Crystalline forms of compound and uses thereof

Abstract

This disclosure provides crystal forms A and B of the free base of the compound shown in formula (I), and uses relating to crystal forms A and B.

Description

Technical Field

[0001] The present disclosure relates to the field of biomedicine, and specifically to a crystal form of a compound and its uses. Prior Art

[0002] Rifamycins are natural products with potential antimicrobial activity. Naturally derived rifamycins (e.g., rifamycin B, rifamycin O, rifamycin R, rifamycin U, rifamycin S, rifamycin SV, and rifamycin Y (Brufani, M., Cerrini, S., Fedeli, W., Vaciago, A. J. Mol. Biol. 1974, 87, 409-435)) have limited therapeutic applications, such as poor pharmacokinetics, low oral bioavailability, weak activity against Gram-negative pathogens, and low distribution in infected tissues. Chemical modification has led to the development of various semisynthetic rifamycin derivatives with improved antimicrobial spectrum and pharmacological properties. Among these semisynthetic compounds, rifampicin and rifabutin have been developed as therapeutic drugs and are currently used to treat tuberculosis and other microbial infections (Farr, B.M. Rifamycins, in Principles and Practice of Infectious Diseases; Mandell, G.L., Bennett, J.E., Dolin, R., Eds.; Churchill 11 Livingstone Philadelphia; pp. 348-361). TNP-2198 is a dual-targeted rifamycin-nitroimidazole conjugate with potent activity against microaerophilic and anaerobic bacterial pathogens, and exhibits good activity against strains resistant to both rifamycins and nitroimidazoles. However, the development and application of this class of innovative antibacterial drug molecules often face challenges in meeting the drugability requirements of formulations due to their high molecular weight, high lipid solubility, low water solubility, and hygroscopicity in their free form, as well as their bioavailability and stability (chemical stability, thermal stability, melting point, and crystalline stability). Therefore, finding and screening new molecular entities (such as salt forms or crystal forms) of such prototype drug molecules plays a vital role in realizing their medicinal significance. Summary of the Invention

[0003] In order to overcome the deficiencies of the aforementioned prior art, the present invention provides a free base crystalline form of a compound that can meet multiple pharmaceutical needs.

[0004] In one aspect, the present disclosure provides a crystalline form A of the free base of the compound represented by formula (I), The X-ray powder diffraction of the crystal form A has characteristic peaks at diffraction angles 2θ of 5.28°±0.2°, 7.17°±0.2°, 8.50°±0.2°, 10.66°±0.2°, 14.33°±0.2°, 15.84°±0.2° and 18.60°±0.2°.

[0005] In some embodiments, the crystalline form A has characteristic peaks at one or more of the diffraction angle 2θ values ​​of 12.61°±0.2°, 14.83°±0.2°, 15.26°±0.2°, 16.57°±0.2°, 19.97°±0.2° and 21.97°±0.2°.

[0006] In some embodiments, the crystalline form A has characteristic peaks at diffraction angles 2θ of 12.61°±0.2°, 14.83°±0.2°, 15.26°±0.2°, 16.57°±0.2°, 19.97°±0.2° and 21.97°±0.2°.

[0007] In some embodiments, the X-ray powder diffraction (XRPD) pattern of Form A is substantially consistent with FIG1 .

[0008] In some embodiments, the differential scanning calorimetry curve of Form A has an endothermic peak at about 169.3°C.

[0009] In some embodiments, the differential scanning calorimetry (DSC) graph of Form A is substantially consistent with Figure 2B.

[0010] In some embodiments, the crystalline Form A is an anhydrate.

[0011] In another aspect, the present disclosure provides a crystalline form A of the free base of the compound represented by formula (I), wherein the differential scanning calorimetry curve of the crystalline form A has an endothermic peak at approximately 169.3°C.

[0012] In some embodiments, the differential scanning calorimetry (DSC) graph of Form A is substantially consistent with Figure 2B.

[0013] In some embodiments, the crystalline Form A is anhydrate and / or free of solvates.

[0014] On the other hand, the present disclosure provides a crystalline form B of the free base of the compound represented by formula (I), wherein the crystalline form B exhibits characteristic peaks in X-ray powder diffraction at diffraction angles 2θ of 4.89°±0.2°, 6.67°±0.2°, 7.12°±0.2°, 13.41°±0.2°, 14.62°±0.2°, 15.19°±0.2°, and 18.23°±0.2°.

[0015] In some embodiments, the X-ray powder diffraction of the crystalline form B has characteristic peaks at one or more of the diffraction angles 2θ values ​​of 7.84°±0.2°, 10.67°±0.2°, 14.25°±0.2°, 16.07°±0.2°, 17.10°±0.2°, 17.41°±0.2°, 17.74°±0.2° and 20.73°±0.2°.

[0016] In some embodiments, the X-ray powder diffraction of the crystalline form B has characteristic peaks at diffraction angles 2θ of 7.84°±0.2°, 10.67°±0.2°, 14.25°±0.2°, 16.07°±0.2°, 17.10°±0.2°, 17.41°±0.2°, 17.74°±0.2° and 20.73°±0.2°.

[0017] In some embodiments, the X-ray powder diffraction (XRPD) pattern of Form B is substantially consistent with FIG. 3 .

[0018] In some embodiments, the differential scanning calorimetry curve of Form B has endothermic peaks at about 85.6°C, about 130.7°C, and about 144.3°C.

[0019] In some embodiments, the differential scanning calorimetry (DSC) graph of Form B is substantially consistent with Figure 4B.

[0020] In some embodiments, the Form B is obtained by converting the Form A described herein in a toluene reagent.

[0021] In some embodiments, the crystalline Form B is a toluene solvate.

[0022] In some embodiments, the molar ratio of the compound represented by formula (I) in the crystalline form B to the toluene molecule is 1:2 to 1:1.

[0023] On the other hand, the present disclosure provides a crystalline form B of the free base of the compound represented by formula (I), wherein the differential scanning calorimetry curve of the crystalline form B has endothermic peaks at approximately 85.6°C, approximately 130.7°C, and approximately 144.3°C.

[0024] In some embodiments, the differential scanning calorimetry (DSC) graph of Form B is substantially consistent with Figure 4B.

[0025] In some embodiments, the Form B is obtained by converting the Form A described herein in a toluene reagent.

[0026] In some embodiments, the crystalline Form B is a toluene solvate.

[0027] In some embodiments, the molar ratio of the compound represented by formula (I) in the crystalline form B to the toluene molecule is 1:2 to 1:1.

[0028] In another aspect, the present disclosure provides a pharmaceutical composition comprising the crystalline form A and / or the crystalline form B described herein, and optionally a pharmaceutically acceptable carrier.

[0029] In some embodiments, the pharmaceutical composition further comprises a second therapeutic agent.

[0030] In some embodiments, the second therapeutic agent is selected from the group consisting of: a proton pump inhibitor, an acid suppressant, an efflux pump inhibitor, an anesthetic, an antifungal agent, an antiviral agent, an antibacterial agent, an antiprotozoal agent, an anti-inflammatory agent, an anticoagulant, a platelet aggregation inhibitor, an antipyretic, a lipid-lowering agent, and a zinc salt.

[0031] In another aspect, the present disclosure provides a kit comprising one or more of the crystalline form A described herein, the crystalline form B described herein, and the pharmaceutical composition described herein.

[0032] In some embodiments, the kit further comprises instructions in physical form and / or machine-readable electronic form.

[0033] In another aspect, the present disclosure provides a method for preparing a drug using the crystalline form A and / or the crystalline form B described herein.

[0034] In another aspect, the present disclosure provides a method for inhibiting or preventing bacterial growth, comprising administering an effective amount of one or more of the crystalline form A, crystalline form B, pharmaceutical composition, and kit described herein.

[0035] In another aspect, the present disclosure provides a method for preventing, treating, or alleviating a disease or a condition related thereto, comprising administering to a patient in need thereof an effective amount of one or more of the crystalline form A, crystalline form B, pharmaceutical composition, and kit described herein.

[0036] In some embodiments, the patient in need thereof has a bacterial infection.

[0037] In some embodiments, the bacteria is selected from the group consisting of Helicobacter pylori, Mycobacterium tuberculosis, nontuberculous mycobacteria, Acinetobacter baumannii, Bacteroides fragilis, Bifidobacterium longum, Ruminococcus, Prevotella, Clostridium perfringens, Clostridium difficile, Lactobacillus acidophilus, Eggertella lentus, Fusobacterium nucleatum, Gardnerella vaginalis, Mobiluncus timidus, Peptostreptococcus, Porphyromonas insaccharolyticus, Prevotella diversa, Propionibacterium acnes, and Veillonella parvum.

[0038] In another aspect, the present disclosure provides uses of the crystalline Form A, the crystalline Form B, the pharmaceutical composition, and / or the kit described herein for inhibiting or preventing bacterial growth.

[0039] In another aspect, the present disclosure provides uses of the crystalline Form A, the crystalline Form B, the pharmaceutical composition, and / or the kit described herein for preparing a medicament for preventing, treating, or alleviating diseases caused by bacterial infection or related symptoms thereof.

[0040] In some embodiments, the bacteria is selected from the group consisting of Helicobacter pylori, Mycobacterium tuberculosis, nontuberculous mycobacteria, Acinetobacter baumannii, Bacteroides fragilis, Bifidobacterium longum, Ruminococcus, Prevotella, Clostridium perfringens, Clostridium difficile, Lactobacillus acidophilus, Eggertella lentus, Fusobacterium nucleatum, Gardnerella vaginalis, Mobiluncus timidus, Peptostreptococcus, Porphyromonas insaccharolyticus, Prevotella diversa, Propionibacterium acnes, and Veillonella parvum.

[0041] In some embodiments, the disease or its associated condition is selected from the group consisting of: gastritis, gastric ulcer, bacterial vaginosis, diarrhea, pneumonia, appendicitis, cholecystitis, otitis media, endocarditis, endometritis, brain abscess, myocardial necrosis, osteomyelitis, peritonitis, empyema, salpingitis, septic arthritis, liver abscess, sinusitis, pelvic inflammatory disease, and bacteremia; and upper respiratory tract infection, lower respiratory tract infection, skin and soft tissue infection, bone and joint infection, lung infection, abdominal infection, eye infection, ear infection, oral infection, and surgical infection.

[0042] In another aspect, the present disclosure provides the pharmaceutical composition or the kit described herein, which is used to prevent, treat, or alleviate diseases caused by bacterial infection or related symptoms thereof.

[0043] In some embodiments, the bacteria is selected from the group consisting of Helicobacter pylori, Mycobacterium tuberculosis, nontuberculous mycobacteria, Acinetobacter baumannii, Bacteroides fragilis, Bifidobacterium longum, Ruminococcus, Prevotella, Clostridium perfringens, Clostridium difficile, Lactobacillus acidophilus, Eggertella lentus, Fusobacterium nucleatum, Gardnerella vaginalis, Mobiluncus timidus, Peptostreptococcus, Porphyromonas insaccharolyticus, Prevotella diversa, Propionibacterium acnes, and Veillonella parvum.

[0044] In some embodiments, the disease or its associated condition is selected from the group consisting of: gastritis, gastric ulcer, bacterial vaginosis, diarrhea, pneumonia, appendicitis, cholecystitis, otitis media, endocarditis, endometritis, brain abscess, myocardial necrosis, osteomyelitis, peritonitis, empyema, salpingitis, septic arthritis, liver abscess, sinusitis, pelvic inflammatory disease, and bacteremia; and upper respiratory tract infection, lower respiratory tract infection, skin and soft tissue infection, bone and joint infection, lung infection, abdominal infection, eye infection, ear infection, oral infection, and surgical infection.

[0045] In another aspect, the present disclosure provides a method for preparing the crystalline form A described herein, comprising crystallizing the compound represented by formula (I) in a solvent comprising an alcohol solvent, wherein the alcohol solvent is selected from one or a combination of more than one of methanol, ethanol, n-propanol, isopropanol, n-butanol, isobutanol, and tertiary butanol.

[0046] Furthermore, the method of preparing Form A disclosed herein further comprises crystallizing the compound represented by formula (I) in an alcohol solvent.

[0047] In some embodiments, the alcohol solvent is methanol, ethanol, or a combination thereof.

[0048] In some embodiments, the method further comprises concentrating the alcohol solvent to obtain a concentrated wet product, and drying the concentrated wet product.

[0049] In another aspect, the present disclosure provides a crystalline form A of the free base of the compound represented by formula (I), wherein the crystalline form A is obtained by the method for preparing the crystalline form A described in the present disclosure.

[0050] In another aspect, the present disclosure provides a method for preparing the crystalline form B described herein, comprising crystallizing the crystalline form A described herein in toluene solvent.

[0051] In another aspect, the present disclosure provides a crystalline form B of the free base of the compound represented by formula (I), wherein the crystalline form B is obtained by the method for preparing the crystalline form B described in the present disclosure.

[0052] Those skilled in the art will readily appreciate other aspects and advantages of the present disclosure from the detailed description that follows. The detailed description that follows merely illustrates and describes exemplary embodiments of the present disclosure. As will be appreciated by those skilled in the art, the present disclosure enables those skilled in the art to modify the disclosed embodiments without departing from the spirit and scope of the inventions herein. Accordingly, the drawings and descriptions herein are intended to be illustrative only and not restrictive. Simple diagram description

[0053] The specific features of the invention disclosed herein are set forth in the accompanying claims. The features and advantages of the invention disclosed herein can be better understood by reference to the exemplary embodiments described in detail below and the accompanying drawings. A brief description of the drawings follows:

[0054] FIG1 shows the XRPD pattern of Form A of the present disclosure.

[0055] FIG2A and FIG2B show the TGA graph and DSC graph of Form A of the present disclosure.

[0056] FIG3 shows the XRPD pattern of Form B of the present disclosure.

[0057] FIG4A and FIG4B show the TGA graph and DSC graph of Form B of the present disclosure.

[0058] FIG5 shows the 1H NMR spectrum of Form A of the present disclosure.

[0059] FIG6A and FIG6B show the PLM observation results of Form A of the present disclosure.

[0060] 7A to 7C show the 1H NMR spectra of Form B of the present disclosure initially and when heated to 115° C. and 140° C., respectively.

[0061] FIG8 shows the XRPD overlay comparison results of Form B of the present disclosure before and after heating.

[0062] 9A to 9C show the XRPD patterns of Forms C1, C2, and C3 of the present disclosure.

[0063] FIG9D shows the XRPD patterns of Forms C1, C2, and C3 after drying.

[0064] FIG10 shows the DVS experimental analysis results of Form A of the present disclosure.

[0065] FIG11 shows the XRPD overlay comparison results of Form A of the present disclosure before and after DVS testing.

[0066] FIG12 shows the XRPD overlay comparison results of Form A of the present disclosure in the solid stability evaluation.

[0067] FIG13 shows the HPLC overlay comparison results of the solid stability evaluation of Form A of the present disclosure.

[0068] FIG14 shows the structural formula of the impurity RRT0.98 in the crude product of the compound of formula (I) disclosed herein. Implementation Method

[0069] The following describes the implementation of the present invention through specific embodiments. People skilled in the art can easily understand other advantages and effects of the present invention from the contents disclosed in this specification. [Definition of terms]

[0070] In the present disclosure, the term "substantially consistent with (Figure)..." generally refers to information such as the number of characteristic peaks in the spectrum, the location (or distribution) of the characteristic peaks, and the geometric topological regularity being substantially the same or similar. For example, the characteristic peaks referred to in the present disclosure may be diffraction peaks in an X-ray powder diffraction (XRPD) spectrum, endothermic peaks in a differential scanning calorimetry (DSC) spectrum, chemical shift peaks in a proton nuclear magnetic resonance (1H NMR) spectrum, or absorption peaks in a high-performance liquid chromatography (HPLC) spectrum. For example, the term "substantially consistent with (Figure)..." may mean that at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% of the characteristic peaks in the spectrum are represented in the referenced figure.

[0071] In this disclosure, the term "2θ (also known as 2th IIta or diffraction peak) value" in reference to an X-ray powder diffraction (XRPD) pattern is expressed in degrees (°). When referring to a pattern and / or data therein, the term "diffraction peak" generally refers to a feature that one skilled in the art would not attribute to background noise. The X-ray powder diffraction peaks of the crystalline forms described herein may be subject to experimental error in the measurement of the 2θ or diffraction peaks in their X-ray powder diffraction patterns. This error may occur from one machine to another and from one sample to another. The measurement of the 2θ or diffraction peaks in the X-ray powder diffraction patterns may vary slightly. The experimental error or difference may be as much as ±0.2 units, ±0.1 units, or ±0.05 units. Therefore, the values ​​of the 2θ or diffraction peaks should not be considered absolute.

[0072] In certain embodiments, the differential scanning calorimetry (DSC) curve of the crystal form may also have experimental errors, which may occur between one machine and another and between one sample and another. The position and peak value of the endothermic peak may be slightly different. The numerical value of the experimental error or difference may be less than or equal to 5°C, or less than or equal to 4°C, or less than or equal to 3°C, or less than or equal to 2°C, or less than or equal to 1°C. Therefore, the peak position or peak value of the DSC endothermic peak cannot be considered absolute.

[0073] In certain embodiments, the thermogravimetric analysis (TGA) of the crystalline form may also have experimental errors, which may occur between one machine and another and between one sample and another. The weight loss temperature and the amount of weight loss may be slightly different. The numerical value of the experimental error or difference may be about ±0.1 unit, about ±0.05 unit, or about ±0.01 unit. Therefore, the numerical values ​​of the weight loss temperature and the amount of weight loss cannot be considered absolute.

[0074] Throughout this disclosure, all numerical values ​​disclosed herein are approximate, regardless of whether the word "about" or "approximately" is used. The numerical value of each numeral may vary by, for example, ±1%, ±2%, or ±5%. The term "about" or "approximately" refers to an acceptable range of error for a particular value, typically determined by one of ordinary skill in the art, which depends in part on how the value is measured or determined, i.e., the limitations of the measurement system. For example, "about" or "approximately" can mean within one or more standard deviations, as practiced in the art. Alternatively, "about" or "approximately" can mean a range of up to 10% or 20% (i.e., ±10% or ±20%). For example, about 3 mg can include any amount between 2.7 mg and 3.3 mg (for 10%) or between 2.4 mg and 3.6 mg (for 20%). Furthermore, particularly with respect to biological systems or processes, the term can mean a value of up to an order of magnitude or up to a factor of five. When specific values ​​or compositions are provided in this specification and the appended claims, unless otherwise indicated, the meaning of "about" or "approximately" should be assumed to be within an acceptable error range for that specific value or composition.

[0075] In this disclosure, the terms "solvate" and "solvate" are used interchangeably and generally refer to an association or complex between one or more solvent molecules and a compound described herein. Examples of solvents that form solvates include, but are not limited to, water, isopropanol, ethanol, methanol, DMSO, ethyl acetate, acetic acid, and ethanolamine.

[0076] In this disclosure, the term "pharmaceutically acceptable carrier" generally refers to one or more non-toxic materials that do not interfere with the effectiveness of the biological activity of the active ingredient. Such formulations may conventionally contain salts, buffers, preservatives, compatible carriers, and, if necessary, other therapeutic agents. Such pharmaceutically acceptable formulations may also include compatible solid or liquid fillers, diluents, or encapsulating materials suitable for administration to humans. Other contemplated carriers, excipients, and / or additives that may be used in the formulations described herein may include, for example, flavorings, antimicrobial agents, sweeteners, antioxidants, antistatic agents, lipids, protein excipients (e.g., serum albumin, gelatin, casein), salt-forming counterions (e.g., sodium), and the like. These and other known pharmaceutical carriers, excipients, and / or additives suitable for use in the formulations described herein are known in the art and are listed, for example, in "Remington: The Science & Practice of Pharmacy," 21st edition, Lippincott Williams & Wilkins (2005) and "Physician's Desk Reference," 60th edition, Medical Economics, Montvale, New Jersey (2005). Suitable pharmaceutically acceptable carriers can be routinely selected based on the desired or required mode of administration, solubility, and / or stability.

[0077] In the present disclosure, the term "therapeutic agent" generally refers to a compound (including but not limited to pharmaceutically acceptable salts, hydrates, solvates, crystal forms, prodrugs, metabolites or deuterated substances thereof), a mixture of compounds, a composition, a biomacromolecule or an extract made from a biological material that can induce a desired therapeutic effect, prevent the occurrence of a certain disease, or alleviate a related disease when properly administered to a patient.

[0078] In this disclosure, the term "bacteria" generally refers to a class of prokaryotes that lack a distinct nucleus and membranous organelles. The bacteria may include spherical, rod-shaped, or spiral-shaped organisms. The bacteria may include species that grow in interlike patterns, such as Escherichia, Salmonella, Shigella, Klebsiella, Vibrio, Pasteurella, Borrelia, Leptospira, Campylobacter, Clostridium, Corynebacterium, Yersinia, Treponema, Rickettsia, Chlamydia, and other genus. a), Mycoplasma, Coxiella, Neisseria, Listeria, Haemophilus, Helicobacter, Legionella, Pseudomonas, Bordetella, Brucella, Staphylococcus, Streptococcus, Enterococcus, Bacillus, Mycobacterium, Nocardia, etc. The term "bacterial infection" generally refers to any disorder caused by the proliferation and / or presence of bacteria as described in the present disclosure in a cell or subject. A bacterial infection can be caused by the growth and reproduction of bacteria (e.g., pathogenic bacteria) and the production of toxins and other metabolic products.

[0079] In this disclosure, the term "patient in need thereof" generally includes human patients and other mammalian subjects receiving prophylactic or therapeutic treatment, including but not limited to non-human primates, laboratory animals such as rabbits, dogs, rats, and mice, and other animals. These "patients in need thereof" may, for example, be subjects diagnosed with a specific disease, subjects currently receiving treatment for a specific disease, subjects at risk of developing a specific disease, and the like.

[0080] In this disclosure, the term "administer" generally refers to introducing a drug or a composition comprising the drug (e.g., a therapeutic agent provided herein) into a patient's body via any route of introduction or delivery. Any method known to those skilled in the art for contacting cells, organs, or tissues with the drug or its composition can be used.

[0081] As used herein, the term "effective amount" generally refers to an amount sufficient to achieve, or at least partially achieve, the desired therapeutic effect. An "effective amount" of a drug or therapeutic agent generally refers to an amount sufficient to cure or at least partially prevent the disease and its complications in a patient already suffering from the disease. The effective amount for this purpose will depend on the severity of the infection and the overall state of the patient's own immune system.

[0082] In this disclosure, the term "comprising" generally refers to including the features specified but not excluding other elements. The terms "above" and "below" generally refer to inclusive situations.

[0083] In this disclosure, the term "selected from" generally refers to a group consisting of a selected group and all combinations thereof. For example, "selected from (:) A, B, and C" means all combinations of A, B, and C, such as A, B, C, A+B, A+C, B+C, or A+B+C. [Detailed description of the invention]

[0084] In one aspect, the present disclosure provides a crystalline form A of the free base of the compound represented by formula (I), wherein the crystalline form A exhibits characteristic peaks in X-ray powder diffraction at diffraction angles 2θ of 5.28°±0.2°, 7.17°±0.2°, 8.50°±0.2°, 10.66°±0.2°, 14.33°±0.2°, 15.84°±0.2°, and 18.60°±0.2°.

[0085] In another aspect, the present disclosure provides a crystalline form A of the free base of the compound represented by formula (I), wherein the differential scanning calorimetry curve of the crystalline form A has an endothermic peak at approximately 169.3°C.

[0086] On the other hand, the present disclosure provides a crystalline form B of the free base of the compound represented by formula (I), wherein the crystalline form B exhibits characteristic peaks in X-ray powder diffraction at diffraction angles 2θ of 4.89°±0.2°, 6.67°±0.2°, 7.12°±0.2°, 13.41°±0.2°, 14.62°±0.2°, 15.19°±0.2°, and 18.23°±0.2°.

[0087] On the other hand, the present disclosure provides a crystalline form B of the free base of the compound represented by formula (I), wherein the differential scanning calorimetry curve of the crystalline form B has endothermic peaks at approximately 85.6°C, approximately 130.7°C, and approximately 144.3°C.

[0088] In another aspect, the present disclosure provides a pharmaceutical composition comprising the crystalline form A and / or the crystalline form B described herein, and optionally a pharmaceutically acceptable carrier.

[0089] In another aspect, the present disclosure provides a kit comprising one or more of the crystalline form A described herein, the crystalline form B described herein, and the pharmaceutical composition described herein.

[0090] In another aspect, the present disclosure provides a method for preparing a drug using the crystalline form A and / or the crystalline form B described herein.

[0091] In another aspect, the present disclosure provides a method for inhibiting or preventing bacterial growth, comprising administering an effective amount of one or more of the crystalline form A, crystalline form B, pharmaceutical composition, and kit described herein.

[0092] In another aspect, the present disclosure provides a method for preventing, treating, or alleviating a disease or a condition related thereto, comprising administering to a patient in need thereof an effective amount of one or more of the crystalline form A, crystalline form B, pharmaceutical composition, and kit described herein.

[0093] In another aspect, the present disclosure provides uses of the crystalline Form A, the crystalline Form B, the pharmaceutical composition, and / or the kit described herein for inhibiting or preventing bacterial growth.

[0094] In another aspect, the present disclosure provides uses of the crystalline Form A, the crystalline Form B, the pharmaceutical composition, and / or the kit described herein for preparing a medicament for preventing, treating, or alleviating diseases caused by bacterial infection or related symptoms thereof.

[0095] In another aspect, the present disclosure provides the pharmaceutical composition or the kit described herein, which is used to prevent, treat, or alleviate diseases caused by bacterial infection or related symptoms thereof. Crystalline form of the free base of the compound of formula (I)

[0096] The present disclosure provides Form A and Form B, and in certain cases, Form C1, Form C2, and Form C3. The following examples will help further understand these forms, their preparation methods, uses, and technical effects described in the present disclosure, but these examples are not intended to limit the scope of the present disclosure. Pharmaceutical compositions

[0097] In some embodiments, the pharmaceutical compositions disclosed herein can be formulated into desired dosage forms, for example, in the form of solutions, aerosols, gels, ointments, sprays, or suspensions. These compositions can be prepared using conventional methods known in the art. For example, the pharmaceutically acceptable carrier can be selected from excipients for increasing solubility, adjuvants for increasing viscosity, and adjuvants for enhancing permeability.

[0098] In some embodiments, the pharmaceutical composition may further comprise a second therapeutic agent. For example, the second therapeutic agent may be selected from another rifamycin or its analog, a proton pump inhibitor, an acid suppressant, an efflux pump inhibitor, an anesthetic, an antifungal agent, an antiviral agent, an antibacterial agent, an antiprotozoal agent, an anti-inflammatory drug (such as a non-steroidal anti-inflammatory drug or a steroid), an anticoagulant, a platelet aggregation inhibitor, an antipyretic, a lipid-lowering agent, and a zinc salt. All therapeutic agents used in the pharmaceutical compositions disclosed herein may be used within the dosage ranges currently known and used in these formulations. Reagent test kit

[0099] In some embodiments, the kits described herein may include the crystal forms and / or pharmaceutical compositions described herein; in addition, the kits may also include at least one container for the crystal forms and / or the pharmaceutical compositions. For example, the kits may include more than one component, and may include second, third, and / or additional containers other than the container, in which the more than one component may be separately placed. For example, the kits may also include various combinations of the crystal forms and / or pharmaceutical compositions in the containers. For example, the kits may further include buffers, devices for mixing the different components, devices for measuring, devices for sorting the components, and / or devices for labeling. For example, the kits may also include packaging for accommodating the various containers. For example, the kits may also include instructions for using the kit components. For example, the instructions may be in physical paper form and / or in machine-readable electronic form. Application method

[0100] In some embodiments, the method for inhibiting or preventing bacterial growth provided herein may include administering an effective amount of a crystalline form, pharmaceutical composition, and / or kit described herein via a desired route. In some embodiments, the method includes contacting a crystalline form, pharmaceutical composition, and / or kit described herein with a bacterially infected site. For example, the infected site may be within or on an animal, within or on a plant.

[0101] In some embodiments, the methods provided herein for preventing, treating, or alleviating a disease or its associated conditions may include administering an effective amount of the crystalline form, pharmaceutical composition, and / or kit described herein to a patient in need thereof via a desired route. In certain embodiments, the methods may further include mixing the crystalline form, pharmaceutical composition, and / or kit described herein with other therapeutic agents. In some embodiments, the methods may include systemically delivering the crystalline form, pharmaceutical composition, and / or kit described herein to a patient in need thereof, such that the crystalline form, pharmaceutical composition, and / or kit described herein are widely exposed to a large portion of the body. This step may be performed by any means known in the art, including but not limited to intravenous, intraarterial, intracavitary, subcutaneous, and intraperitoneal delivery. In other embodiments, the methods may include locally delivering the crystalline form, pharmaceutical composition, and / or kit described herein to a patient in need thereof, such that the crystalline form, pharmaceutical composition, and / or kit described herein are directly delivered to a target site within an organism or to a bacterially infected site on an organism's surface, or by direct contact with a bacterially infected site on the body surface. For example, local delivery does not preclude systemic pharmacological effects. In certain embodiments, the method may comprise administering an effective amount of the crystalline form described herein, the pharmaceutical composition described herein, and / or the kit described herein to a patient in need thereof by intramuscular injection, subcutaneous or intradermal injection, intravenous injection, intrathecal injection, inhalation, oral administration, or topical application. Diseases caused by bacteria and bacterial infections or related conditions

[0102] In some embodiments, the patient in need described in the present disclosure is infected with a bacteria, or suffers from a disease caused by a bacterial infection or a condition related thereto. For example, the bacteria can be selected from: Helicobacter pylori, Mycobacterium tuberculosis, nontuberculous mycobacteria, Acinetobacter baumannii, Bacteroides fragilis, Bifidobacterium longum, Ruminococcus, Prevotella, Clostridium perfringens, Clostridium difficile, Lactobacillus acidophilus, Eggertella lentus, Fusobacterium nucleatum, Gardnerella vaginalis, Mobiluncus timidus, Peptostreptococcus, Porphyromonas insaccharolyticus, Prevotella diversa, Propionibacterium acnes, and Veillonella parvum. In the present disclosure, the bacteria may also include drug-resistant strains of the above-mentioned bacteria. For example, the drug-resistant strain may be resistant to rifamycins alone, resistant to nitroimidazoles alone, or resistant to both rifamycins and nitroimidazoles. For example, the resistant strain may also be resistant to other antibiotics, including resistance to macrolides such as clarithromycin, azithromycin, and roxithromycin; resistance to fluoroquinolones such as ciprofloxacin, levofloxacin, and moxifloxacin; resistance to aminoglycosides such as streptomycin and amikacin; resistance to β-lactams such as ampicillin and amoxicillin; resistance to tetracyclines such as tetracycline, tigecycline, and minocycline; resistance to oxazolidinones such as linezolid and tedizolid; resistance to nitrofurans such as furazolidone; resistance to glycopeptides such as vancomycin; resistance to diarylquinolines such as bedaquiline and clofazimine, etc.

[0103] For example, the disease can be selected from gastritis, gastric ulcer, bacterial vaginosis, diarrhea, pneumonia, appendicitis, cholecystitis, otitis media, endocarditis, endometritis, brain abscess, myocardial necrosis, osteomyelitis, peritonitis, empyema, salpingitis, septic arthritis, liver abscess, sinusitis, pelvic inflammatory disease and bacteremia. For example, the disease can be selected from upper respiratory tract infection, lower respiratory tract infection, skin and soft tissue infection, bone and joint infection, lung infection, abdominal cavity infection, eye infection, ear infection, oral infection and surgical infection.

[0104] Without intending to be bound by any theory, the following examples are merely intended to illustrate the crystal forms, preparation methods, and uses of the disclosed compounds, and are not intended to limit the scope of the disclosed invention. [Example] [Example 1]

[0105] Preparation and characterization of Form A and Form B disclosed herein (1) Preparation of Form A

[0106] Weigh 40.05 g of the crude compound of formula (I) and mix it with 5 times the weight of methanol or ethanol. Stir at 25°C for 30 minutes, at which point a noticeable solid precipitate will appear. After continuing stirring for 2-3 hours, filter the wet cake and wash it with 80 mL of methanol or ethanol. Dry the wet cake under vacuum at 42°C for 52 hours to obtain 36.12 g of the crystalline product, with a yield of approximately 67.9%. The purity, as determined by high-performance liquid chromatography (HPLC), was 99.6%. Samples of this crystalline product were then analyzed by X-ray powder diffraction (XRPD), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), solution 1H NMR, and polarizing microscopy (PLM). The results are shown in Figure 1, Table 1, Figures 2A and 2B, Figures 5, and Figures 6A and 6B.

[0107] Characterization of Form A reveals XRPD diffraction peaks (Figure 1) indicating high crystallinity. 1H NMR (Figure 5) reveals no residual solvent, suggesting Form A is anhydrous and / or ansolvate-free. TGA / DSC (Figures 2A-2B) reveal a 1.36% weight loss upon heating of the Form A sample to 150°C, with an endothermic peak at 169.3°C (peak temperature). PLM (Figures 6A-6B) demonstrate the sample's flattened rod-like shape with a particle size of approximately 10-50 μm. (2) Preparation of Crystal Forms C1-C3

[0108] Weigh 40.05 g of the crude compound of Formula (I) and mix it with 5 times the mass of ethanol. Stir at 25°C for 30 minutes, at which point a clear solid precipitate will appear. After stirring for 2-3 hours, filter the wet cake and wash it with 80 mL of ethanol. Three solvate crystal forms C1, C2, and C3 with different structures were detected in the undried wet product of the compound of Formula (I) formed in ethanol. Their XRPD results are shown in Figures 9A to 9C, Tables 2-1, 2-2, and 2-3. However, after drying, Forms C1, C2, and C3 all converted to Form A, as shown in Figure 9D. (3) Preparation of Form B

[0109] Form B was obtained by shaking the crystalline product (Form A) in Example (1) in toluene solvent at room temperature for 24 hours. After drying at room temperature for 24 hours, the crystalline form remained unchanged. The XRPD results are shown in Figure 3 and Table 3. TGA / DSC results (Figures 4A-4B) show that when the Form B sample was heated to 120°C, the sample had a weight loss of 9.33%, and when further heated to 150°C, the sample had a weight loss of 5.36%. The sample also had three endothermic peaks at 85.6°C, 130.7°C, and 144.3°C (peak temperatures). 1H NMR results (Figure 7A) showed that the molar ratio of residual solvent Toluene to API in the sample was 1.6 (13.5 wt%). To further investigate the large TGA weight loss of the Form B sample, a heating experiment was performed on it. XRPD results (Figure 8) show that the Form B sample remains unchanged after heating to 115°C and cooling to room temperature. However, the Form B sample, heated to 140°C and cooled to room temperature, transforms to Form A, but with poorer crystallinity. 1H NMR results (Figures 7B and 7C) show that the molar ratio of residual solvent, Toluene, to API, is 1.2 (10.5 wt%) after heating to 115°C and cooling to room temperature. No residual Toluene solvent is detected after heating to 140°C and cooling to room temperature. Given the crystal transformation upon heating, combined with the significant TGA weight loss and residual solvent revealed by the NMR results after heating, Form B is presumed to be a Toluene solvate. [Example 2]

[0110] Evaluation of Form A in this disclosure (1) Hygroscopicity test (dynamic water vapor sorption test or DVS)

[0111] DVS curves were collected on SMS (Surface Measurement Systems) DVS Intrinsic and DVS Intrinsic plus. Relative humidity at 25°C was calibrated using the deliquescent points of LiCl, Mg(NO₃)₂, and KCl. The DVS results (Figure 10) show that the Form A sample had a water adsorption of 2.880% at 25°C / 80% RH, indicating hygroscopicity. The amorphous form, under the same test conditions, had a hygroscopicity of 5.941%, indicating that Form A has superior hygroscopicity. Furthermore, XRPD results of Form A before and after DVS testing (Figure 11) show that no polymorphic transformation occurred, indicating that Form A exhibits superior stability. In contrast, Forms B, C1, C2, and C3 exhibit less stability and can be converted to Form A upon heating or drying. (2) Solid stability

[0112] Form A samples were exposed at 60°C for 24 hours, and at 25°C / 60% RH and 40°C / 75% RH for one week. The physical and chemical stability of the samples was evaluated by XRPD and HPLC. The stability evaluation results are summarized in Table 4, with the XRPD results shown in Figure 12 and the HPLC results shown in Table 5 and Figure 13. The results show that Form A samples did not undergo significant purity changes or crystal form transformation after exposure to the three conditions. (3) Purification / impurity removal effect

[0113] This example also evaluates and compares the effects of Form A samples and amorphous samples of the compound of formula (I) in the purification and impurity removal processes of the crude compound of formula (I).

[0114] Amorphous phase slurrying step: Approximately 0.5 g of the compound of formula (I) was weighed into a 25 mL glass vial equipped with a magnetic stirrer. 5 mL of various solvents were added, and the mixture was slurried at room temperature. The mixture was filtered, and the filter cake was analyzed for purity by high-performance liquid chromatography. The various solvents were selected by mixing a solvent with high solubility for the compound of formula (I) (e.g., methanol, ethanol, isopropanol, acetone, acetonitrile, ethyl acetate (EA), isopropyl acetate (IPAC), tetrahydrofuran (THF), toluene, dichloromethane (DCM), dimethylformamide (DMF), 2-methyltetrahydrofuran (2-MeTHF), dimethylsulfoxide (DMSO)) in a 1:1 volume ratio with a solvent with low solubility for the compound of formula (I) (e.g., water, methyl tertiary butyl ether (MTBE), and n-heptane) to identify a solvent system that precipitated solids. The selected amorphous phase slurrying solvent systems and their corresponding purification results are shown in Table 6.

[0115] Purification steps for Form A: Weigh 3.5 g of the crude compound of formula (I) into a 50 mL reaction flask equipped with a magnetic stirrer, add 17.5 mL of ethanol, and stir the mixture at 25°C for 15 min. Filter and rinse the filter cake with 5 mL of ethanol. The wet product is dried under vacuum to obtain the crystalline compound of formula (I). The purity is determined by high performance liquid chromatography.

[0116] The comparison of the effects of the two purification methods is summarized in Table 6. It can be seen that compared with the HPLC results of the crude product of the compound of formula (I), the use of various solvent mixture systems to slurry and purify the amorphous sample has basically no impurity removal effect. In contrast, the purification effect of Form A is significant. It can not only increase the purity of the crude product before purification from 92.95% to 98.2%, but also completely remove individual impurities such as RRT0.54, RRT0.92, RRT0.97 and RRT1.08. For impurities that are difficult to remove by the amorphous slurry method, such as RRT0.63, RRT0.85, RRT0.92, RRT0.95, RRT0.97 and RRT1.21, the purification method of Form A crystallization has a more significant purification effect than that of the amorphous form.

[0117] The ability of Form A to remove difficult-to-remove impurities was also investigated by comparing purification methods using column chromatography followed by ethanol / water slurrying with Form A crystallization, as shown in Table 7. The results show that Form A achieved relatively good removal of impurities with RRT0.83 and RRT0.98, which are difficult to remove using column chromatography. In particular, Form A crystallization was able to control the impurity RRT0.98 (structural formula shown in Figure 14) below the detection limit. On the other hand, column chromatography purification is time-consuming and labor-intensive, with high production costs, demanding process equipment, and challenging impurity control. Purification using Form A crystallization is more environmentally friendly and offers advantages such as lower production costs.

Claims

1. A crystal form A of the free base of the compound shown in formula (I), formula (I), wherein the X-ray powder diffraction of crystal form A has characteristic peaks at diffraction angles 2θ of 5.28°±0.2°, 7.17°±0.2°, 8.50°±0.2°, 10.66°±0.2°, 14.33°±0.2°, 15.84°±0.2° and 18.60°±0.2°.

2. Crystal form A as claimed in claim 1, wherein crystal form A has a characteristic peak at one or more of the diffraction angles 2θ of 12.61°±0.2°, 14.83°±0.2°, 15.26°±0.2°, 16.57°±0.2°, 19.97°±0.2° and 21.97°±0.2°.

3. Crystal form A as claimed in claim 1 or 2, wherein crystal form A has characteristic peaks at diffraction angles 2θ of 12.61°±0.2°, 14.83°±0.2°, 15.26°±0.2°, 16.57°±0.2°, 19.97°±0.2° and 21.97°±0.2°.

4. Crystal form A as described in claim 1, wherein the X-ray powder diffraction (XRPD) pattern of crystal form A is substantially consistent with that in Figure 1.

5. A pharmaceutical composition comprising crystal form A as described in any one of claims 1 to 4, and a pharmaceutically acceptable carrier as desired.

6. A kit comprising crystal form A as described in any one of claims 1 to 4, and / or a pharmaceutical composition as described in claim 5.

7. The kit as claimed in claim 6, wherein the kit further comprises instructions for use in physical form and / or machine-readable electronic form.

8. Use of a crystal form A as described in any one of claims 1 to 4, a pharmaceutical composition as described in claim 5, and / or a kit as described in claim 6 or 7 for inhibiting or preventing bacterial growth, wherein the bacteria are selected from: Helicobacter pylori, Mycobacterium tuberculosis, nontuberculous mycobacteria, Bacteroides fragilis, Bifidobacterium longum, Prevotella, Clostridium perfringens, Clostridium difficile, Egertella tarda, Clostridium nucleoides, Gardnerella vaginalis, Movula tibeticum, Peptostreptococcus, Prevotella bisporus, and Veillonella microphylla.

9. Use of a crystal form A as described in any one of claims 1 to 4, a pharmaceutical composition as described in claim 5, and / or a kit as described in claim 6 or 7 for the preparation of a medicament for the treatment or relief of a disease caused by a bacterial infection or a related condition.

10. The use as claimed in claim 9, wherein the bacteria is selected from: Helicobacter pylori, Mycobacterium tuberculosis, nontuberculous mycobacteria, Bacteroides fragilis, Bifidobacterium longum, Prevotella, Clostridium perfringens, Clostridium difficile, Egertella tarda, Clostridium nucleoides, Gardnerella vaginalis, Movula tibeticum, Peptostreptococcus, Prevotella bisporus, and Veillonella septembin.

11. The use as described in claim 10, wherein the disease or related symptoms are selected from: gastritis, gastric ulcer, bacterial vaginosis, diarrhea, pneumonia, endometritis, peritonitis, salpingitis, sinusitis, pelvic inflammatory disease; and upper respiratory tract infection, lower respiratory tract infection, skin and soft tissue infection, lung infection, abdominal infection, oral infection and surgical infection.

12. A method for preparing crystal form A as described in any one of claims 1 to 4, the method comprising crystallizing the compound of formula (I) in a solvent containing an alcohol solvent.

13. The method of claim 12, wherein the alcohol solvent is selected from one or more combinations of methanol, ethanol, n-propanol, isopropanol, n-butanol, isobutanol and tert-butanol.

14. The method as claimed in claim 12 or 13, wherein the alcohol solvent is methanol, ethanol, or a combination thereof.

15. The method of claim 12, wherein crystallization in a solvent containing an alcohol solvent further comprises crystallization in an alcohol solvent.

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