SBIR-STTR Award

The goal of this project is to develop a therapeutic acting specifically against Helicobacter pylori, the causative agent of peptic ulcer and gastric carcinoma. Roughly every other person carries the pathogen, and there are an estimated 500,000 cases annually of active infection in the US. The currently-used triple therapy is a combination of a proton pump inhibitor and broad spectrum antimicrobials, usually amoxicillin and clarithromycin. A recent meta-analysis of clinical data showed that treatment failure is 22%. An estimated 70% of failures are due to antibiotic resistance. Considering the total number of cases, treatment failure is very high, and H. pylori is emerging as one of the most significant drug-resistant pathogens, and there is a considerable unmet need for novel treatments. The obstacles for discovering a new therapeutic are formidable - the last class of antibiotics acting against Gram negative species, the fluoroquinolones, was introduced 40 years ago. However, we reasoned that it should be considerably easier to develop a narrow-spectrum antimicrobial acting against H. pylori. Demands on a compound acting against a single target are less as compared to a broad- spectrum which needs to inhibit many proteins of an orthologous group. H. pylori also have a large number of unique essential proteins which could serve as targets for new antimicrobials. Poor permeability into Gram negative bacteria is another major obstacle for developing broad-spectrum compounds, but H. pylori do not have a strong permeability barrier. These considerations suggest that novel anti-H. Pylori compounds could be discovered in an HTS of commercial compounds libraries that failed to produce broad-spectrum antimicrobials. H. pylori grow under microaerophilic conditions, which are incompatible with standard HTS. We were able to develop a first HTS against H. pylori, and a pilot screen produced a large number of diverse hits. A major problem in HTS is a large number of toxic and promiscuous compounds. We solved this problem with a counter-screen against gut symbionts. This resulted in leads that are specific against H. pylori and will be free of side-effects such as diarrhea associated with broad-spectrum compounds that harm the gut flora. Validation of the hits resulted in a potent lead, 2MP, with an MIC and MBC of 0.04 g/mL, low cytotoxicity, low resistance frequency, reasonable ADME, and an SAR, making it suitable for further development. The Phase I project will focus on closing SAR around the lead series, which will inform medicinal chemistry optimization in Phase II. Results from the pilot screen suggest that we have a validated discovery platform for selective anti-H. pylori compounds. We will take advantage of this, and will perform a larger HTS in order to identify a suitable back- up series. Iterative medicinal chemistry optimization will be combined with detailed validation of each series in Phase II. in vitro validation will include: potency, spectrum of activity, resistance development, acid stabilit, cytotoxicity, absorption, metabolic stability and plasma binding studies. Candidates suitable for animal testing will emerge from medicinal chemistry using iterative design-make-test cycles aimed at multifunctional optimization of the microbiological, pharmacologic and safety properties of each series. Next, compounds will undergo in vivo validation for suitable oral bioavailability and efficacy in a mouse model of H. pylori infection. Mechanism of action studies will be initiated for leads that exhibit animal efficacy. The end result will be validated leads that will enable us o enter into a partnership with a Pharmaceutical Company for further preclinical development leading towards and IND, clinical trials, marketing a sales of a new selective therapeutic for peptic ulcer.

Public Health Relevance:
The aim of this project is to identify compounds to treat Helicobacter pylori infection. H. pylori cause acid reflux, ulcers and stomach cancer. However, currently available therapeutics is broad spectrum antibiotics, which cause high levels of resistance and unwanted side-effects. We will develop an antibiotic that specifically targets H. pylori.

The goal of this project is to develop a therapeutic acting specifically against Helicobacter pylori, the causative agent of peptic ulcer and gastric carcinoma. Roughly every other person carries the pathogen, and there are an estimated 500,000 cases annually of active infection in the US. The currently-used triple therapy is a combination of a proton pump inhibitor and broad spectrum antimicrobials, usually amoxicillin and clarithromycin. A recent meta-analysis of clinical data showed that treatment failure is 22%. An estimated 70% of failures are due to antibiotic resistance. Considering the total number of cases, treatment failure is very high, and H. pylori is emerging as one of the most significant drug-resistant pathogens, and there is a considerable unmet need for novel treatments. The obstacles for discovering a new therapeutic are formidable - the last class of antibiotics acting against Gram negative species, the fluoroquinolones, was introduced 40 years ago. However, we reasoned that it should be considerably easier to develop a narrow-spectrum antimicrobial acting against H. pylori. Demands on a compound acting against a single target are less as compared to a broad- spectrum which needs to inhibit many proteins of an orthologous group. H. pylori also have a large number of unique essential proteins which could serve as targets for new antimicrobials. Poor permeability into Gram negative bacteria is another major obstacle for developing broad-spectrum compounds, but H. pylori do not have a strong permeability barrier. These considerations suggest that novel anti-H. Pylori compounds could be discovered in an HTS of commercial compounds libraries that failed to produce broad-spectrum antimicrobials. H. pylori grow under microaerophilic conditions, which are incompatible with standard HTS. We were able to develop a first HTS against H. pylori, and a pilot screen produced a large number of diverse hits. A major problem in HTS is a large number of toxic and promiscuous compounds. We solved this problem with a counter-screen against gut symbionts. This resulted in leads that are specific against H. pylori and will be free of side-effects such as diarrhea associated with broad-spectrum compounds that harm the gut flora. Validation of the hits resulted in a potent lead, 2MP, with an MIC and MBC of 0.04 ¿g/mL, low cytotoxicity, low resistance frequency, reasonable ADME, and an SAR, making it suitable for further development. The Phase I project will focus on closing SAR around the lead series, which will inform medicinal chemistry optimization in Phase II. Results from the pilot screen suggest that we have a validated discovery platform for selective anti-H. pylori compounds. We will take advantage of this, and will perform a larger HTS in order to identify a suitable back- up series. Iterative medicinal chemistry optimization will be combined with detailed validation of each series in Phase II. in vitro validation will include: potency, spectrum of activity, resistance development, acid stabilit, cytotoxicity, absorption, metabolic stability and plasma binding studies. Candidates suitable for animal testing will emerge from medicinal chemistry using iterative design-make-test cycles aimed at multifunctional optimization of the microbiological, pharmacologic and safety properties of each series. Next, compounds will undergo in vivo validation for suitable oral bioavailability and efficacy in a mouse model of H. pylori infection. Mechanism of action studies will be initiated for leads that exhibit animal efficacy. The end result will be validated leads that will enable us o enter into a partnership with a Pharmaceutical Company for further preclinical development leading towards and IND, clinical trials, marketing a sales of a new selective therapeutic for peptic ulcer.

Public Health Relevance Statement:
The aim of this project is to identify compounds to treat Helicobacter pylori infection. H. pylori cause acid reflux, ulcers and stomach cancer. However, currently available therapeutics is broad spectrum antibiotics, which cause high levels of resistance and unwanted side-effects. We will develop an antibiotic that specifically targets H. pylori.

Project Terms:
absorption; Accounting; Acids; Adverse effects; Amoxicillin; analog; animal efficacy; Animal Testing; Antibiotic Resistance; Antibiotics; antimicrobial; Antimicrobial Resistance; Back; base; Benchmarking; Binding (Molecular Function); Biological Availability; Bismuth; Buffers; Chemicals; Clarithromycin; Clinical; Clinical Data; Clinical Trials; Combined Modality Therapy; counterscreen; Custom; cytotoxicity; design; Development; Diarrhea; Dose; Drug Delivery Systems; Drug Kinetics; Drug resistance; efficacy testing; Evaluation; Exhibits; Failure (biologic function); Fluoroquinolones; Frequencies (time pattern); genome sequencing; Goals; Gram-Negative Bacteria; Helicobacter Infections; Helicobacter pylori; improved; In Vitro; in vivo; Incubated; Infection; innovation; iterative design; Killings; Lead; lead series; Libraries; malignant stomach neoplasm; Mammalian Cell; Marketing; Measures; member; Meta-Analysis; Metabolic; Microbiology; mouse model; Mus; mutant; novel; novel therapeutics; Oral; Organism; pathogen; Peptic Ulcer; Permeability; Persons; Pharmaceutical Chemistry; Pharmacologic Substance; Phase; Plasma; pre-clinical; Problem Solving; Property; Protein Binding; Proteins; Proton Pump Inhibitors; Reflux; Regimen; Resistance; Resistance development; resistant strain; Rest; Safety; Sales; screening; Series; Site; Solubility; Species Specificity; Specificity; Staphylococcus aureus; Stomach; Stomach Carcinoma; Technology; Testing; Therapeutic; therapeutic development; Therapeutic Index; Toxic effect; Treatment Failure; Triage; Ulcer; Validation