Mark L. Smythe

Proteolytic degradation of host hemoglobin by schistosomes.

Schistosomes acquire amino acids for growth, development, and reproduction by catabolizing hemoglobin obtained from ingested host erythrocytes. While the biochemical pathway(s) involved has not been determined definitively, a number of proteases including schistosome legumain and cathepsin L-, D-, B- and C-like enzymes have been ascribed roles in the degradation of hemoglobin to diffusible peptides. Transcripts encoding these schistosome proteases, which appear to be expressed in the gastrodermis and cecum of the schistosome, have been reported. Because these enzymes are candidate targets at which to direct novel anti-schistosomal therapies, the comparative biochemistry of these and their counterpart mammalian proteases is now the focus of research in a number of laboratories. This paper reviews reports dating from 40 years ago to the present on how schistosomes digest host-derived hemoglobin, and interprets apparent anomalies in some earlier compared to later reports, the latter having benefited from the availability of PCR and gene cloning technologies. More specifically, the review concentrates on five proteolytic enzymes, and their associated genes, which have been ascribed key roles in the pathway of hemoglobin degradation.

Exploring privileged structures: the combinatorial synthesis of cyclic peptides.

Head-to-tail cyclic peptides have been reported to bind to multiple, unrelated classes of receptor with high affinity. They may therefore be considered to be privileged structures. This review outlines the strategies by which both macrocyclic cyclic peptides and cyclic dipeptides or diketopiperazines have been synthesised in combinatorial libraries. It also briefly outlines some of the biological applications of these molecules, thereby justifying their inclusion as privileged structures.

Exploring privileged structures: The combinatorial synthesis of cyclic peptides

Head-to-tail cyclic peptides have been reported to bind to multiple, unrelated classesof receptor with high affinity. They may therefore be considered to beprivileged structures. This review outlines the strategies by which bothmacrocyclic cyclic peptides and cyclic dipeptides or diketopiperazines havebeen synthesised in combinatorial libraries. It also briefly outlines someof the biological applications of these molecules, thereby justifying theirinclusion as privileged structures.

Sigma-class glutathione transferases

Mammalian cytosolic glutathione transferases (GSTs) can be grouped into seven classes. Of these, the sigma class is also widely distributed in nature, with isoforms found in both vertebrates and invertebrates. It contains examples of proteins that have evolved specialized functions, such as the cephalopod lens S-crystallins, the mammalian hematopoietic prostaglandin D2 synthase, and the helminth 28-kDa antigen. In mammals, the sigma-class GST has both anti- and proinflammatory functions, depending on the type of immune response, and an immunomodulatory function is also associated with the enzyme from helminth parasites. In the fly, it is associated with a specific detoxication activity toward lipid oxidation products. Mice genetically depleted of the sigma-class GST, or transgenically overexpressing it, have provided insight into the physiological roles of the GST. Inhibitors of the mammalian enzyme developed by structure-based methods are effective in controlling allergic response. This review covers the structure, function, and pharmacology of vertebrate and invertebrate GSTs.

Development of small molecules that mimic the binding of ω-conotoxins at the N-type voltage-gated calcium channel

Cone snails (Conidae) are marine predators with some extraordinary features. Their venom contains a hundred or more peptides that target numerous ion channels and receptors in mammals, including several that are involved in disease. ω-Conotoxins from fish hunting snails are 24–27 residue peptides with a rigid 4-loop cysteine framework that target the N-type voltage-gated calcium channel (VGCC). Two ω-conotoxins, MVIIA and CVID are currently in clinical development for chronic pain management (Ziconotide or Prialt, and AM336, respectively). In an attempt to develop small molecule equivalents of CVID, we defined the Cα–Cβ vectors of the residues believed to be important for binding to the N-type VGCC. Using these vectors, we undertook a virtual screening of virtual libraries approach to identify compounds that matched the pharmacophore. Cyclic pentapeptides containing residues of loop 2 of CVID, with one or more being a D-amino acid were designed and synthesised and were found to be active at the N-type VGCC (IC50∼ 20 μM). Agreeing with the specificity profile of CVID, molecules were inactive at the P/Q-type VGCC.

Discovery and Characterization of a Potent Interleukin-6 Binding Peptide with Neutralizing Activity In Vivo

Interleukin-6 (IL-6) is an important member of the cytokine superfamily, exerting pleiotropic actions on many physiological processes. Over-production of IL-6 is a hallmark of immune-mediated inflammatory diseases such as Castleman’s Disease (CD) and rheumatoid arthritis (RA). Antagonism of the interleukin IL-6/IL-6 receptor (IL-6R)/gp130 signaling complex continues to show promise as a therapeutic target. Monoclonal antibodies (mAbs) directed against components of this complex have been approved as therapeutics for both CD and RA. To potentially provide an additional modality to antagonize IL-6 induced pathophysiology, a peptide-based antagonist approach was undertaken. Using a combination of molecular design, phage-display, and medicinal chemistry, disulfide-rich peptides (DRPs) directed against IL-6 were developed with low nanomolar potency in inhibiting IL-6-induced pSTAT3 in U937 monocytic cells. Targeted PEGylation of IL-6 binding peptides resulted in molecules that retained their potency against IL-6 and had a prolongation of their pharmacokinetic (PK) profiles in rodents and monkeys. One such peptide, PN-2921, contained a 40 kDa polyethylene glycol (PEG) moiety and inhibited IL-6-induced pSTAT3 in U937 cells with sub-nM potency and possessed 23, 36, and 59 h PK half-life values in mice, rats, and cynomolgus monkeys, respectively. Parenteral administration of PN-2921 to mice and cynomolgus monkeys potently inhibited IL-6-induced biomarker responses, with significant reductions in the acute inflammatory phase proteins, serum amyloid A (SAA) and C-reactive protein (CRP). This potent, PEGylated IL-6 binding peptide offers a new approach to antagonize IL-6-induced signaling and associated pathophysiology.

Cyclic tetrapeptides via the ring contraction strategy: Chemical techniques useful for their identification

Cyclic tetrapeptides are a class of natural products that have been shown to have broad ranging biological activities and good pharmacokinetic properties. In order to synthesise these highly strained compounds a ring contraction strategy had previously been reported. This strategy was further optimised and a suite of techniques, including the Edman degradation and mass spectrometry/mass spectrometry, were developed to enable characterisation of cyclic tetrapeptide isomers. An NMR solution structure of a cyclic tetrapeptide was also generated. To illustrate the success of this strategy a library of cyclic tetrapeptides was synthesised.

Development and characterization of new inhibitors of the human and mouse hematopoietic prostaglandin D(2) synthases.

The hematopoietic prostaglandin D(2) synthase has a proinflammatory effect in a range of diseases, including allergic asthma, where its product prostaglandin D(2) (PGD(2)) has a role in regulating many of the hallmark disease characteristics. Here we describe the development and characterization of a novel series of hematopoietic prostaglandin D(2) synthase inhibitors with potency similar to that of known inhibitors. Compounds N-benzhydryl-5-(3-hydroxyphenyl)thiophene-2-carboxamide (compound 8) and N-(1-amino-1-oxo-3-phenylpropan-2-yl)-6-(thiophen-2-yl)nicotinamide (compound 34) demonstrated low micromolar potency in the inhibition of the purified enzyme, while only 34 reduced Toll-like receptor (TLR) inducible PGD(2) production in both mouse primary bone marrow-derived macrophages and the human megakaryocytic cell line MEG-01S. Importantly, 34 demonstrated a greater selectivity for inhibition of PGD(2) synthesis versus other eicosanoids that lie downstream of PGH(2) (PGE(2) and markers of prostacyclin (6-keto PGF(1alpha)) and thromboxane (TXB(2))) when compared to the known inhibitors HQL-79 (compound 1) and 2-phenyl-5-(1H-pyrazol-3-yl)thiazole (compound 2). Compound 34 therefore represents a selective hematopoietic prostaglandin D(2) synthase inhibitor.

Identification and characterisation of new inhibitors for the human hematopoietic prostaglandin D-2 synthase

Prostaglandin D(2) synthesised by the hematopoietic prostaglandin D(2) synthase has a pro-inflammatory effect in allergic asthma, regulating many hallmark characteristics of the disease. Here we describe identification of hematopoietic prostaglandin D(2) synthase inhibitors including cibacron blue, bromosulfophthalein and ethacrynic acid. Expansion around the drug-like ethacrynic acid identified a novel inhibitor, nocodazole, and a fragment representing its aromatic core. Nocodazole binding was further characterised by docking calculations in combination with conformational strain analysis. The benzyl thiophene core was predicted to be buried in the active site, binding in the putative prostaglandin binding site, and a likely hydrogen bond donor site identified. X-ray crystallographic studies supported the predicted binding mode.

Topological side-chain classification of β-turns: Ideal motifs for peptidomimetic development

Summaryβ-turns are important topological motifs for biological recognition of proteins and peptides. Organic molecules that sample the side chain positions of β-turns have shown broad binding capacity to multiple different receptors, for example benzodiazepines. β-turns have traditionally been classified into various types based on the backbone dihedral angles (φ2, ψ2, φ3 and ψ3). Indeed, 57–68% of β-turns are currently classified into 8 different backbone families (Type I, Type II, Type I′, Type II′, Type VIII, Type VIa1, Type VIa2 and Type VIb and Type IV which represents unclassified β-turns). Although this classification of β-turns has been useful, the resulting β-turn types are not ideal for the design of β-turn mimetics as they do not reflect topological features of the recognition elements, the side chains. To overcome this, we have extracted β-turns from a data set of non-homologous and high-resolution protein crystal structures. The side chain positions, as defined by Cα–Cβ vectors, of these turns have been clustered using the kth nearest neighbor clustering and filtered nearest centroid sorting algorithms. Nine clusters were obtained that cluster 90% of the data, and the average intra-cluster RMSD of the four Cα–Cβ vectors is 0.36. The nine clusters therefore represent the topology of the side chain scaffold architecture of the vast majority of β-turns. The mean structures of the nine clusters are useful for the development of β-turn mimetics and as biological descriptors for focusing combinatorial chemistry towards biologically relevant topological space.