A regional outbreak of pneumonia in Wuhan, Hubei Province of China in late 2019 was associated with a novel coronavirus. Rapid release of genomic data for the isolated virus enabled the construction of first-generation homology models of the new CoV 3CL pro cysteine protease. Whilst the overall viral genome was most closely associated with bat coronaviruses, the main protease is most closely related (96% identity) to SARS CoV protease.

A regional outbreak of pneumonia in Wuhan, Hubei Province of China in late 2019 was associated with a novel coronavirus. Rapid release of genomic data for the isolated virus enabled the construction of first-generation homology models of the new CoV 3CLpro cysteine protease. Whilst the overall viral genome was most closely associated with bat coronaviruses, the main protease is most closely related (96% identity) to SARS CoV protease.

The December 2019 outbreak of pneumonia in Wuhan, Hubei Province of China was rapidly linked to a novel coronavirus 2019-nCoV. The rapid spread and severity of the virus has led the World Health Organization to declare it a Public Health Emergency of International Concern. We recently described the first homology models of the main 3CL protease from 2019-nCoV, and now present models of the other viral protease, the papain-like protease or PLpro. Whilst the overall viral genome is most closely associated with bat coronaviruses, no bat PLpro crystal structures are known. Wuhan 2019-nCoV PLpro is most closely related to a bat coronavirus PLpro (97% identity), then SARS (80 %) and MERS (29%) and the most promising models presented here are prepared from SARS crystal structure templates.

The selection of a core scaffold or template is of enormous importance in medicinal chemistry. Benzimidazoles are a recurring fragment in medicinal chemistry, and the 2-amino derivative is a versatile example in lead generation. Alkylated and acylated examples abound, however, alternative linkage chemistries leading do more diverse structures are needed.Here we discuss the regiochemistry of nucleophilic addition of 2-aminobenzimidazole to nitriles, leading to imidamide (amidine) adducts. Additionally, we use extensive NMR analysis and ultimately X-ray crystallography to demonstrate both the regiochemistry and stereochemistry of the addition products, arising from derivatisation of the exocylic 2-amino group.

The formal cycloaddition adduct of 1,4-benzoquinone with two equivalents of cyclopentadiene is a scaffold with two non-conjugated alkenes. Both alkenes undergo endo [4+2] cycloaddition with a diene to form a rigid U-shaped molecular cleft. Here we show experimental, computational and structural evidence that π interactions between the alkenes affect structural rigidity, Diels–Alder reactivity, cleft formation and host–guest capture.

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 bioavailability are analyzed, including molecular weight, octanol water partitioning, hydrogen bond donors/acceptors, rotatable bonds, and polar surface area. The cyclic peptides violated to different degrees all of the limits traditionally considered to be important for oral bioavailability;of drug-like small molecules, although fewer hydrogen bond donors and reduced flexibility generally favored oral absorption.

Dengue Virus (DENV) infection is responsible for the world's most significant insect-borne viral disease. Despite an increasing global impact, there are neither prophylactic nor therapeutic options available for the effective treatment of DENV infection. An attractive target for antiviral drugs is the virally encoded trypsin-like serine protease (NS3pro) and its associated cofactor (NS2B). The NS2B NS3pro complex is responsible for cleaving the viral polyprotein into separate functional viral proteins, and is therefore essential for replication. Recombinant expression of an active NS2B-NS3 protease has primarily been based on constructs linking the C-terminus of the approximately 40 amino acid hydrophilic cofactor domain of NS2B to the N-terminus of NS3pro via a flexible glycine linker. The resulting complex can be expressed in high yield, is soluble and catalytically active and has been used for most in vitro screening, inhibitor, and X-ray crystallographic studies over the last 15 years. Despite extensive analysis, no inhibitor drug candidates have been identified yet. Moreover, the effect of the artificial linker introduced between the protease and its cofactor is unknown. Two alternate methods for bacterial expression of non-covalently linked, catalytically active, NS2B-NS3pro complex are described here along with a comparison of the kinetics of substrate proteolysis and binding affinities of substrate-based aldehyde inhibitors. Both expression methods produced high yields of soluble protein with improved substrate proteolysis kinetics and inhibitor binding compared to their glycine-linked equivalent. The non-covalent association between NS2B and NS3pro is predicted to be more relevant for examining inhibitors that target cofactor-protease interactions rather than the protease active site. Furthermore, these approaches offer alternative strategies for the high yield co-expression of other protein assemblies. (C) 2015 Elsevier Inc. All rights reserved.

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, which revealed long-lasting interactions that trap the antagonist within the receptor. Despite negligible oral bioavailability, 3D53 was much more orally efficacious than W54011 or JJ47 in preventing repeated agonist insults to induce rat paw oedema over 24 h. Thus, residence time on a receptor can trump drug-likeness in determining efficacy, even oral efficacy, of pharmacological agents.

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.

David P Fairlie, Mei-Kwan Yau, Johan K Hamidon, Ranee Singh, Junxian Lim, Jacky Y Suen, Jessica A Rowley, Rink-Jan Lohman, Martin J. Stoermer, Abishek Iyer, and Robert C Reid Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, Brisbane, Queensland, 4072, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Queensland, Brisbane, Queensland, 4072, Australia; Centre for Inflammation and Disease Research, Institute for Molecular Bioscience, Brisbane, Queensland, 4072, Australia

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 from the less homologous template protein, human ORL-1. The results suggest that virtual screening against multiple homology models of the same GPCR can produce structurally diverse antagonists and that this may be desirable even when some models have less sequence homology with the target protein.

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.

ChemInformVolume 45, Issue 15 Heterocyclic Compounds ChemInform Abstract: Lithium Perchlorate Accelerated Friedel—Crafts Addition of Furans to β-Nitrostyrenes. Martin J. Stoermer, Martin J. Stoermer Inst. Mol. Biosci., Univ. Queensland, St. Lucia, Queensl. 4072, AustraliaSearch for more papers by this authorHans-Matthias Richter, Hans-Matthias Richter Inst. Mol. Biosci., Univ. Queensland, St. Lucia, Queensl. 4072, AustraliaSearch for more papers by this authorDieter E. Kaufmann, Dieter E. Kaufmann Inst. Mol. Biosci., Univ. Queensland, St. Lucia, Queensl. 4072, AustraliaSearch for more papers by this author Martin J. Stoermer, Martin J. Stoermer Inst. Mol. Biosci., Univ. Queensland, St. Lucia, Queensl. 4072, AustraliaSearch for more papers by this authorHans-Matthias Richter, Hans-Matthias Richter Inst. Mol. Biosci., Univ. Queensland, St. Lucia, Queensl. 4072, AustraliaSearch for more papers by this authorDieter E. Kaufmann, Dieter E. Kaufmann Inst. Mol. Biosci., Univ. Queensland, St. Lucia, Queensl. 4072, AustraliaSearch for more papers by this author First published: 27 March 2014 https://doi.org/10.1002/chin.201415112Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume45, Issue15April 15, 2014 RelatedInformation

The G-protein coupled receptor (C3aR) for human inflammatory protein complement C3a is an important component of immune, inflammatory, and metabolic diseases. A flexible compound (N2-[(2,2-diphenylethoxy)acetyl]-l-arginine, 4), known as a weak C3aR antagonist (IC50 μM), was transformed here into potent agonists (EC50 nM) of human macrophages (Ca(2+) release in HMDM) by incorporating aromatic heterocycles. Antagonists were also identified. A linear correlation between binding affinity for C3aR and calculated hydrogen-bond interaction energy of the heteroatom indicated that its hydrogen-bonding capacity influenced ligand affinity and function mediated by C3aR. Hydrogen-bond accepting heterocycles (e.g., imidazole) conferred the highest affinity and agonist potency (e.g., 21, EC50 24 nM, Ca(2+), HMDM) with comparable efficacy and immunostimulatory activity as that of C3a in activating human macrophages (Ca(2+), IL1β, TNFα, CCL3). These potent and selective modulators of C3aR, inactivated by a C3aR antagonist, are stable C3a surrogates for interrogating roles for C3aR in physiology and disease.