Methods for treating and preventing clostridium difficile infection

Abstract

The present invention relates to methods for treating and preventing Clostridium difficile infection. Methods of treating or preventing Clostridium difficile infection and associated pathological conditions associated with Clostridium difficile infection are disclosed.

Description

This application is a divisional application of Chinese patent application 201780032098.0, filed on March 24, 2017, “Methods for treating and preventing Clostridium difficile infection”. Technical Field The present invention is directed to methods of treating or preventing Clostridium difficile infection and related pathological conditions associated with Clostridium difficile infection.

[0001] Related Applications This application claims the benefit of U.S. Provisional Application Serial No. 62 / 312,996, filed on March 24, 2016, and U.S. Provisional Application Serial No. 62 / 320,053, filed on April 8, 2016. The entire contents of each of the foregoing applications are incorporated herein by reference. Background Art Clostridium difficile (C. difficile) is a Gram-positive, spore-forming bacterial species that is ubiquitous in nature and is particularly prevalent in soil. Pathogenic C. difficile strains produce a variety of toxins, the most well characterized of which are enterotoxins (C. difficile toxin A) and cytotoxins (C. difficile toxin B), both of which can produce diarrhea and inflammation in infected patients. Toxins A and B are glucosyltransferases that target and inactivate the Rho family of GTPases. Toxin B (cytotoxin) induces actin depolymerization through a mechanism associated with a decrease in ADP-ribosylation of low molecular weight GTP-binding Rho proteins. Another toxin, binary toxin, has also been described previously, but its role in causing the pathological conditions associated with C. difficile infection is not fully understood.

[0003] C. difficile is transmitted from person to person via the fecal-oral route. However, the organism forms heat-resistant spores that are not killed by alcohol-based hand cleaners or conventional surface cleaning. Therefore, these spores survive for long periods of time in clinical settings. Therefore, the bacteria can be cultured from almost any surface. Once the spores are ingested, their acid resistance allows them to pass through the stomach unharmed. They germinate in the colon and multiply into vegetative cells when exposed to bile acids.

[0004] Infection of the gut by C. difficile is thought to occur when this bacterium replaces the damaged normal intestinal flora, usually after antibiotic treatment for an unrelated infection. Disturbances in normal healthy bacteria can provide an opportunity for C. difficile to overtake the intestinal microbiome. Therefore, C. difficile-associated diarrhea (CDAD) is a type of antibiotic-associated diarrhea, and mild cases of CDAD can often be treated by interrupting the offending antibiotic. Ironically, more severe cases require targeted antibiotic therapy, such as treatment with vancomycin or metronidazole, and recurrences of CDAD have been reported in up to 20% of cases.

[0005] C. difficile infection can lead to pseudomembranous colitis or intestinal inflammation, and infectious diarrhea CDAD, which is the most common cause of death associated with gastroenteritis in the health care system (Johanesen et al., Genes (Basel), 6, 1347-60, 2015; Cohen et al., Infect. Control Hosp. Epidemiol., 31 (5), 431-55, 2010). Recent surveillance studies reported an estimated 450,000 infections and 29,000 deaths in the United States in 2011 due to C. difficile infection (Lessa et al., N. Engl. J. Med. 372 (9): 825-34, 2015). The annual cost associated with C. difficile infection is estimated to be approximately $4.8 billion (Lessa et al., N. Engl. J. Med. 372 (9): 825-34, 2015).

[0006] Due to antibiotic resistance and physiological factors (spore formation and the protective effect of pseudomembrane) of bacteria, antibiotic treatment of C. difficile infection may be difficult. In 2005, the emergence of new highly toxic C. difficile strains was reported, which resisted fluoroquinolone antibiotics such as ciprofloxacin and levofloxacin and were said to have caused geographically dispersed outbreaks in North America. The Centers for Disease Control (CDC) in Atlanta, USA, warned of the emergence of epidemic strains with increased virulence, antibiotic resistance or both.

[0007] Therefore, more effective methods for treating and preventing C. difficile infection and CDAD are needed. Summary of the invention Omadacycline, also known as Compound A, is the first in the class of aminomethylcyclines with the structure shown below (Honeyman et al., Antimicrob. Agents Chemother. 59(11), 7044-53, 2015):

[0009] It has been surprisingly found that omadacycline exhibits unusually high activity against C. difficile. It has also been surprisingly observed that, unlike other antibiotics, omadacycline is not associated with an increased risk of developing C. difficile infection.

[0010] Accordingly, in some embodiments, the present invention relates, at least in part, to a method of treating a Clostridium difficile infection in a subject in need thereof, the method comprising administering to the subject an effective amount of a compound or a salt thereof, wherein the compound is Compound A' having the following structural formula: Such that a Clostridium difficile infection in a subject is treated.

[0011] In some embodiments, the C. difficile infection is a recurrent C. difficile infection. In some embodiments, the compound is administered in combination with at least one or more additional therapies for treating C. difficile infection. In one embodiment, the therapy comprises administration of an antibiotic, such as metronidazole or vancomycin. In another embodiment, the therapy comprises administration of a probiotic. In another embodiment, the therapy comprises administration of a fecal transplant.

[0012] In some embodiments, the present invention also provides a method for treating a bacterial infection in a subject at risk of developing a Clostridium difficile infection without causing a Clostridium difficile infection, the method comprising administering to the subject an effective amount of a compound or a salt thereof, wherein the compound is a compound A' having the following structural formula: Such that a bacterial infection in a subject is treated without causing a C. difficile infection.

[0013] In some embodiments, the present invention also provides a method for treating a bacterial infection in a subject at risk of developing a Clostridium difficile infection without substantially disrupting the intestinal microbiome, the method comprising administering to the subject an effective amount of a compound or a salt thereof, wherein the compound is a compound A' having the following structural formula: Such that a bacterial infection in a subject is treated without substantially disrupting the intestinal microbiome.

[0014] In certain aspects, treating the bacterial infection without substantially disrupting the gut microbiome does not result in a Clostridium difficile infection in the subject.In some aspects, the methods of the invention further comprise, prior to administering, selecting a subject at risk of developing a Clostridium difficile infection.

[0015] In some embodiments, the present invention provides a method of treating a bacterial infection in a subject prone to developing a Clostridium difficile infection, the method comprising administering to the subject an effective amount of a compound or a salt thereof, wherein the compound is Compound A' having the following structural formula: Such that a bacterial infection in a subject is treated.

[0016] In certain aspects, the present invention also provides a method of treating a bacterial infection in a subject at risk of developing a Clostridium difficile infection, the method comprising the steps of: Selecting subjects at risk for developing a C. difficile infection; and An effective amount of a compound is administered to a subject, wherein the compound is a compound A' or a salt thereof having the following structural formula: Such that a bacterial infection in a subject is treated.

[0017] In some aspects, the bacterial infection is selected from the group consisting of a skin or skin structure infection, community acquired bacterial pneumonia (CABP), and a urinary tract infection (UTI).

[0018] In some aspects, bacterial infection is caused by gram-positive bacteria (for example gram-positive anaerobic bacteria). In other aspects, bacterial infection is caused by gram-negative bacteria (for example gram-negative rods (GNR)). In a further embodiment, bacterial infection is caused by belonging to the bacterium selected from the following species: Escherichia coli (E.coli), Staphylococcus aureus (S.aureus), Enterococcus faecalis (E.faecalis), Klebsiella pneumoniae (K.pneumoniae), Enterococcus hirae (E.hirae), Acinetobacter baumanii (A.baumanii), B.catarrhalis, Haemophilus influenzae (H.influenza), Pseudomonas aeruginosa (P.aeruginosa) and Enterococcus faecium (E.faecium).

[0019] In a further aspect, Staphylococcus aureus is methicillin-sensitive Staphylococcus aureus (MSSA) or methicillin-resistant Staphylococcus aureus (MRSA), including hospital-related and community-related MRSA. In one embodiment, infection is hospital-related MRSA infection. In another embodiment, infection is community-related MRSA infection.

[0020] In one aspect, the bacterial infection is caused by Streptococci (e.g., Streptococcus pneumoniae, penicillin-resistant Streptococcus pneumoniae (PRSP), Streptococcus pyogenes, and Streptococcus agalactiae), Viridans Streptococci, Enterococci, or a combination thereof.

[0021] In yet another aspect, the bacterial infection is caused by a bacterium belonging to a genus selected from the group consisting of Salmonella and Streptococcus.

[0022] In one embodiment, the bacterial infection may be resistant to other antibiotics such as penicillin or tetracycline.

[0023] In some embodiments, the compound used in the methods of the present invention is Compound A having the following structural formula:

[0024] In certain aspects, the subject at risk of developing a Clostridium difficile infection is a subject who has recently been treated with one or more antibiotics, such as a broad-spectrum antibiotic. In one aspect, the subject at risk of developing a Clostridium difficile infection is a subject who has undergone gastrointestinal surgery. In another aspect, the subject at risk of developing a Clostridium difficile infection is a subject with a colon disease, such as inflammatory bowel disease or colorectal cancer. In one aspect, the subject at risk of developing a Clostridium difficile infection is a subject with a weakened immune system. In another aspect, the subject at risk of developing a Clostridium difficile infection is a subject undergoing chemotherapy. In yet another aspect, the subject at risk of developing a Clostridium difficile infection is a subject who has previously suffered from a Clostridium difficile infection. In yet another aspect, the subject at risk of developing a Clostridium difficile infection is an advanced age, such as a subject of 65 years of age or more. In yet another aspect, the subject at risk of developing a Clostridium difficile infection is a subject with kidney disease. In one embodiment, the subject at risk of developing a Clostridium difficile infection is a subject taking a proton pump inhibitor.

[0025] In one embodiment, a subject at risk of developing a C. difficile infection is a subject living in an environment that predisposes the subject to developing a C. difficile infection. In a further aspect, an environment that predisposes the subject to developing a C. difficile infection comprises a hospital, a nursing home, or an assisted living facility.

[0026] In one embodiment, the compound is administered orally. In another embodiment, the compound is administered intravenously. In a further embodiment, the compound is administered as at least one intravenous dose followed by at least one oral dose. In a further aspect, at least one oral dose is administered about 24 hours after at least one intravenous dose.

[0027] In one embodiment, the compound is administered once a day or twice a day.

[0028] In some embodiments, the compound is administered at a dose of about 100 mg, about 200 mg, about 300 mg, about 600 mg, or about 900 mg.

[0029] In some embodiments, the subject is treated for up to and including about 14 days, up to and including about 10 days, up to and including about 9 days, up to and including about 8 days, or up to and including about 7 days.

[0030] In one aspect, the pharmaceutically acceptable salt of the compound of the invention is the hydrochloride salt. In another aspect, the pharmaceutically acceptable salt of the compound of the invention is the tosylate salt. The present invention relates to the following scheme: 1. A method for treating Clostridium difficile infection in a subject in need thereof, the method comprising administering to the subject an effective amount of a compound or a salt thereof, wherein the compound is a compound A' having the following structural formula: Such that the Clostridium difficile infection in the subject is treated. 2. The method of claim 1, wherein the Clostridium difficile infection is a recurrent Clostridium difficile infection. 3. The method of claim 1, wherein the compound is administered in combination with at least one or more additional therapies for treating Clostridium difficile infection. 4. The method of claim 3, wherein the additional therapy comprises administration of an antibiotic. 5. The method of claim 4, wherein the antibiotic is metronidazole or vancomycin. 6. The method of claim 3, wherein the additional therapy comprises administration of a probiotic. 7. The method of claim 3, wherein the additional therapy comprises administration of a fecal transplant. 8. A method of treating a bacterial infection in a subject at risk of developing a Clostridium difficile infection without causing a Clostridium difficile infection, the method comprising administering to the subject an effective amount of a compound or a salt thereof, wherein the compound is Compound A' having the following structural formula: Such that the bacterial infection in the subject is treated without causing a C. difficile infection. 9. A method of treating a bacterial infection in a subject at risk of developing a Clostridium difficile infection without substantially disrupting the intestinal microbiome, the method comprising administering to the subject an effective amount of a compound or a salt thereof, wherein the compound is Compound A' having the following structural formula: Such that the bacterial infection in the subject is treated without substantially disrupting the intestinal microbiome. 10. The method of claim 9, wherein treating the bacterial infection without substantially disrupting the intestinal microbiome does not result in a Clostridium difficile infection in the subject. 11. The method of any one of schemes 1-10, further comprising, prior to administering, selecting a subject at risk of developing a Clostridium difficile infection. 12. A method of treating a bacterial infection in a subject prone to developing a Clostridium difficile infection, the method comprising administering to the subject an effective amount of a compound or a salt thereof, wherein the compound is Compound A' having the following structural formula: Such that the bacterial infection in the subject is treated. 13. A method of treating a bacterial infection in a subject at risk of developing a Clostridium difficile infection, the method comprising the steps of: Selecting subjects at risk for developing a C. difficile infection; and An effective amount of a compound is administered to the subject, wherein the compound is a compound A' or a salt thereof having the following structural formula: Such that the bacterial infection in the subject is treated. 14. The method of any one of schemes 8-13, wherein the bacterial infection is selected from the group consisting of skin or skin structure infection, community-acquired bacterial pneumonia (CABP), and urinary tract infection (UTI). 15. The method of any one of schemes 8-13, wherein the bacterial infection is caused by a Gram-positive bacterium. 16. The method of any one of schemes 8-13, wherein the bacterial infection is caused by a Gram-negative bacterium. 17. The method of any one of schemes 8-14, wherein the bacterial infection is caused by a bacterium belonging to a species selected from the group consisting of Escherichia coli (E. coli), Staphylococcus aureus (S. aureus), Enterococcus faecalis (E. faecalis), Klebsiella pneumoniae (K. pneumoniae), Enterococcus hirae (E. hirae), Acinetobacter baumanii (A. baumanii), B. catarrhalis, Haemophilus influenzae (H. influenza), Pseudomonas aeruginosa (P. aeruginosa) and Enterococcus faecium (E. faecium). 18. The method of claim 17, wherein the Staphylococcus aureus is methicillin-resistant Staphylococcus aureus (MRSA) or methicillin-sensitive Staphylococcus aureus (MSSA). 19. The method of any one of claims 8 to 14, wherein the bacterial infection is caused by a bacterium belonging to a genus selected from the group consisting of Salmonella and Streptococcus. 20. The method of any one of Schemes 1-19, wherein the compound is Compound A having the following structural formula: 21. The method of any one of schemes 1-20, wherein the subject at risk of developing a Clostridium difficile infection is a subject recently treated with one or more antibiotics. 22. The method of claim 21, wherein the antibiotic is a broad-spectrum antibiotic. 23. The method of any one of schemes 1-20, wherein the subject at risk of developing a Clostridium difficile infection is a subject who has undergone gastrointestinal surgery. 24. The method of any one of schemes 1-20, wherein the subject at risk of developing a Clostridium difficile infection is a subject suffering from colon disease. 25. The method of claim 24, wherein the colon disease is inflammatory bowel disease or colorectal cancer. 26. The method of any one of schemes 1-20, wherein the subject at risk of developing a Clostridium difficile infection is a subject with a weakened immune system. 27. The method of any one of schemes 1-20, wherein the subject at risk of developing a Clostridium difficile infection is a subject undergoing chemotherapy. 28. The method of any one of schemes 1-20, wherein the subject at risk of developing a Clostridium difficile infection is a subject who previously had a Clostridium difficile infection. 29. The method of any one of schemes 1-20, wherein the subject at risk of developing a Clostridium difficile infection is a subject 65 years of age or older. 30. The method of any one of claims 1-20, wherein the subject at risk of developing a Clostridium difficile infection is a subject with kidney disease. 31. The method of any one of schemes 1-20, wherein the subject at risk of developing a Clostridium difficile infection is a subject taking a proton pump inhibitor. 32. The method of any one of schemes 1-20, wherein the subject at risk of developing a Clostridium difficile infection is a subject living in an environment that predisposes the subject to developing a Clostridium difficile infection. 33. The method of claim 26, wherein the environment comprises a hospital. 34. The method of claim 26, wherein the environment comprises a nursing home. 35. The method of claim 26, wherein the environment comprises an assisted living facility. 36. The method of any one of schemes 1-35, wherein the compound is administered orally. 37. The method of any one of schemes 1-35, wherein the compound is administered intravenously. 38. The method of any one of schemes 1-35, wherein the compound is administered as at least one intravenous dose followed by at least one oral dose. 39. The method of claim 38, wherein the at least one oral dose is administered about 24 hours after the at least one intravenous dose. 40. The method of any one of regimens 1-39, wherein the compound is administered once a day or twice a day. 41. The method of any one of schemes 1-40, wherein the compound is administered at a dose of about 100 mg, about 200 mg, about 300 mg, about 600 mg, or about 900 mg. 42. The method of any one of regimens 1-40, wherein the subject is treated for up to and including about 14 days, up to and including about 10 days, up to and including about 9 days, up to and including about 8 days, or up to and including about 7 days. 43. The method of any one of schemes 1-40, wherein the compound. 44. The method of any one of schemes 1, 8, 9, 12 or 13, wherein the salt is a hydrochloride salt. 45. The method of any one of schemes 1, 8, 9, 12 or 13, wherein the salt is a tosylate salt. BRIEF DESCRIPTION OF THE DRAWINGS Figure 1 is a Kaplan-Meier plot of percent survival of hamsters infected with C. difficile following treatment with omadacycline and comparator.

[0032] Figure 2 is a schematic diagram showing the experimental time frame for the intestinal model experiment described in Example 3.

[0033] Figure 3 Figure 2 shows the intestinal microbial community population (log 10 cfu / mL). Figure 2 as shown in .

[0034] Figure 4 Figure 3 shows the intestinal microbial community population (log 10 cfu / mL). Figure 2 as shown in .

[0035] Figure 5 is a graph showing the C. difficile count (log 10 cfu / mL), toxin titer (relative unit RU) and active omadacycline (OMA) concentration (mg / L). Figure 2 Defined in.

[0036] Figure 6 is a graph showing the C. difficile count (log 10 cfu / mL), toxin titer (relative unit RU) and active omadacycline (OMA) concentration (mg / L). Figure 2 Defined in.

[0037] Figure 7 is a graph showing the C. difficile count (log 10 cfu / mL), toxin titer (relative unit RU) and active omadacycline (OMA) concentration (mg / L). Figure 2 Defined in.

[0038] Figure 8 Figure 2 shows the intestinal microbial community population (log 10 cfu / mL). Figure 2 The horizontal dashed line indicates the detection limit with respect to viable counts.

[0039] Fig. 9 Figure 2 shows the intestinal microbial community population (log 10 cfu / mL). Figure 2 The horizontal dashed line indicates the detection limit with respect to viable counts.

[0040] Fig.10 is a graph showing the C. difficile count (log 10 cfu / mL), toxin titer (relative unit RU) and active omadacycline (OMA) concentration (mg / L). Figure 2 The horizontal dashed line indicates the detection limit with respect to viable counts.

[0041] Fig.11 is a graph showing the C. difficile count (log 10 cfu / mL), toxin titer (relative unit RU) and active omadacycline (OMA) concentration (mg / L). Figure 2 The horizontal dashed line indicates the detection limit with respect to viable counts.

[0042] Fig.12 is a graph showing the C. difficile count (log 10 cfu / mL), toxin titer (relative unit RU) and active omadacycline (OMA) concentration (mg / L). Figure 2 The horizontal dashed line indicates the detection limit with respect to viable counts.

[0043] Fig.13 is a graph showing the intestinal microbial community population (log 10 cfu / mL). Figure 2 The horizontal dashed line indicates the detection limit with respect to viable counts.

[0044] Fig.14 is a graph showing the intestinal microbial community population (log 10 cfu / mL). Figure 2 The horizontal dashed line indicates the detection limit with respect to viable counts.

[0045] Fig.15 is a graph showing the C. difficile count (log 10 cfu / mL), toxin titer (relative unit RU). Figure 2 The horizontal dashed line indicates the detection limit with respect to viable counts.

[0046] Fig.16 is a graph showing the C. difficile count (log 10 cfu / mL), toxin titer (relative unit RU). Figure 2 The horizontal dashed line indicates the detection limit with respect to viable counts.

[0047] Fig.17 is a graph showing the C. difficile count (log 10 cfu / mL), toxin titer (relative unit RU). Figure 2 The horizontal dashed line indicates the detection limit with respect to viable counts. DETAILED DESCRIPTION Treatment of Clostridium difficile infection The present invention is based on the surprising discovery that omadacycine exhibits unexpectedly high activity against Clostridium difficile. Accordingly, in some embodiments, the present invention relates at least in part to a method of treating Clostridium difficile infection in a subject in need thereof, such as a human subject, comprising administering to the subject an effective amount of a compound or a salt thereof, wherein the compound is a compound A' having the following structural formula: Such that a Clostridium difficile infection in a subject is treated.

[0049] In some embodiments, the compound used in the methods of the present invention is Compound A having the following structural formula:

[0050] In some embodiments, the C. difficile infection may be a recurrent C. difficile infection. After treatment of an initial C. difficile infection (CDI) with metronidazole or vancomycin, recurrence of C. difficile infection may occur in 20-30% of subjects. Such recurrence is frustrating because there is no approved treatment alternative that provides a lower probability of recurrence once again. After the second recurrence, subsequent episodes occur in up to 40%-60% of subjects. Recurrent CDI may be the result of infection by resident spores or contamination from the local environment. It is therefore difficult to distinguish between recurrence and reinfection. Both metronidazole and vancomycin suppress the growth of normal microbial flora, and thereby destroy natural colonization resistance.

[0051] In some embodiments, the C. difficile infection is a superinfection.

[0052] In some embodiments, the subject who develops a C. difficile infection, such as a recurrent C. difficile infection or a C. difficile superinfection is a subject who lives in an environment that predisposes the subject to develop a C. difficile infection. Such an environment may include any environment in a health care setting, including a hospital, a nursing home, or an assisted living facility. The environment in a health care setting may become contaminated with C. difficile spores, and the degree of contamination is proportional to the number of patients with CDAD. Although asymptomatic, colonized patients may also serve as a source of contamination.

[0053] The compounds of the present invention, such as compound (A') or compound (A), may be administered in combination with at least one or more additional therapies for treating Clostridium difficile infection. For example, treatment may include administration of antibiotics for treating Clostridium difficile infection, such as metronidazole or vancomycin. Additional therapies may also include administration of probiotics, such as preparations containing Lactobacillus rhamnosus (L. rhamnosus) or Saccharomyces boulardii. In another embodiment, additional therapies include administration of fecal transplants. Without wishing to be bound by a particular theory, it is believed that administration of fecal transplants reduces damage to the intestinal microbiota, allowing Clostridium difficile infection to be controlled.

[0054] Identification of subjects with C. difficile infection can be accomplished using methods generally known in the art. Such methods include, but are not limited to, stool culture of C. difficile; molecular testing for toxins A and / or B produced by C. difficile, such as by PCR-based assays, tissue culture cytotoxicity assays, or enzyme immunoassays; and the presence of C. difficile antigens using, for example, latex agglutination or immunochromatographic assays.

[0055] Treatment of bacterial infections The present invention also provides a method for treating a bacterial infection in a subject at risk of developing a Clostridium difficile infection, such as a human subject, without causing a Clostridium difficile infection, the method comprising administering to the subject an effective amount of a compound or a salt thereof, wherein the compound is a compound A' having the following structural formula: Such that a bacterial infection in a subject is treated without causing a C. difficile infection.

[0056] In some embodiments, the compound used in the methods of the present invention is Compound A having the following structural formula:

[0057] It has now been found that treating bacterial infections with omadacycline does not increase the risk of developing C. difficile infection. This is in contrast to treating bacterial infections with other common antibiotics, which increase the risk of developing C. difficile infection and related CDAD. Specifically, as described in subsequent Example 3, increased omadacycline exposure in the in vitro intestinal model did not result in any signs of simulated C. difficile infection. Specifically, the total viable count (TVC) of C. difficile remained approximately equal to the spore count throughout the experiment, indicating that all C. difficile remained as spores, and no vegetative cell proliferation was observed. In addition, no C. difficile toxins were detected throughout the experiment (see also Figure 5 , 6 and 7).

[0058] In some embodiments, omadacycline exposure or administration of omadacycline to a subject does not promote proliferation of C. difficile in vivo.

[0059] In some embodiments, omadacycline exposure or administration of omadacycline to a subject has a low potential for inducing a Clostridium difficile infection.

[0060] In some embodiments, the present invention also provides a method for treating a bacterial infection in a subject, such as a human subject, at risk of developing a Clostridium difficile infection without substantially disrupting the intestinal microbiome, the method comprising administering to the subject an effective amount of a compound or a salt thereof, wherein the compound is a compound A' having the following structural formula: Such that a bacterial infection in a subject is treated without substantially disrupting the intestinal microbiome.

[0061] In some embodiments, the compound used in the methods of the present invention is Compound A having the following structural formula:

[0062] The term "does not substantially disrupt the intestinal microbiome" refers to the level of regulation of the bacterial population in the intestine following treatment with an antibiotic, such as omadacycline, such as Compound (A) or Compound (A'), which is not associated with an increased risk of developing a Clostridium difficile infection. The term includes embodiments in which treatment of a bacterial infection with a compound of the invention, such as omadacycline, may result in some disruption of the intestinal microbiome, but the extent of the disruption does not result in a Clostridium difficile infection in the subject or an increased risk of developing a Clostridium difficile infection. For example, some disruption may occur, but a Clostridium difficile infection is inhibited or prevented by the presence of omadacycline. In at least one embodiment, when the flora or intestinal microbiome in the gastrointestinal tract is extensively disrupted, omadacycline has a low propensity to induce a Clostridium difficile infection when administered to a subject.

[0063] When an oral dose of omadacycline, e.g., Compound (A) or Compound (A'), is administered to a subject, a large proportion of the oral dose, e.g., about 60% of the absorbed omadacycline, is eliminated in the intestine, i.e., via the biliary / fecal elimination pathway. Because a large portion of an oral dose of omadacycline is eliminated in the intestine, the finding that omadacycline can be administered to a subject without substantially disrupting the intestinal microbiome is surprising and unexpected. Because Clostridium difficile infection occurs when the intestinal microbiome is substantially disrupted, the finding that omadacycline does not increase the risk of a subject developing a Clostridium difficile infection when administered to a subject for the treatment of a bacterial infection is also surprising and unexpected.

[0064] In some embodiments, treating the bacterial infection without substantially disrupting the gut microbiome does not result in a Clostridium difficile infection in the subject. In some aspects, the methods of the invention further comprise, prior to administering, selecting a subject at risk of developing a Clostridium difficile infection or a subject prone to developing a Clostridium difficile infection.

[0065] In some embodiments, the present invention also provides a method for treating a bacterial infection in a subject, such as a human subject, that is prone to developing a Clostridium difficile infection, the method comprising administering to the subject an effective amount of a compound or a salt thereof, wherein the compound is a compound A' having the following structural formula: Such that a bacterial infection in a subject is treated.

[0066] In certain aspects, the present invention also provides a method of treating a bacterial infection in a subject at risk of developing a Clostridium difficile infection, the method comprising the steps of: Selecting subjects at risk for developing a C. difficile infection; and An effective amount of a compound is administered to a subject, wherein the compound is a compound A' or a salt thereof having the following structural formula: Such that a bacterial infection in a subject is treated.

[0067] In some embodiments, the compound used in the methods of the present invention is Compound A having the following structural formula:

[0068] The term "subject at risk of developing a C. difficile infection" or "subject predisposed to developing a C. difficile infection" refers to a subject who is more likely to develop a C. difficile infection than a healthy subject. The term "subject at risk of developing a C. difficile infection" or "subject predisposed to developing a C. difficile infection" also refers to a subject living in an environment that predisposes the subject to developing a C. difficile infection. Factors that may predispose a subject to developing a C. difficile infection may include, but are not limited to, the following: (a) recent treatment with antibiotics, such as broad-spectrum antibiotics; (b) recent surgical procedures, especially those involving the gastrointestinal tract; (c) suffering from colon disease, such as inflammatory bowel disease or colorectal cancer; (d) have a weakened immune system, for example due to illness or due to treatment with chemotherapy; (e) had at least one previous Clostridium difficile infection; (f) advanced age, e.g. 65 years or above; (g) suffering from kidney disease; (h) taking proton pump inhibitors; and (i) Living in an environment that predisposes the subject to develop C. difficile infection. Such environments may include any environment in a health care setting, including a hospital, a nursing home, or an assisted living facility. Environments in health care settings may become contaminated with C. difficile spores, and the degree of contamination is proportional to the number of patients with CDAD. Although asymptomatic, colonized patients may also serve as a source of contamination.

[0069] Accordingly, in some embodiments, a subject at risk of developing a C. difficile infection or a subject prone to developing a C. difficile infection can belong to at least one of the following categories of subjects: (a) Subjects who have recently been treated with antibiotics, such as broad-spectrum antibiotics; (b) subjects who had undergone recent surgical procedures, especially those involving the gastrointestinal tract; (c) subjects suffering from colon diseases, such as inflammatory bowel disease or colorectal cancer; (d) subjects with a weakened immune system, for example due to disease or due to treatment with chemotherapy; (e) Subjects with at least one previous Clostridium difficile infection; (f) elderly subjects, e.g. subjects aged 65 years or above; (g) Subjects with kidney disease; (h) subjects taking proton pump inhibitors; and (i) Subjects living in an environment that predisposes them to develop C. difficile infection. Such environments may include any environment in a health care setting, including a hospital, a nursing home, or an assisted living facility. Environments in health care settings may become contaminated with C. difficile spores, and the degree of contamination is proportional to the number of patients with CDAD. Although asymptomatic, colonized patients may also serve as a source of contamination.

[0070] In at least one embodiment, the subject at risk of developing a C. difficile infection or a subject prone to developing a C. difficile infection does not fall into category (f) as listed above, ie, the subject is not of advanced age, eg, 65 years or older.

[0071] In some embodiments, the subject at risk of developing a C. difficile infection or a subject prone to developing a C. difficile infection is older than 81 years old. In further embodiments, the subject at risk of developing a C. difficile infection or a subject prone to developing a C. difficile infection is older than 85 years old, older than 90 years old, or older than 95 years old.

[0072] In some embodiments, a subject at risk of developing a Clostridium difficile infection or a subject prone to developing a Clostridium difficile infection belongs to at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, or all 9 subject categories as listed above in (a)-(i).

[0073] Bacterial infections that may be treated with omadacycline without an increased risk of developing C. difficile infection may include skin or skin structure infections (ABSSSI), community-acquired bacterial pneumonia (CABP), and urinary tract infections (UTI).

[0074] Bacterial infection can be caused by gram-positive bacteria or gram-negative bacteria. Bacterial infection can be caused by bacteria belonging to species selected from: Escherichia coli, Staphylococcus aureus such as methicillin-resistant Staphylococcus aureus (MRSA) or methicillin-sensitive Staphylococcus aureus (MSSA), Enterococcus faecalis, Klebsiella pneumoniae, Enterococcus hirae, Acinetobacter baumannii, B.catarrhalis, Haemophilus influenzae, Pseudomonas aeruginosa and Enterococcus faecium. Bacterial infection can also be caused by bacteria belonging to the genus selected from: Salmonella and Streptococcus. Treatment of bacterial infection by compounds of the present invention, such as omadacycline, is described in, for example, U.S. Patent Nos. 7,553,828 and 9,265,740, the entire contents of which are incorporated herein by reference.

[0075] In one embodiment, the compound is administered orally. In another embodiment, the compound is administered intravenously. In a further embodiment, the compound is administered as at least one intravenous dose followed by at least one oral dose. In a further aspect, at least one oral dose is administered about 24 hours after at least one intravenous dose.

[0076] In one embodiment, the compound may be administered once daily or twice daily.

[0077] Subjects may be treated for up to and including about 60 days, up to and including 30 days, up to and including 21 days, up to and including 14 days, up to and including about 10 days, up to and including about 9 days, up to and including about 8 days, or up to and including about 7 days.

[0078] The pharmaceutically acceptable salt of the compound of the present invention may be a hydrochloride or a tosylate.

[0079] Administration of the compounds of the present invention The compound of the present invention, eg, omadacycline, eg, Compound (A') or Compound (A), or a salt thereof, may be administered as part of a pharmaceutical composition, optionally comprising a pharmaceutically acceptable carrier.

[0080] The term "pharmaceutically acceptable carrier" includes substances that can be co-administered with the compounds of the invention, such as omadacycline, and that allow the compounds of the invention to perform their intended functions, such as treating or preventing bacterial infections, such as Clostridium difficile infections. Suitable pharmaceutically acceptable carriers include, but are not limited to, water, saline solutions, alcohols, vegetable oils, polyethylene glycols, gelatin, lactose, amylose, magnesium stearate, talc, silicic acid, viscous paraffin, perfume oils, fatty acid monoglycerides and diglycerides, petroleum ether (petroethral) fatty acid esters, hydroxymethylcellulose, polyvinylpyrrolidone, and the like. The pharmaceutical composition can be sterilized and, if necessary, can be mixed with auxiliary agents, such as lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for affecting osmotic pressure, buffers, colorants, flavorings, and / or aromatic substances, etc., which do not react harmfully with the active compounds of the invention.

[0081] The tetracycline compounds of the present invention, such as omadacycline, are capable of forming a wide variety of salts with various inorganic and organic acids. Acids that can be used to prepare pharmaceutically acceptable acid addition salts of the compounds of the present invention are acids that form non-toxic acid addition salts, i.e., salts containing pharmaceutically acceptable anions, such as hydrochloride, hydrobromide, hydroiodide, nitrate, sulfate, bisulfate, phosphate, acid phosphate, isonicotinate, acetate, lactate, salicylate, citrate, acid citrate, tartrate, pantothenate, bitartrate, ascorbate, succinate, maleate, gentisate, fumarate, gluconate, glucuronate, saccharate, formate, benzoate, glutamate, methanesulfonate, ethanesulfonate, benzenesulfonate, p-toluenesulfonate, and palmitate [i.e., 1,1'-methylene-bis-(2-hydroxy-3-naphthoic acid)] salts. Although such salts must be pharmaceutically acceptable for application to a subject, such as a mammal, such as a human, it is often desirable in practice to initially separate the compound of the present invention as a pharmaceutically unacceptable salt from the reaction mixture, then simply convert the latter back to the free base compound by treating with an alkaline agent, and subsequently convert the latter free base to a pharmaceutically acceptable acid addition salt. The acid addition salt of the base compound of the present invention is easily prepared by: in an aqueous solvent medium or in a suitable organic solvent such as methanol or ethanol, the base compound is treated with a substantially equivalent amount of a selected inorganic or organic acid. After careful evaporation of the solvent, the desired solid salt is easily obtained. Preferably, the compound of the present invention is administered as a toluenesulfonate (e.g., p-toluenesulfonate) salt or as a free base orally or as a hydrochloride intravenously.

[0082] Compounds of the invention, such as salts of omadacycline, are described, for example, in U.S. Pat. Nos. 8,383,610 and 9,227,921, the entire contents of which are incorporated herein by reference.

[0083] In yet a further embodiment, the compounds of the invention may be administered at doses of about 110 to about 490 mg, about 120 to about 480 mg, about 130 to about 470 mg, about 140 to about 460 mg, about 150 to about 450 mg, about 160 to about 440 mg, about 170 mg to about 430 mg, about 180 mg to about 420 mg, about 190 mg to about 410 mg, about 200 mg to about 400 mg, about 210 mg to about 390 mg, about 220 mg to about 380 mg, about 230 mg to about 370 mg, about 240 mg to about 360 mg, about 250 mg to about 350 mg, about 260 mg to about 340 mg, about 270 mg to about 330 mg, about 280 mg to about 320 mg, about 290 mg to about 310 mg, or to about 300 mg of a compound of the invention, e.g., omadacycline.

[0084] In some embodiments, the compounds of the invention, e.g., Compound A' or Compound A, can be administered at a dose of about 10 to about 1000 mg, about 20 to about 750 mg, about 50 to about 500 mg, about 75 to about 400 mg, about 100 to about 300 mg, about 110 to about 290 mg, about 120 to about 280 mg, about 130 to about 270 mg, about 140 to about 260 mg, about 150 to about 250 mg, about 160 to about 240 mg, about 170 mg to about 230 mg, about 180 mg to about 220 mg, about 190 mg to about 210 mg, or about 200 mg. In another embodiment, the compound of the present invention, such as Compound A' or Compound A, can be administered intravenously at a dose of about 5 to about 500 mg, about 10 to about 400 mg, about 25 to about 300 mg, about 50 to about 200 mg, about 50 to about 150 mg, about 60 to about 140 mg, about 70 mg to about 130 mg, about 80 mg to about 120 mg, about 90 mg to about 110 mg, or about 100 mg. In one embodiment, the compound of the present invention, such as Compound A' or Compound A, can be administered orally at a dose of about 5 to about 800 mg, about 10 to about 700 mg, about 25 to about 600 mg, about 50 to about 500 mg, about 100 to about 400 mg, about 150 to about 350 mg, about 200 mg to about 340 mg, about 250 mg to about 330 mg, about 270 mg to about 320 mg, about 280 to about 310, or about 300 mg.

[0085] In some embodiments, the compounds of the invention are administered at doses of about 1 mg, about 5 mg, about 10 mg, about 15 mg, about 20 mg, about 25 mg, about 30 mg, about 35 mg, about 40 mg, about 45 mg, about 50 mg, about 55 mg, about 60 mg, about 65 mg, about 70 mg, about 75 mg, about 80 mg, about 85 mg, about 90 mg, about 95 mg, about 100 mg, about 105 mg, about 110 mg, about 115 mg, about 120 mg, about 125 mg, about 130 mg, about 135 mg, about 140 mg, about 145 mg, about 150mg, about 155mg, about 160mg, about 165mg, about 170mg, about 175mg, about 180mg, about 185mg, about 190mg, about 195mg, about 200mg, about 205mg, about 210mg, about 215mg, about 220mg, about 225mg, about 230mg, about 235mg, about 240mg, about 245mg, about 250mg, about 255mg, about 260mg, about 265mg, about 270mg, about 275mg, about 280mg, about 285mg, about 290mg, about 295mg, about 3 00mg, about 305mg, about 310mg, about 315mg, about 320mg, about 325mg, about 330mg, about 335mg, about 340mg, about 345mg, about 350mg, about 355mg, about 360mg, about 365mg, about 370mg, about 375mg, about 380mg, about 385mg, about 390mg, about 395mg, about 400mg, about 405mg, about 410mg, about 415mg, about 420mg, about 425mg, about 430mg, about 435mg, about 440mg, about 445mg, about 450 In some embodiments, the dosage is an intravenous dose. In some embodiments, the dosage is an intravenous dose. In some embodiments, the dosage is an oral dose.

[0086] It should be understood that the dosage range comprising the above dosage is also included in the present invention. For example, any one of the above dosages can be the lower part or the higher part of the dosage range included in the present invention. Even further, it should be understood that all numerical values ​​used throughout the application are listed or set and are also expected to include any one of the numerical values ​​listed therein can be the lower part or the higher part of the numerical range of the range. These ranges are expected to be included in the present invention.

[0087] In one embodiment, the compound of the invention, such as Compound A' or Compound A, can be administered intravenously at a dose of about 100 mg, about 200 mg, or about 300 mg. In another embodiment, the compound of the invention, such as Compound A' or Compound A, can be administered orally at a dose of about 300 mg, about 600 mg, or about 900 mg.

[0088] In one embodiment, the oral dose of the compound of the invention, eg, Compound A' or Compound A, is 3 times the intravenous dose of the compound of the invention, eg, Compound A' or Compound A.

[0089] It is understood that for all listed embodiments, the dosage of a compound of the invention, eg, Compound A' or Compound A, is also an effective amount of a compound of the invention, eg, Compound A' or Compound A.

[0090] In one embodiment, when administered orally, an effective amount of a compound of the invention, e.g., Compound A or Compound A', is about 10 to about 1000 mg, about 20 to about 750 mg, about 50 to about 500 mg, about 75 to about 400 mg, about 100 to about 300 mg, about 110 to about 290 mg, about 120 to about 280 mg, about 130 to about 270 mg, about 140 to about 260 mg, about 150 to about 250 mg, about 160 to about 240 mg, about 170 mg to about 230 mg, about 180 mg to about 220 mg, about 190 mg to about 210 mg, or about 200 mg. In another embodiment, when administered intravenously, an effective amount of a compound of the invention, e.g., Compound A or Compound A', is about 5 to about 500 mg, about 10 to about 400 mg, about 25 to about 300 mg, about 50 to about 200 mg, about 50 to about 150 mg, about 60 to about 140 mg, about 70 mg to about 130 mg, about 80 mg to about 120 mg, about 90 mg to about 110 mg, or about 100 mg.

[0091] The compounds of the invention, such as omadacycline and pharmaceutically acceptable salts thereof, can be administered via oral, parenteral or topical routes. In general, the compounds of the invention are most desirably administered at effective doses, which depend on the weight and condition of the subject to be treated and the specific route of administration selected. Variations may occur depending on the species of the subject to be treated and its individual response to the drug, as well as the type of pharmaceutical formulation selected and the period and interval under which such administration is performed.

[0092] The pharmaceutical composition of the present invention can be used alone or in combination with other known compositions for treating bacterial infections in subjects such as mammals. Mammals include pets (such as cats, dogs, ferrets, etc.), farm animals (cattle, sheep, pigs, horses, goats, etc.), experimental animals (rats, mice, monkeys, etc.) and primates (chimpanzees, people, gorillas). The wording and known compositions "combination" are expected to include the simultaneous administration of the compound of the present invention and the known composition, first administering the compound of the present invention, followed by the known composition, and first administering the known composition, followed by the compound of the present invention. Any of the therapeutic compositions known in the art for treating bacterial infections, such as Clostridium difficile infections, can be used in the method of the present invention.

[0093] The compounds of the present invention can be administered alone or in combination with a pharmaceutically acceptable carrier or diluent by any of the aforementioned routes, and administration can be performed in a single dose or multiple doses. For example, the compounds of the present invention can be advantageously administered in a wide variety of different dosage forms, that is, it can be combined with various pharmaceutically acceptable inert carriers in the form of tablets, capsules, lozenges, lozenges, hard candies, powders, sprays, creams, ointments, suppositories, gels, gels, pastes, lotions, ointments, aqueous suspensions, injectable solutions, elixirs, syrups, etc. Such carriers include solid diluents or fillers, sterile aqueous media, and various non-toxic organic solvents, etc. In addition, oral pharmaceutical compositions can be appropriately sweetened and / or flavored. In general, the compounds of the present invention are present in such dosage forms, and their concentration levels range from about 5.0% to about 70% by weight.

[0094] For oral administration, tablets containing various excipients such as microcrystalline cellulose, sodium citrate, calcium carbonate, dicalcium phosphate and glycine can be used with various disintegrants such as starch (and preferably corn, potato or tapioca starch), alginic acid and certain complex silicates together with granulating binders such as polyvinyl pyrrolidone, sucrose, gelatin and acacia. In addition, lubricants such as magnesium stearate, sodium lauryl sulfate and talc are generally very suitable for tableting purposes. Solid compositions of similar types can also be used as fillers in gelatin capsules; in this regard, preferred materials also include lactose or milk sugar and high molecular weight polyethylene glycols.

[0095] When aqueous suspensions and / or elixirs are required for oral administration, the active ingredient, i.e., omadacycline, may be combined with various sweetening or flavoring agents, coloring agents or dyes and, if desired, with emulsifying and / or suspending agents, together with such diluents as water, ethanol, propylene glycol, glycerin, and various similar combinations thereof.

[0096] For parenteral administration (including intraperitoneal, subcutaneous, intravenous, intradermal or intramuscular injection), a solution of a compound of the invention, such as omacillin, in sesame or peanut oil or aqueous propylene glycol may be employed. If necessary, the aqueous solution should be suitably buffered (e.g., having a pH greater than 8), and the liquid diluent first rendered isotonic.

[0097] These aqueous solutions are suitable for intravenous injection purposes. Oily solutions are suitable for intra-articular, intramuscular and subcutaneous injection purposes. The preparation of all these solutions under sterile conditions is readily accomplished by standard pharmaceutical techniques well known to those skilled in the art. For parenteral use, examples of suitable formulations include solutions, preferably oily or aqueous solutions, and suspensions, emulsions or implants, including suppositories. Omacycline can be formulated in sterile form in multiple or single dose forms, for example dispersed in a fluid carrier such as sterile saline or 5% saline dextrose solution commonly used with injections.

[0098] For enteral use, tablets, dragees or capsules with talc and / or carbohydrate carrier binders and the like are particularly suitable, the carrier being preferably lactose and / or corn starch and / or potato starch. Syrups, elixirs and the like may be used, wherein a sweetened vehicle is employed. Sustained release compositions may be formulated, including those in which the active ingredient is protected with a differentially degradable coating, such as by microencapsulation, multilayer coatings and the like.

[0099] In addition to the treatment of human subjects, the therapeutic methods of the invention will also have significant veterinary applications, e.g., for treating livestock such as cattle, sheep, goats, cows, pigs, etc.; poultry such as chickens, ducks, geese, turkeys, etc.; horses; and pets such as dogs and cats.

[0100] In some embodiments, the compounds of the invention, such as Compound A or Compound A', can be administered for at least 3 days, at least 7 days, at least 14 days, at least 21 days, at least 30 days, or at least 60 days. For example, the administration of the compounds of the invention can last from 3 days to 7 days, from 3 days to 14 days, from 3 days to 21 days, from 3 days to 30 days, from 3 days to 60 days, from 7 days to 14 days, from 7 days to 21 days, from 7 days to 30 days, from 7 days to 60 days, from 14 days to 21 days, from 14 days to 30 days, from 14 days to 60 days, from 21 days to 30 days, from 21 days to 60 days, or from 30 days to 60 days.

[0101] For example, a compound of the invention, e.g., Compound A or Compound A', can be administered for 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 days.

[0102] In some embodiments, the method comprises administering to the subject one or more loading doses of the compound, followed by one or more maintenance doses of the compound. In one embodiment, the one or more loading doses may be greater than the one or more maintenance doses.

[0103] In some embodiments, administering a compound of the invention, such as Compound A or Compound A', to a subject may include administering one or more loading doses of the compound, followed by one or more maintenance doses of the compound. In some embodiments, the one or more loading doses of the compound may be greater than the one or more maintenance doses of the compound. For example, the loading dose may be about 200 mg, while the maintenance dose may be about 150 mg, 100 mg, or 50 mg; or the loading dose may be about 400 mg, while the maintenance dose may be about 300 mg, 250 mg, 200 mg, 150 mg, 100 mg, or 50 mg; or the loading dose may be about 100 mg, while the maintenance dose may be about 75 mg, about 50 mg, or about 25 mg.

[0104] The loading dose of the compound of the present invention and the maintenance dose of the compound of the present invention can be administered via the same route or different routes. For example, one or more loading doses can be administered intravenously, and the maintenance dose can be administered orally. In other embodiments, one or more loading doses and the maintenance dose can be administered orally, or one or more loading doses and the maintenance dose can be administered intravenously.

[0105] In some embodiments, the loading dose of the compound of the present invention, such as Compound A' or Compound A, may be an oral dose or intravenous dose administered twice a day, and the maintenance dose may be an oral dose or intravenous dose administered once a day. For example, the compound of the present invention, such as Compound A' or Compound A, may be administered as an intravenous loading dose of 100 mg twice a day, followed by an intravenous maintenance dose of 100 mg once a day. In another example, the compound of the present invention, such as Compound A' or Compound A, may be administered as an intravenous loading dose of 100 mg twice a day, followed by an oral maintenance dose of 300 mg once a day. In another example, the compound of the present invention, such as Compound A' or Compound A, may be administered as an oral loading dose of 300 mg twice a day, followed by an oral maintenance dose of 300 mg once a day.

[0106] In another embodiment, a compound of the invention, eg, Compound A or Compound A', can be administered once or twice daily, intravenously or orally.

[0107] The terms "treating" or "treatment" refer to the amelioration or alleviation of one or more symptoms of the condition being treated, eg, a bacterial infection.

[0108] The terms "prophylaxis," "prevent," or "prevention" mean preventing or reducing the risk of a bacterial infection.

[0109] The term "resistance" or "resistant" refers to antibiotic / organism standards as defined by the Clinical and Laboratories Standards Institute (CLSI) and / or the Food and Drug Administration (FDA).

[0110] The term "subject" includes animals that are subject to bacterial infection. Examples of objects include animals such as farm animals (e.g., cattle, pigs, horses, goats, rabbits, sheep, chickens, etc.), laboratory animals (mice, rats, monkeys, chimpanzees, etc.), pets (e.g., dogs, cats, ferrets, hamsters, etc.), birds (e.g., chickens, turkeys, ducks, geese, crows, ravens, sparrows, etc.), primates (e.g., monkeys, gorillas, chimpanzees, bonobos, and humans), and other animals (e.g., squirrels, raccoons, mice, rats, etc.). In one embodiment, the object is a mouse or a rat. In one embodiment, the object is a cattle, a pig, or a chicken. In one embodiment, the object is a human.

[0111] The term "effective amount" includes the amount of the compound of the present invention required to treat or prevent bacterial infection. For example, an effective amount describes an effective level sufficient to achieve the desired therapeutic effect by killing bacteria and / or inhibiting bacterial growth. In one embodiment, the effective amount is sufficient to eradicate one or more bacteria causing the infection.

[0112] The term "about" refers to a range of values ​​that can be 15%, 10%, 8%, 5%, 3%, 2%, 1% or 0.5% more or less than a specified value. For example, "about 10%" can be 8.5% to 11.5%. In one embodiment, the term "about" refers to a range of values ​​that are 5% more or less than a specified value. In another embodiment, the term "about" refers to a range of values ​​that are 2% more or less than a specified value. In another embodiment, the term "about" refers to a range of values ​​that are 1% more or less than a specified value.

[0113] The structures of the compounds of the present invention include double bonds or asymmetric carbon atoms. Such compounds can exist as racemates, racemic mixtures, single enantiomers, individual diastereomers, diastereomeric mixtures, and cis- or trans- or E- or Z-double bond isomeric forms. Such isomers can be obtained in substantially pure form by classical separation techniques and by stereochemically controlled synthesis. In addition, the structures and other compounds and moieties discussed in the present invention also include all tautomers thereof.

[0114] It should be understood that whenever values ​​and ranges are provided herein, for example, in the age of the subject population, dosage and duration, etc., all values ​​and ranges encompassed by these values ​​and ranges are intended to be encompassed within the scope of the present invention. In addition, all values ​​in these values ​​and ranges may also be the upper or lower limit of the range.

[0115] The compounds of the present invention can be synthesized and purified according to the synthetic schemes shown below and as described in US 2008 / 0287401, the entire contents of which are incorporated herein by reference.

[0116] The efficacy of the compounds of the present invention in treating or preventing bacterial infections can be evaluated using common methods known in the art. In one embodiment, efficacy can be determined by a minimum inhibitory concentration (MIC) assay. For example, the compounds of the present invention can be serially diluted and then added to a growth medium, such as cation-regulated MuellerHinton broth (CAMHB) for bacterial culture. The lowest concentration (i.e., MIC) at which the compounds of the present invention inhibit 50% or 90% bacterial growth is determined. 50 or MIC 90 ) and, if necessary, the MIC of other antibiotics 50 or MIC 90Comparison. In another embodiment, efficacy can be determined by in vivo assays known in the art (e.g., animal experiments). For example, the compounds of the present invention are applied to experimental animals (e.g., mice and rats) in decreasing amounts. Determine the minimum amount of the compounds of the present invention that treats experimental animals (e.g., improves the symptoms of bacterial infection, prolongs the survival time of animals, and allows animals to survive after bacterial infection), or prevents experimental animals from being infected by bacteria or developing any symptoms of infection, and, if necessary, compares with the minimum amount of other antibiotics that achieve the same results.

[0117] Embodiments of the present invention Example 1. In vitro activity of omadacycline (Compound A) against Clostridium difficile strains Materials and methods The activity of omadacycline was tested in vitro for 27 clinical isolates of Clostridium difficile. The activity was compared with the activity of other comparator antibiotics for Clostridium difficile, including cefotaxime, doxycycline, amoxicillin-clavulanate, metronidazole, imipenem and clindamycin. According to the Clinical and Laboratory Standards Institute (CLSI) guidelines, broth and agar microdilution method were used to experiment. Wilkins-Chalgren broth containing each test antibiotic with a final concentration of 0.016mg / mL to 16mg / mL was added to 96-well plates, and the 96-well plates were incubated for 48 hours under anaerobic conditions. Each test was run in duplicate.

[0118] result The minimum inhibitory concentration (MIC) of omadacycline and other antibiotics 50 and MIC 90 ) are shown in Table 1. Specifically, regarding the MIC of omadacycline against Clostridium difficile 90 0.06 mg / L by broth dilution and 0.12 mg / L by agar dilution. Omadacycline is higher than doxycycline (MIC by broth 90 0.5 mg / L and diluted to 1 mg / L by agar) was more active.

[0119] Table 1 Minimum inhibitory concentrations of omadacycline and comparator antibiotics against C. difficile strains (N=27) by broth and agar dilution methods.

[0120] The results shown in Table 1 indicate that omadacycline exhibited potent in vitro activity against C. difficile that was similar to the activity of the comparator antibiotics.

[0121] Example 2. In vitro and in vivo activity of omacillin against C. difficile in a hamster model of C. difficile-associated diarrhea.

[0122] Materials and methods The activity of omadacycline was determined in a hamster model of Clostridium difficile-associated diarrhea (ViviSource Laboratories, Inc., Waltham MA). Male LGV-Golden Syrian hamsters weighing 80-100 g were used (Charles River Laboratories Inc., Wilmington, MA). The hamsters were kept in a room maintained at 64-76°F (17.8-24.4°C), with humidity set at 40%-70%, and standard rodent diet and water were available without restriction. Hamsters were pretreated with a subcutaneous (SC) dose of 10 mg / kg clindamycin 24 hours before injection.

[0123] C. difficile strain ATCC 43596 was obtained from the American Type Culture Collection (Manassas, VA) and cultured from frozen stocks on Brucella agar with 5% sheep blood under anaerobic conditions. Hamsters were infected with a suspension of a 48-hour culture of C. difficile ATCC 43596 24 hours after pretreatment with clindamycin using a dose of 10 mL / kg administered by oral gavage. This resulted in approximately 1.3 x 10 7 Inoculum of CFU / hamster. At 24 hours post infection, groups of animals (N=10) received oral doses of 50 mg / kg / day of omadacycline; 50 mg / kg / day of vancomycin or vehicle (sterile water) for 5 days. Animals were observed daily to assess general health, and body weights were recorded at least 3 times per week. The in vitro activity of clindamycin, tigecycline, vancomycin, and metronidazole was also determined.

[0124] The survival percentage of each group was determined for up to 21 days after infection. Kaplan-Meier survival analysis was performed using a step plot. P values, significant differences in the curves, and median survival were determined using Log Rank data analysis.

[0125] result Omacycline was active in vitro against the infection model C. difficile strain ATCC 43596 as was tigecycline, metronidazole and vancomycin (MIC90 = 0.06 mg / L for all drugs), whereas clindamycin showed no activity. The results of in vitro testing against the infection model strain ATCC 43596 are presented in Table 2.

[0126] Table 2 Minimum inhibitory concentrations (MIC90) of omadacycline and comparator antibiotics against Clostridium difficile strain ATCC 43596. Plates A and B are duplicates.

[0127] Figure 1 Shown in the table are Kaplan-Meier analyses of the percent survival of hamsters infected with C. difficile following treatment with omadacycline and comparator antibiotics. Specifically, on day 2 post infection, 100% of the omadacycline treated animals were alive, compared to 40% of animals receiving vancomycin and 0% of animals receiving vehicle control. Hamsters that received only clindamycin pretreatment demonstrated a 10% survival rate on day 2 post infection. For omadacycline treated animals, survival dropped to 60% by day 3 and remained at 60% until day 13 when it dropped to 40% and to 0% on day 16. Animals treated with vancomycin that survived the initial 2 days post infection showed a 30% survival rate by day 11, and all animals succumbed to infection by day 14. In summary, the median survival for omadacycline treated animals was day 12, compared to 2 days for vancomycin and 4 days for clindamycin pretreatment, as shown in the table below.

[0128] Table 3 .Median survival of hamsters after treatment with omadacycline and comparator antibiotics. Test compound Median survival (days) P-value* Omadacycline 12 0.0004 Vancomycin 2 0.0293 Clindamycin 4 ＜0.0001 *Kaplan-Meier analysis using the log rank test.

[0129] Figure 1 The data presented in Tables 2 and 3 demonstrate that omadacycline exhibits potent in vitro and in vivo activity against C. difficile in the hamster model of C. difficile-associated diarrhea. In vivo, this activity is superior to that of vancomycin.

[0130] Example 3. Effects of omadacycline on intestinal microflora and Clostridium difficile germination, proliferation and toxin production in an in vitro model of the human intestine Target Using an in vitro model of Clostridium difficile infection (CDI), the effects of omadacycline instillation on normal intestinal microflora populations were determined and the propensity of omadacycline to induce C. difficile germination, proliferation, and toxin production was investigated.

[0131] introduction The in vitro intestinal model is used to study the effect of omadacycline instillation on normal microbial community and Clostridium difficile. The intestinal model has been validated for intestinal contents from sudden death victims, and provides a very close simulation of bacterial activity and composition in different areas of the hindgut (Macfarlane et al., Microb.Ecol.35,180-7,1998). The model consists of three containers aligned in series and fed with a complex growth medium top. All three containers are continuously stirred, maintained anaerobically at 37°C and adjusted to reflect the in vivo differences from the proximal to the distal colon, including pH. Three anaerobic fermentation containers are maintained at increased alkalinity (pH 5.5 ± 0.2 about container 1; pH 6.2 ± 0.2 about container 2; and pH 6.8 ± 0.2 about container 3). The increasing alkalinity combined with nutrient restriction conditions is designed to simulate the human intestine from the proximal to the distal colon. Inoculation with combined human feces (from healthy elderly volunteers) is followed by a balance period during which the bacterial population responds to its environmental conditions and reaches a steady state. At this stage, dietary ingredients, probiotics, pathogens and / or antibiotics can be added and the bacterial population monitored. The specific components of the intestinal flora and associated pathogens can be closely monitored and their behavior analyzed.

[0132] The intestinal model has been used previously to simulate CDI using epidemic virulent strains (Freeman et al., J. Antimicrob. Chemother. 52, 96-102, 2003). Cefotaxime, an antibiotic well known for its ability to predispose subjects to CDI, was shown to promote C. difficile germination and toxin production in the intestinal model. In contrast, piperacillin-tazobactam and tigecycline, antibiotics considered to have a low propensity to induce CDI, did not promote C. difficile germination and toxin production (Baines et al., J. Antimicrob. Chemother. 55, 974-82, 2005; Baines et al., J. Antimicrob. Chemother., 58, 1062–5, 2006). Clindamycin also caused significant toxin production in the intestinal model, but this could be reversed by dosing the model with the therapeutic agent (Freeman et al., J. Antimicrob. Chemother., 56, 717-25, 2005).

[0133] It is believed that the intestinal model avoids many of the problems encountered during in vivo studies; including the variability of data derived from fecal specimens, and the ethical issues associated with animal testing. In addition, larger experimental controls provide researchers with a degree of reproducibility that would be difficult to achieve in vivo without a large number of subjects / animals. In summary, the intestinal model is believed to predictably reflect CDI induction. Knowledge of the propensity of novel antimicrobials to induce CDI is critical to informing prescribing practices.

[0134] method like Figure 2 The intestinal model was established as shown in Figure 1. The intestinal model was inoculated with pooled fecal slurry (5 volunteers ≥60 years old, with no history of antibiotic treatment in the previous 3 months) and left for 2 weeks to allow the bacterial population to reach a steady state. On day 14, a single inoculum (~10 7 cfu / mL) of C. difficile spores (PCR RNA type 027 strain 210) were added to container 1 of the intestinal model. One week later, on day 21, a second aliquot of C. difficile spores was added and antibiotic instillation was started. Omadacycline instillation (430 mg / L, once a day for 7 days) was started on day 21.

[0135] By culturing on selective and non-selective agar, the intestinal microbiota bacterial population and total live and spore counts of C. difficile were counted daily. The C. difficile population was monitored in all three containers, and all other bacterial groups (total obligate anaerobes, total facultative anaerobes, lactic acid fermenting Enterobacteriaceae, Enterococci, total Clostridium, Lactobacillus, Bifidobacterium, Bacteroides fragilis group) were monitored only in containers 2 and 3. Container 3 had the greatest physiological relevance in terms of the tendency to induce CDI. Total live and spore counts of C. difficile were monitored using live counts and differential alcohol shock live counts on selective agar.

[0136] Starting from day 14, C. difficile cytotoxins were measured using a quantitative VERO cell cytotoxicity assay. 1 mL of the sample was centrifuged at 16,000 x g for 15 minutes and the supernatant was removed. The culture supernatant from the intestinal model was serially diluted 1:10 to 10 -6 20 μL of the appropriate dilution was added to the Vero cell monolayer and a further 20 μL aliquot of C. perfringens antitoxin (1:10 dilution in sterile distilled water) was placed in the corresponding antitoxin row. 2 Monolayers were examined after 24 and 48 hours of incubation in , with positive results indicated by the presence of cell rounding, accompanied by simultaneous neutralization of the effects of C. perfringens antitoxin. Cytotoxin titers (relative units, RU) are arbitrary log 10scale, and cytotoxic titers are reported as the highest dilution with >70% cell rounding, i.e., 10 0 =1RU, 10 -1 =2RU, 10 -2 =3RU. Samples were collected daily starting from day 21 to determine the antimicrobial concentration in the intestinal model container by bioassay. The concentration of omadacycline was measured by large plate bioassay using Wilkins Chalgren agar, using Kocuria rhizophila as an indicator organism.

[0137] result Omadacycline exposure model In vessels 1, 2, and 3 of the omadacycline exposure model, bioactive omadacycline concentrations peaked at ∼370 mg / L, ∼150 mg / L, and ∼150 mg / L, respectively ( Figure 5 , 6 and 7).

[0138] Changes in the gut microbiome population were similar in vessels 2 and 3 ( Figure 3 and 4 Omadacycline instillation causes Clostridia (~6log 10 cfu / mL) and Bifidobacteria (~6log 10 cfu / mL) population, which was below the detection limit. A significant decrease was also observed in the Bacteroides fragilis group (~3 log 10 cfu / mL), Lactobacillus spp. (~2log 10 cfu / mL) and Enterococcus spp. (~4log 10 cfu / mL). Overall, Enterobacteriaceae populations remained undisturbed. All populations recovered after omadacycline dosing ended and returned to steady-state levels approximately 1 week after antimicrobial exposure.

[0139] Despite the extensive disruption of the intestinal microbial community, omadacycline exposure did not result in any signs of simulated C. difficile infection. The total viable count (TVC) of C. difficile remained approximately equal to the spore count in all three containers throughout the experiment, indicating that all C. difficile remained as spores. No vegetative cell proliferation was observed. No toxins were detected in any container throughout the experiment ( Figure 5 , 6 and 7).

[0140] discuss Despite causing extensive disruption of the intestinal microbial community, omadacycline exposure did not induce any signs of simulated CDI in the in vitro human intestinal model. This model has been shown to be clinically reflective. Antibiotics known to have a high propensity to induce CDI clinically induced CDI in this model, such as clindamycin, cephalosporins, and co-amoxyclav, while antibiotics clinically described as "low risk" for CDI did not induce simulated CDI in the intestinal model, such as tigecycline and piperacillin-tazobactam. See Saxton et al., Antimicrob. Agents and Chemother., 53, 412-420, 2009; Freeman et al., J. Antimicrob. Chemother. 52, 96-102, 2003; Chilton et al., J. Antimicrob. Chemother., 67(4), 951-4, 2012; Baines et al., J. Antimicrob. Chemother., 58, 1062-5, 2006; Baines et al., J. Antimicrob. Chemother., 55, 974-82, 2005. Current data indicate that despite the disruptive effects on the intestinal flora, omadacycline is associated with a low risk for CDI induction.

[0141] Example 4. Effects of omadacycline on intestinal microflora and Clostridium difficile germination, proliferation and toxin production in an in vitro model of the human intestine Target Using an in vitro model of Clostridium difficile infection (CDI), the effects of omadacycline instillation on normal intestinal microflora populations were determined and the propensity of omadacycline to induce C. difficile germination, proliferation, and toxin production was investigated.

[0142] method like Figure 2 The intestinal model was established as shown in Figure 1. The intestinal model was inoculated with pooled fecal slurry (5 volunteers ≥60 years old, with no history of antibiotic treatment in the previous 3 months) and left for 2 weeks to allow the bacterial population to reach a steady state. On day 14, a single inoculum (~10 7 cfu / mL) of C. difficile spores (PCR RNA type 027 strain 210) were added to container 1 of the intestinal model. One week later, on day 21, a second aliquot of C. difficile spores was added and antibiotic instillation was started. Model A (LHS) was exposed to moxifloxacin (43 mg / L once a day for 7 days) and model B (RHS) was exposed to omadacycline (430 mg / L once a day for 7 days), which started on day 21.

[0143] Selective agar was used to monitor the bacterial population in the intestinal model to count live bacterial colonies. The population was monitored every other day for the first 2 weeks until steady state was reached, and was monitored every day thereafter. The C. difficile population was monitored in all three containers, and all other bacterial groups (total obligate anaerobes, total facultative anaerobes, lactic acid fermentation Enterobacteriaceae, Enterococcus, total Clostridium, Lactobacillus, Bifidobacterium, Bacteroides fragilis group) were monitored only in containers 2 and 3. In terms of the tendency to induce CDI, container 3, which represents the distal colon, has the greatest physiological relevance. Using viable counts and differential alcohol shock viable counts on selective agar, the total viable count and spore count of C. difficile were monitored. Starting from the 14th day, C. difficile cytotoxins were measured using quantitative VERO cell cytotoxicity assays. Each 1 mL sample was centrifuged at 16,000 x g for 15 minutes, and the supernatant was removed. Six 1:10 serial dilutions (to 10 -6 20 μL of the appropriate dilution was added to the VERO cell monolayer and a further 20 μL of C. perfringens antitoxin (1:10 dilution in sterile distilled water) was placed in the corresponding antitoxin row. 2 Monolayers were examined after 24 and 48 hours of incubation in , with positive results indicated by the presence of cell rounding, accompanied by simultaneous neutralization of the effects of C. perfringens antitoxin. Cytotoxin titers (relative units, RU) are arbitrary log 10 scale, and cytotoxic titers are reported as the highest dilution with >70% cell rounding, i.e., 10 0 =1RU, 10 -1 =2RU, 10 -2 =3RU. Samples were collected daily starting from day 21 to determine the antimicrobial concentration in the intestinal model container by bioassay. The concentration of moxifloxacin was determined using Isosensitest agar, using Escherichia coli as an indicator organism. The concentration of omadacycline was determined using Wilkins Chalgren agar, using Coxiella rhizophila as an indicator organism.

[0144] result Omadacycline exposure model Changes in the gut microbiome population were similar in vessels 2 and 3 ( Figure 8 and 9 Omadacycline instillation caused Bifidobacterium spp. (~8log 10 cfu / mL), Bacteroides fragilis group (~8log 10 cfu / mL), Lactobacillus (~6log 10 cfu / mL) and Enterococcus species populations (~6log 10cfu / mL), all of which were below the detection limit. Clostridium was also observed (~5 log 10 cfu / mL) and lactose-fermenting Enterobacteriaceae (~5log 10 cfu / mL). During omadacycline exposure, the Enterobacteriaceae population increased, particularly in container 2. These observations corresponded to a ~5 log increase in the total anaerobic population. 10 There was an overall decrease in cfu / mL. However, total facultative anaerobes remained fairly stable throughout. All populations recovered after omadacycline administration ended and returned to pre-antibiotic exposure levels by the end of the experiment.

[0145] Despite the extensive disruption of the intestinal microbial community, omadacycline exposure did not result in any signs of simulated CDI. The total viable count (TVC) of C. difficile remained approximately equal to the spore count in all three containers throughout the experiment, indicating that all C. difficile remained as spores. No vegetative cell proliferation was observed. No toxins were detected in any container throughout this intestinal model experiment ( Fig.10 , 11 and 12).

[0146] Moxifloxacin exposure model Changes in the gut microbiota population were similar in vessels 2 and 3 ( Fig.13 and 14 Moxifloxacin instillation caused a population of Bacteroides fragilis (~8 log in container 2). 10 cfu / mL and container 3 ~4log 10 cfu / mL); Enterococcus population (~4 log in both container 2 and container 3) 10 cfu / mL); and Lactobacillus population (~3 log in both container 2 and container 3 10 All populations returned to pre-antibiotic levels by ~1 week after antibiotic exposure ended.

[0147] In all three containers, C. difficile remained as spores during the internal control period (B), but during the moxifloxacin instillation, an increase in total viable counts compared to spore counts was observed, indicating spore germination and vegetative cell proliferation. The total viable count in container 1 increased by ~4.5 log 10 cfu / mL and peaked at ~6 log in containers 2 and 3. 10The increase in total viable counts was accompanied by the detection of C. difficile cytotoxin, which reached a peak titer of 2 relative units in container 1 and 3 relative units in containers 2 and 3. At the end of the experiment, both total viable counts and toxin titers decreased, and toxin was undetectable in all containers by day 42.

[0148] discuss In this study, moxifloxacin instillation induced simulated CDI in the intestinal model, and toxins were detected in all three vessels. This is consistent with previous data, confirming that moxifloxacin instillation causes substantial intestinal microbial community destruction and induces Clostridium difficile spore germination, proliferation, and toxin production (Saxton K et al., Antimicrob. Agents Chemother.; 53: 412-420, 2009). Moxifloxacin instillation has a significant effect on many components of the intestinal microbiota, including Bacteroides species (6log 10 cfu / mL decreased), lactose-fermenting Enterobacteriaceae (6log 10 cfu / mL decreased) and Enterococcus spp. (4log 10 cfu / mL decreased), which was below the detection limit (Saxton et al., Antimicrob. Agents Chemother.; 53:412-420, 2009), similar to the effect observed here. This disruption of the intestinal microbial community was followed by C. difficile spore germination, vegetative cell proliferation, and detectable toxins.

[0149] Despite causing extensive disruption of the intestinal microbial community, omadacycline exposure did not induce any signs of simulated CDI in an in vitro human intestinal model. This model has been shown to be clinically reflective. Antibiotics known to have a high propensity to induce CDI clinically induced CDI in this model (e.g., clindamycin, cephalosporins, amoxicillin), while antibiotics clinically considered to be 'low risk' for CDI did not induce simulated CDI in the intestinal model (e.g., tigecycline and piperacillin-tazobactam). This study provides data indicating that omadacycline may be a low risk for CDI induction, despite the intestinal microbial community effect that disrupts 'colonization resistance'. It is noteworthy that the lack of CDI induction by tigecycline and piperacillin-tazobactam in the intestinal model is also despite the obvious intestinal microbial community disruption (Baines et al., J. Antimicrob. Chemother. 55, 974-982, 2005; Baines et al., J. Antimicrob. Chemother., 58, 1062-1065, 2006). Even when potential niches have been generated by antibiotic exposure, the high intrinsic activity of omadacycline, tigecycline and piperacillin-tazobactam against C. difficile is likely to prevent its expansion. In addition, the relatively rapid reconstruction of the intestinal microbial community population after antibiotic cessation will provide further protection against CDI.

[0150] When compared to the results of published and unpublished studies demonstrating that clinically relevant concentrations of moxifloxacin induce simulated CDI in an intestinal model, the data presented in Example 4 indicate that omadacycline is less likely to induce CDI than moxifloxacin and other fluoroquinolones.

[0151] Comparison with Example 3 The effect of omadacycline on the anaerobic gut microbiota population in Example 4 was similar to that observed in Example 3, with all measured anaerobic populations being affected. The main difference between the data presented in Example 3 and Example 4 was observed in the facultative anaerobic population, for which a greater decrease following omadacycline exposure was observed in Example 4 compared to Example 3. As in Example 3, no signs of C. difficile germination, vegetative cell proliferation, or toxin production were observed, indicating that omadacycline is less likely to induce CDI than other commonly used antibiotics. In Example 4, the comparator antibiotic moxifloxacin was also tested. The data in Example 4 indicate that omadacycline is less likely to induce CDI than moxifloxacin.

[0152] Equivalent solution Those skilled in the art will recognize or be able to determine many equivalents of the specific embodiments and methods described herein using no more than routine experimentation. Such equivalents are expected to be encompassed by the scope of the present invention. All patents, patent applications and references cited herein are expressly incorporated herein by reference.

Claims

1. A method for treating Clostridium difficile infection in a subject in need thereof, the method comprising administering to the subject an effective amount of a compound or a salt thereof, wherein the compound is a compound A' having the following structural formula: Such that the Clostridium difficile infection in the subject is treated.

2. The method of claim 1, wherein the Clostridium difficile infection is a recurrent Clostridium difficile infection.

3. The method of claim 1, wherein the compound is administered in combination with at least one or more additional therapies for treating Clostridium difficile infection.

4. The method of claim 3, wherein the additional therapy comprises administration of an antibiotic.

5. The method of claim 4, wherein the antibiotic is metronidazole or vancomycin.

6. The method of claim 3, wherein the additional therapy comprises administration of probiotics.

7. The method of claim 3, wherein the additional therapy comprises administration of a fecal transplant.

8. A method of treating a bacterial infection in a subject at risk of developing a Clostridium difficile infection without causing a Clostridium difficile infection, the method comprising administering to the subject an effective amount of a compound or a salt thereof, wherein the compound is Compound A' having the following structural formula: Such that the bacterial infection in the subject is treated without causing a C. difficile infection.

9. A method of treating a bacterial infection in a subject at risk of developing a Clostridium difficile infection without substantially disrupting the intestinal microbiome, the method comprising administering to the subject an effective amount of a compound or a salt thereof, wherein the compound is Compound A' having the following structural formula: Such that the bacterial infection in the subject is treated without substantially disrupting the intestinal microbiome.

10. The method of claim 9, wherein treating the bacterial infection without substantially disrupting the intestinal microbiome does not result in a Clostridium difficile infection in the subject.

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