US20040033986A1 - Anti tubercular drug: compositions and methods - Google Patents

Anti tubercular drug: compositions and methods Download PDF

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Publication number
US20040033986A1
US20040033986A1 US10/440,017 US44001703A US2004033986A1 US 20040033986 A1 US20040033986 A1 US 20040033986A1 US 44001703 A US44001703 A US 44001703A US 2004033986 A1 US2004033986 A1 US 2004033986A1
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Prior art keywords
hydrogen
diamine
substituted ethylene
amine
amino
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US10/440,017
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English (en)
Inventor
Marina Protopopova
Richard Lee
Richard Slayden
Clifton Barry
Elena Bogatcheva
Leo Einck
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Priority claimed from US10/147,587 external-priority patent/US6951961B2/en
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Priority to US10/440,017 priority Critical patent/US20040033986A1/en
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    • C07C323/23—Thiols, sulfides, hydropolysulfides or polysulfides substituted by halogen, oxygen or nitrogen atoms, or by sulfur atoms not being part of thio groups containing thio groups and nitrogen atoms, not being part of nitro or nitroso groups, bound to the same carbon skeleton
    • C07C323/24—Thiols, sulfides, hydropolysulfides or polysulfides substituted by halogen, oxygen or nitrogen atoms, or by sulfur atoms not being part of thio groups containing thio groups and nitrogen atoms, not being part of nitro or nitroso groups, bound to the same carbon skeleton having the sulfur atoms of the thio groups bound to acyclic carbon atoms of the carbon skeleton
    • C07C323/25—Thiols, sulfides, hydropolysulfides or polysulfides substituted by halogen, oxygen or nitrogen atoms, or by sulfur atoms not being part of thio groups containing thio groups and nitrogen atoms, not being part of nitro or nitroso groups, bound to the same carbon skeleton having the sulfur atoms of the thio groups bound to acyclic carbon atoms of the carbon skeleton the carbon skeleton being acyclic and saturated
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    • A61K31/13—Amines
    • A61K31/132—Amines having two or more amino groups, e.g. spermidine, putrescine
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    • A61K31/33—Heterocyclic compounds
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    • A61P1/04—Drugs for disorders of the alimentary tract or the digestive system for ulcers, gastritis or reflux esophagitis, e.g. antacids, inhibitors of acid secretion, mucosal protectants
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    • C07C211/41—Compounds containing amino groups bound to a carbon skeleton having amino groups bound to carbon atoms of rings other than six-membered aromatic rings of an unsaturated carbon skeleton containing condensed ring systems
    • C07C211/42—Compounds containing amino groups bound to a carbon skeleton having amino groups bound to carbon atoms of rings other than six-membered aromatic rings of an unsaturated carbon skeleton containing condensed ring systems with six-membered aromatic rings being part of the condensed ring systems
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    • C07C215/06—Compounds containing amino and hydroxy groups bound to the same carbon skeleton having hydroxy groups and amino groups bound to acyclic carbon atoms of the same carbon skeleton the carbon skeleton being saturated and acyclic
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    • C07C2602/10—One of the condensed rings being a six-membered aromatic ring the other ring being six-membered, e.g. tetraline
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07C—ACYCLIC OR CARBOCYCLIC COMPOUNDS
    • C07C2602/00—Systems containing two condensed rings
    • C07C2602/36—Systems containing two condensed rings the rings having more than two atoms in common
    • C07C2602/42—Systems containing two condensed rings the rings having more than two atoms in common the bicyclo ring system containing seven carbon atoms
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07C—ACYCLIC OR CARBOCYCLIC COMPOUNDS
    • C07C2603/00—Systems containing at least three condensed rings
    • C07C2603/56—Ring systems containing bridged rings
    • C07C2603/58—Ring systems containing bridged rings containing three rings
    • C07C2603/70—Ring systems containing bridged rings containing three rings containing only six-membered rings
    • C07C2603/74—Adamantanes
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
    • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Definitions

  • the present invention relates to methods and compositions for treating disease caused by microorganisms, particularly tuberculosis.
  • the present invention also relates to methods and compositions having improved anti-mycobacterial activity, namely compositions comprising novel substituted ethylene diamine compounds.
  • Mycobacterial infections often manifest as diseases such as tuberculosis.
  • Human infections caused by mycobacteria have been widespread since ancient times, and tuberculosis remains a leading cause of death today.
  • mycobacterial diseases still constitute a leading cause of morbidity and mortality in countries with limited medical resources.
  • mycobacterial diseases can cause overwhelming, disseminated disease in immunocompromised patients.
  • the eradication of mycobacterial diseases has never been achieved, nor is eradication imminent.
  • tuberculosis TB
  • Tuberculosis is the cause of the largest number of human deaths attributable to a single etiologic agent (see Dye et al., J. Am. Med. Association, 282, 677-686, (1999); and 2000 WHO/OMS Press Release).
  • M. tuberculosis are increasingly found in opportunistic infections that plague the AIDS patient.
  • Enormous numbers of MAC are found (up to 10 10 acid-fast bacilli per gram of tissue), and consequently, the prognosis for the infected AIDS patient is poor.
  • the World Health Organization continues to encourage the battle against TB, recommending prevention initiatives such as the “Expanded Program on Immunization” (EPI), and therapeutic compliance initiatives such as “Directly Observed Treatment Short-Course” (DOTS).
  • EPI Program on Immunization
  • DAS Directly Observed Treatment Short-Course
  • diagnosis, treatment, and prevention are equally important. Rapid detection of active TB patients will lead to early treatment by which about 90% cure is expected. Therefore, early diagnosis is critical for the battle against TB.
  • therapeutic compliance will ensure not only elimination of infection, but also reduction in the emergence of drug-resistance strains.
  • M. tuberculosis M. avium intracellulare
  • M. kansasii M. fortuitum
  • M. chelonae M. leprae.
  • the most prevalent mycobacterial disease in humans is tuberculosis (TB) which is predominantly caused by mycobacterial species comprising M. tuberculosis, M. bovis, or M. africanum (Merck Manual 1992).
  • Infection is typically initiated by the inhalation of infectious particles which are able to reach the terminal pathways in lungs.
  • the bacilli Following engulfment by alveolar macrophages, the bacilli are able to replicate freely, with eventual destruction of the phagocytic cells. A cascade effect ensues wherein destruction of the phagocytic cells causes additional macrophages and lymphocytes to migrate to the site of infection, where they too are ultimately eliminated.
  • the disease is further disseminated during the initial stages by the infected macrophages which travel to local lymph nodes, as well as into the blood stream and other tissues such as the bone marrow, spleen, kidneys, bone and central nervous system. (See Murray et al. Medical Microbiology, The C. V. Mosby Company 219-230 (1990)).
  • M. avium bacilli occur in several distinct colony forms. Bacilli which grow as transparent, or rough, colonies on conventional laboratory media are multiplicable within macrophages in tissue culture, are virulent when injected into susceptible mice, and are resistant to antibiotics. Rough or transparent bacilli, which are maintained on laboratory culture media, often spontaneously assume an opaque R colony morphology, at which time they are not multiplicable in macrophages, are avirulent in mice, and are highly susceptible to antibiotics. The differences in colony morphology between the transparent, rough and opaque strains of M.
  • avium are almost certainly due to the presence of a glycolipid coating on the surface of transparent and rough organisms which acts as a protective capsule.
  • This capsule, or coating is composed primarily of C-mycosides which apparently shield the virulent M. avium organisms from lysosomal enzymes and antibiotics.
  • the non-virulent opaque forms of M. avium have very little C-mycoside on their surface. Both the resistance to antibiotics and the resistance to killing by macrophages have been attributed to the glycolipid barrier on the surface of M. avium.
  • PCR polymerase chain reaction
  • MTD amplified mycobacterium tuberculosis direct test
  • tuberculin skin test One diagnostic test that is widely used for detecting infections caused by M. tuberculosis is the tuberculin skin test.
  • many versions of the skin test are available, typically one of two preparations of tuberculin antigens are used: old tuberculin (OT), or purified protein derivative (PPD).
  • OTD old tuberculin
  • PPD purified protein derivative
  • the antigen preparation is either injected into the skin intradermally, or is topically applied and is then invasively transported into the skin with the use of a multiprong inoculator (Tine test).
  • Tine test multiprong inoculator
  • Several problems exist with the skin test diagnosis method For example, the Tine test is not generally recommended because the amount of antigen injected into the intradermal layer cannot be accurately controlled. (See Murray et al. Medical Microbiology , The C. V. Mosby Company 219-230 (1990)).
  • tuberculin skin tests are widely used, they typically require two to three days to generate results, and many times, the results are inaccurate since false positives are sometimes seen in subjects who have been exposed to mycobacteria, but are healthy.
  • instances of mis-diagnosis are frequent since a positive result is observed not only in active TB patients, but also in persons vaccinated with Bacille Calmette-Guerin (BCG), and those who had been infected with mycobacteria, but have not developed the disease. It is hard therefore, to distinguish active TB patients from the others, such as household TB contacts, by the tuberculin skin test.
  • BCG Bacille Calmette-Guerin
  • tuberculin test often produces a cross-reaction in those individuals who were infected with mycobacteria other than M. tuberculosis (MOTT). Therefore, diagnosis using the skin tests currently available is frequently subject to error and inaccuracies.
  • MOTT mycobacteria other than M. tuberculosis
  • the standard treatment for tuberculosis caused by drug-sensitive organisms is a six-month regimen consisting of four drugs given for two months, followed by two drugs given for four months.
  • the two most important drugs, given throughout the six-month course of therapy, are isoniazid and rifampin.
  • the regimen is relatively simple, its administration is quite complicated. Daily ingestion of eight or nine pills is often required during the first phase of therapy; a daunting and confusing prospect. Even severely ill patients are often symptom free within a few weeks, and nearly all appear to be cured within a few months. If the treatment is not continued to completion, however, the patient may experience a relapse, and the relapse rate for patients who do not continue treatment to completion is high.
  • Ethambutol is a widely used antibiotic for the treatment of TB, with over 300 million doses delivered for tuberculosis therapy in 1988.
  • Ethambutol developed by Lederle Laboratories in the 1950s, has low toxicity and is a good pharmacokinetic. However, ethambutol has a relatively high Minimum Inhibition Concentration (MIC) of about 5 ⁇ g/ml, and can cause optic neuritis.
  • MIC Minimum Inhibition Concentration
  • the present invention comprises methods and compositions comprising ethylene diamine compounds effective for the treatment of infectious disease.
  • the present invention also provides methods and compositions comprising substituted ethylene diamines having improved anti-mycobacterial activity, including substituted ethylene diamines having improved anti-tuberculosis activity.
  • the present invention contemplates substituted ethylene diamines, which can derive from a variety of amine compounds.
  • the substituted ethylene diamines are based on the following structure.
  • the substituted ethylene diamine compounds described herein are synthesized and screened for activity as follows.
  • a chemical library of substituted ethylene diamines is prepared on a solid polystyrene support using split and pool technologies. This technique allows for the synthesis of a diverse set of substituted ethylene diamines.
  • These diamines are screened for anti-TB activity using in vitro, biological assays, including a High-Throughput Screening (HTS) assay, based on the recently completed genomic sequence of M. tuberculosis , and a Minimum Inhibition Concentration (MIC) assay.
  • HTS High-Throughput Screening
  • MIC Minimum Inhibition Concentration
  • the methods and compositions described herein comprise substituted ethylene diamines that are effective against disease caused by infectious organisms, including, but not limited to, bacteria and viruses.
  • One embodiment of the invention provides methods and compositions comprising substituted ethylene diamines that are effective against mycobacterial disease.
  • Another embodiment of the invention provides methods and compositions comprising substituted ethylene diamines that have MIC of 50 ⁇ M or lower for mycobacterial disease.
  • Another embodiment of the present invention comprises substituted ethylene diamines that have an MIC of 25 ⁇ M or lower for mycobacterial disease.
  • Yet another embodiment of the present invention comprises substituted ethylene diamines that have an MIC of 12.5 ⁇ M or lower for mycobacterial disease.
  • Another embodiment of the present invention comprises substituted ethylene diamines that have an MIC of 5 ⁇ M or lower for mycobacterial disease
  • the methods and compositions comprise substituted ethylene diamines with HTS Luc activity of 10% or greater.
  • the methods and compositions comprise substituted ethylene diamines, wherein one amine group is derived from a primary amine, and wherein the other amine group is derived from a primary or secondary amine.
  • the methods and compositions comprise substituted ethylene diamines, wherein one amine is derived from cis-( ⁇ )myrtanylamine, cyclooctylamine, 2,2-diphenylethylamine, 3,3-diphenylpropylamine, (+)-bornylamine, 1-adamantanemethylamine, (+)-isopinocampheylamine; or ( ⁇ )-isopinocampheylamine.
  • the present invention contemplates various salt complexes and other substituted derivatives of the substituted ethylene diamines.
  • the present invention also contemplates enantiomers and other stereoisomers of the substituted ethylene diamines and their substituted derivatives.
  • the present invention further contemplates treatment for animals, including, but not limited to, humans.
  • Another object of the present invention is to provide methods and compositions for the treatment and prevention of mycobacterial disease, including but not limited to, tuberculosis.
  • Yet another object of the present invention is to provide methods and compositions for the treatment and prevention of infectious diseases using compositions comprising substituted ethylene diamines.
  • Another object of the present invention is to provide methods and compositions for the treatment and prevention of mycobacterial disease using compositions comprising substituted ethylene diamines.
  • Still another object of the present invention is to provide methods and compositions for the treatment and prevention of tuberculosis using compositions comprising substituted ethylene diamines.
  • Another object of the present invention is to provide methods and compositions for the treatment and prevention of tuberculosis using compositions comprising substituted ethylene diamines, wherein the diamine has an MIC of 50 ⁇ M, or less.
  • Another object of the present invention is to provide methods and compositions for the treatment and prevention of tuberculosis using compositions comprising substituted ethylene diamines, wherein the diamine has an MIC of 25 ⁇ M, or less.
  • Another object of the present invention is to provide methods and compositions for the treatment and prevention of tuberculosis using compositions comprising substituted ethylene diamines, wherein the diamine has an MIC of 12.5 ⁇ M, or less.
  • Yet another object of the present invention is to provide methods and compositions for the treatment and prevention of tuberculosis using compositions comprising substituted ethylene diamines, wherein the diamine has an MIC of 5 ⁇ M, or less.
  • Yet another object of the present invention is to provide methods and compositions for the treatment and prevention of tuberculosis using compositions comprising substituted ethylene diamines, wherein the diamine has HTS/Luc activity of 10% or greater.
  • Another object of the present invention is to provide methods and compositions for the treatment and prevention of tuberculosis using compositions comprising substituted ethylene diamines, wherein one amine group is derived from a primary amine, and the other amine group is derived from a primary or secondary amine.
  • Yet another object of the present invention is to provide methods and compositions for the treatment and/or prevention of tuberculosis using compositions comprising substituted ethylene diamines, wherein one amine is derived from cis-( ⁇ )myrtanylamine, cyclooctylamine, 2,2-diphenylethylamine, 3,3-diphenylpropylamine, (+)-bornylamine, 1-adamantanemethylamine, (+)-isopinocampheylamine; or ( ⁇ )-isopinocampheylamine.
  • Yet another object of the present invention is to provide composition for the therapeutic formulation for the treatment and prevention of mycobacterial disease.
  • Another object of the present invention is to provide compositions for therapeutic formulations for the treatment and prevention of mycobacterial disease caused by mycobacterial species comprising M. tuberculosis complex, M. avium intracellulare, M. kansarii, M. fortuitum, M. chelonoe, M. leprae, M. africanum, M. microti , or M. bovis.
  • FIG. 1 represents a flow chart schematic showing various solid support syntheses used to prepare substituted ethylene diamines.
  • FIGS. 2 ( a )- 2 ( ac ) provide chemical structures of a variety of primary amines.
  • FIGS. 3 ( a )- 3 ( f ) provide chemical structures of a variety of acyclic secondary amines.
  • FIGS. 4 ( a )- 4 ( i ) provide chemical structures of a variety of cyclic secondary amines.
  • FIG. 5 represents a flow schematic for a representative reaction pool of ten substituted ethylene diamines.
  • FIG. 6 is a graph of Luminescence Count per Second (LCPS) versus concentration showing HTS Luc assay results for pooled substituted ethylene diamine compounds.
  • FIG. 7 is a graph of LCPS versus concentration showing HTS Luc assay results for individual substituted ethylene diamine compounds.
  • FIG. 8 is a graph of LCPS versus concentration showing HTS Luc assay results for individual substituted ethylene diamine compounds.
  • FIG. 9 is a bar graph providing a summary of MIC activities for discrete substituted ethylene diamines.
  • FIG. 10 is a bar graph providing a summary of Luciferase activity of discrete substituted ethylene diamines with at least 10% activity in reference to ethambutol at 3.1 ⁇ M.
  • FIG. 11 is a bar graph showing the frequency of occurrences of the selected amine monomers in the substituted ethylene diamine compounds that were active against TB. Amine monomers are represented by their numerical designations.
  • FIG. 12 represents a flow schematic showing a synthesis of N-Geranyl-N′-(2-adamanthyl)ethane-1,2-diamine (compound 109).
  • FIG. 13 is a flow schematic showing a synthesis of N-(Cyclooctyl)-N′-(1R, 2R, 3R, 5S)-( ⁇ )-isopinocampheyletbane-1,2-diamine as hydrochloride (compound 59).
  • FIG. 14 is a mass spec profile for one representative sample well containing pooled substituted ethylene diamine compounds.
  • FIG. 15 is a mass spec profile for compound 109, N-Geranyl-N 1 -(2-adamanthyl) ethane-1,2-diamine.
  • FIG. 16 is a proton NMR profile for compound 109, N-Geranyl-N 1 -(2-adamanthyl) ethane-1,2-diamine.
  • FIG. 17 is a bar graph of data from a Colony Forming Units/Lung (CFU/Lung) study showing CFU/Lung growth over time in days for various compounds.
  • FIG. 18 is a bar graph of data from a CFU/Lung study showing CFU/Lung growth over time in days for various compounds.
  • FIG. 19 is a bar graph of data from a CFU/Lung study showing CFU/Lung growth over time in days for various compounds.
  • FIG. 20 is a bar graph of data from a lesion study showing visible lesions over time after treatment with various compounds.
  • FIG. 21 provides a schematic demonstrating the identification of a drug candidate
  • FIG. 22 provides the compounds tested for in vivo efficacy.
  • FIG. 23 is a graph showing the results of in vivo studies of compounds 73 and 109 at 1 and 10 mg/kg doses (spleen).
  • FIG. 24 is a graph showing the results of in vivo studies of compounds 73 and 109 at 1 and 10 mg/kg doses (lungs).
  • FIG. 25 is a graph showing in vivo studies of compounds 59 and 111 at 1 and 10 mg/kg doses (spleen).
  • FIG. 26 is a graph showing in vivo studies of compounds 59 and 111 at 1 and 10 mg/kg doses (lungs).
  • FIG. 27 is a graph showing the results of efficacy testing of the compounds 58, 73, 109, and 111 in C57BL.6 mice infected with M.tuberculosis H37Rv (spleen). Mice were infected i.v. with 5 ⁇ 10 6 CFU M.tuberculosis H37Rv; treatment with drugs started 18 days following infection. EC - EC—early control, CFU in lungs of mice at the day of chemotherapy start. Mice received: 1—untreated mice, 2—INH (25 mg/kg), 3—EMB (100 mg/kg), 4—comp. 109 (25 mg/kg), 4*—comp.109 (10 mg/kg), 4**—comp. 109 (0.1 mg/kg), 5—comp. 58 (25 mg/kg), 6—comp.73 (25 mg/kg), 7—comp. 111 (25 mg/kg).
  • FIG. 28 is a graph showing the results of efficacy testing of the compounds 58, 73, 109, and 111 in C57BL.6 mice infected with M.tuberculosis H37Rv (lungs). Mice were infected i.v. with 5 ⁇ 10 6 CFU M.tuberculosis H37Rv; treatment with drugs started 18 days following infection. EC - EC—early control, CFU in lungs of mice at the day of chemotherapy start. Mice received: 1—untreated mice, 2—INH (25 mg/kg), 3—EMB (100 mg/kg), 4—comp. 109 (25 mg/kg), 4*—comp.109 (10 mg/kg), 4**—comp. 109 (0.1 mg/kg), 5—comp. 58 (25 mg/kg), 6—comp.73 (25 mg/kg), 7—comp. 111 (25 mg/kg).
  • FIG. 29 provides LC/MS data of tested compounds.
  • FIG. 30 provides a graph showing results of PK studies with a cassette dosing of tested compounds to mice. Oral delivery.
  • Compound NSC 722039 in the study reads as the compound 37, NSC 722040—compound 59, NSC 722041—compound 109.
  • FIG. 31 provides a graph showing results of PK studies with a cassette dosing of tested compounds to mice. Peritoneal delivery.
  • Compound NSC 722039 in the study reads as the compound 37, NSC 722040—compound 59, NSC 722041—compound 109.
  • FIG. 32 provides a graph showing results of PK studies with a cassette dosing of tested compounds to mice. Intravenous delivery.
  • Compound NSC 722039 in the study reads as the compound 37, NSC 722040—compound 59, NSC 722041—compound 109.
  • FIG. 33 provides a graph showing the results of PK Studies of the compound 109 in mice.
  • FIG. 34 Tissue distribution of 109 in mice (i.v., 3 mg/kg).
  • FIG. 35 Tissue distribution of 109 in mice (p.o., 25 mg/kg).
  • FIG. 36 Metabolism of the compound 109 in mouse urine.
  • FIG. 37 No glucoronidation metabolites of 109 were found in mouse urine.
  • FIG. 41 Scheme 1. Synthesis of 100,000 compound library of ethambutol analogues on solid support.
  • FIG. 41 Scheme 2. Attempts to synthesize SQBisAd on solid support.
  • FIG. 42 provides structures of representative targeted diamines prepared via acylation by amino acids.
  • FIG. 43 provides Table 25 summarizing data for synthesized plates of diamines for the prepared library of targeted 20,000 ethambutol analogs.
  • FIG. 44 provides Scheme 5 showing the synthesis of the diamine library using amino acids as linkers.
  • FIG. 45 provides a schematic showing the occurrence of amine monomers in the hits that were generated in the original 100,000 compound library of EMB analogs.
  • FIG. 46 provides a schematic showing structural diversity among primary amines.
  • FIG. 47 provides Table 26 listing the amino acids that were used in the prepartion of the diamine library.
  • FIG. 48 provides carbonyl compounds used as reagents in the synthesis of the diamine library.
  • FIG. 49 provides Table 27 showing carbonyl compounds used in the masterplate for the synthesis of the diamine library.
  • FIG. 50 provides representative examples of MIC and Lux data for the diamine library.
  • FIG. 51 provides a schematic showing the occurrence of alkylating monomers in final diamine products with anti-TB activity.
  • FIG. 52 provides the layout of a representative 96-well deconvolution plate.
  • FIG. 53 provides a list of compound hits and structures for the modified linker diamine library.
  • Tuberculosis is the cause of the largest number of human deaths attributed to a single etiologic agent with two to three million people infected with tuberculosis dying each year. Areas where humans are crowded together, or living in substandard housing, are increasingly found to have persons affected with mycobacteria. Individuals who are immunocompromised are at great risk of being infected with mycobacteria and dying from such infection. In addition, the emergence of drug-resistant strains of mycobacteria has led to treatment problems of such infected persons.
  • Chemotherapy is a standard treatment for tuberculosis. Some current chemotherapy treatments require the use of three or four drugs, in combination, administered daily for two months, or administered biweekly for four to twelve months. Table 1 lists several treatment schedules for standard tuberculosis drug regimens. TABLE 1 Treatment Schedules for Standard TB Drug Regimens.
  • the present invention provides methods and compositions comprising a class of substituted ethylene diamine compounds effective in treatment and prevention of disease caused by microorganisms including, but not limited to, bacteria.
  • the methods and compositions of the present invention are effective in inhibiting the growth of the microorganism, M. tuberculosis .
  • the methods and compositions of the present invention are intended for the treatment of mycobacteria infections in human, as well as other animals.
  • the present invention may be particularly useful for the treatment of cows infected by M. bovis.
  • the term “tuberculosis” comprises disease states usually associated with infections caused by mycobacteria species comprising M. tuberculosis complex.
  • the term “tuberculosis” is also associated with mycobacterial infections caused by mycobacteria other than M. tuberculosis (MOTT).
  • MOTT mycobacterial species include M. avium - intracellulare, M. kansarii, M. fortuitum, M. chelonae, M. leprae, M. africanum , and M. microti, M. avium paratuberculosis, M. intracellulare, M. scrofulaceum, M. xenopi, M. marinum, M. ulcerans.
  • the present invention further comprises methods and compositions effective for the treatment of infectious disease, including but not limited to those caused by bacterial, mycological, parasitic, and viral agents.
  • infectious agents include the following: staphylococcus, streptococcaceae, neisseriaaceae, cocci, enterobacteriaceae, pseudomonadaceae, vibrionaceae, campylobacter, pasteurellaceae, bordetella, francisella, brucella, legionellaceae, bacteroidaceae, gram-negative bacilli, clostridium, corynebacterium, propionibacterium, gram-positive bacilli, anthrax, actinomyces, nocardia, mycobacterium, treponema, borrelia, leptospira, mycoplasma, ureaplasma, rickettsia, chlamydiae, systemic mycoses, op
  • the present invention further provides methods and compositions useful for the treatment of infectious disease, including by not limited to, tuberculosis, leprosy, Crohn's Disease, aquired immunodeficiency syndrome, lyme disease, cat-scratch disease, Rocky Mountain Spotted Fever and influenza.
  • the anti-infective methods and compositions of the present invention contain one or more substituted ethylene diamine compounds.
  • these compounds encompass a wide range of substituted ethylene diamine compounds having the following general formula:
  • R 1 NH is typically derived from a primary amine
  • R 2 R 3 N is typically derived from a primary or secondary amine.
  • the ethylene diamines of the present invention are prepared by a modular approach using primary and secondary amines as building blocks, and coupling the amine moieties with an ethylene linker building block. Representative primary amines, acyclic secondary amines, and cyclic secondary amines are shown in FIGS. 2, 3, and 4 , respectively.
  • chemical moieties R 1 , R 2 , and R 3 of the ethylene diamine compounds of the present invention are independently selected from H, alkyl; aryl; alkenyl; alkynyl; aralkyl; aralkenyl; aralkynyl; cycloalkyl; cycloalkenyl; heteroalkyl; heteroaryl; halide; alkoxy; aryloxy; alkylthio; arylthio; silyl; siloxy; a disulfide group; a urea group; amino; and the like, including straight or branched chain derivatives thereof, cyclic derivatives thereof, substituted derivatives thereof, heteroatom derivatives thereof, heterocyclic derivatives thereof, functionalized derivatives thereof, salts thereof, such salts including, but not limited to hydrochlorides and acetates, isomers thereof, or combinations thereof.
  • nitrogen-containing heterocyclic moieties include, but are not limited to, groups such as pyridinyl (derived from pyridine, and bonded through a ring carbon), piperidinyl (derived from piperidine and bonded through the ring nitrogen atom or a ring carbon), and pyrrolidinyl (derived from pyrrolidine and bonded through the ring nitrogen atom or a ring carbon).
  • substituted, or functionalized, derivatives of R 1 , R 2 , and R 3 include, but are not limited to, moieties containing substituents such as acyl, formyl, hydroxy, acyl halide, amide, amino, azido, acid, alkoxy, aryloxy, halide, carbonyl, ether, ester, thioether, thioester, nitrile, alkylthio, arythio, sulfonic acid and salts thereof, thiol, alkenyl, alkynyl, nitro, imine, imide, alkyl, aryl, combinations thereof, and the like.
  • the alkyl substituent may be pendant to the recited chemical moiety, or used for bonding to the amine nitrogen through the alkyl substituent.
  • Examples of chemical moieties R 1 , R 2 , and R 3 of the present invention include, but are not limited to: H; methyl; ethyl; propyl; butyl; pentyl; hexyl; heptyl; octyl; ethenyl; propenyl; butenyl; ethynyl; propynyl; butynyl; cyclopropyl; cyclobutyl; cyclopentyl; cyclohexyl; cyclooctyl cyclobutenyl; cyclopentenyl; cyclohexenyl; phenyl; tolyl; xylyl; benzyl; naphthyl; pyridinyl; furanyl; tetrahydro-1-napthyl; piperidinyl; indolyl; indolinyl; pyrrolidinyl; 2-(methyl;
  • R 1 , R 2 , and R 3 of the present invention include, but are not limited to, the following species or substituted or alkylated derivatives of the following species, covalently bonded to the amine nitrogen: furan; tetrahydrofuran; indole; piperazine; pyrrolidine; pyrrolidinone; pyridine; quinoline; anthracene; tetrahydroquinoline; naphthalene; pyrazole; imidazole; thiophene; pyrrolidine; morpholine; and the like.
  • One feature of the recited species or substituted or alkylated derivatives of these species, is that they may be covalently bonded to the amine nitrogen in any fashion, including through the pendant substituent or alkyl group, through the heteroatom as appropriate, or through a ring atom as appropriate, as understood by one of ordinary skill in the art.
  • the chemical moieties R 1 , R 2 , and R 3 of the present invention also include, but are not limited to, cyclic alkanes and cyclic alkenes, and include bridged and non-bridged rings.
  • bridged rings include, but are not limited to, the following groups: isopinocamphenyl; bornyl; norbornyl; adamantanetetyl; cis-( ⁇ )myrtanyl; adamantyl; noradamantyl; 6-azabicyclo[3.2.1]octane; exo-norbomane; and the like.
  • NR 2 R 3 is derived from a cyclic secondary amine.
  • a cyclic chemical moiety, NR 2 R 3 of the present invention include, but are not limited to, 4-benzyl-piperidine; 3-piperidinemethanol; piperidine; tryptamine; moropholine; 4-piperidinopiperidine; ethyl 1-piperazine carboxylate; 1-(2-amino-ethyl)-piperazine; decahydroquinoline; 1,2,3,4-tetrahydro-pyridoindole (reaction at either amine); 3-amino-5-phenyl pyrazole; 3-aminopyrazole; 1-(2-fluorophenyl) piperazine; 1-proline methyl ester; histidinol; 1-piperonyl-piperazine; hexamethyleimine; 4-hydroxypiperidine; 2-piperidinemethanol; 1,3,3-trimethyl-6-azabicy
  • the R 1 HN substituent is derived from a primary amine.
  • the R 2 R 3 N substituent is typically derived from a primary or secondary amine, but may also arise from an amino acid, or an amino acid precursor.
  • the amino acid can transform into an amino alcohol.
  • the precursor compound may be selected from, among others, the following compounds and their derivatives: d,1-tryptophan methyl ester; 1-methionine ethyl ester; 1-lysine methyl ester (via reaction at either primary amine); (S)-benzyl-1-cysteine ethyl ester; 1-arginine methyl ester (via reaction at either primary amine); 1-glutamic acid ethyl ester; 1-histidine methyl ester; or (3S (3a, 4Ab), 8A b)-N-t-butyl-D-ecahydro-3-iso-quino linecarboxamide.
  • R 4 moiety of the substituted ethylene diamine compounds of the present invention is typically selected from H, alkyl or aryl, but R 4 can also constitute alkenyl, alkynyl, aralkyl, aralkenyl, aralkynyl, cycloalkyl, cycloalkenyl, and the like.
  • R 4 chemical moiety examples include, but are not limited to: H; methyl; ethyl; propyl; butyl; pentyl; hexyl; heptyl; octyl; ethenyl; propenyl; butenyl; ethynyl; propynyl; butynyl; cyclobutyl; cyclopentyl; cyclohexyl; cyclobutenyl; cyclopentenyl; cyclohexenyl; phenyl; tolyl; xylyl; benzyl; naphthyl; straight or branched chain derivatives thereof, cyclic derivatives thereof; substituted, functionalized, and heteroatom derivatives thereof; and heterocyclic derivatives thereof, and the like.
  • R 4 is selected from H, methyl, ethyl, butyl or phenyl.
  • R 4 is “H” the ethylene diamine does not contain
  • a majority of the ethylene diamine compounds described hrein are preferably prepared using a solid support synthesis, as set forth in one of the representative reaction schemes shown in FIG. 1.
  • R 4 is H
  • the reaction does not proceed well when sterically hindered amines are used for R 1 NH 2 , or when diamines, such as amino alkylenemorpholine, or aminoalkylene-piperidines, are used for R 1 NH 2 .
  • R 4 is methyl, or phenyl
  • sterically hindered amines used for R 3 R 2 NH do not work well due to steric hindrance at the reaction site.
  • a competing hydrolysis reaction producing the corresponding amino alcohols, and incomplete reduction of the amidoethyleneamines, interfere with the reaction scheme.
  • the desired diamine products form in low yields.
  • the preparation of the ethylene diamines is preferably accomplished in six steps, using a rink-acid resin.
  • the first step of the synthesis is converting the rink-acid resin to rink-chloride by treatment with triphenylphosphine and hexachloroethane in tetrahydrofuran (THF). This step is followed by addition of the primary amine in the presence of Hunig's base (EtN(i-Pr) 2 ) in dichloroethane.
  • the third step is the acylation of the resin-attached amine using either one of the two acylation routes shown in FIG. 1.
  • the acylation step is preferably accomplished using either ⁇ -chloroacetyl chloride, ⁇ -bromo- ⁇ -methyl acetylbromide, ⁇ -bromo- ⁇ -ethylacetyl bromide, ⁇ -bromo- ⁇ -butyl acetylbromide, or ⁇ -chloro- ⁇ -phenyl-acetylchloride, each in the presence of pyridine in THF.
  • Other acylation reagents known to those skilled in the art may also be used, however, the ⁇ -bromoacetyl halides result in low product yields, which may be attributed to HBr elimination.
  • the acylation may also be accomplished via a peptide coupling mechanism using ⁇ -bromo- ⁇ -methylacetic acid, or ⁇ -chloro- ⁇ -methylacetic acid, in the presence of benzotriazole-1-yl-oxy-tris-pyrrolidino-phosphonium hexafluorophosphate (PyBrop) and N 1 N-diisopropylethyl amine (EtN(i-Pr) 2 ) in dichloromethane (DCM) and dimethylformamide (DMF).
  • PyBrop benzotriazole-1-yl-oxy-tris-pyrrolidino-phosphonium hexafluorophosphate
  • EtN(i-Pr) 2 N 1 N-diisopropylethyl amine
  • DCM dichloromethane
  • DMF dimethylformamide
  • the acylation step is preferably performed twice to achieve better acylated product yields.
  • the solid support syntheses, shown in FIG. 1, are preferably used to prepare a substituted ethylene diamine library.
  • Solid phase synthesis offers at least three principal advantages: (i) a reduced need for chromatographic procedures, (ii) the use of excess reagents to drive a reaction forward in high yields, and (iii) the use of split and pool technologies for the synthesis of a large number of compounds.
  • Solid support syntheses of 1,2-diamine libraries have previously been accomplished by the reduction of short peptides (Cuervo et al., Peptides 1994: Proceedings of the European Peptide Symposium; Maia HSL Ed., Esom: Leiden, 1995, 465-466).
  • an ethylene diamine library is created using amines, rather than simple amino acids, to allow for greater diversity in the building-block monomers.
  • the synthesizer handles up to twenty simultaneous reactions in 5 ml or 10 ml reaction vessels to allow for rapid synthesis of target compounds.
  • the synthesizer provides programmable temperature control and agitation, and the automated delivery of solvents into the reaction vessels.
  • the addition of the second amine, the reduction with Red-Al, and the cleavage from the solid support are carried out in 2 ml wells in a 96-well, chemically resistant plate.
  • each amine within numbers 1 to 288, as shown in FIGS. 2, 3, and 4 , is dissolved in DMF as a one molar solution, and organized in three, 96-well plates (one amine per well), to yield three master plates of these amines.
  • Individual haloacetyl amides are then pooled into groups of ten or thirty. A suspension of the pooled resins in a 2:1 mixture of DCM/THF is evenly distributed into one, two or three reaction plates to assure 15-20 mg of the suspension per well.
  • FIG. 5 provides a flow schematic for a representative pool. Each reaction occurs in a separate well, in the presence of Hunig's base in DMF at 70-75° C. for 16-20 hours. Each resulting amine-amide is reduced using 65+w % Red-Al at room temperature. The reduction is followed by cleavage with 10% vol. TFA in DCM. The solvents in each reaction well are evaporated, and the TFA salts of the diamines analyzed (mass spec), and screened against M. tuberculosis. One plate of pooled diamines are screened against M. smegmatis. Two randomly selected rows in each plate; i.e., 24 samples per 96-well plate, or 25% of the library, are examined by mass spectroscopy. Specific protocols and detailed methods are provided below in the Examples.
  • FIG. 6 represents typical assay data in a luciferase reporter strain containing an Rv0341 EMB-inducible promoter.
  • FIG. 6 represents percent maximum Luminescense Count per Second (% Max. LCPS) for pooled compound mixtures in one row (row D) in one of the 96-well plates.
  • the M. tuberculosis screening revealed approximately 300 active compounds mixtures that were selected for deconvolution.
  • Deconvolutions were performed by discrete re-synthesis of each substituted ethylene diamine compound in each active compound pool.
  • the pooled compounds in each active well were individually synthesized, and screened. Syntheses of the targeted diamine compounds in each active pool were done in the 96-well plates using stored archived ⁇ -haloacetyl amides (resin attached haloacetyl amides), according to the previously described reaction steps (the addition of the second amine, the reduction with Red-Al, and the cleavage from the solid support).
  • the archived resins were stored as individual compounds at 4° C.
  • the 96-well plates were used for the remaining synthesis steps as previously described.
  • FIGS. 7 and 8 represent the Luminescence Count per Second (LCPS) for individual compounds.
  • FIG. 9 summarizes the MIC data for all synthesized discrete compounds with an MIC of 50 ⁇ M or less.
  • FIG. 10 summarizes Luc assay data for all compounds that exhibit at least 10% activity at each concentration (the results are not cumulative). The MIC and Luc activities were obtained for non-purified samples, with chemical yields of approximately 20%, based on an assumed 80% yield at each reaction step. In the Luc assay, 32 compounds exhibited activity at 1.56 ⁇ M, and in the MIC assay, at least 11 compounds had an MIC of 3.13 ⁇ M.
  • #105a (1R,2R,3R,5S)-( ⁇ )-Isopinocampheylamine
  • the present invention is also directed to a new library of diamine compounds useful against infectious disease.
  • a synthetic scheme to incorporate amino acids into a bridging linker between the two amine components has been developed.
  • the use of amino acids allowed for diverse linker elements, as well as chirality see FIG. 42 for representative examples.
  • the diamine compounds were prepared on mmol scale in 96-well format in pools of 10 compounds per well (for the vast majority of the plates).
  • Table 25 (FIG. 43) summarizes data for the synthesized plates.
  • Attachment of the first amine to the support was done according to the Garigipati protocol.
  • Rink acid resin (Novabiochem) was converted into the Rink-chloride upon treatment with triphenylphosphine and dichloroethane in THF.
  • This activated resin was then loaded by addition of an amine N1 in presence of Hunig's base in dichloroethane.
  • the amine N1 includes, but is not limited to, alkyl and aryl primary amines. Out of 177 primary amines that had been previously used as N1 for 100,000 library preparation, only 30 were selected in this Scheme, based upon in vitro activity data of their ethylenediamine derivatives (from the previous ⁇ 100K library) as well as structural diversity (FIGS. 45 and 46).
  • Therapeutics including compositions containing the substituted ethylene diamine compounds of the present invention, can be prepared in physiologically acceptable formulations, such as in pharmaceutically acceptable carriers, using known techniques. For example, a substituted ethylene diamine compound is combined with a pharmaceutically acceptable excipient to form a therapeutic composition.
  • compositions of the present invention may be administered in the form of a solid, liquid or aerosol.
  • solid compositions include pills, creams, soaps and implantable dosage units. Pills may be administered orally.
  • Therapeutic creams and anti-mycobacteria soaps may be administered topically.
  • Implantable dosage units may be administered locally, for example, in the lungs, or may be implanted for systematic release of the therapeutic composition, for example, subcutaneously.
  • liquid compositions include formulations adapted for injection intramuscularly, subcutaneously, intravenously, intraarterially, and formulations for topical and intraocular administration.
  • aerosol formulations include inhaler formulations for administration to the lungs.
  • a sustained release matrix is a matrix made of materials, usually polymers, which are degradable by enzymatic or acid/base hydrolysis, or by dissolution. Once inserted into the body, the matrix is acted upon by enzymes and body fluids.
  • the sustained release matrix is chosen desirably from biocompatible materials, including, but not limited to, liposomes, polylactides, polyglycolide (polymer of glycolic acid), polylactide co-glycolide (coplymers of lactic acid and glycolic acid), polyanhydrides, poly(ortho)esters, polypeptides, hyaluronic acid, collagen, chondroitin sulfate, carboxylic acids, fatty acids, phospholipds, polysaccharides, nucleic acids, polyamino acids, amino acids such as phenylalanine, tyrosine, isoleucine, polynucleotides, polyvinyl propylene, polyvinylpyrrolidone and silicone.
  • a preferred biodegradable matrix is a matrix of one of either polylactide, polyglycolide, or polylactide co-glycolide.
  • the dosage of the composition will depend on the condition being treated, the particular composition used, and other clinical factors, such as weight and condition of the patient, and the route of administration.
  • a suitable dosage may range from 100 to 0.1 mg/kg.
  • a more preferred dosage may range from 50 to 0.2 mg/kg.
  • a more preferred dosage may range from 25 to 0.5 mg/kg.
  • Tablets or other forms of media may contain from 1 to 1000 mg of the substituted ethylene diamine. Dosage ranges and schedules of administration similar to ethambutol or other anti-tuberculosis drugs may be used.
  • compositions may be administered in combination with other compositions and procedures for the treatment of other disorders occurring in combination with mycobacterial disease.
  • tuberculosis frequently occurs as a secondary complication associated with acquired immunodeficiency syndrome (AIDS).
  • AIDS acquired immunodeficiency syndrome
  • Rink-acid resin was obtained from NOVABIOCHEM® Inc., San Diego, Calif. Solvents: acetonitrile, dichloromethane, dimethylformamide, ethylenedichloride, methanol and tetrahydrofuran were purchased from ALDRICH®, Milwaukee, Wis., and used as received. All other reagents were purchased from SIGMA-ALDRICH®, West Monroe Highland, Ill.
  • Solid phase syntheses were performed on a QUEST® 210 Synthesizer, from ARGONAUT TECHNOLOGIES®, Foster City, Calif., with the aid of combinatorial chemistry equipment, from WHATMAN® POLYFILTRONICS® (Kent, England; Rockland, Mass.) and ROBBINS SCIENTIFIC®, Sunnyvale, Calif. Evaporation of solvents was done using SPEEDVAC® AES, from SAVANT®, Holbrook, N.Y. All necessary chromatographic separations were performed on a WATERS' ALLIANCE HT SYSTEM®, Milford, Mass. Analytical thin-layer chromatography was performed on MERCK® silica gel 60F 254 plates, purchased from SIGMA-ALDRICH®, West Monroe Highland, Ill.
  • the Rink-acid resin had a coverage of 0.43-0.63 mmol of linker per gram resin.
  • Four to five grams of this resin were suspended in 80 ml of a 2:1 mixture of dichloromethane and tetrahydrofuran (THF), and distributed into ten, 10 ml tubes, with 8 ml of resin suspension per tube. Each suspension was filtered and washed twice with THF.
  • a solution of triphenylphosphine (3.80 g, 14.5 mmol) in 30 ml of THF was prepared, and 3 ml of this solution was added to each tube, followed by the addition of 3 ml of a solution of hexachloroethane in THF (3.39 g/14.3 mmol hexachloroethane in 30 ml THF). After agitation for six hours at room temperature, each activated resin was washed twice with THF and twice with dichloromethane.
  • each tube, containing the activated rink resin was charged with 3 ml of dichloroethane, 0.3 ml (1.74 mmol) N 1 N-diisopropylethylamine (EtN(iPr) 2 ) and the corresponding amine (around 1 mmol). If the selected amine was a solid at room temperature, it was added as a solution, or a suspension in DMF. Enough dichloroethane was added to each tube for a final volume of 8 ml. The reaction mixture was heated at 45° C. for 6-8 hours. The resins were filtered, washed with a 2:1 mixture of dichloromethane and methanol (1 ⁇ 8 ml), then with methanol (2 ⁇ 8 ml), and then dried under argon for 10 minutes.
  • dichloroethane 0.3 ml (1.74 mmol) N 1 N-diisopropylethylamine (EtN(iPr) 2 ) and the corresponding amine
  • the acylation was repeated using the same loading of reagents, but a shorter reaction time of 4 hours at 45° C., and 2 hours at room temperature. Each resin was then filtered, washed with a 2:1 mixture of dichloromethane and methanol (1 ⁇ 8 ml), and then with methanol (3 ⁇ 8 ml). Each resin was dried under argon for 10 minutes. Each resin was then transferred into a vial and dried in a desiccator under vacuum for 1 hour.
  • each resin was then filtered, washed with dichcloromethane (2 ⁇ 8 ml) and methanol (2 ⁇ 8 ml), and the acylation was repeated.
  • Each resin was then filtered, washed with dichloromethane (2 ⁇ 8 ml), methanol (3 ⁇ 8 ml), and dried under argon for about 10 minutes.
  • Each resin was transferred into a vial, and dried in a desiccator under vacuum for one hour.
  • the distributed suspension was then filtered using a filtration manifold, a small lightweight manifold that is generally used for drawing solvents and reagents from the chambers of the 96-well reaction plates.
  • the reaction plates were transferred into COMBICLAMPS® (Huntington, W. Va.), and 10% EtN(iPr) 2 in DMF was added at 0.2 ml per well (0.21 mmole of EtN(iPr) 2 per well), followed by the addition of a 1.0M solution of the appropriate amine from the corresponding master plate, 0.1 ml per well (0.1 mmole amine per well).
  • the COMBICLAMPS® are used to accommodate 96-well reaction plates during synthesis, allowing for the addition of reagents into the plates, and a proper sealing that maintains reagents and solvents for hours at elevated temperatures.
  • These clamps consist of a top and bottom cover provided with changeable, chemically resistant sealing gaskets. They are designed to accommodate 96-well reaction plates between the top and bottom covers.
  • the reaction plates were sealed and kept in an oven at 70-75° C. for 16 hours. After cooling to room temperature, the resins were filtered, washed with a 1:1 mixture of DCM/methanol (1 ⁇ 1 ml), methanol (2 ⁇ 1 ml), and then dried in a desiccator under vacuum for 2 hours.
  • reaction plates were placed into COMBICLAMPS®.
  • a 1:6 mixture of Red-Al (65+w % in toluene) and THF was added, at 0.6 ml per well (0.28 mmole of Red-Al per well), and allowed to react for 4 hours.
  • Each resin was then filtered, washed with THF (2 ⁇ 1 ml), and methanol (3 ⁇ 1 ml). The addition of methanol should proceed with caution. Each resin was then dried under vacuum.
  • This step was carried out using a cleavage manifold, a Teflon coated aluminum, filter/collection vacuum manifold, designed for recovering cleavage products from the reaction plates into collection plates.
  • the manifold is designed to ensure that the filtrate from each well is directed to a corresponding well in a receiving 96-well collection plate.
  • the reaction plates placed on the top of the collection plates in this manifold) were charged with a 10:85:5 mixture of TFA, dichloromethane, and methanol (0.5 ml of mixture per well). After fifteen minutes, the solutions were filtered and collected into proper wells on the collection plates. The procedure was repeated. Solvents were evaporated on a SPEED VAC®, Holbrook, N.Y., and the residual samples (TFA salts) were tested without further purification.
  • Deconvolution of the active wells was performed by re-synthesis of discrete compounds, from the archived ⁇ -haloacetyl amide resins (10 resins, 0.05-0.10 g each), which were set aside at the end of the acylation step before the pooling. Each resin was assigned a discrete column (1, or 2, or 3, etc., see the template) in a 96 well filterplate, and was divided between X rows (A, B, C, etc), where X is the number of hits discovered in the original screening plate.
  • reaction plates were sealed and kept in an oven at 70-75° C. for 16 hours. After cooling to room temperature, the resins were filtered, washed with a 1:1 mixture of DCM and methanol (1 ⁇ 1 ml), methanol (2 ⁇ 1 ml), and dried in desiccator under vacuum for 2 h. Reduction and cleavage were performed according to steps 5 and 6 in the original synthetic protocol. The product wells from the cleavage were analyzed by ESI-MS (Electro Spray Ionization Mass Spectroscopy) to ensure the identity of the actives, and were tested in the same Luc and MIC assays.
  • ESI-MS Electro Spray Ionization Mass Spectroscopy
  • Rink-acid resin Synthesis of Rink-Cl resin.
  • Rink-acid resin, coverage (linker) of 0.43 to 0.63 mmol/g (0.8 g, 0.5 mmol) was placed into one of the 10 ml tubes of QUEST® 210 Synthesizer, and washed twice with THF.
  • a solution of triphenylphosphine (0.380 g, 1.45 mmol) in THF (3 ml) was added, followed by the addition of a solution of hexachloroethane (0.4 g, 1.43 mmol) in THF (3 ml).
  • THF was added up to the volume of the tube (approximately 2 ml). After 6 hours, the resin was filtered, washed with THF (2 ⁇ 8 ml) and dichloromethane (2 ⁇ 8 ml).
  • the resin was filtered, washed with a 2:1 mixture of dichloromethane and methanol (1 ⁇ 8 ml), methanol (2 ⁇ 8 ml), and THF, and the acylation was repeated using the same loads of the reagents, but shorter reaction time: 4 hours at 45° C. and 2 hours at room temperature.
  • the ⁇ -chloroacetamide loaded resin was filtered, washed with a 2:1 mixture of dichloromethane and methanol (1 ⁇ 8 ml), methanol (3 ⁇ 8 ml), and suck dried for 15 min under argon.
  • the resin was filtered, washed with THF (1 ⁇ 8 ml), a 1:1 mixture of THF and methanol (1 ⁇ 8 ml) (addition of MeOH should proceed with caution), methanol (3 ⁇ 8 ml), and then dried.
  • reaction mixture was diluted with 150 ml of ethyl ether, and washed with 1M NaOH solution (2 ⁇ 50 ml). The organic layer was washed with brine (1 ⁇ 50 ml), dried over MgSO 4 , and concentrated to dryness on the rotory evaporator.
  • the residue (11.04 g) as brown oil was purified on COMBIFLASK® (Isco, Lincoln, Nebr., USA), using Silicagel catridges commercially available from BIOTAGE® (Biotage, Inc.
  • Mass spectra data were obtained by Elecrospray Ionization technique on a PERKIN ELMER®/SCIEX®, API-300, TQMS with an autosampler, manufactured by SCIEX®, Toronto, Canada.
  • Mass spectroscopy served as a means for monitoring the reaction results of the library of ethylenediamines. Mass spectroscopy was done on two randomly selected rows (24 samples) per reaction plate, for roughly 28,000 compounds in pool of 10 or 30 compounds per well. Thus, if ten compounds per well were synthesized, the mass spectra for each well should contain ten signals, correlating with the proper molecular ions for each compound. The presence or absence of a particular signal indicated the feasibility of the particular synthesis. Based on the mass spectral data, and on a general analysis of the reactivity of the various amines, it is estimated that 67,000 compounds were formed out of 112,000 compounds.
  • FIG. 14 is a representative mass spec profile for one sample well. Mass spectra for a representative ethylene diamine compound is shown in FIG. 15. Tables 5 to 8, below, list illustrative examples of mass spec data for representative reaction wells, with each well containing ten substituted ethylene diamines. TABLE 5 ILLUSTRATIVE EXAMPLES OF MASS SPEC DATA FOR REPRESENTATIVE ETHYLENEDIAMINES (TEN COMPOUNDS PER WELL).
  • the substituted ethylene diamines were analyzed according to the following procedure.
  • the diamines were dried in a speed vacuum to an approximate concentration of 6.3 mmoles per well.
  • Each diamine, or diamine mixture was then resuspended or dissolved in 200 ⁇ l of methanol for a concentration of 31.5 mM diamine(s).
  • the diamine(s) solution was diluted to a concentration of 200 ⁇ M in 7H9 broth medium (a 1:15.75 dilution of the 31.5 mM stock, followed by a 1:10 dilution; each dilution in 7H9 broth medium).
  • the following substrates were prepared: a buffer solution containing 50 mM HEPES at pH 7.0 and 0.4% Triton X-100. Then, 0.25 ml of 1M DTT, and 14 ⁇ l of 10 mg/ml luciferin in DMSO were added to 5 ml of the buffer solution. This final solution (50 ⁇ l) was added to each of the twelve wells, immediately after the incubation period had run. The luminescence from each well was measured 20 minutes after the luciferin substrate was added, using a TOPCOUNT® (Downers, Grove, Ill.) NXT luminometer (55/well).
  • FIGS. 6 - 8 show typical assay data for the luciferase reporter strain containing an Rv0341 EMB-inducible promoter with serial dilution of 12 wells (1 row) of a 96-well library plate.
  • FIG. 10 shows the number of substituted ethylene diamines with at least 10% luciferase activity, based on the activity of ethambutol at 3.1 ⁇ M.
  • FIG. 6 represents typical assay data in the luciferase reporter strain containing an Rv0341 EMB-inducible promoter.
  • the data represents values obtained from the HTS Luc assay for compound mixtures of one row (row D) in the 96-well library. Row D was subject to several serial dilutions. The effectiveness of the compound mixture in the assay was measured by the intensity of luminescence, and compared to ethambutol (100% intensity, 99% purity) at 3.1 ⁇ M. Each curve in FIG. 6 represents one well, or ten compounds. Results are reported in percent maximum Luminescence Count per Second (% Max. LCPS). During the screening, a theoretical 100% chemical yield was assumed for every unpurified compound. Concentrations are given for a single compound. Based on this initial screening, 300+ compound mixtures showed anti-TB activity.
  • the Minimum Inhibition Concentration is the concentration of the growth inhibitor, here a substituted ethylene diamine, at which there is no multiplication of seeded cells.
  • a microdilution method was used to determine the MIC of the substituted ethylene diamines, capable of inhibiting the growth of Mycobacteriun tuberculosis in vitro.
  • bacteria the H37Rv strain of Mycobacterium tuberculosis ( M.tb ) was cultivated in 7H9 medium to a density of 0.2 OD (optical density) at 600 nm. The bacterial culture was then diluted 1:100 in 7H9 broth medium.
  • Table 9 A representative plate layout, listing concentration in each well, is shown in Table 9.
  • Table 10 lists MIC and LD50 data for selected compounds.
  • the LD50 is the concentration of the substituted ethylene diamine at which 50% of the cells (H37Rv strain of M.tb ) are killed.
  • Table 11 lists MIC data for purified substituted ethylene diamines in comparison to ethambutol (EMB).
  • FIG. 9 shows the number of substituted ethylene diamine compounds with MIC activity at various concentration levels.
  • MDR Strain TN576 is classified as a W1 strain (STP R , INH R , RIF R , EMB R , ETH R , KAN R , CAP R ) strain TN587 is classified as a W strain (STP R , INH R , RIF R , EMB R , KAN R ), and the third strain TN3086 is classified as a W1 strain (STP R , INH R , RIF R , EMB R , KAN R ).
  • Each MDR strain is highly resistant to ethambutol with MIC values exceeding 12.5-25 ⁇ M.
  • mice aerosolized with M. tuberculosis H37R v were examined for 10 to 12 weeks following inoculation.
  • Drugs substituted ethylene diamines
  • esophageal cannula gavage 7 days/week, starting at either 14 or 21 days post infection.
  • Bacterial load in the lungs of five mice per group were determined at approximately one-week intervals by viable colony counts.
  • the drugs tested were directly compared to the front line anti-tuberculosis drug isoniazid, and to the second line drug, ethambutol. Isoniazid and ethambutol were tested at 25 mg/kg and 100 mg/kg, respectively.
  • FIGS. 17 to 19 represent data from three, independent CFU Lung studies. In each study, the number of colony forming units (CFU) that were recoverable and cultivatable, were determined during various time intervals (days).
  • CFU colony forming units
  • Toxicity was assessed using a dose escalation study. This study was performed with ten C57BL/6 mice per candidate. Every two days, the mice were administered an increased concentration of the drug, and monitored for detrimental effects.
  • the administration scheme was 50, 100, 200, 400, 600, 800 and 1000 mg/kg. The maximum limit of 1000 kg/mg was based on the goal of dose escalation, and the solubility of the drugs in the delivery vehicle.
  • Compound 37 was toxic in mice at 100 kg/mg.
  • Compound 59 and compound 109 were tolerated in mice at 1000 mg/kg and 800 mg/kg, respectively.
  • Compounds 58, 59, 73, 109, and 111 were selected for in vivo efficacy studies in a mouse model of TB.
  • Compounds 58 and 59 share the same cyclooctyl fragment in their molecules; compounds 58, 73, and 109 share adamantly moiety, and 109 and 111—the geranyl fragment (FIG. 22).
  • mice Female C57BL/6 mice of 8 weeks old were purchased from Charles River (Raleigh, N.C.), housed in BSL-2 facility of BIOCAL, Inc. (Rockville, Md.), and were allowed to acclimate at least 4 days prior infection.
  • Mycobacteria An example of frozen and thawed of M.tuberculosis H37Rv Pasteur was added to 5 ml 7H10 broth medium, with 0.5% BSA and 0.05% Tween 80, incubated 1 week at 37° C., and then 1 ml was added into 25 ml medium (2-d passage during 2 weeks).
  • Infection Frozen sample of culture was thawed, and diluted for concentration about 10 6 CFU/ml. Mice were infected with M.tuberculosis H37Rv intravenously through lateral tail vein in corresponded dose in 0.2 ml of PBS.
  • Protocol of drug treatment Treatment of mice with compounds was initiated 20 days following infection. Compounds were dissolved in 10% ethanol in water and administered by gavage (0.2 ml per mouse). Therapy was given 5 days per week and continued for four or six weeks. Two, four and six weeks following chemotherapy start mice (6 mice per group) were sacrificed, lungs and spleens were removed and homogenized in sterile in 2 ml PBS with 0.05% Tween-80. Homogenates were plated in serial dilutions on 7H10 agar dishes, and incubated at 37° C. CFU counts were calculated three weeks later.
  • FIGS. 21 - 24 In vivo activities of new compounds. The activities of these compounds are presented in FIGS. 21 - 24 .
  • mice were infected with 5 ⁇ 10 5 CFU M.tuberculosis H37Rv and chemotherapy was started 20 days following infection. Mice were treated with INH (25 mg/kg), EMB (100 mg/kg), compounds 73 and 109 (both 1 mg/kg and 10 mg/kg). The results indicate that in the spleen, compounds 73 and 109 have activities equal to that of EMB at 100 mg/kg (FIG. 21). In spleen there are no statistical differences between activities of these compounds at 1 mg/kg or 10 mg/kg.
  • compound 109 at concentration 10 mg/kg after 4 and 6 weeks was more effective than EMB at 100 mg/kg.
  • statistically sufficient difference was shown for compound 109 at concentrations 1 mg/kg and 10 mg/kg (FIG. 22). INH was the most active drug in both spleen and lung.
  • INH showed higher activity than EMB and other compounds decreasing load of bacteria in organs on 2-3 logs during 4-6 weeks of chemotherapy; new compounds similar to EMB (100 mg/kg) decreased load of bacteria on 1.0-2.0 logs.
  • studied compounds 73 and 109 are the most preferable, because the highest capacity to decrease mycobacteria in organs and its parameters of toxicity and pharmacology kinetics.
  • Compound 109 was mostly used in the form of dihydrochloride at five different doses, and 37—solely as hydrochloride salt at two doses.
  • mice were given a one-time dose of the compounds at concentrations 100, 300 or 1000 mg/kg using the gavage method. Each dose of each compound consisted of one group of 3 mice. Monitoring of the mice was done twice a day for the duration of the experiment. Mice surviving one week post-drug administration were sacrificed; critical organs were aseptically removed and observed for abnormalities and evidence of drug toxicity. The MTD (mg/kg) is the highest dose that results in no lethality/tissue abnormality.
  • mice C57BL/6 female mice (6-8 weeks in age) are given a one-time dose of the compound at concentrations 100, 300 or 1000 mg/kg using the gavage method.
  • the compounds are dissolved in the appropriate concentration of ethanol in distilled water and administered in a volume of 0.2 ml per mouse.
  • mice will be observed 4 and 6 hours post administration, then twice daily for one week. Survival and body weight of mice will be closely monitored throughout the study.
  • Compound SQBisAd can be prepared by “wet chemistry” using the same route, Scheme 3 (FIG. 41), it is documented that 2-adamantamine (used as commercially available hydrochloride) does provide products when used on the 1 and 2 steps. Due to the symmetrical nature, this compound can be synthesized by alternative routes.
  • SQBisAd by reductive alkylation of ethylnediamine by 2-adamantanone using sodium cyanoborohydride. Final product (without additional purification) demonstrated MIC (Minimal Inhibitory Concentration) equal or better than compound 109.
  • Step 1 Activation of the Rink-acid Resin.
  • each tube was charged with 3 ml of dichloroethane, EtNiPr 2 , (0.2 ml, 1.15 mmol), and the corresponding amine (1 mmol). (When a selected amine was a solid, it was added as a solution or a suspension in DMF). Dichloroethane was added to each tube to fill up the volume 4 ml. The reaction was carried for 8 h at 45° C. and 6-8 h at room temperature. The resins were filtered, washed with a 2:1 mixture of dichloromethane and methanol (1 ⁇ 4 ml), then with methanol (2 ⁇ 4 ml), and suck dry.
  • the resins were filtered, washed with 1:1 mixture of DMF and dichloromethane (1 ⁇ 3 ml), and methanol (3 ⁇ 3 ml), sucked dry (on Quest) for 30 min and transferred into vials (one resin per vial), and dried in a desiccator under vacuum for 1 h. After this step all resins were subjected for quality control using MS spectra.
  • Step 4. Alkylation of the Amino Group.
  • This step was carried out using a cleavage manifold.
  • the reaction plates placed on the top of the collection plates in this manifold) were charged with a 10:85:5 mixture of TFA, dichloromethane, and methanol, 0.5 ml per well. After 15 min, the solutions were filtered and collected into proper wells of the collection plates. The procedure was repeated. Solvents were evaporated on a speedvac, and the residual samples were ready for testing.
  • Deconvolution of the active wells was performed by re-synthesis of discrete compounds, from the archived FMOC-protected ⁇ -aminoacetamide resins (10 resins, 0.05-0.10 g each), which were set aside at the end of the acylation step before the pooling. Each resin was assigned a discrete column (1, or 2, or 3, etc.) in a 96-well filterplate, and was divided between X rows (A, B, C, etc), where X is the number of hits discovered in the original screening plate.
  • a selected carbonyl compound (present in the hit) was added along with other required reagents: the first selected carbonyl compound was added to the resins in the row “A”, the second carbonyl compound—to the resins in the row “B”, the third carbonyl compound—to the resins in the row “C”, etc.
  • a lay-out of a representative 96-well deconvolution plate is shown in Table 28, FIG. 52.

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