles, and clinical efficacy.
Germs such as bacteria develop the ability to overcome the medicines designed to kill them, which limits our ability to successfully treat bacterial infections and leads to millions of additional deaths worldwide each year. Tuberculosis—caused by a bacterial infection—is currently responsible for more deaths annually than any other infectious disease, representing a significant global public health threat. Of growing concern is the rapid emergence of drug-resistant tuberculosis strains that do not respond to traditional antibiotic medicines. To address this critical need for better tuberculosis medicines, this project aims to develop novel therapeutic candidates that are highly potent against drug-resistant strains of the tuberculosis bacteria yet produce fewer side effects than existing treatments.
The adenosine receptor (AR) family is an important class of physiologically and therapeutically relevant GPCRs that can benefit substantially from more selective drug targeting. Although all four AR subtypes are expressed in the mammalian heart, the well-known protective effects of adenosine in this tissue are predominantly mediated by the adenosine A1 receptor (A1AR) subtype, especially under conditions of ischemia and reperfusion injury. Unfortunately, the transition of A1AR agonists into the clinic has been severely hindered because of high doses causing on-target bradycardia, atrioventricular block, and hypotension.
As a consequence, clinical trials of AR agonists have had limited success because of the suboptimal dose of agonist that can be used. We have designed a novel bitopic A1AR ligand (MIPS746) - a hybrid molecule comprising adenosine linked to a positive allosteric modulator to engender biased signaling at the A1AR. This compound was able to act as cardioprotective agent without affecting heart rate, providing proof of concept that bitopic ligands can be designed as biased agonists to promote on-target efficacy without on-target side effects.
In an extension of this research we aim to further modify the allosteric component of this interesting bitopic ligand to obtain more drug-like derivatives.
Reference: Valant et al. PNAS, 2014, 111, 4614-4619.
Noscapine is an phthalideisoquinoline alkaloid isolated from the opium poppy, Papaver somniferum, that has been used as a cough suppressant since the mid-1950s. More recently, noscapine was found to act as a weak inhibitor of microtubule polymerization which has generated interest in developing anticancer agents based on noscapine. The usefulness of microtubule targeting agents in the treatment of cancer has been validated by the successful use of a number of taxanes and vinca alkaloids in the therapy of a variety of cancers. Although noscapine has exhibits modest activity in this respect, it's favorable toxicity profile and oral bioavailability make it an appealing target for further study. A number of semi-synthetic derivatives of noscapine have been prepared by ourselves and others that exhibit improved cytotoxic activity (e.g. CEFNA and MIPS1361).
However, only a limited number of structural modifications have been investigated to date and there is considerable scope for further research. Accordingly, the goal of this project is to explore the structure-activity relationships of this interesting molecule and identify noscapine derivatives with enhanced potency as anticancer agents. A structure-activity guided optimization will be pursued in parallel to a structure-based design approach in order to gain a greater understanding of the structural features that are important for noscapine's anticancer activity and identify derivatives with improved potency.
Reference: The Discovery and Development of Noscapine and Derivatives as Anti-cancer Agents, A. DeBono, B. Capuano, P.J. Scammells, J. Med. Chem. 2015, 58, 5699-5727.
We are applying structure-based drug discovery approaches to the development of therapeutically useful inhibitors of two important aminopeptidase enzymes.
1) PfMAP Inhibitors. Malaria remains a global health issue, as up to 48% of the world’s population (3 billion people), now live in areas at risk of malaria. The malaria parasite Plasmodium falciparum's metalloaminopeptidases (PfMAPs), M1, M17 and M18 are essential for parasite fitness. Agents that inhibit the PfMAPs in combination is desirable as this would reduce the likelihood of parasites being able to rapidly evolve resistance.
In this project, biochemistry and protein crystallography will be used to identify how molecules are trafficked to the buried active sites of multimeric PfMAPs and SAR-guided and structure-based drug design approaches will be applied to the development of novel dual and tripeptidase inhibitors.
2) APN Inhibitors. Aminopeptidase N (APN) is a zinc-dependent aminopeptidase that plays a significant role in cancer proliferation, metastasis, and cancer-induced angiogenesis. Dysregulation of APN is associated with ovary, prostate, colon, kidney, and lung cancers. Inhibitors of APN can mediate cancer cell-death and have shown clinical efficacy alone and in combination chemotherapy.
The known APN inhibitors, Bestatin and Tosedostat, have shown clinical efficacy for the treatment of many cancer types including acute myeloid leukaemia and lung cancer. In our preliminary studies, we have identified a number of novel APN inhibitors, two of which demonstrate an approximate 10-fold improvement over current clinical candidates, and show sub-micromolar cellular efficacy against leukemic cell lines. The central goal of this project is to develop these compounds into potent anticancer lead compounds that possess the physicochemical properties appropriate for a drug.
Fragment-based drug design (FBDD) is a technique that has been developed for the rapid and efficient identification of key building-blocks for drug development. FBDD relies on the measurement of interactions between a therapeutic target and small molecular ‘fragments’ that are not, in themselves, candidate drug molecules but represent pieces of the sorts of chemical entities commonly found in drugs. Determining the structure of these fragments in complex with the target protein provides critical information for assembly of the fragments into potent drug candidates. The structures of fragments bound to their target proteins are normally obtained using X-ray crystallography.
However, many drug targets are not amenable to this approach. Although NMR spectroscopy can also be used to determine structures of complexes, it is generally regarded as being too slow to support programs of structure-based drug design. In this project you will develop techniques to enable rapid structure determination by NMR. These will exploit recent advances in protein expression, selective isotope labelling, non-uniform acquisition and conjugation with paramagnetic lanthanides and be applied to therapeutically relevant proteins that are not amenable to crystallography.
Fragment-based drug design enables the identification of small, low affinity (Kd ~5mM-500uM) but highly ligand efficient compounds binding to the target of interest. These hits represent good starting points for the development of cell permeable inhibitors and drugs. Hence, the next major hurdle in development of the weak affinity hit is to increase affinity and size to give lead structures which can be used to probe biology or undergo further development. Off-rate screening uses Surface Plasmon Resonance (SPR) to observe the kinetics of ligand-target interactions.
Affinity (Kd) is related to the association rate (ka) and dissociate rate (kd) of the ligand-target complex and higher affinity compounds are predominantly obtained by reducing the dissociation rate of the complex. Hence screening for compounds with slower dissociation rates provides an efficient method for finding higher affinity analogues. Another advantage of screening for slow dissociation rates by SPR is that low purity mixtures can be used. Hence chemistry can be conducted in parallel (~96 at a time) on microscale (~10 uL per reaction) without the need for purification and screened directly by SPR.
This project has a number of aspects from computational chemistry and medicinal chemistry associated with the design of the library for synthesis, conducting the microscale parallel synthesis and screening the products by SPR and would provide the opportunity to work across computational chemistry, organic chemistry and biophysical screening fields.
Epigenetics describes the management of the genetic code to influence protein expression in cells and organisms. It is a major driver of cellular transformation in cancer and many other diseases. We are developing novel inhibitors of epigenetic regulators, utilizing structure-based drug design principles and stereoselective synthesis, combined with biochemical and cell based assays.
1. epigenetic drug discovery - fragment based design of bromodomain inhibitors
2. solid phase synthesis of chromodomain epigenetic reader proteins and peptidomimetic inhibitors.
3. combination kinase and bromodomain inhibitors - knocking down Myc in cancer