SBIR-STTR Award

The alarming increase in incidence of infections caused by drug-resistant bacteria has created an urgent need for new antibacterial agents. We have discovered and optimized a novel class of antibiotics targeting PolC, the replicative DNA polymerase in Gram-positive bacteria. These agents exhibit broad spectrum activity against Gram-positive bacteria, including clinically important pathogens such as methicillin-resistant Staphylococcus aureus (MRSA), penicillin-resistant Streptococcus pneumoniae (PRSP), Streptococcus pyogenes (Group A strep), vancomycin-resistant enterococcus (VRE) and Clostridium difficile. In addition, compounds of this class are currently being evaluated for antibacterial activity in Gram-positive biothreat pathogens such as Bacillus anthracis. These agents demonstrate bactericidal activity, oral bioavailability, in vivo efficacy, a low propensity for toxicity and a low rate of spontaneous resistance. The mechanism of action has been unambiguously defined: the compounds inhibit an essential and novel molecular target involved in bacterial DNA synthesis and consequently circumvent existing mechanisms of antibiotic resistance. Although mechanistically similar to previously described PolC inhibitors of the anilino uracil class (Daly et al., 2000, Antimicrob. Agents Chemother. 44:2217), this compound series is chemically distinct, and displays more favorable microbiological potency and more desirable physical properties for drug development. We seek funding to advance this program from its current preclinical stage of lead optimization to the point of selecting a candidate compound for clinical development. The research plan leading to Investigational New Drug (IND) candidate selection comprises three stages. First, we will leverage information from our current structure- activity relationship (SAR) data coupled with a collection of 15 target-inhibitor co-crystals to perform structure- based lead optimization. Resulting compounds will be synthesized and will undergo extensive microbiological profiling. Compounds meeting the desired thresholds for potency and selectivity will progress to the second step, consisting of in vitro screens for metabolic stability and toxicity. This includes measuring degradation rates in human liver microsomes in order to estimate oral bioavailability and overall plasma exposure levels. Receptor binding assays that are predictive of known toxicity pathways have proven utility and help to ensure that the promising safety profile of these compounds is maintained throughout the lead optimization process. Compounds that pass the in vitro screens will progress to the final stage, consisting of in vivo testing of pharmacokinetics, efficacy and preliminary multi-dose toxicity. Collectively, these data should provide a detailed characterization of several lead compounds, supporting selection of the final IND candidate. A successful outcome would provide a long-term public health benefit in combating the rising tide of antibiotic- resistant infections that pose an acute threat to the general population, even those without predisposing risk factors. The alarming increase in incidence of infections caused by drug-resistant bacteria has created an urgent need for new antibacterial agents. The agents we have discovered and wish to develop represent a novel antibiotic class with broad spectrum Gram-positive antibacterial activity. The novel mechanism of action means that extant bacterial populations lack natural resistance. In the last forty years, very few new antibiotic classes have been brought to market, highlighting the pressing need for novel agents to combat resistance.

Thesaurus Terms:
"1-(3-(Dimethylamino)Propyl)-4-((Hydroxyimino)Methyl)Pyridinium, Chloride; 2,4(1h,3h)-Pyrimidinedione; 2,4-Dioxopyrimidine; 2,4-Pyrimidinediol; 2-Hydroxy-4-(3h)-Pyrimidione; 4-Hydroxy-2-(1h)-Pyrimidione; 4-Hydroxyiminomethyl-1-(3-N,N-Dimethylaminopropyl)Pyridinium Chloride; Acute; Adverse Effects; Animals; Anti-Bacterial Agents; Antibacterial Agents; Antibiotic Agents; Antibiotic Drugs; Antibiotic Resistance; Antibiotics; Assay; B. Anthracis; Bacillus Anthracis; Bacterial Dna; Binding; Binding (Molecular Function); Bioassay; Bioavailability; Biochemical; Biologic Assays; Biologic Availability; Biological Assay; Biological Availability; Blood; Blood Plasma; Blood Serum; C. Difficile; C.Difficile; Cell Culture Techniques; Chemicals; Chemistry, Pharmaceutical; Clinical; Clostridium Difficile; Collection; Common Rat Strains; Coupled; D. Pneumoniae; D.Pneumoniae; Dna Polymerase Inhibitor; Dna Polymerases; Dna Replication; Dna Synthesis; Dna Biosynthesis; Dna-Dependent Dna Polymerases; Dna-Directed Dna Polymerase; Data; Deoxynucleoside-Triphosphate[{..}]dna Deoxynucleotidyltransferase (Dna-Directed); Development; Diplococcus Pneumoniae; Dose; Drug Kinetics; Drug Resistance; Drug Resistant Bacterium; Drug Toxicity; Drugs; Drugs, Investigational; E. Faecalis; E.Faecalis; Ec 2.7.7.7; Ensure; Enterococcus Faecalis; Evaluation; Exhibits; Funding; General Population; General Public; Goals; Government; Gram-Positive Bacteria; Health Benefit; Human; Human, General; In Vitro; Incidence; Infection; Investigational Drugs; Investigational New Drugs; Lead; Linezolid; Liver; Liver Microsomes; Lytotoxicity; Mrsa; Mammalian Cell; Mammals, Mice; Mammals, Rats; Man (Taxonomy); Man, Modern; Marketing; Measures; Medication; Medicinal Chemistry; Metabolic; Methicillin Resistant S. Aureus; Methicillin Resistant Staphylococcus Aureus; Mice; Microsomes; Miscellaneous Antibiotic; Modeling; Molecular Interaction; Molecular Target; Murine; Mus; N-((3-(3-Fluoro-4-Morpholinylphenyl)-2-Oxo-5-Oxazolidinyl)Methyl)Acetamide; Natural Resistance; Oral; Outcome; Pathway Interactions; Pb Element; Penicillin Resistance; Persons; Pharmaceutic Chemistry; Pharmaceutic Preparations; Pharmaceutical Chemistry; Pharmaceutical Preparations; Pharmacokinetics; Physiologic Availability; Plasma; Plasma Proteins; Pneumococcus; Population; Programs (Pt); Programs [publication Type]; Property; Property, Loinc Axis 2; Protein Binding; Public Health; Rat; Rattus; Receptor Protein; Research; Resistance; Resistance To Antibiotics; Resistance, Antibiotic; Resistant To Antibiotics; Reticuloendothelial System, Blood; Reticuloendothelial System, Serum, Plasma; Risk Factors; S. Aureus; S. Faecalis; S. Pneumoniae; S. Pyogenes; S.Aureus; S.Faecalis; S.Pyogenes; Sched; Safety; Schedule; Screening Procedure; Series; Serum; Serum, Plasma; Staging; Staphylococcus Aureus; Streptococcus Group A; Streptococcus Group D; Streptococcus Faecalis; Streptococcus Pneumoniae; Streptococcus Pyogenes; Structure; Structure-Activity Relationship; Testing; Thigh; Thigh Structure; Toxic Effect; Toxicities; Treatment Side Effects; Uracil; Vancomycin Resistant Enterococcus; Vancomycin-Resistant Enterococci; Zyvox; Anthracis; Anti-Bacterial; Antibacterial; Antibiotic Resistant; Bactericidal; Bactericide; Base; Bio-Threat; Bioavailability Of Drug; Biothreat; Body System, Hepatic; Candidate Selection; Chemical Structure Function; Combat; Compound 30; Cytotoxicity; Drug Candidate; Drug Development; Drug Resistant; Drug Resistant Bacteria; Drug/Agent; Heavy Metal Pb; Heavy Metal Lead; Improved; In Vivo; Inhibitor; Inhibitor/Antagonist; Meetings; Methicillin Resistant Staphylococcus Aureus (Organism); Novel; Organ System, Hepatic; Pathogen; Pathway; Penicillin Resistant; Physical Property; Pre-Clinical; Preclinical; Process Optimization; Programs; Public Health Medicine (Field); Receptor; Receptor Binding; Resistance To Drug; Resistance To Penicillin; Resistant; Resistant To Drug; Resistant To Penicillin; Response; Screening; Screenings; Side Effect; Structure Function Relationship; Therapy Adverse Effect; Treatment Adverse Effect"

The alarming increase in incidence of infections caused by drug-resistant bacteria has created an urgent need for new antibacterial agents. We are developing a novel class of small molecule antibiotics ("TZUs") targeting PolC, the replicative DNA polymerase in Gram-positive bacteria. These agents exhibit broad-spectrum activity against Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA), penicillin-resistant Streptococcus pneumoniae (PRSP), Streptococcus pyogenes (Group A strep), vancomycin resistant enterococcus (VRE), Bacillus anthracis, Listeria monocytogenes and Clostridium difficile. TZUs demonstrate bactericidal activity, oral bioavailability, in vivo efficacy, a low propensity for toxicity and a low rate of spontaneous resistance. TZUs inhibit a novel bacterial target, thereby circumventing existing mechanisms of antibiotic resistance. We have made compelling progress during Phase I, having already met several key goals. In particular, we have identified several TZUs with in vitro potency exceeding that of linezolid, the only orally active drug approved for MRSA. We seek Phase II funding to enable completion of pivotal studies required for filing of an Investigational New Drug (IND) application. The research plan is divided into three stages. Aim 1 focuses on in-depth characterization of three top TZUs; each exhibits key attributes including in vivo efficacy following oral administration and outstanding microbiological potency. Aim 1 studies will include in vivo pharmacodynamics (PD) dose response studies, determination of pharmacokinetic (PK) parameters in two species, determination of the PK-PD index, evaluation of in vitro and in vivo toxicity, and determination of rates of resistance development. Based on these results, the TZU that best exemplifies the target product profile will be selected as the IND candidate. In Aim 2, process chemistry work will commence, focusing on improving synthetic yields, lowering cost, and making the synthetic process more scalable (e.g., by elimination of chromatographic steps). At this stage, the goal will be to develop a synthetic route appropriate for 1-10 kilogram scale synthesis at a cost of less than $25,000 per kg. Exploratory toxicology and toxicokinetic studies will be performed under non-GLP conditions in two species to support dose selection, toxicology endpoints and toxicokinetic time points for GLP-compliant studies. Analytical and bioanalytical methods will be validated under Good Laboratory Practice (GLP) conditions. Comprehensive microbiological characterization will be performed, including MIC90 testing in several Gram-positive species, evaluation of cross-resistance, post antibiotic effect (PAE) and synergy with other antibiotics. In Aim 3, a 5-10 kg GLP-toxicology batch will be synthesized, and GLP-compliant toxicology and safety pharmacology studies will be performed. Successful completion of these IND-enabling studies would support advancement of this program into human clinical trials. This project represents a compelling opportunity to combat the rising tide of antibiotic-resistant infections, providing a much-needed public health benefit.

Public Health Relevance:
The alarming increase in incidence of infections caused by drug-resistant bacteria has created an urgent need for new antibacterial agents. The drug we wish to develop represents a brand new antibiotic class with broad-spectrum Gram-positive antibacterial activity. Existing bacterial populations are highly susceptible to this drug, highlighting the truly life-saving potential of this new agent.

Public Health Relevance Statement:
: The alarming increase in incidence of infections caused by drug-resistant bacteria has created an urgent need for new antibacterial agents. The drug we wish to develop represents a brand new antibiotic class with broad-spectrum Gram-positive antibacterial activity. Existing bacterial populations are highly susceptible to this drug, highlighting the truly life-saving potential of this new agent.

Project Terms:
Acute; analog; Animal Model; Anti-Bacterial Agents; Antibiotic Resistance; Antibiotics; Bacillus anthracis; bactericide; base; Biodistribution; Biological Availability; Cardiovascular system; Categories; Chemistry; Childhood; Chromosome abnormality; Clinical Trials; Clostridium difficile; combat; cost; Development; DNA-Directed DNA Polymerase; Dose; drug candidate; Drug Formulations; Drug Kinetics; drug resistant bacteria; Enterococcus; Evaluation; Evaluation Indexes; evaluation/testing; Exhibits; Frequencies (time pattern); Funding; Genus staphylococcus; Goals; good laboratory practice; Gram-Positive Bacteria; Health Benefit; Human; improved; In Vitro; in vivo; Incidence; indexing; Infection; inhibitor/antagonist; Intravenous; Investigational Drugs; Investigational New Drug Application; Kilogram; Label; Lead; Life; Linezolid; Listeria monocytogenes; Macrolide-resistance; Measures; meetings; methicillin resistant Staphylococcus aureus (organism); Methods; Micronucleus Tests; Minimum Inhibitory Concentration measurement; Modeling; Multi-Drug Resistance; Mutagenesis; Mutagenicity Tests; National Institute of Allergy and Infectious Disease; Neurologic; New Agents; novel; Oral; Oral Administration; pathogen; Penicillin Resistance; Pharmaceutical Preparations; Pharmacodynamics; Pharmacology; Phase; Population; Process; programs; Protein Binding; public health medicine (field); Radiolabeled; radiotracer; receptor binding; Research; Resistance; Resistance development; response; Risk; Rodent; Route; Safety; Serum Proteins; small molecule; Staging; Streptococcus; Streptococcus pneumoniae; Streptococcus pyogenes; Tablets; Temperature; Testing; Time; Toxic effect; Toxicokinetics; Toxicology; United States Food and Drug Administration; Vancomycin resistant enterococcus; Work