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The mechanism of action of AFN-1252, a selective inhibitor of Staphylococcus aureus enoyl-acyl carrier protein reductase (FabI), which is involved in fatty acid biosynthesis, was confirmed by using biochemistry, macromolecular synthesis, genetics, and cocrystallization of an AFN-1252–FabI complex. AFN-1252 demonstrated a low propensity for spontaneous resistance development and a time-dependent reduction of the viability of both methicillin-susceptible and methicillin-resistant S. aureus , achieving a ≥2-log 10 reduction in S. aureus counts over 24 h, and was extremely potent against clinical isolates of S. aureus (MIC 90 , 0.015 μg/ml) and coagulase-negative staphylococci (MIC 90 , 0.12 μg/ml), regardless of their drug resistance, hospital- or community-associated origin, or other clinical subgroup. AFN-1252 was orally available in mouse pharmacokinetic studies, and a single oral dose of 1 mg/kg AFN-1252 was efficacious in a mouse model of septicemia, providing 100% protection from an otherwise lethal peritoneal infection of S. aureus Smith. A median effective dose of 0.15 mg/kg indicated that AFN-1252 was 12 to 24 times more potent than linezolid in the model. These studies, demonstrating a selective mode of action, potent in vitro activity, and in vivo efficacy, support the continued investigation of AFN-1252 as a targeted therapeutic for staphylococcal infections.

Over the past decade, the sequences of microbial genomes have accumulated, changing the strategies for the discovery of novel anti-infective agents. Targets have become plentiful, yet new antimicrobial agents have been slow to emerge from this effort. In part, this reflects the long discovery and development times needed to bring new drugs to market. In addition, bottlenecks have been revealed in the antimicrobial drug discovery process at the steps of identifying good leads, and optimizing those leads into drug candidates. The fruit of structural genomics may provide opportunities to overcome these bottlenecks and fill the antimicrobial pipeline, by using the tools of structure guided drug discovery (SGDD).

The pharmaceutical industry has embraced genomics as a means to identify new biological targets for target-based drug discovery approaches. Now, genomics is driving a substantial effort in protein structure determination and structure prediction. These structures will provide the opportunity to undertake structure-guided drug discovery programs in the search for new classes of broad-spectrum antibiotics. In addition, these structures could provide structure-based criteria to prioritize certain targets for focused drug discovery programs.

A Staphylococcus aureus mutant conditionally defective in DNA ligase was identified by isolation of complementing plasmid clones that encode the S. aureus lig A gene. Orthologues of the putative S. aureus NAD + -dependent DNA ligase could be identified in the genomes of Bacillus stearothermophilus and other gram-positive bacteria and confirmed the presence of four conserved amino acid motifs, including motif I, KXDG with lysine 112, which is believed to be the proposed site of adenylation. DNA sequence comparison of the ligA genes from wild type and temperature-sensitive S. aureus strain NT64 identified a single base alteration that is predicted to result in the amino acid substitution E46G. The S. aureus ligA gene was cloned and overexpressed in Escherichia coli , and the enzyme was purified to near homogeneity. NAD + -dependent DNA ligase activity was demonstrated with the purified enzyme by measuring ligation of 32 P-labeled 30-mer and 29-mer oligonucleotides annealed to a complementary strand of DNA. Limited proteolysis of purified S. aureus DNA ligase by thermolysin produced products with apparent molecular masses of 40, 22, and 21 kDa. The fragments were purified and characterized by N-terminal sequencing and mass analysis. The N-terminal fragment (40 kDa) was found to be fully adenylated. A fragment from residues 1 to 315 was expressed as a His-tagged fusion in E. coli and purified for functional analysis. Following deadenylation with nicotinamide mononucleotide, the purified fragment could self-adenylate but lacked detectable DNA binding activity. The 21- and 22-kDa C-terminal fragments, which lacked the last 76 amino acids of the DNA ligase, had no adenylation activity or DNA binding activity. The intact 30-kDa C terminus of the S. aureus LigA protein expressed in E. coli did demonstrate DNA binding activity. These observations suggest that, as in the case with the NAD + -dependent DNA ligase from B. stearothermophilus , two independent functional domains exist in S. aureus DNA ligase, consisting of separate adenylation and DNA binding activities. They also demonstrate a role for the extreme C terminus of the ligase in DNA binding. As there is much evidence to suggest that DNA ligase is essential for bacterial survival, its discovery in the important human pathogen S. aureus indicates its potential as a broad-spectrum antibacterial target for the identification of novel antibiotics.

A temperature-sensitive lethal mutant ofStaphylococcus aureuswas found to harbor a mutation in the uncharacterized two-component histidine kinase (HK)-response regulator (RR) pair encoded byyycFG; orthologues ofyycFGcould be identified in the genomes ofBacillus subtilisand other gram-positive bacteria. Sequence analysis of the mutant revealed a point mutation resulting in a nonconservative change (Glu to Lys) in the regulator domain of the RR at position 63. To confirm that this signal transduction system was essential, a disrupted copy of either the RR (yycF) or the HK (yycG) was constructed with a set of suicide vectors and used to generate tandem duplications in the chromosome. Resolution of the duplications, leaving an insertion in either theyycFor theyycGcoding region, was achieved only in the presence of an additional wild-type copy of the two open reading frames. Phenotypic characterization of the conditional lethal mutant showed that at permissive growth conditions, the mutant was hypersusceptible to macrolide and lincosamide antibiotics, even in the presence of theermBresistance determinant. Other mutant phenotypes, including hypersensitivity to unsaturated long-chain fatty acids and suppression of the conditional lethal phenotype by high sucrose and NaCl concentrations, suggest that the role of the two-component system includes the proper regulation of bacterial cell wall or membrane composition. The effects of this point mutation are strongly bactericidal at the nonpermissive temperature, indicating that this pathway provides an excellent target for the identification of novel antibiotics.

This review provides the current status of structure-guided drug discovery, with examples from antibiotic drug discovery. The article aims to show where and when structural biology has been used “early and often” during the process of antibiotic drug discovery, primarily against novel antibacterial targets. The vast majority of examples are derived from the use of protein crystallization and diffraction information and the high-resolution protein structures that those tools provide. The review provides key examples and a range of methods that have effectively used structural information in various stages of the antibacterial drug discovery process. The starting point for structure-guided drug discovery is most often a high-resolution structure of the target protein. Over the past decade, the publicly funded Protein Structure Initiatives have solved a large number of bacterial protein structures, often from clinically important bacterial species. The public release of these high-resolution structures has enabled structure-guided efforts for antibacterial drug discovery. Many structure-guided methods overcome challenges raised by the limited chemical diversity found in existing chemical diversity libraries.

A temperature-sensitive (ts) mutant of Salmonella typhimurium that accumulated unmodified murein prolipoprotein at 42 degrees C but not at 30 degrees C was identified. In vivo and in vitro studies of the biosynthesis of Braun's lipoprotein revealed that this mutant (SE5221) was defective in the glyceryl modification of prolipoprotein. The ts mutation was mapped to 60.6 min of the S. typhimurium chromosome and was linked to argA and cysH. A clone with a 1.4-kilobase S. typhimurium DNA insert that complemented the ts mutation and restored the prolipoprotein modification activity both in vivo and in vitro was isolated. DNA sequencing of the complementing region revealed an open reading frame encoding a protein with 291 amino acids lacking NH2-terminal signal sequence. This open reading frame is immediately 5' to the thyA gene and is allelic to umpA of Escherichia coli. Wild-type strains harboring the cloned gene exhibited elevated levels of prolipoprotein modification activity. At the non-permissive temperature, the mutation affected both growth and viability, and the mutant cells exhibited anomalous cell morphology. The ts phenotype was suppressed by the introduction of a lpp::Tn10 mutation. These results suggest that the cloned gene encodes prolipoprotein glyceryl transferase (lgt), and in the wild-type background, this prolipoprotein modification enzyme is essential for the growth and viability of S. typhimurium.

On screening 440 temperature-sensitive (ts) mutants of Salmonella typhimurium, a mutant strain SE5312 which accumulated apolipoprotein (ALP) at 42 degrees C was identified. In vitro assay of apolipoprotein N-acyltransferase activity indicated that the mutant cell envelope contained reduced activity as compared to the wild-type strain. Transduction with a Mud-P22 mapping set placed the ts mutation to 14-17 min region of the S. typhimurium chromosome. P22 transduction using transposon insertions in this region revealed a linkage of the ts mutation to cobD (6%), nag (8%), and corC68 (99%). The ts phenotype was complemented by a 2.3-kilobase EcoRI subclone derived from lambda-phage 170 of Kohara's bank of Escherichia coli. Restriction enzyme analysis of the cloned DNA revealed that this 2.3-kilobase EcoRI fragment included the copper transport (cutE) gene in E. coli. The mutant strain SE5312 was copper-sensitive at 30 degrees C, and the complementing clone conferred copper resistance and restored the ALP N-acyltransferase activity in the mutant cell. Wild-type strain of S. typhimurium harboring this clone exhibited elevated levels of ALP N-acyltransferase activity. These results suggest that the cloned gene encodes the ALP N-acyltransferase. Upon shift to the non-permissive temperature, the viability of the mutant cells decreased, and the mutant cells assumed anomalous morphology. Temperature-resistant revertants could be readily isolated, and a subset of tr revertants contained no detectable lipoprotein. A lpp::Tn10 derivative of the mutant SE5312 was also temperature-resistant. These observations suggest that ALP N-acyltransferase is essential for the growth and viability of S. typhimurium, and this requirement is decreased in the absence of major outer membrane lipoprotein.

Gene products required for in vivo growth and survival of microbial pathogens comprise a unique functional class and may represent new targets for antimicrobial chemotherapy, vaccine construction, or diagnostics. Although some factors governingStaphylococcus aureuspathogenicity have been identified and studied, a comprehensive genomic analysis of virulence functions will be a prerequisite for developing a global understanding of interactions between this pathogen and its human host. In this study, we describe a genetic screening strategy and demonstrate its use in screening a collection of 6,300S. aureusinsertion mutants for virulence attenuation in a murine model of systemic infection. Ninety-five attenuated mutants were identified, reassembled into new pools, and rescreened using the same murine model. This effort identified 24 highly attenuated mutants, each of which was further characterized for virulence attenuation in vivo and for growth phenotypes in vitro. Mutants were recovered in numbers up to 1,200-fold less than wild type in the spleens of systemically infected animals and up to 4,000-fold less than wild type in localized abscess infections. Genetic analysis of the mutants identified insertions in 23 unique genes. The largest gene classes represented by these mutants encoded enzymes involved in small-molecule biosynthesis and cell surface transmembrane proteins involved in small-molecule binding and transport. Additionally, three insertions defined two histidine kinase sensor-response regulator gene pairs important forS. aureusin vivo survival. Our findings extend the understanding of pathogenic mechanisms employed byS. aureusto ensure its successful growth and survival in vivo. Many of the gene products we have identified represent attractive new targets for antibacterial chemotherapy.

Type II fatty acid biosynthesis systems are essential for membrane formation in bacteria, making the constituent proteins of this pathway attractive targets for antibacterial drug discovery. The third step in the elongation cycle of the type II fatty acid biosynthesis is catalyzed by beta-hydroxyacyl-(acyl carrier protein) (ACP) dehydratase. There are two isoforms. FabZ, which catalyzes the dehydration of (3R)-hydroxyacyl-ACP to trans-2-acyl-ACP, is a universally expressed component of the bacterial type II system. FabA, the second isoform, as has more limited distribution in nature and, in addition to dehydration, also carries out the isomerization of trans-2- to cis-3-decenoyl-ACP as an essential step in unsaturated fatty acid biosynthesis. We report the structure of FabZ from the important human pathogen Pseudomonas aeruginosa at 2.5 A of resolution. PaFabZ is a hexamer (trimer of dimers) with the His/Glu catalytic dyad located within a deep, narrow tunnel formed at the dimer interface. Site-directed mutagenesis experiments showed that the obvious differences in the active site residues that distinguish the FabA and FabZ subfamilies of dehydratases do not account for the unique ability of FabA to catalyze isomerization. Because the catalytic machinery of the two enzymes is practically indistinguishable, the structural differences observed in the shape of the substrate binding channels of FabA and FabZ lead us to hypothesize that the different shapes of the tunnels control the conformation and positioning of the bound substrate, allowing FabA, but not FabZ, to catalyze the isomerization reaction.

Over the past decade, the availability of complete microbial genome sequences has led to changes in the strategies that are used to search for novel anti-infectives. However, despite the identification of many new potential drug targets, novel antimicrobial agents have been slow to emerge from these efforts. In part, this reflects the long discovery and development times that are needed to bring new drugs to market and the bottlenecks at the stages of identifying good lead compounds and optimizing these leads into drug candidates. Structural genomics will hopefully provide opportunities to overcome these bottlenecks and populate the antimicrobial pipeline.

Triclosan MIC determination showed that recent Staphylococcus aureus clinical isolates ( n = 100) were highly susceptible to triclosan, with a 50% minimal inhibitory concentration (MIC 50 ) of 0.12 μg/ml and a MIC 90 of 0.25 μg/ml. Staphylococcus epidermidis isolates ( n = 96) were less susceptible, with a MIC 50 of 0.12 μg/ml and a MIC 90 of 8 μg/ml. Decreased susceptibility to triclosan was more prevalent among methicillin-resistant S. epidermidis than among methicillin-sensitive S. epidermidis isolates.

Genomics has changed our view of the biological world in the past decade, providing both new information and new tools to characterise biological systems. Over 100 microbial genomes - including many of substantial clinical importance - have been fully or partially sequenced, pushing the search for novel antimicrobial compounds into the post-genomic era. Genomic information and associated new technologies have the potential to revolutionise the drug discovery process. Genomic methods have created a wealth of potential new antimicrobial targets; strategies are evolving to provide validation for these targets before chemical inhibitors are identified. The ability to obtain large amounts of purified target proteins and advances in X-ray crystallography have caused significant increases in available protein structures, which may foreshadow an increased effort in structure-based drug design. The post-genomics strategies used in antimicrobial drug discovery may have application for small molecule drug discovery in numerous therapeutic areas.

With the completion of numerous bacterial genome sequences, the discovery of antibacterial drugs has fully entered the genomic era. The strategies for effectively using genomic information for target identification, target characterization, screen development and compound evaluation are emerging, and have greatly increased the number of antibacterial targets available for screening. Fortunately, simultaneous efforts in improving miniaturization, robotics and database tools are underway so that the potential of genomics can be realized.

An integrative approach highlights the challenge of identifying new antibiotic drug targets.

The murB gene of Salmonella typhimurium was cloned and found to be 75% and 82% identical to the DNA and protein sequences, respectively, of the same gene in Escherichia coli. These identities are among the lowest recorded between the two bacteria. Nevertheless, wild-type S. typhimurium murB complemented the known temperature-sensitive E. coli mutant, and wild-type E. coli murB complemented three temperature-sensitive mutants of S. typhimurium. The 5S rRNA gene, rrfB, and the region between murB and rrfB were also cloned and sequenced. The rrfB gene of S. typhimurium differs from rrfB of E. coli in only 2 of 120 nt, but the region between murB and rrfB has diverged greatly and includes a sequence that elosely resembles a repetitive extragenic palindrome of the type normally associated with E. coli. Previous comparisons of gene divergence have suggested that the chromosomal mutation rate is lower in the vicinity of the origin of replication. However, the S. typhimurium murB gene, located 6 map minutes from the origin of replication, is highly substituted at synonymous sites and the sequence between murB and rrfB is significantly modified as well. Thus, murB is an exception to the general observation that genes near the origin of replication show less divergence than do genes elsewhere in the bacterial chromosome.

In the past few years, two new DNA topoisomerases have been discovered in bacteria, bringing the total number of DNA topoisomerases in E. coli to four. Two classes of topoisomerases, type 1 and type 2, are distinguishable by their amino acid homology and their apparent reaction mechanism. Of the four E. coli topoisomerases, there are two type 1 and two type 2 enzymes. In eukaryotes, the existence of multiple type 1 and type 2 enzymes has also become apparent. The existence of these multiple enzymes provokes a question whose answer has both evolutionary and physiological implications: are these topoisomerases functionally redundant, or have they acquired sufficient specialization that they now perform unique biological reactions? In bacteria, there is evidence for both specialization and redundancy in the functions of topoisomerases.

Mutants in bacterial topoisomerase (topo) IV are deficient in chromosomal partitioning. To investigate the basis of this phenotype, we examined plasmid DNA topology in conditionally lethal topo IV mutants. We found that dimeric catenated plasmids accumulated in vivo after topo IV inhibition. The catenanes were supercoiled, contained from 2 to > 32 nodes, and were the products of DNA synthesis. Electron microscopy and recombination tests proved that the catenanes have the unique structure predicted for replication intermediates. These data provide strong evidence for a model in which unlinking of the double helix can occur in two stages during DNA replication and for the critical role of topo IV in the second stage. The interlocks in the catenanes appear to be sequestered from DNA gyrase, perhaps by compartmentalization in an enzyme complex dedicated to partitioning.

Two internal promoters in the his operon of Salmonella typhimurium have been precisely mapped genetically. The internal promoters are found in, or very close to, gene border regions in the his operon. The his operon was examined for the presence of additional internal promoters whose transcripts were sensitive to rho-mediated transcription termination and therefore had escaped detection. No new internal promoters were found. It is argued that the internal promoters described here are not likely to be fortuitous message start sites, but may play a physiologically important role in operon expression.

Generalized transducing fragments that have redundant sequences in direct order can circularize during transduction events. The length of the required redundant sequences can be at least as short as IS10 (1.4 kb) (KLECRNER 1977).The circular transduced fragment is able to recombine with homologous sequences in the chromosome. Circularization and insertion of transduced fragments allow addition of segments to the bacterial chromosome rather than replacement of recipient segments as in a normal transductional cross. It also provides a method for translocation of bacterial genes to a variety of specific sites on the chromosome in either orientation. The significance of these events to bacterial eiolution is discussed.

Promoters located within the Tn10 insertion element cause transcription of "host" sequences adjacent to both ends of the inserted Tn10 element. These promoters are usually not observed in genetic experiments because their transcripts are efficiently terminated at nearby rho-dependent termination sites. The observations presented here provide an explanation for several confusing aspects of transposon behavior and suggest the possibility that many transposons possess promoters that have escaped detection for similar reasons.

In bacteria there appear to be two distinct levels of DNA condensation: the organization of independently supercoiled domains of DNA (averaging 100 kbp in size) and the organization of shorter segments of DNA (60–120 bp) with abundant DNA-binding proteins.

The biotechnology industry has historically had a strong focus on innovation and research. As the industry has matured, companies have become intensely focused on commercialising their products. This study assesses the current functional composition of the pharmaceutical and biotechnology workforce, and compares differences in workforce needs among companies of different sizes, ages and product commercialisation maturities. Sample sets of the largest pharmaceutical and biotechnology companies were selected, as were a set of smaller and younger companies. Job openings posted on the websites of these companies were categorised. Five functional categories of job openings were created – Laboratory, Manufacturing, General & Administrative, Regulatory/Clinical Affairs and Sales/Marketing – and each open position was placed into one of these five categories. Companies with products on the market had an average of 17 per cent of job openings in the laboratory category, and 83 per cent of openings in the remaining non-laboratory categories. Smaller companies without products on the market had a higher percentage of jobs categorised as laboratory. This study identifies the need for individuals with a blend of science and business skills, and makes clear the importance of educating scientifically trained individuals for scientifically oriented, but non-laboratory positions.