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BackgroundGlutamate racemase (MurI) is a cofactor-independent enzyme that is essential to the bacterial peptidoglycan biosynthesis pathway and has therefore been considered an attractive target for the development of antimicrobial drugs. While in our previous study the essentiality of themurIgene was shown inStreptococcus mutans, the primary aetiologic agent of human dental caries, studies onS. mutansMurI have not yet provided definitive results. This study aimed to produce and characterize the biochemical properties of the MurI from theS. mutansUA159 genome.MethodsStructure characterization prediction and multiple sequence alignment were performed by bioinformatic analysis. Recombinant His6-taggedS. mutansMurI was overexpressed in the expression vector pColdII and further purified using a Ni2+affinity chromatography method. Protein solubility, purity and aggregation state were analyzed by SDS–PAGE, Western blotting, native PAGE and SEC-HPLC. Kinetic parameters were assessed by a circular dichroism (CD) assay. Kinetic constants were calculated based on the curve fit for the Michaelis–Menten equation. The effects of temperature and pH on enzymatic activity were determined by a series of coupled enzyme reaction mixtures.ResultsThe glutamate racemase gene fromS. mutansUA159 was amplified by PCR, cloned and expressed inEscherichia coliBL21 (DE3). The 264-amino-acid protein, as a mixture of dimeric and monomeric enzymes, was purified to electrophoretic homogeneity. In the CD assay,S. mutansMurI displayed unique kinetic parameters (Km,d-Glu→l-Glu= 0.3631 ± 0.3205 mM,Vmax,d-Glu→l-Glu= 0.1963 ± 0.0361 mM min−1,kcat,d-Glu→l-Glu= 0.0306 ± 0.0065 s−1,kcat/Km,d-Glu→l-Glu= 0.0844 ± 0.0128 s−1mM−1, withd-glutamate as substrate;Km,l-Glu→d-Glu= 0.8077 ± 0.5081 mM,Vmax,l-Glu→d-Glu= 0.2421 ± 0.0418 mM min−1,kcat,l-Glu→d-Glu= 0.0378 ± 0.0056 s−1,kcat/Km,l-Glu→d-Glu= 0.0468 ± 0.0176 s−1mM−1, withl-glutamate as substrate).S. mutansMurI possessed an assay temperature optimum of 37.5 °C and its optimum pH was 8.0.ConclusionThe findings of this study provide insight into the structure and biochemical traits of the glutamate racemase inS. mutansand supply a conceivable guideline for employing glutamate racemase in anti-caries drug design.

Treatment of hepatitis C patients with direct-acting antiviral drugs involves the combination of multiple small-molecule inhibitors of distinctive mechanisms of action. ACH-806 (or GS-9132) is a novel, small-molecule inhibitor specific for hepatitis C virus (HCV). It inhibits viral RNA replication in HCV replicon cells and was active in genotype 1 HCV-infected patients in a proof-of-concept clinical trial (1). Here, we describe a potential mechanism of action (MoA) wherein ACH-806 alters viral replication complex (RC) composition and function. We found that ACH-806 did not affect HCV polyprotein translation and processing, the early events of the formation of HCV RC. Instead, ACH-806 triggered the formation of a homodimeric form of NS4A with a size of 14 kDa (p14) both in replicon cells and in Huh-7 cells where NS4A was expressed alone. p14 production was negatively regulated by NS3, and its appearance in turn was associated with reductions in NS3 and, especially, NS4A content in RCs due to their accelerated degradation. A previously described resistance substitution near the N terminus of NS3, where NS3 interacts with NS4A, attenuated the reduction of NS3 and NS4A conferred by ACH-806 treatment. Taken together, we show that the compositional changes in viral RCs are associated with the antiviral activity of ACH-806. Small molecules, including ACH-806, with this novel MoA hold promise for further development and provide unique tools for clarifying the functions of NS4A in HCV replication.

Previous work has shown that incorporation of either 1-aminocyclohexanecarboxylic acid (Ac6c) or alpha-methyl-p-phosphonophenylalanine ((alpha-Me)Ppp) in the phosphotyrosyl (pTyr) C-proximal position (pY + 1 residue) of Grb2 SH2 domain binding peptides confers high affinity. The tetralin-based (S)-2-amino-6-phosphonotetralin-2-carboxylic acid (Atc(6-PO3H2)) simultaneously presents structural features of both (alpha-Me)Ppp and Ac6c residues. The current study compares the affinity of this tetralin hybrid Atc(6-PO3H2) versus Ac6c and (alpha-Me)Ppp residues when incorporated into the pY + 1 position of a high-affinity Grb2 SH2 domain binding tripeptide platform. The highest binding affinity (KD = 14.8 nM) was exhibited by the (alpha-Me)Ppp-containing parent, with the corresponding Ac6c-containing peptide being nearly 2-fold less potent (KD = 23.8 nM). The lower KD value was attributable primarily to a 50% increase in off-rate. Replacement of the Ac6c residue with the tetralin-based hybrid resulted in a further 4-fold decrease in binding affinity (KD = 97.8 nM), which was the result of a further 6-fold increase in off-rate, offset by an approximate 45% increase in on-rate. Therefore, by incorporation of the key structural components found in (alpha-Me)Ppp into the Ac6c residue, the tetralin hybrid does enhance binding on-rate. However, net binding affinity is decreased due to an associated increase in binding off-rate. Alternatively, global conformational constraint of an (alpha-Me)Ppp-containing peptide by beta-macrocyclization did result in pronounced elevation of binding affinity, which was achieved primarily through a decrease in the binding off-rate. Mathematical fitting using a simple model that assumed a single binding site yielded an effective KD of 2.28 nM. However this did not closely approximate the data obtained. Rather, use of a complex model that assumed two binding sites resulted in a very close fit of data and provided KD values of 97 pM and 72 nM for the separate sites, respectively. Therefore, although local conformational constraint in the pY + 1 residue proved to be deleterious, global conformational constraint through beta-macrocyclization achieved higher affinity. Similar beta-macrocyclization may potentially be extended to SH2 domain systems other than Grb2, where bend geometries are required.

INTRODUCTION: The complement system is a pivotal player in multiple hematological conditions that include paroxysmal nocturnal hemoglobinuria (PNH). The current standard of care for PNH is intravenous infusion of eculizumab, a humanized monoclonal antibody that targets the terminal complement protein C5 and thereby efficiently impairs intravascular hemolysis. However, a significant fraction of PNH patients in clinical practice respond incompletely to eculizumab due to extravascular hemolysis by immune cells as eculizumab does not prevent erythrocyte opsonization. Additionally, a non-responsive sub-population has been identified with a rare genetic polymorphism in C5 that renders the variant incapable of binding eculizumab. Therefore, an unmet medical need remains for regimens that improve efficacy and that can be administered orally. To achieve this goal, we initiated a discovery program for small molecule inhibitors of complement factor D, a serine protease that is the rate limiting enzyme of the alternative complement pathway. We have obtained high resolution (1.5 Å) crystal structure of inhibitor-bound factor D. Through structure-guided optimization, we have discovered novel inhibitors of factor D that possess high potency and specificity as well as pharmacokinetic properties suitable for oral administration. Herein, we present a biochemical characterization of lead compounds and studies of their activities in various complement-mediated processes. METHODS: The binding affinity to factor D was determined by surface plasmon resonance (Biacore) analysis. The inhibitory effect on factor D protease was evaluated biochemically using both a nonspecific synthetic substrate and a natural substrate consisting of C3b and the complement factor B. The alternative pathway (AP) hemolytic assay was conducted with unsensitized rabbit erythrocytes, 8% human or non-human primate serum, and 10 mM MgEGTA. The classical pathway (CP) hemolytic assay was conducted with antibody-sensitized sheep erythrocytes and 0.5% human serum. To assess inhibition of CP activation through the AP-dependent amplification loop, inhibition of terminal complement complex (TCC) formation by 50% human serum was quantitated following activation by the CP-specific activator HAIGG. Inhibition of complement opsonization and lysis of PNH-like erythrocytes exposed to acidified serum (Ham test) was assessed ex vivo. Finally, selected lead compounds were administered to non-human primates to evaluate the efficacy of factor D inhibitors for blockade of alternative pathway-mediated events. RESULTS: Lead compounds obtained through optimization bound to factor D with Kd values below 1 nM. Tight binding to factor D of the compounds resulted in potent inhibition of factor D proteolytic activity assessed using a synthetic nonspecific substrate as well as a natural substrate. When evaluated in an AP hemolytic assay with human serum, the most potent compounds inhibited cell lysis with EC50 values below 10 nM. Similar inhibitory activity was observed when compounds were assessed in AP hemolytic assays with non-human primate serum, but not with rodent serum. The compounds showed no activity in a CP hemolytic assay using highly diluted human serum and antibody-coated erythrocytes, indicating specificity for factor D. When evaluated in the presence of 50% human serum and with TCC formation as an endpoint, however, the compounds blocked approximately 75% of TCC formation upon CP activation, a consequence of blockage of the AP-dependent amplification loop. Furthermore, the compounds prevented both opsonisation and lysis of PNH-like cells in the Ham test. Finally, when selected compounds were administered to non-human primates, potent inhibition of TCC formation following ex vivo AP activation was observed with EC50 values below 50 nM. CONCLUSIONS: Highly potent and specific factor D inhibitors that block both the terminal pathway and opsonization were discovered using structure-guided design. These orally deliverable inhibitors hold promise as a novel therapeutic approach for treatment of complement-mediated hematological conditions including PNH. Disclosures Morgan: Swedish Orphan Biovitrum: Consultancy, Research Funding; Glaxo Smith Kline: Consultancy; Achillion Pharmaceuticals: Consultancy, Research Funding. Thanassi:Achillion Pharmaceuticals: Employment. Podos:Achillion Pharmaceuticals : Employment. Phadke:Achillion Pharmaceuticals: Employment. Gadhachanda:Achillion Pharmaceuticals: Employment. Pais:Achillion Pharmaceuticals: Employment. Hashimoto:Achillion Pharmaceuticals: Employment. Wang:Achillion Pharmaceuticals: Employment. Chen:Achillion Pharmaceuticals: Employment. Wang:Achillion Pharmaceuticals: Employment. Agarwal:Achillion Pharmaceuticals: Employment. Deshpande:Achillion Pharmaceuticals: Employment. Huang:Achillion Pharmaceuticals: Employment. Wiles:Achillion Pharmaceuticals: Employment. Huang:Achillion Pharmaceuticals: Employment.