5-Aminomethylbenzimidazoles as potent ITK antagonists

Benzamide 1 demonstrated good potency as a selective ITK inhibitor, however the amide moiety was found to be hydrolytically labile in vivo, resulting in low oral exposure and the generation of mutagenic aromatic amine metabolites. Replacing the benzamide with a benzylamine linker not only addressed the toxicity issue, but also improved the cellular and functional potency as well as the drug-like properties. SAR studies around the benzylamines and the identification of 10n and 10o as excellent tools for proof-of-concept studies are described.     

Synthesis and evaluation of novel tricyclic benzo[4.5]cyclohepta[1.2]pyridine derivatives as NMDA/NR2B antagonists

A novel series of annulated tricyclic compounds was synthesized and evaluated as NMDA/NR2B antagonists. Structure–activity development was directed towards in vitro optimization of NR2B activity and selectivity over the hERG K⁺ channel. Preferred compounds were subsequently evaluated for selectivity in an α₁-adrenergic receptor binding counter-screen and a cell-based assay of NR2B activity.     

Backbone structure of a small helical integral membrane protein: A unique structural characterization

The structural characterization of small integral membrane proteins pose a significant challenge for structural biology because of the multitude of molecular interactions between the protein and its heterogeneous environment. Here, the three‐dimensional backbone structure of Rv1761c from Mycobacterium tuberculosis has been characterized using solution NMR spectroscopy and dodecylphosphocholine (DPC) micelles as a membrane mimetic environment. This 127 residue single transmembrane helix protein has a significant (10 kDa) C‐terminal extramembranous domain. Five hundred and ninety distance, backbone dihedral, and orientational restraints were employed resulting in a 1.16 Å rmsd backbone structure with a transmembrane domain defined at 0.40 Å. The structure determination approach utilized residual dipolar coupling orientation data from partially aligned samples, long‐range paramagnetic relaxation enhancement derived distances, and dihedral restraints from chemical shift indices to determine the global fold. This structural model of Rv1761c displays some influences by the membrane mimetic illustrating that the structure of these membrane proteins is dictated by a combination of the amino acid sequence and the protein's environment. These results demonstrate both the efficacy of the structural approach and the necessity to consider the biophysical properties of membrane mimetics when interpreting structural data of integral membrane proteins and, in particular, small integral membrane proteins.     

Simple sequence repeat (SSR)-based gene diversity in <Emphasis Type="Italic">Burkholderia pseudomallei</Emphasis> and <Emphasis Type="Italic">Burkholderia mallei</Emphasis>

Pathogens Burkholderia pseudomallei (Bp) and Burkholderia mallei (Bm) contain a large number (> 12,000) of Simple Sequence Repeats (SSRs). To study the extent to which these features have contributed to the diversification of genes, we have conducted comparative studies with nineteen genomes of these bacteria. We found 210 genes with characteristic types of SSR variations. SSRs with nonamer repeat units were the most abundant, followed by hexamers and trimers. Amino acids with smaller and nonpolar R-groups are preferred to be encoded by the variant SSRs, perhaps due to their minimal impacts to protein functionality. A majority of these genes appears to code for surface or secreted proteins that may directly interact with the host factors during pathogenesis or other environmental factors. There also are others that encode diverse functions in the cytoplasm, and this protein variability may reflect an extensive involvement of phase variation in survival and adaptation of these pathogens.     

Lack of Adaptation of Chimeric GB Virus B/Hepatitis C Virus in the Marmoset Model: Possible Effects of Bottleneck

Approximately 3% of the world population is chronically infected with hepatitis C virus (HCV). GB virus B (GBV-B), a surrogate model for HCV, causes hepatitis in tamarins and is the virus phylogenetically most closely related to HCV. Previously we described a chimeric GBV-B containing an HCV insert from the 5′ noncoding region (NCR) that was adapted for efficient replication in tamarins (Saguinus species). We have also demonstrated that wild-type (WT) GBV-B rapidly adapts for efficient replication in a closely related species, the common marmoset (Callithrix jacchus). Here, we demonstrate that the chimeric virus failed to adapt during serial passage in marmosets. The chimeric virus was passaged four times through 24 marmosets. During passage, two marmoset phenotypes were observed: susceptible and partially resistant. Although appearing to adapt in a resistant animal during a prolonged and gradual increase in viremia, the chimeric GBV-B failed to replicate efficiently upon passage to a naïve marmoset. The resistance was specific to the chimeric virus, as the chimeric virus-resistant animals were susceptible to marmoset-adapted WT virus during rechallenge studies. Three isolates of the chimeric virus were sequenced, and 20 nucleotide changes were observed, including eight amino acid changes. Three unique changes were observed in the 5′ NCR chimeric insert, an area that is highly conserved in HCV. We speculate that the failure of the chimeric virus to adapt in marmosets might be due to a bottleneck that occurs at the time of infection of resistant animals, which may lead to a loss of fitness upon serial passage.Worldwide, approximately 170 million people are chronically infected with hepatitis C virus (HCV). The current approved therapy involves the combination of pegylated alpha interferon and ribavirin and has response rates for sustained viral clearance of 42% and 82% for genotypes 1 and 2/3, respectively (15, 29). However, a significant proportion of the population still develops serious disease as a consequence of HCV infection. HCV infection is the leading cause for liver transplantation in the United States (1, 50), and liver cancer due to HCV infection is one of the most rapidly increasing types of cancer in the United States (20).GB virus B (GBV-B) is a hepatotropic virus that causes hepatitis in tamarins and is the virus phylogenetically most closely related to HCV (33, 36, 44), and as such, GBV-B represents an important small-primate surrogate model for HCV infections. The history of the GB agent is complex and originates with the inoculation of tamarins with serum obtained from a surgeon with hepatitis (for a review, see reference 3); however there is little doubt that GBV-B is a tamarin virus, despite the fact that it has never been isolated from tamarins a second time. GBV-B has a very narrow host range for tamarins, marmosets, and other closely related New World monkeys (6, 23, 54). The GBV-B model overcomes a number of limitations encountered when working with HCV (3, 22). Due to the limited availability of tamarins, our lab and others (5, 16, 21, 23) initiated GBV-B studies in common marmosets (Callithrix jacchus), a small New World primate closely related to the tamarin (Saguinus sp.). The marmoset and tamarin represent less expensive, more readily available, and smaller animal models than the chimpanzee. While replication in marmosets is typically higher than what is observed in HCV-infected chimpanzees, reproducible infection profiles require some adaptation to this host (5, 54). Although robust replication of HCV in vitro is now possible using specific adapted strains of HCV (derivatives of the JFH1 and H77-S) and the Huh-7.5 cell line (4, 27, 52, 55, 56), the GBV-B primary hepatocyte culture system (2) may be more suitable for some studies, especially those involving specific aspects of the innate immune response and other viral host interactions.The organization of the GBV-B genome is very similar to that of HCV and the GBV-B polyprotein gene encodes 10 proteins analogous to the HCV proteins. The polyprotein of GBV-B has approximately 25 to 30% homology to that of HCV at the amino acid level (33), while the 5′ and 3′ noncoding regions (NCRs) are more divergent (7, 33, 40). The HCV and GBV-B 5′ NCRs are essential for both replication and translation. The structures are similar; however, GBV-B domain I is predicted to fold into two stem-loops (SL), compared to one SL in HCV, and the GBV-B 5′ NCR is longer due mainly to additional SL IIB and IIC that are not present in HCV (Fig. ​(Fig.1A)1A) (40). The 5′ NCR contains the internal ribosomal entry site (IRES), which can directly bind the 40S ribosomal subunit in order to initiate translation of the viral RNA (19, 38). cis RNA elements involved in RNA replication are also located in the HCV 5′ NCR (for a review, see reference 49). In GBV-B, 5′ NCR segments essential for genome replication have recently been identified (53).Open in a separate windowFIG. 1.(A) Predicted structures of the GBV-B (left) and HCV (right) 5′ NCRs. The scissors on GBV-B represent the sequence that was excised and replaced by the HCV insert, which is represented by scissors on the HCV 5′ NCR. The locations of mutations detected during sequencing are boxed: the first box identifies the deletion (ΔC) in a run of cytosines, and the second box identifies the polymorphisms present at two adjacent uracils (C, C/U). (Adapted from reference 40.) (B) Schematic of the GBV-B genome. During passage of GB/III^HC in tamarins, nine mutations were identified in virus from the T2 serum used to inoculate M1, and these nine mutations remained fixed in all marmoset isolates sequenced. Amino acid changes are indicated by dark arrows, silent mutations are indicated by asterisks, and NCR changes are indicated by dotted arrows.The utility of the GBV-B model was increased by the development of infectious cDNA clones that induced hepatitis upon intrahepatic inoculation of tamarins with in vitro-transcribed RNA (7, 31, 45). In order to further increase the use of GBV-B as a model for HCV, chimeras between GBV-B and HCV were constructed (16, 43, 48). In one chimera, a portion of the GBV-B 5′ NCR containing domain III, which is within the IRES functional domain, was replaced by an analogous region of HCV (40-43). The chimeric GB/III^HC retained IRES translational function and supported replication in tamarins (43). In this study, we examined the host range of this chimeric virus during serial passage in marmosets. We found that chimeric GBV-B failed to adapt during passage in marmosets. Marmosets infected with GB/III^HC displayed variable phenotypes ranging from susceptible to resistant, which appear to be due to a polymorphism in the marmoset population that also affects wild-type (WT) GBV-B (54). The failure of chimeric virus to adapt to replication in marmosets with the resistant phenotype was specific to the chimeric virus, and not the WT, and may involve several factors, including reduced replication capacity and the requirement to acquire multiple adaptive mutations. These barriers cumulatively may result in GB/III^HC experiencing a bottleneck in the resistant marmoset host.     

Severe Acute Respiratory Syndrome Coronavirus Protein 6 Is Required for Optimal Replication

Severe acute respiratory syndrome coronavirus (SARS-CoV) encodes several accessory proteins of unknown function. One of these proteins, protein 6 (p6), which is encoded by ORF6, enhances virus replication when introduced into a heterologous murine coronavirus (mouse hepatitis virus [MHV]) but is not essential for optimal SARS-CoV replication after infection at a relatively high multiplicity of infection (MOI). Here, we reconcile these apparently conflicting results by showing that p6 enhances SARS-CoV replication to nearly the same extent as when expressed in the context of MHV if cells are infected at a low MOI and accelerates disease in mice transgenic for the human SARS-CoV receptor.The genome of severe acute respiratory syndrome coronavirus (SARS-CoV) encodes several structural proteins, including the spike, nucleocapsid, membrane, and envelope proteins (13). Integrated between and within these structural proteins are eight accessory proteins (6, 8, 10, 15, 16, 18, 21-27). Our laboratory showed previously that one of these SARS-CoV-specific accessory proteins, encoded by ORF6, showed a clearly recognizable phenotype when introduced into a heterologous attenuated murine coronavirus, mouse hepatitis virus (MHV) strain J2.2-V-1 (rJ2.2.6). rJ2.2.6 grew more rapidly and to higher titers in tissue culture cells and in the murine central nervous system than control viruses, and the presence of p6 increased mortality in mice from 10 to 20% to 80% (7, 19, 20). However, the absence of p6 did not diminish SARS-CoV growth in tissue culture cells when cells were infected with 1 PFU/cell (31). In addition to a role in enhancing virus replication, when expressed in the context of a SARS-CoV infection or by transfection, p6 blocked interferon (IFN)-induced STAT1 nuclear translocation by retention of the nuclear import adaptor molecule karyopherin alpha 2 in the cytoplasm, indicating a role in thwarting innate immune effectors (5, 11). In contrast, p6 did not significantly diminish IFN sensitivity when expressed in the context of rJ2.2 (20).The results described above were puzzling, because p6 seemed to be required for the optimal replication of a heterologous coronavirus but not for that of SARS-CoV. Thus, the objective of this study was to determine whether p6 could enhance SARS-CoV replication in tissue culture cells under any conditions. For this purpose, we examined its function by comparing the growth of a recombinant SARS-CoV (rSARS-CoV) in which p6 was deleted (rSARS-CoVΔ6) with that of wild-type rSARS-CoV at a range of multiplicities of infection (MOIs). Normal mice infected with SARS-CoV readily cleared the infection, making it difficult to detect a role for p6 in vivo. However, mice that are transgenic for expression of the human receptor angiotensin-converting enzyme 2 (hACE2) are exquisitely sensitive to infection with SARS-CoV and are useful for identifying an in vivo role for p6 (14).     

The complete genome sequence of Bacillus anthracis Ames "Ancestor"

The pathogenic bacterium Bacillus anthracis has become the subject of intense study as a result of its use in a bioterrorism attack in the United States in September and October 2001. Previous studies suggested that B. anthracis Ames Ancestor, the original Ames fully virulent plasmid-containing isolate, was the ideal reference. This study describes the complete genome sequence of that original isolate, derived from a sample kept in cold storage since 1981.