WO2023232838A1

WO2023232838A1 - Bedaquiline for use in the treatment of leprosy

Info

Publication number: WO2023232838A1
Application number: PCT/EP2023/064481
Authority: WO
Inventors: Zuleima AGUILAR; Miao Wang; Nyasha Dorothea BAKARE
Original assignee: Janssen Pharmaceutica Nv
Priority date: 2022-05-31
Filing date: 2023-05-31
Publication date: 2023-12-07

Abstract

The present invention relates to a new use of bedaquiline.

Description

BEDAQUILINE FOR USE IN THE TREATMENT OF LEPROSY

Field of the Invention

The present invention relates to a new use of bedaquiline, in the treatment of leprosy. In particular, it relates to the clinical use of bedaquiline in such treatment, for instance measured by specific end points using a mouse footpad assay.

Background of the Invention

Leprosy, also known as Hansen’s disease is an infection caused by slow-growing bacteria, specifically Mycobacterium leprae (CK Mycobacterium lepromatosis). And typically the disease is found in developing countries. It can affect the nerves, skin, eyes and lining of the nose. The bacteria attach to the nerves, which can become swollen under the skin. This can cause the affected areas to lose the ability to sense touch and pain. Further, physical symptoms may manifest such as lighter or darker skin colour, often dry or flaky, with loss of feeling or reddish skin colour due to inflammation. If left untreated, the nerve damage can result in paralysis of hands and feet. In very advanced cases, the person may have multiple injuries due to lack of sensation and eventually display other drastic symptoms, including apparent loss of toes and fingers, corneal ulcers, eyebrow loss and saddle-nose deformity. In addition, there remains a lot of stigma and prejudice about the disease and those suffering from it - often being discriminated against and forcing those people into isolation.

Leprosy spreads slowly, also due to the slow growing bacteria Mycobacterium leprae, and it may take up to 20 years to develop signs of the infection. It can be spread between people, although it has a low pathogenicity and 95% of those who contract the Mycobacterium leprae do not develop the disease. Early diagnosis is clearly preferred and, once diagnosed, it can be treated - currently with multidrug therapy - for instance paucibacillary leprosy may be treated with the medications dapsone, rifampicin and clofazimine for six months and multibacillary leprosy for 12 months. For instance, the WHO recommends such multi-drug therapy (MDT) in adults where rifampicin is administered at 600mg once a month, clofazimine at 300mg once a month and 50mg daily and dapsone at lOOmg daily for either the 12-month (multibacillary leprosy) or 6-month (paucibacillary leprosy) duration. Clearly, alternatives to the typical three antibiotics are desirable, including shorter, better-tolerated and/or more effective therapies/regimes. Bedaquiline, or (lR,2S)-l-(6-bromo-2-methoxyquinolin-3-yl)-4-(dimethylamino)-2- naphthalen-l-yl-l-phenylbutan-2-ol, is a mycobacterium adenosine 5 ’-triphosphate (ATP) synthase inhibitor that has been developed as a part of a combination therapy for the treatment of pulmonary multidrug-resistant tuberculosis (MDR-TB) in adult patients. Bedaquiline, in the form of a fumarate salt, has been approved for that indication under certain conditions under the tradename Sirturo® in territories including the US, Brazil, Japan, Russia, the EU, South Africa and the Republic of Korea.

The marketed bedaquiline product Sirturo® is a tablet containing bedaquiline fumarate, or (1R, 2S)-l-(6-bromo-2 -methoxy quinolin-3-yl)-4-(dimethylamino)-2 -naphthal en-l-yl- l-phenylbutan-2-ol, fumarate salt, with 100 mg of bedaquiline active ingredient. The fumarate salt can be prepared by reacting the corresponding free base of bedaquiline with fumaric acid in the presence of a suitable solvent, such as for example isopropanol. In the adult population, the first approval in Europe relates to the use of Sirturo® as a part of a combination regimen for pulmonary MDR-TB under certain conditions (when an effective treatment regimen cannot otherwise be composed for reasons of resistance or tolerability). Therein it is indicated (amongst other things) that Sirturo® should be used in combination with at least three other medicinal products to which the patient’s isolate has been shown to be susceptible in vitro. If in vitro testing results are unavailable, treatment may be initiated with Sirturo® in combination with at least four medicinal products to which the patient’s isolate is likely to be susceptible. The product may also be administered by directly observed therapy (DOT). The recommended dosage is: (i) Weeks 1-2: 400 mg (4 tablets of 100 mg) once daily; and (ii) Weeks 3-24: 200 mg (2 tablets of 100 mg) three times per week (with at least 48 hours between doses). The total duration of treatment with Sirturo® is 24 weeks. Other medicinal products that are used in combination may or should continue after completion of treatment with Sirturo®.

Bedaquiline is known to show activity against Mycobacteria including drug resistant strains, in particular AT. tuberculosis, M. bovis, M. avium, M. leprae, M. marinum, M. leprae, M. kansasii, and M. abscessus. The active ingredient, including salt thereof, shows activity against active, sensitive, susceptible Mycobacteria strains and latent, dormant, persistent Mycobacteria strains.

International Patent Application Publication No. WO 2004/011436 disclosed the activity of the free base of bedaquiline against Mycobacteria, including Mycobacterium leprae. Later documents such as International Patent Application Publication Nos. WO 2005/117875 and WO 2006/067048 disclose the use of bedaquiline in the treatment of inter alia drug resistant tuberculosis and latent tuberculosis. International Patent Application Publication No. WO 2008/068231 described the suitability of the fumarate salt as a drug product indicating its acceptable bioavailability. The fumarate salt of bedaquiline is described as non-hygroscopic and stable. This document also discloses the preparation of certain formulations and tablets containing bedaquiline fumarate. Further, international patent application WO 2020/144197 discloses bedaquiline as a part of a regimen in the treatment of a disease associated with nontuberculosis mycobacteria (Mycobacterium avium), pulmonary disease.

In addition to bedaquiline’ s ATP synthase mode of action and in vitro activity against mycobacteria (specifically Mycobacterium leprae), there is also evidence of its activity in mouse models, for instance in Ji et al, Antimicrobial Agents and Chemotherapy, 2006 Apr, 50(4): 1558-1560 (where it is referred to as R207910) where the mouse model is of a non-established infection, and Gelber et al, Antimicrobial Agents and Chemotherapy, 2009 Sep, 53(9): 3989-3991 where there was an established infection in the mouse model and bedaquiline (R207910) was seen to be bactericidal against Mycobacterium leprae in mice at low dose when administered intermittently.

However, bedaquiline had not been tested in humans for treating leprosy.

As described herein, there is currently a need for new effective clinical treatments for leprosy. There is now provided evidence that bedaquiline is effective clinically, which efficacy can be measured with specific end points. In fact there is now provided the first proof of concept of the efficacy of bedaquiline in treating a disease due to Mycobacterium leprae (including the harder to treat multibacillary leprosy disease due to Mycobacterium leprae).

In an embodiment of the invention, there is provided bedaquiline, or a pharmaceutically acceptable salt thereof (e.g. a fumarate salt form), for human use in the treatment of a (leprosy) disease due to Mycobacterium leprae (M leprae), wherein the bedaquiline, or pharmaceutically acceptable salt thereof, is safe and effective at killing the M leprae in the human subject. In a further embodiment, the leprosy disease due to Mycobacterium leprae is multibacillary (MB) leprosy disease, which is essentially the form that is harder to treat and is the biggest unmet need within leprosy. In an embodiment, the human subject that is being treated is treatment naive. In a further embodiment, there is provided bedaquiline, or a pharmaceutically acceptable salt thereof, for human use in the treatment of MB Mycobacterium leprae disease, wherein such disease: a) is defined as 6 or more skin lesions or extensive confluent lesions or diffuse skin involvement, and is either borderline lepromatous or polar lepromatous, as determined using Ridley and Jopling classification system; and b) has a bacteriological index of >=4+ from the lesion biopsy obtained at screening, and a bacteriological index of >= 1+ from each of 4 slit skin smear assessments taken at screening.

In an embodiment, there is provided bedaquiline, or a pharmaceutically acceptable salt thereof, for human use in the treatment of a leprosy disease due to M leprae (e.g. MB leprosy disease), wherein the bedaquiline is part of a treatment regimen, and is itself administered in a dosing regimen comprising 200 mg of bedaquiline or a pharmaceutically acceptable salt thereof once daily for two weeks followed by 100 mg of bedaquiline or a pharmaceutically acceptable salt thereof three times weekly for six weeks (for instance, with at least 48 hours between doses). In such an embodiment, there is further provided such a treatment regimen (of which bedaquiline is a part) that comprises co-administration of bedaquiline (or a pharmaceutically acceptable salt thereof) for those eight weeks with one or more other antibacterials that are effective at killing M leprae. In a further embodiment, such a treatment regimen continues after 8 weeks, for instance up to six months or up to a year, which in an embodiment may:

- continue with the same antibacterials as for the first 8 weeks

- continues with the same antibacterials as for the first 8 weeks, but without bedaquiline.

In an embodiment, there is also provided a treatment regimen for use in the treatment of a leprosy disease due toM leprae (e.g. MB mycobacterium leprae) comprising (or consisting of):

- bedaquiline, or pharmaceutically acceptable salt thereof, that is safe and effective at killing the M leprae in a human subject; and

- one or more other antibacterials that are effective at killing M leprae.

For instance, in an embodiment, such a treatment regimen as defined above, may comprise one wherein:

- the bedaquiline is administered in a dosing regimen comprising 200 mg of bedaquiline or a pharmaceutically acceptable salt thereof once daily for two weeks followed by 100 mg of bedaquiline or a pharmaceutically acceptable salt thereof three times weekly for six weeks (for instance, with at least 48 hours between doses).

For instance, in an embodiment, such a treatment regimen as defined above, may further comprise one or more other antibacterials that are co-administered with bedaquiline for the first 8 weeks. In an embodiment, there is also provided a treatment regimen, wherein after the first 8 weeks treatment is continued (optionally without bedaquiline) for up to six months or up to a year.

In a key embodiment, there is also provided a process for preparing a combination treatment regimen as defined hereinbefore, which comprises:

- bringing into association each of the components (e.g. as separate pharmaceutical formulations) of the combination product and co-packaging (e.g. as a kit of parts) or indicating that the intended use is in combination (with the other components) - for instance to form a blister pack, with instructions on dosing regimen of each of the components; and/or

- bringing into association each of the components in the preparation of a pharmaceutical formulation comprising such components.

In an embodiment of the invention, there is provided a method of treating a disease due to Mycobacterium leprae (e.g. multibacillary leprosy disease), the method comprising administering to a subject in need thereof a therapeutically effective amount of bedaquiline or a pharmaceutically acceptable salt thereof. For instance, in an embodiment, there is provided a method of treating a disease due to Mycobacterium leprae (e.g. MB leprosy disease), the method comprising administration to a subject in need thereof using a dosing regimen comprising (or consisting of) 200 mg of bedaquiline or a pharmaceutically acceptable salt thereof once daily for two weeks followed by 100 mg of bedaquiline or a pharmaceutically acceptable salt thereof three times weekly for six weeks (for instance, with at least 48 hours between doses). In an embodiment, the subject in need thereof has a) multibacillary (MB) leprosy, defined as 6 or more skin lesions or extensive confluent lesions or diffuse skin involvement, and is either borderline lepromatous or polar lepromatous, as determined using Ridley and Jopling classification system; and b) has a bacteriological index of >=4+ from the lesion biopsy obtained at screening, and a bacteriological index of >= 1+ from each of 4 slit skin smear assessments taken at screening. In a further embodiment, the subject to be treated (for a disease due to M leprae) as mentioned herein is a human subject that may be treatment naive.

In an embodiment, there is provided a method of medical treatment as hereinbefore described, further comprising administering to the subject, after termination of the dosing regimen, one or more further antibacterials for treating Mycobacterium leprae or administering a known multi-drug dosing regimen for leprosy. In a further embodiment, the multi-drug dosing regimen for leprosy comprises rifampicin, clofazimine, and dapsone.

The drug components described herein can be used in free drug form or as a pharmaceutically acceptable salt or co-crystal thereof. The drug components (including free forms and salt or co-crystal forms) can be used in solvate forms with suitable solvents, including water (e.g., hydrate form or alcoholate form, in particular a hydrate form such as a hydrate, monohydrate, or dihydrate). Bedaquiline can be used in a free base form or as a suitable pharmaceutically acceptable salt form, such as an acid addition salt form. In an embodiment, bedaquiline is administered in the form of a salt thereof, such as bedaquiline fumarate. In particular, it is administered in the form marketed currently (for tuberculosis) known as Sirturo®.

The pharmaceutically acceptable acid addition salts are defined to comprise the therapeutically active non-toxic acid addition salt forms that bedaquiline is able to form. Said acid addition salts can be obtained by treating the free form of the drug component with an appropriate acid, for example an inorganic acid, for example hydrohalic acid, in particular hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid and phosphoric acid ; or an organic acid, for example acetic acid, hydroxyacetic acid, propanoic acid, lactic acid, pyruvic acid, oxalic acid, malonic acid, succinic acid, maleic acid, fumaric acid, malic acid, tartaric acid, citric acid, methanesulfonic acid, ethanesulfonic acid, benzenesulfonic acid, p-toluenesulfonic acid, cyclamic acid, salicyclic acid, p-aminosalicylic acid and pamoic acid. Conversely, the acid addition salt forms can be converted into the free forms by treatment with an appropriate base. In particular, the fumarate salt is considered for bedaquiline, given that this is the form employed in the already -marketed product Sirturo®. The fumarate salt of bedaquiline can be prepared by reacting the corresponding free base with fumaric acid in the presence of a suitable solvent, such as for example isopropanol. For the drug components discussed herein, each drug component may be used in a single stereoisomeric form or as a mixture of stereoisomers, if applicable. Whenever reference to bedaquiline is employed herein, we refer to the single stereoisomeric form that is employed in the marketed product Sirturo®, and which is disclosed in Inti. Pat. Appln. Publ. No. W02004/011436 as an antimycobacterial agent.

For instance, bedaquiline may be administered as a tablet, e.g. formulated as the fumarate salt and containing 100 mg of the active ingredient bedaquiline.

The treatment regimen described herein may be considered alongside the WHO guidelines. In an embodiment, bedaquiline is administered after food (for instance, straight after food or with food), as that may increase the bioavailability of the drug.

Due to its unique mode of action (inhibition of ATP synthase), bedaquiline represents a new class of anti-mycobacterial compounds and currently, no other drugs belonging to the same pharmacological class are available, thus minimizing the potential for crossresistance. The combinations of the treatment regimens described herein thus have an advantage that bedaquiline is a component thereof.

Bedaquiline, or its pharmaceutically acceptable salt thereof, or treatment regimens of the invention containing bedaquiline (or its salt) as described herein may be considered safe and effective, and the first proof of concept (of killing Mycobacterium leprae,' and hence safe and effective in treating a leprosy disease) in human subjects. This has the potential therefore to lead to a lot of clinical innovation to ultimately lead to further drugs/regimens that could be placed on the market in order to help Mycobacterium leprae patient populations, especially patients with multibacillary (MB) mycobacterium leprae (or a MB leprosy disease due to M leprae).

The term “safe”, as it relates to a dose, dosage regimen, treatment or method of the present invention, refers to a favorable risk:benefit ratio with an acceptable frequency and/or acceptable severity of treatment-emergent adverse events (referred to as AEs or TEAEs) compared to the standard of care or to another comparator. An adverse event is an untoward medical occurrence in a patient administered a medicinal product. Specifically, in relation to the invention, safety and tolerability would be monitored throughout the 8-week study (at specific time points that may be predetermined), and “safe” may be assessed based on safety parameters that would include adverse events, clinical laboratory tests (chemistry, hematology, coagulation, and urinalysis), 12-lead electrocardiogram (ECG) (performed in triplicate), vital signs (body temperature, blood pressure, pulse rate, and respiratory rate), weight, and physical examinations. Subjects would also be assessed for emergence of new or worsening lepra reactions and specific toxicities (including aspartate aminotransferase [AST] and/or alanine aminotransferase [ALT] elevations, pancreatic amylase elevation, gastrointestinal system toxicities, musculoskeletal system and cardiac muscle toxicities, and cardiac rhythm disturbances); further during the follow-up period (Week 8 to Week 12), safety assessments will include 12-lead ECGs, and clinical laboratory tests as indicated in a predetermined schedule specifying such time points. Subjects who meet certain QTcF and/or laboratory criteria would also have safety assessments at Weeks 14 and 16; thereafter survival status may be monitored - these parameters are all considered in the context of “safe”.

The term “safe and effective” amount refers to an amount of an active ingredient that elicits the desired biological or medicinal response in a subject’s biological system without the risks outweighing the benefits of such response in accordance with the Federal Food, Drug, and Cosmetic Act, as amended (secs. 201-902, 52 Stat. 1040 et seq., as amended; 21 U.S.C. §§ 321-392). Safety is often measured by toxicity testing to determine the highest tolerable dose or the optimal dose of an active pharmaceutical ingredient needed to achieve the desired benefit. Studies that look at safety also seek to identify any potential adverse effects that may result from exposure to the drug. Efficacy is often measured by determining whether an active pharmaceutical ingredient demonstrates a health benefit over a placebo or other intervention when tested in an appropriate situation, such as a tightly controlled clinical trial.

The terms "efficacy" and “effective” as used herein in the context of a dose, dosage regimen, treatment or method refer to the effectiveness of a particular dose, dosage or treatment regimen. For instance, specifically in the context of the invention, efficacy at killing leprae may be measured by: full bactericidal effect by Week 8 (e.g. in all human subjects), as measured using the mouse foot pad assay marked clinical improvement in skin lesions (e.g. in all human subjects) by Week 7 or Week 8; and/or

- undetectable AL leprae (e.g. in all human subjects) as measured by qRT-qPCR at Week 8

For instance, a treatment may be effective if bacterial growth is decreased after treatment, relative to baseline, as evidenced by a mouse footpad assay, or, if there is inhibition of bacterial growth in a biological sample (e.g. a human biological sample, a mouse biological sample), after administration of the treatment.

As used herein, “effective amount” may also refer to the amount of each of the components of the combinations of the invention, or any pharmaceutically acceptable salts thereof, that elicits the biological or medicinal response in a tissue system (e.g., blood, plasma, biopsy) or warm-blooded animal (e.g., human), that is being sought by a health care provider, which includes alleviation of the symptoms of the disease being treated.

As mentioned herein, the combination of drug components as described herein may be co-administered, sequentially administered, or administered substantially simultaneously (as described herein). Hence the individual dosage forms of each of the drug components can be administered as separate forms (e.g. as separate tablets or capsules) as described herein.

In an embodiment, there is provided a process for preparing a combination product as defined herein comprising:

- bringing into association each of the components (e.g. as separate pharmaceutical formulations) of the combination product and co-packaging (e.g. as a kit of parts) or indicating that the intended use is in combination (with the other components) - for instance a blister pack as described herein; and/or

All dosage amounts mentioned in this disclosure refer to the free base equivalent (i.e. calculated with respect to the free base form of the particular drug component). The values given below represent free-form equivalents, i.e., quantities as if the free form would be administered. If salts are administered the amounts need to be calculated in function of the molecular weight ratio between the salt and the free form.

The daily doses described herein are calculated for an average body weight of about 70 kg and should be recalculated in case of paediatric applications, or when used with patients with a substantially diverting body weight.

There may be a need to have alternative regimens to the current leprosy regimens. For instance, the regimens of the invention may have the advantage that they are more efficacious (for instance, as measured through a number of means, including by assays such as those described herein, visual improvements including through photographs or certain scales used in the field), have a better safety profile, have a shorter treatment duration, be better tolerated and/or have fewer side effects than existing or recommended treatment regimens (e.g. recommended by WHO).

The following examples are merely illustrative and are not intended to limit the disclosure to the materials, conditions, or process parameters set forth therein

Examples

Example 1: Clinical testing - An open-label Study to Evaluate the Efficacy and Safety of TMC207 (bedaquiline fumarate, Sirturo®) in Subjects with Multibacillary leprosy

OBJECTIVES

Primary Objective

While ongoing, the primary objective was to assess the efficacy of an 8-week TMC207 (bedaquiline fumarate, marketed as Sirturo®) regimen in human subjects with treatment-naive multibacillary (MB) leprosy.

Secondary Objectives

The secondary objective was to assess the overall safety of TMC207 in subjects with MB leprosy. There were also several exploratory objectives.

ENDPOINTS

Primary Endpoint

In the human subjects, the change was measured from baseline in the odds of Mycobacterium leprae (M leprae) growth in mouse footpads following 8 weeks of treatment with TMC207, using a mouse footpad assay to assess the viability of M. leprae in skin biopsy samples collected from the human subjects (after the 8-week course of TMC207 monotherapy).

Change from baseline in the odds of M. leprae growth in mouse footpads would be evaluated. M. leprae bacilli extracted from the human subjects’ skin biopsy samples would be inoculated in footpads of mice, according to the method of Shepard. M. leprae growth would be determined by technologists trained and experienced in mouse footpad procedures, at 1 year after inoculation (or at mouse death or humane endpoint, if it occurs greater than or equal to [>=] 6 months after footpad inoculation). The number of footpads with positive growth (>= 10^A5 M. leprae) will be counted and used to determine the odds of bacterial growth.

Secondary Endpoints

The secondary endpoints were number and severity of adverse events (up to 124 weeks, as the study is ongoing).

Number of Participants with Adverse Events (AEs): An adverse event is any untoward medical event that occurs in a participant administered an investigational product, and it does not necessarily indicate only events with clear causal relationship with the relevant investigational product.

Number of Participants with AEs by Severity: Severity of adverse events would be graded by using division of microbiology and infectious diseases (DMID) adult toxicity scale to estimate grade of severity. Severity scale ranges from Grade 1 (Mild) to Grade 4 (Life-threatening). Grade 1= Mild, Grade 2= Moderate, Grade 3= Severe, and Grade 4= Life-threatening.

The exploratory endpoints included an analysis of viable Mycobacterium leprae in mouse footpads following 8 weeks of treatment with TMC207, as compared with baseline, as well as an assessment by an investigator of skin lesions (from the human subjects) and a sponsor assessment of clinical photographs (of various parts of the human subjects, including the face and ears, depending on exactly where the lesions were; hence including frontal face, left and right side of head/neck, and front and back of upper and lower body), following 8 weeks of treatment with TMC207 as compared with baseline.

Study Design

This was an open-label study to assess the potential efficacy of TMC207 for the treatment of leprosy. Approximately 10 subjects were enrolled in order to have at least 8 completed subjects with evaluable biopsy data. Subjects with MB leprosy (either borderline lepromatous or polar lepromatous), without a history of leprosy treatment or lepra reactions requiring treatment with prohibited therapies, and with a high lesion biopsy bacteriological index (>4+) and a bacteriological index of >1+ in slit skin smears from at least 4 anatomical sites were recruited. This study consisted of an eligibility screening examination (between 28 days and 1 day prior to the first dose), an 8-week open-label treatment period, and a 112-week follow-up period.

During the open-label treatment period, subjects received an initial dose of TMC207 200 mg daily for 2 weeks, and subsequently 100 mg 3 times per week (tiw) for 6 weeks (for instance with at least 48 hours between doses - however, in the event that there would be a minor protocol deviation, e.g. of a time period of minutes or hours, this was assessed to not have a major clinical impact).

At the completion of the 8-week open-label treatment period, subjects were treated for MB leprosy as directed by their physician. Following the last dose of TMC207, subjects returned to the clinic during Weeks 10 and 12 for follow up safety assessments during the transition to new pharmacotherapy. Subjects who meet certain QTcF and/or laboratory criteria would also have safety assessments at Weeks 14 and 16. Thereafter, subjects would be contacted every 18 weeks (±2 weeks) through Week 120 to obtain their survival status.

The total study duration for each subject would be up to 124 weeks (approximately), including screening. The end of the trial is defined as the last planned trial-related contact of the last subject.

Subject Population

Approximately 10 subjects, aged 18 to 65, inclusive, were enrolled in order to have at least 8 completed subjects with evaluable biopsy data. Subjects with MB leprosy without a history of leprosy treatment with a high bacteriological index (>4+) in the lesion biopsy and a bacteriological index of >1+ in slit skin smears from at least 4 anatomical sites were recruited.

Additional subjects could be enrolled if replacement subjects were required.

Dosage and Administration

Subjects enrolled in the open-label treatment period would receive 200 mg TMC207, administered as two 100 mg tablets daily for 2 weeks, and subsequently 100 mg TMC207, tiw for the next 6 weeks.

Efficacy Evaluations

Prior to the initiation of TMC207 (baseline) and predose (or prior to dosing) on Days 14, 28, and 56, subjects would undergo skin lesion punch biopsies, and M. leprae bacilli from these samples would be inoculated in footpads of mice, according to the method of Shepard (Shepard CC). The experimental disease that follows the injection of human leprosy bacilli into footpads of mice. J Exp Med. 1960; 112:445- 454). M. leprae viability and growth will be determined by technologists trained and experienced in mouse footpad procedures, at 1 year after infection (or at mouse death or humane endpoint, if it occurs >6 months after footpad inoculation).

Clinical evaluations were performed at visits as specified in the Time and Events Schedule. Lesion changes will be graded numerically in comparison with baseline as: worse (-1), no change (0), some improvement (1), or marked improvement (2), and in comparison with the most recent assessment as: worse, no change, or improved. Data will be summarized using descriptive statistics and frequency tables.

Pharmacokinetic Evaluations

Blood samples for measurement of plasma levels of TMC207 and its M2 metabolite would be collected during the study. Blood samples for PK evaluations would be collected at specified time periods. For the avoidance of doubt, the M2 metabolite of bedaquiline is known, it is active and is essentially the methyl-substituted metabolite, formed as a result of N-dem ethylation of the di-methyl substituted amino group.

Pharmacodynamic Evaluations

Tissue from skin punch biopsies would be used to determine the viability of M. leprae using qRT-PCR. The viability of the M. leprae in each sample would be determined on the bacterial complementary deoxyribonucleic acid (cDNA), using Taqman technology, the standard curve method, and primers and probes specific for

leprae hspl8 and esxA transcripts

Assessment of TMC207 Resistance

To assess the development of mechanism-based resistance to TMC207, M. leprae DNA extracted from skin biopsies would be used to sequence the atpE gene (if bacterial load allows sufficient amplification).

Safety Evaluations

Safety and tolerability would be monitored throughout the study (at specific time points).

During the TMC207 treatment period (Week 1 to Week 8), safety parameters would include adverse events, clinical laboratory tests (chemistry, hematology, coagulation, and urinalysis), 12-lead electrocardiogram (ECG) (performed in triplicate), vital signs (body temperature, blood pressure, pulse rate, and respiratory rate), weight, and physical examinations. Subjects would also be assessed for emergence of new or worsening lepra reactions and specific toxicities (including aspartate aminotransferase [AST] and/or alanine aminotransferase [ALT] elevations, pancreatic amylase elevation, gastrointestinal system toxicities, musculoskeletal system and cardiac muscle toxicities, and cardiac rhythm disturbances).

During the follow-up period (Week 8 to Week 12), safety assessments would include 12-lead ECGs, and clinical laboratory tests as indicated in the Time and Events Schedule. Subjects who meet certain QTcF and/or laboratory criteria would also have safety assessments at Weeks 14 and 16. During the remainder of the follow-up period subjects will be contacted every 18 weeks (±2 weeks) (at ~Weeks 30, 48, 66, 84, 102 and at Week 120) to check survival status.

STATISTICAL METHODS

The sample size was determined as 8 subjects with MB leprosy. A target of 10 subjects would be enrolled to allow for at least 8 subjects to complete treatment and all assessments through Week 8.

Efficacy Analyses: To assess viability from biopsy samples (baseline, and Days 14, 28, and 56) the number of bacilli obtained from the hind footpads of mice infected with 5000, 500, and 50 AL leprae per footpad (except for the Day 56 biopsy for which only inoculum sizes of 5000 and 500 M. leprae per footpad would be used) would be enumerated 1 year after infection (or at mouse death or humane endpoint, if either occurs >6 months after footpad infection). It was planned that 10 individual footpads from each inoculum size would be harvested. The number of footpads with positive growth (>10 M. leprae) would be counted. A logistic regression would be used, with inoculation size and time points as variables, to model the binary outcomes of each footpad (growth versus no growth of M. leprae). The occurrence of bacterial growth would be modeled as a function of day and initial inoculum size; an interaction of the two predictor variables would be included if an effect could be identified. Random effects would be included to account for repeated measures from each subject. The efficacy of the treatment would be determined by testing whether the odds of bacterial growth were significantly decreased after 8 weeks, relative to baseline. Exploratory Efficacy Endpoints: Clinical Evaluation data would be summarized using descriptive statistics and frequency tables. The percentage of viable M. leprae in mouse footpads infected with inocula created from subjects’ biopsy samples collected at baseline and following 8 weeks of treatment with TMC207 would be calculated, and the probability that killing occurred and the probability that differences in M. leprae viabilities were recognized would be assessed by the method of Spearman and Karber (Shepard CC. Statistical analysis of results obtained by two methods for testing drug activity against Mycobacterium leprae. Int J Lepr. 1982; 50:96-101).

ARMS AND INTERVENTIONS

Treatment arm: participants received bedaquiline 200mg (2xl00mg tablets) once daily for 2 weeks followed by lOOmg tablet three times weekly (tiw) for 6 weeks (for instance with at least 48 hours between doses)

Inclusion Criteria

• Participant has: a) multibacillary (MB) leprosy, defined as 6 or more skin lesions or extensive confluent lesions or diffuse skin involvement, and is either borderline lepromatous or polar lepromatous, as determined using Ridley and Jopling classification system; and b) has a bacteriological index of >=4+ from the lesion biopsy obtained at screening, and a bacteriological index of >= 1+ from each of 4 slit skin smear assessments taken at screening

• Otherwise healthy on the basis of physical examination, medical history, vital signs, and 12-lead electrocardiogram (ECG) performed at screening. If there are abnormalities, they must be consistent with the underlying illness in the study population. This determination must be recorded in the participant's source documents and initialled by the investigator

• Otherwise healthy on the basis of clinical laboratory tests performed at screening. If the results of the serum chemistry panel, including liver enzymes, other specific tests, blood coagulation, hematology, or urinalysis are outside the normal reference ranges, the participant may be included only if the investigator judges the abnormalities or deviations from normal to be not clinically significant or to be appropriate and reasonable for the population under study. This determination must be recorded in the participant's source documents and initialled by the investigator • A man must agree not to donate sperm throughout treatment with TMC207 and for 3 months after treatment is stopped

• Willing and able to adhere to the prohibitions, restrictions, and long-term follow up requirements specified in this protocol

• If a woman is of childbearing potential, must be practising a highly effective method of birth control (failure rate of <1% per year when used consistently and correctly) before entry, and must also agree to use a barrier contraceptive method (that is, male or female condom, diaphragm or cervical cap) plus spermicide. Participant must also agree to continue to use a highly effective method of contraception plus a barrier method throughout treatment with TMC207 and until 6 months after treatment is stopped

Exclusion Criteria

• Has experienced or is experiencing a lepra reaction requiring treatment with a prohibited therapy

• Has a contraindication limiting the implementation of a medically accepted MB leprosy regimen

• a) Has ever received pharmacotherapy for leprosy; b) has ever been treated with a drug that is a component of the primary World Health Organization (WHO) regimen for the treatment of MB leprosy (example, dapsone, rifampicin, clofazimine). Short-term (<=2 weeks) pharmacotherapy with any antibiotic that could be used as a second line treatment for leprosy (eg, of the macrolide, quinolone, or tetracycline class) is acceptable as long as the last administration occurred >=4 weeks before first dose of study drug (TMC207)

• Has a concomitant infection that requires an additional systemic antimicrobial agent

• Has tuberculosis (TB), as determined by medical history and chest x-ray

• Is a woman who is pregnant, or breast-feeding, or planning to become pregnant while enrolled in this study or within 6 months after the last dose of study drug

MOUSE FOOT PAD (MFP) ASSAY

The MFP assay is described in Gelber et al., Antimicrobial Agents & Chemotherapy, Sept 2008, p. 3113-3117 (Powerful Bactericidal Activity of Moxifloxacin in Human Leprosy) as well as in Gelber etal., Antimicrobial Agents & Chemotherapy, Sept 2009, p. 3989-3991 (The Diarylquinoline R207910 Is Bactericidal against Mycobacterium leprae in Mice at Low Dose and Administered Intermittently). Essentially the method is one previously reported by Shepard, C. C. 1967, Int. J. Lepr. 35: 429-435 (A kinetic method for the study of activity of drugs against mycobacterium leprae in mice) as well as in other Shepard articles mentioned herein.

Essentially, several skin biopsies (from human subjects) for mycobacterium leprae were performed prior to therapy and on certain days after initiation of therapy, and mycobacterium leprae bacilli were therein inoculated in groups of hind footpads of mice in amounts of 50, 500 and 5000 (so 10-fold changes of dilution) mycobacterium leprae/footpad.

MFP Assay monitoring for patients in this clinical study

- Mouse foot pads were injected with dilutions of mycobacterium leprae isolated from skin biopsies at the indicated timepoints

Growth of 10⁵ mycobacterium leprae bacilli was considered evidence that the initial inoculum was viable (ideally 12 months after inoculation - viability from each biopsy sample was assessed, the number of bacilli obtained from the hind footpads is enumerated, preferably one year after infection (or at mouse death, if that death occurs 6 or more months after footpad infection))

Results

Preliminary Data Show Full Bactericidal Effect by Week 4 in First 3 Patients (MFP

Assay Primary Data)

- Preliminary data in first three participants show full bactericidal effect by Week 4

* Subject 2 not to be included in the final MFP data analysis (due to a major protocol deviation) - Subjects 4, 5 and 7 showed no footpads growing M. leprae as of Week 2, and

Subject 6 showed no footpads growing after Week 4

The selection of the primary endpoint (i.e., change in the odds of M. leprae growth following 8 weeks of treatment with TMC207, as measured in the mouse footpad assay) is, as mentioned, the gold standard. There is also an absence of other validated methods of assessing AT. leprae viability. The dosing duration of 8 weeks is expected to provide an adequate time period for a pilot assessment of the bactericidal efficacy of TMC207. In studies in the literature, 8 weeks has been sufficient to demonstrate complete killing of M. leprae with moxifloxacin, ofloxacin, clarithromycin, and minocycline (as measured by the mouse foot pad assay). As indicated, after 8 weeks, all subjects transitioned to the standard of care for leprosy (e.g., WHO regimen) upon completion of this study.

EVIDENCE OF SKIN LESION IMPROVEMENT

Skin lesion improvement is a key measurement of efficacy. Indeed, over the 8 weeks, the patients’ lesions were assessed (also through photographic assessment), and it was clear that the subjects had a marked improvement after 8 weeks of TMC 207 treatment. The improvement was seen even before 8 weeks, and even as early as after 1 week.

Results to show clinical evaluation of skin lesion improvement (n = number of subjects - and in fact 11 subjects were recruited) - this was an exploratory endpoint

n = the number of subjects this was not completed for one subject at the Week 4 visit

** one subject discontinued treatment in Week 5 due to use of prohibited medication

Preliminary data showed marked improvement in ten (10) participants by Week 7 - specifically, there was a demonstrated marked clinical improvement in skin lesions by Week 7. (However, one of those participants had a major protocol deviation.)

MOLECULAR VIABILITY ASSAY

A protocol has been developed to detect M. leprae mRNA in biopsies by Week 8 (which was an exploratory endpoint). The methodology may be found in the journal article “A Sensitive and Quantitative Assay to Enumerate and Measure Mycobacterium leprae Viability in Clinical and Experimental Specimens” by Linda Adams et al, Current Protocols e359, Volume 2 (doi: 10.1002/cpzl.359). Results

8 out of 10 of the subjects started with having detectable M leprae mRNA in skin biopsies, measured as being at least 10² hspl8 expression equivalents per 150 M leprae organisms (for instance at least about 10³ equivalents) - and hence it was detected by qRT-qPCR in 8 out of 10 patients

After 8 weeks, using this measurement, M leprae was undetectable in all subjects (one patient discontinued following use of a prohibited medication) OTHER RESULTS/CONCLUSIONS

- Marked and rapid skin lesion improvement was seen in enrolled patients with multibacillary leprosy following bedaquiline monotherapy, with a rapid bactericidal effect observed

Compared with baseline, PK data showed increased and sustained bedaquiline concentrations in the blood after the treatment started

- No safety concerns were identified as related to bedaquiline

Treatment was safe and well tolerated (up to now), based on the data generated to date from 11 enrolled subjects (at the dose being tested)

Claims

1. Bedaquiline, or a pharmaceutically acceptable salt thereof (e.g. a fumarate salt form), for human use in the treatment of a disease due to Mycobacterium leprae (M leprae), wherein the bedaquiline, or pharmaceutically acceptable salt thereof, is safe and effective at killing M leprae in the human subject.

2. Bedaquiline, or a pharmaceutically acceptable salt thereof, for human use as claimed in Claim 1, wherein the disease due to Mycobacterium leprae is multibacillary (MB) leprosy disease.

3. Bedaquiline, or a pharmaceutically acceptable salt thereof, for human use as claimed in Claim 2, wherein the MB leprosy disease: a) is defined as 6 or more skin lesions or extensive confluent lesions or diffuse skin involvement, and is either borderline lepromatous or polar lepromatous, as determined using Ridley and Jopling classification system; and b) has a bacteriological index of >=4+ from the lesion biopsy obtained at screening, and a bacteriological index of >= 1+ from each of 4 slit skin smear assessments taken at screening

4. Bedaquiline, or a pharmaceutically acceptable salt thereof, for human use as claimed in any one of the preceding claims, wherein the human subject is treatment naive.

5. Bedaquiline, or a pharmaceutically acceptable salt thereof, for human use as claimed in any one of the preceding claims, wherein the bedaquiline is part of a treatment regimen, and is itself administered in a dosing regimen comprising 200 mg of bedaquiline or a pharmaceutically acceptable salt thereof once daily for two weeks followed by 100 mg of bedaquiline or a pharmaceutically acceptable salt thereof three times weekly for six weeks (for instance, with at least 48 hours between doses).

6. Bedaquiline, or a pharmaceutically acceptable salt thereof, for human use as claimed in Claim 5, wherein the treatment regimen (of which bedaquiline is a part) comprises co-administration of bedaquiline (or a pharmaceutically acceptable salt thereof) for those eight weeks with one or more other antibacterials that are effective at killing M leprae.

7. Bedaquiline, or a pharmaceutically acceptable salt thereof, for human use as claimed in Claim 5 or 6, wherein the treatment regimen continues after 8 weeks, for instance up to six months or up to a year.

8. Bedaquiline, or a pharmaceutically acceptable salt thereof, for human use as claimed in Claim 7, wherein the treatment regimen:

- continues with the same antibacterials as for the first 8 weeks

9. Bedaquiline, or a pharmaceutically acceptable salt thereof, for use as claimed in any one of the preceding claims, wherein the efficacy at killing M. leprae is measured by: full bactericidal effect by Week 8 (e.g. in all human subjects), as measured using the mouse foot pad assay marked clinical improvement in skin lesions (e.g. in all human subjects) by Week 7 or Week 8; and/or

- undetectable M. leprae (e.g. in all human subjects) as measured by qRT-qPCR at Week 8

10. Bedaquiline, or a pharmaceutically acceptable salt thereof, for use as claimed in Claim 9, wherein the efficacy at killing M. leprae is measured by: full bactericidal effect by Week 8 (e.g. in all human subjects), as measured using the mouse foot pad assay

11. A treatment regimen, or combination product, for use in the treatment of a disease due to M leprae (e.g. MB leprosy disease) comprising (or consisting of):

- one or more other antibacterials that are effective at killing M leprae.

12. The treatment regimen, or combination product, as claimed in Claim 11, wherein:

13. The treatment regimen, or combination product, as claimed in Claim 12, wherein one or more other antibacterials are co-administered with bedaquiline for the first 8 weeks.

14. The treatment regimen, or combination product, as claimed in Claim 13, wherein after the first 8 weeks treatment is continued (optionally without bedaquiline) for up to six months or up to a year.

15. A process for preparing a treatment regimen or combination product as defined in any one of Claims 11-14, which comprises:

- bringing into association each of the components (e.g. as separate pharmaceutical formulations) of the combination product and co-packaging (e.g. as a kit of parts) or indicating that the intended use is in combination (with the other components); and/or

16. A combination product as claimed in any one of Claims 11-14 (for use in the treatment of a disease due to M leprae, including MB leprosy disease), which comprises either:

- each of the components (e.g. as separate pharmaceutical formulations) of the combination product together with instructions indicating that the intended use is in combination (with the other components)

- each of the components co-packaged (e.g. as a kit of parts, for instance a blister pack)

17. A method of treating a disease due o Mycobacterium leprae (e.g. multibacillary leprosy disease), the method comprising administering to a human subject in need thereof a therapeutically safe and effective amount of bedaquiline or a pharmaceutically acceptable salt thereof (and for instance, the bedaquiline is safe and effective at killing the M leprae).

18. A method of treating a disease due to Mycobacterium leprae (e.g. MB leprosy disease), the method comprising administration to a human subject in need thereof a dosing regimen comprising (or consisting of) 200 mg of bedaquiline or a pharmaceutically acceptable salt thereof once daily for two weeks followed by 100 mg of bedaquiline or a pharmaceutically acceptable salt thereof three times weekly for six weeks (for instance with at least 48 hours between doses (and for instance, wherein the bedaquiline is safe and effective at killing the M leprae)).

19. The method of claim 17 or 18, wherein the subject in need thereof has a) multibacillary (MB) leprosy, defined as 6 or more skin lesions or extensive confluent lesions or diffuse skin involvement, and is either borderline lepromatous or polar lepromatous, as determined using Ridley and Jopling classification system; and b) has a bacteriological index of >=4+ from the lesion biopsy obtained at screening, and a bacteriological index of >= 1+ from each of 4 slit skin smear assessments taken at screening.

20. The method of claim 19, wherein the human subject is treatment naive.

21. The method of claim 20, further comprising administering to the human subject, after termination of the dosing regimen, one or more further antibacterials for treating Mycobacterium leprae or administering a multi-drug dosing regimen for leprosy.

22. The method of claim 21, wherein the multi-drug dosing regimen for leprosy comprises rifampicin, clofazimine, and dapsone.

23. The method of any one of Claims 17-20, wherein bacterial growth is decreased after treatment, relative to baseline, as evidenced by a mouse footpad assay.

24. A method of inhibiting bacterial growth in a biological sample (e.g. a human biological sample, a mouse biological sample), comprising administering to a subject in need thereof a safe and effective amount of bedaquiline or a pharmaceutically acceptable salt thereof.