David Fairlie | The University of Queensland, Australia (original) (raw)

Papers by David Fairlie

European Journal of Organic Chemistry, Dec 4, 2017

British journal of pharmacology, 2014

Journal of Pharmacology and Experimental Therapeutics, 2011

Many trypsin-like serine proteases like β-tryptase are involved in the pathogenesis of colitis an... more Many trypsin-like serine proteases like β-tryptase are involved in the pathogenesis of colitis and inflammatory bowel diseases. Inhibitors of individual proteases show limited efficacy in treating such conditions, but also likely disrupt digestive and defensive functions of proteases. Here we investigate whether This article has not been copyedited and formatted. The final version may differ from this version.

Current Medicinal Chemistry, 2006

American Journal of Physiology-Renal Physiology, 2013

Protease-activated receptor-2 (PAR2) is a G protein-coupled receptor abundantly expressed in the ... more Protease-activated receptor-2 (PAR2) is a G protein-coupled receptor abundantly expressed in the kidney. The aim of this study was to profile inflammatory gene and protein expression induced by PAR2 activation in human kidney tubular epithelial cells (HTEC). A novel PAR2 antagonist, GB88, was used to confirm agonist specificity. Intracellular Ca2+ (iCa2+) mobilization, confocal microscopy, gene expression profiling, qRTPCR, and protein expression were used to characterize PAR2 activation. PAR2 induced a pronounced increase in iCa2+ concentration that was blocked by the PAR2 antagonist. Treatment with SLIGKV-NH2 at the apical or basolateral cell surface for 5 h induced expression of a range of inflammatory genes by greater than fourfold, including IL-1β, TRAF1, IL-6, and MMP-1, as assessed by cDNA microarray and qRTPCR analysis. Using antibody arrays, GM-CSF, ICAM-1, TNF-α, MMP-1, and MMP-10 were among the induced proteins secreted. Cytokine-specific ELISAs identified three- to sixfo...

Chemical Communications, 2019

Rule-of-five parameters and membrane permeabilities are not the only determinants of oral bioavai... more Rule-of-five parameters and membrane permeabilities are not the only determinants of oral bioavailability.

Chemical reviews, Jan 28, 2017

Peptides and proteins are not orally bioavailable in mammals, although a few peptides are intesti... more Peptides and proteins are not orally bioavailable in mammals, although a few peptides are intestinally absorbed in small amounts. Polypeptides are generally too large and polar to passively diffuse through lipid membranes, while most known active transport mechanisms facilitate cell uptake of only very small peptides. Systematic evaluations of peptides with molecular weights above 500 Da are needed to identify parameters that influence oral bioavailability. Here we describe 125 cyclic peptides containing four to thirty-seven amino acids that are orally absorbed by mammals. Cyclization minimizes degradation in the gut, blood, and tissues by removing cleavable N- and C-termini and by shielding components from metabolic enzymes. Cyclization also folds peptides into bioactive conformations that determine exposure of polar atoms to solvation by water and lipids and therefore can influence oral bioavailability. Key chemical properties thought to influence oral absorption and bioavailabili...

Nature communications, Aug 24, 2017

Complement C3a is an important protein in innate and adaptive immunity, but its specific roles in... more Complement C3a is an important protein in innate and adaptive immunity, but its specific roles in vivo remain uncertain because C3a degrades rapidly to form the C3a-desArg protein, which does not bind to the C3a receptor and is indistinguishable from C3a using antibodies. Here we develop the most potent, stable and highly selective small molecule modulators of C3a receptor, using a heterocyclic hinge to switch between agonist and antagonist ligand conformations. This enables characterization of C3 areceptor-selective pro- vs. anti-inflammatory actions in human mast cells and macrophages, and in rats. A C3a receptor-selective agonist induces acute rat paw inflammation by first degranulating mast cells before activating macrophages and neutrophils. An orally administered C3a receptor-selective antagonist inhibits mast cell degranulation, thereby blocking recruitment and activation of macrophages and neutrophils, expression of inflammatory mediators and inflammation in a rat paw edema ...

The Journal of pharmacology and experimental therapeutics, 2017

Small molecule histone deacetylase (HDAC) inhibitors with anti-inflammatory activity may be candi... more Small molecule histone deacetylase (HDAC) inhibitors with anti-inflammatory activity may be candidates for targeting intestinal inflammatory pathways in inflammatory bowel disease (IBD). This study investigated whether treatment with a potent HDAC6 inhibitor, BML-281, could protect against colonic inflammation and prevent inflammatory cell infiltration into the colon to drive disease pathology in a mouse model of acute dextran sodium sulfate (DSS) colitis. Control and acute DSS-colitis mice were treated with BML-281 (1 mg/kg per day s.c. and 10 mg/kg per day s.c.) for 8 days. Changes in disease pathology, colonic structure, function, alterations in inflammatory milieu, together with colonic inflammatory cell flux, were assessed by weight loss and disease activity index in vivo and by flow cytometry, gene expression, and histology ex vivo. Anti-inflammatory responses of BML-281 on human polymorphonuclear leukocytes were assessed in vitro. Administration of BML-281 to DSS-treated mice...

ACS Medicinal Chemistry Letters, 2016

Scientific reports, Jan 20, 2016

Drug discovery and translation are normally based on optimizing efficacy by increasing receptor a... more Drug discovery and translation are normally based on optimizing efficacy by increasing receptor affinity, functional potency, drug-likeness (rule-of-five compliance) and oral bioavailability. Here we demonstrate that residence time of a compound on its receptor has an overriding influence on efficacy, exemplified for antagonists of inflammatory protein complement C5a that activates immune cells and promotes disease. Three equipotent antagonists (3D53, W54011, JJ47) of inflammatory responses to C5a (3nM) were compared for drug-likeness, receptor affinity and antagonist potency in human macrophages, and anti-inflammatory efficacy in rats. Only the least drug-like antagonist (3D53) maintained potency in cells against higher C5a concentrations and had a much longer duration of action (t1/2 ~ 20 h) than W54011 or JJ47 (t1/2 ~ 1-3 h) in inhibiting macrophage responses. The unusually long residence time of 3D53 on its receptor was mechanistically probed by molecular dynamics simulations, w...

Bioorganic & medicinal chemistry letters, Jan 17, 2015

Activation of protease activated receptor 2 (PAR2) has been implicated in inflammatory and metabo... more Activation of protease activated receptor 2 (PAR2) has been implicated in inflammatory and metabolic disorders and its inhibition may yield novel therapeutics. Here, we report a series of PAR2 antagonists based on C-terminal capping of 5-isoxazolyl-l-cyclohexylalanine-l-isoleucine, with benzylamine analogues being effective new PAR2 antagonists. 5-Isoxazolyl-l-cyclohexylalanine-l-isoleucine-2-methoxybenzylamine (10) inhibited PAR2-, but not PAR1-, induced release of Ca(2+) (IC50 0.5μM) in human colon cells, IL-6 and TNFα secretion (IC50 1-5μM) from human kidney cells, and was anti-inflammatory in acute rat paw inflammation (ED50 5mg/kg sc). These findings show that new benzylamide antagonists of PAR2 have anti-inflammatory activity.

The Journal of pharmacology and experimental therapeutics, Jan 10, 2015

Vorinostat and other inhibitors of different histone deacetylase (HDAC) enzymes are currently bei... more Vorinostat and other inhibitors of different histone deacetylase (HDAC) enzymes are currently being sought to modulate a variety of human conditions, including chronic inflammatory diseases. Some HDAC inhibitors are anti-inflammatory in rodent models of arthritis and colitis, usually at cytotoxic doses that may cause side effects. Here, we investigate the dose-dependent pro- and anti- inflammatory efficacy of two known inhibitors of multiple HDACs, Vorinostat and BML281, in human macrophages and in a rat model of collagen-induced arthritis by monitoring effects on disease progression, histopathology and immunohistochemistry. Both HDAC inhibitors differentially modulated lipopolysaccharide (LPS)-induced cytokine release from human macrophages, suppressing release of some inflammatory mediators (IL12p40, IL6) at low concentrations (< 3 µM) but amplifying production of others (TNF, IL1β) at higher concentrations (>3 µM). This trend translated in vivo to rat arthritis, with anti-i...

Chembiochem : a European journal of chemical biology, Jan 4, 2015

Cyclic peptides and macrocycles have the potential to be membrane permeable and orally bioavailab... more Cyclic peptides and macrocycles have the potential to be membrane permeable and orally bioavailable, despite often not complying with the rule-of-five used in medicinal chemistry to guide discovery of oral drugs. Here we compare solvent-dependent three dimensional structures of three cyclic hexapeptides containing D-amino acids, prolines, and intramolecular hydrogen bonds. Conformational rigidity rather than flexibility resulted in higher membrane permeability, metabolic stability and oral bioavailability, consistent with less polar surface exposure to solvent and a reduced entropy penalty for transition between polar and nonpolar environments.

Peptides 2015, Proceedings of the 24th American Peptide Symposium, 2015

PLOS ONE, 2015

Antibacterial drugs with novel scaffolds and new mechanisms of action are desperately needed to a... more Antibacterial drugs with novel scaffolds and new mechanisms of action are desperately needed to address the growing problem of antibiotic resistance. The periplasmic oxidative folding system in Gram-negative bacteria represents a possible target for anti-virulence antibacterials. By targeting virulence rather than viability, development of resistance and side effects (through killing host native microbiota) might be minimized. Here, we undertook the design of peptidomimetic inhibitors targeting the interaction between the two key enzymes of oxidative folding, DsbA and DsbB, with the ultimate goal of preventing virulence factor assembly. Structures of DsbB-or peptides-complexed with DsbA revealed key interactions with the DsbA active site cysteine, and with a hydrophobic groove adjacent to the active site. The present work aimed to discover peptidomimetics that target the hydrophobic groove to generate non-covalent DsbA inhibitors. The previously reported structure of a Proteus mirabilis DsbA active site cysteine mutant, in a non-covalent complex with the heptapeptide PWATCDS, was used as an in silico template for virtual screening of a peptidomimetic fragment library. The highest scoring fragment compound and nine derivatives were synthesized and evaluated for DsbA binding and inhibition. These experiments discovered peptidomimetic fragments with inhibitory activity at millimolar concentrations. Although only weakly potent relative to larger covalent peptide inhibitors that interact through the active site cysteine, these fragments offer new opportunities as templates to build non-covalent inhibitors. The results suggest that non-covalent peptidomimetics may need to interact with sites beyond the hydrophobic groove in order to produce potent DsbA inhibitors.

Journal of chemical information and modeling, Jan 22, 2015

Protease activated receptor 2 (PAR2) is an unusual G-protein coupled receptor (GPCR) involved in ... more Protease activated receptor 2 (PAR2) is an unusual G-protein coupled receptor (GPCR) involved in inflammation and metabolism. It is activated through cleavage of its N-terminus by proteases. The new N-terminus functions as a tethered ligand that folds back and intramolecularly activates PAR2, initiating multiple downstream signaling pathways. The only compounds reported to date to inhibit PAR2 activation are of moderate potency. Three structural models for PAR2 have been constructed based on sequence homology with known crystal structures for bovine rhodopsin, human ORL-1 (also called nociceptin/orphanin FQ receptor), and human PAR1. The three PAR2 model structures were compared and used to predict potential interactions with ligands. Virtual screening for ligands using the Chembridge database, and either ORL-1 or PAR1 derived PAR2 models led to identification of eight new small molecule PAR2 antagonists (IC50 10-100 μM). Notably, the most potent compound 1 (IC50 11 μM) was derived ...

Proceedings of the National Academy of Sciences of the United States of America, Jan 9, 2014

Enhancing the oral bioavailability of peptide drug leads is a major challenge in drug design. As ... more Enhancing the oral bioavailability of peptide drug leads is a major challenge in drug design. As such, methods to address this challenge are highly sought after by the pharmaceutical industry. Here, we propose a strategy to identify appropriate amides for N-methylation using temperature coefficients measured by NMR to identify exposed amides in cyclic peptides. N-methylation effectively caps these amides, modifying the overall solvation properties of the peptides and making them more membrane permeable. The approach for identifying sites for N-methylation is a rapid alternative to the elucidation of 3D structures of peptide drug leads, which has been a commonly used structure-guided approach in the past. Five leucine-rich peptide scaffolds are reported with selectively designed N-methylated derivatives. In vitro membrane permeability was assessed by parallel artificial membrane permeability assay and Caco-2 assay. The most promising N-methylated peptide was then tested in vivo. Here...

ACS medicinal chemistry letters, Jan 9, 2014

Development of peptide-based drugs has been severely limited by lack of oral bioavailability with... more Development of peptide-based drugs has been severely limited by lack of oral bioavailability with less than a handful of peptides being truly orally bioavailable, mainly cyclic peptides with N-methyl amino acids and few hydrogen bond donors. Here we report that cyclic penta- and hexa-leucine peptides, with no N-methylation and five or six amide NH protons, exhibit some degree of oral bioavailability (4-17%) approaching that of the heavily N-methylated drug cyclosporine (22%) under the same conditions. These simple cyclic peptides demonstrate that oral bioavailability is achievable for peptides that fall outside of rule-of-five guidelines without the need for N-methylation or modified amino acids.

Nature Communications, 2013

A significant challenge in chemistry is to rationally reproduce the functional potency of a prote... more A significant challenge in chemistry is to rationally reproduce the functional potency of a protein in a small molecule, which is cheaper to manufacture, non-immunogenic, and also both stable and bioavailable. Synthetic peptides corresponding to small bioactive protein surfaces do not form stable structures in water and do not exhibit the functional potencies of proteins. Here we describe a novel approach to growing small molecules with protein-like potencies from a functionally important amino acid of a protein. A 77-residue human inflammatory protein (complement C3a) important in innate immunity is rationally transformed to equipotent small molecules, using peptide surrogates that incorporate a turninducing heterocycle with correctly positioned hydrogen-bond-accepting atoms. Small molecule agonists (molecular weight o500 Da) examined for receptor affinity and cellular responses have the same high potencies, functional profile and specificity of action as C3a protein, but greater plasma stability and bioavailability.