Method for synthesizing 9-aminomethyltetracycline compounds

Abstract

A method for synthesizing 9-aminomethyltetracycline compounds is disclosed. The method includes the steps of a) reacting minocycline and a hydroxymethylamide derivative to form 2,9-(methylamide substituted) minocycline and 2-(methylamide substituted) minocycline, b) reacting the 2,9-(methylamide substituted) minocycline from step a) with an amine or diamine to form a 9-aminomethyltetracycline intermediate, and c) reacting the 9-aminomethyltetracycline intermediate from step b) with an aldehyde in the presence of a reducing agent to form a 9-aminomethyltetracycline compound, or d) reacting the 9-aminomethyltetracycline intermediate from step b) with an alkyl halide or alkyl reagent to form a 9-aminomethyltetracycline compound. Step b) may be operated in the absence of a hydrogenation reaction. The method may be a semi-continuous or continuous flow process. Optionally, in a semi-continuous flow process, two of steps a), b) and c) or d) can be carried out without the use of a batch reactor and without the need to isolate intermediate products between reaction steps, for example steps b) and c) or steps b) and d) can be operated continuously using the 9-aminomethyltetracycline intermediate formed in step b) directly in step c) or d). The 9-aminomethyltetracycline compound formed in step c) or d) can be omadacycline.

Description

[Technical field]

[0001] The present invention relates to new and improved processes for the preparation of 9-aminomethyltetracycline compounds known from the prior art (US Pat. No. 9,365,500), including, but not limited to, omadacycline. [Background technology]

[0002] Antibiotics are essential life-saving drugs that have revolutionized medicine starting with the discovery of penicillin in 1928 (Singh, S.; Barrett, J. Empirical Antibacterial Drug Discovery-Foundation in Natural Products. Biochem. Pharmacol. 2006, 71, 1006-1015). Since then, a large number of highly effective antibiotics have been discovered and developed for clinical use in the treatment of bacterial infections (Brown, E.; Wright, G. Antibacterial Drug Discovery in the Resistance Era. Nature 2016, 529, 336-343). Many of these antibiotics have broad-spectrum activity and are effective in treating infections caused by gram-positive and gram-negative bacteria, while others are only effective against gram-positive bacteria. An ideal antibiotic would be an antibacterial agent that kills or inhibits the growth of harmful bacteria in the host regardless of the site of infection, without affecting beneficial microorganisms (such as gut / skin flora). In either case, whether ideal or not, antibiotics have not remained effective forever, mainly due to over- or inappropriate prescription, leading to the emergence and increasing spread of multidrug-resistant bacteria (Singh, S.B.; Young, K.; Silver, L.L. What Is an “Ideal” Antibiotic? Discovery Challenges and Path Forward. Biochem. Pharmacol. 2017, 133, 63-73).

[0003] Antimicrobial resistance (AMR) reduces our ability to treat infections and threatens our ability to perform routine surgery. It is a problem of global concern with serious health and economic consequences, as highlighted in the EU One Health Action Plan on AMR (European Commission. A European One Health Action Plan against Antimicrobial Resistance (AMR); 2017) and the US government report on the threat of antibiotic resistance (US Department of Health and Human Services, Antibiotic Resistance Threats in the United States-Report 2019; 2019). A key challenge is the excessive and inappropriate use of antimicrobials in veterinary and human healthcare, leading to the emergence of resistance, which is estimated to result in 33,000 deaths annually in the EU / EEA and over 35,000 deaths in the US (Cassini, A.; Hogberg, LD; Plachouras, D.; Quattrocchi, A.; Hoxha, A.; Simonsen, GS; Colomb-Cotinat, M.; Kretzschmar, ME; Devleesschauwer, B.; Cecchini, M.; Ouakrim, DA; Oliveira, TC; Struelens, MJ; Suetens, C.; Monnet, DL Attributable Deaths and Disability-Adjusted Life-Years Caused by Infections with Antibiotic-Resistant Bacteria in the EU and the European Economic Area in 2015: A Population-Level Modelling Analysis. Lancet 2019,19,56-66).It is currently estimated that someone dies every minute and 23 seconds due to drug-resistant infections, and by 2050, if research and development of new drugs and treatments continues at this pace, the death toll could be a staggering 1 every 3 seconds (O'Neill, J. Tackling Drug-Resistant Infections Globally: Final Report and Recommendations; 2016). Current incentive models do not provide a sustainable solution, and new business approaches are needed, including new incentives and new pricing systems for developing antimicrobials.

[0004] Investment in research and development for innovative medicines and treatments is essential to advance disease prevention and treatment. Access to safe, high-quality and effective medicines is a key component of societal well-being (European Commission. Pharmaceutical Strategy for Europe 2020;2020). The continued development of new antibacterial agents is recognized as crucial for human health. In the face of increasing resistance, new antibacterial agents suitable for the treatment of infections in patients are needed. Furthermore, in recent years, there have been efforts to reevaluate the dosage regimens of some approved drugs to maximize their efficacy and minimize the risk of selecting resistant bacteria (EMEA Guideline on the Evaluation of Medicinal Products Indicated for Treatment of Bacterial Infections (Draft). EMEA Eur. Med. Agency 2010,44 (February),1-26). However, few new antibiotics have been brought to the market due to lack of commercial interest (Wright, GDPerspective Antibiotics: A New Hope. Chem. Biol. 2012, 19(1), 3-10). Currently, due to lack of commercial interest or limitations in science, investments are not always focused on the greatest unmet needs. For example, there is a lack of development of new antibacterial agents, treatments, or vaccines for emerging health threats (including those such as the COVID-19 pandemic, such as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) or Middle East Respiratory Syndrome (MERS)), and a lack of treatments for certain population groups, such as pregnant and breastfeeding women and the elderly. Given the lack of treatment options to address AMR, the development of novel antibacterial agents or alternatives is a prime example of unmet medical need. Identification of new biochemical targets to create different classes of drugs is complex, and in that case, there are economic challenges associated with low return on investment.As new antibiotics continue to develop and enter the market without bacterial resistance, the guidelines are to reserve these drugs as a last resort when all other treatment options have failed, and therefore sales are limited. To compensate for this issue, many antibiotics, including low-cost generic versions, are already present in the clinic (Sertkaya, A.; Eyraud, J.; Birkenbach, A.; Franz, C.; Ackerley, N.; Overton, V. Analytical Framework for Examining the Value of Antibacterial Products.; Washington DC, 2014).

[0005] In 2012, GAIN (Generating Antibiotic Incentives Now) was signed into law as part of the US Food and Drug Administration Safety and Innovation Act. Incentives were created for sponsors to bring to market antibiotics and antifungals intended to treat serious or life-threatening infections (known as QIDPs-Qualified Infectious Disease Products). Sponsors may request a GAIN for their drugs, and the FDA will review the request and respond within 60 days of submission (FDA Generating Antibiotics Incentive Now; 2017).

[0006] Sponsors who develop and submit applications for QIDPs may be eligible to receive incentives through GAIN. The primary incentive included in GAIN is that designation as a QIDP qualifies the company for an additional five years of marketing exclusivity to the certain exclusivity already provided by the Food, Drug, and Cosmetic Act. GAIN also manufactures drugs designated as QIDPs that qualify for fast track designation. Finally, GAIN requests that FDA grant priority review to the first application submitted for approval of a QIDP.

[0007] tetracycline Tetracyclines, a broad-spectrum class of antibiotics, are inhibitors of bacterial growth by inhibiting protein synthesis. In general, they bind to the bacterial 30S ribosomal subunit and prevent the addition of amino acids to the growing polypeptide chain. (U.S. Pat. No. 9,365,500, Bradford, P.; Jones, C. Antibiotic Discovery and Development-Chapter 5(Tetracyclines); Springer, Boston, MA, 2012). Since the first tetracycline was discovered, tetracyclines have been proven safe and effective for 70 years (Bradford, P.; Jones, C. Antibiotic Discovery and Development-Chapter 5(Tetracyclines); Springer, Boston, MA, 2012).

[0008] [ka]

[0009] In 1945, Benjamin Duggar isolated 7-chlorotetracycline (compound 1, formula 2) from a bacterial culture (Duggar, BMAureomycin: A Product of the Continuing Search for New Antibiotics. Ann. NY Acad. Sci. 1948, 51, 177-181) which was approved for human use in 1948 (Lederle Laboratories: https: / / www.accessdata.fda.gov / scripts / cder / daf / index.cfm?event=overview.process&ApplNo=050404). Two years later, 5-oxytetracycline (compound 2, formula 2) was isolated by Pfizer scientists (Finally, A.; Hobby, G.; Regna, P.; Routien, J.; Seeley, D.; Shull, G. Terramycin, a New Antibiotic. Science (80) 1950, 11 (27), 85-85) and approved by the FDA for human use (Pfizer. https: / / www.accessdata.fda.gov / scripts / cder / daf / index.cfm?event=overview.process&ApplNo=050286) (US Department of Health and Human Services. Antibiotic Resistance Threats in the United States-Report 2019;2019). In 1953, chemists at Pfizer modified 7-chlorotetracycline to produce a molecule known as tetracycline (compound 3, formula 2Error! Reference source not found), a more active antibiotic (Bradford, P.; Jones, C. Antibiotic Discovery and Development-Chapter 5 (Tetracyclines); Springer, Boston, MA, 2012).

[0010] While Lederle Laboratories led this discovery effort, Pfizer and, more recently, Paratek Pharmaceuticals and Tetraphase have added value to the tetracycline class of antibiotics.Unfortunately, over the past decade, efforts to discover and develop new and modified antibacterial agents that are not susceptible to common bacterial tetracycline resistance mechanisms have declined (Bradford, P.; Jones, C. Antibiotic Discovery and Development-Chapter 5(Tetracyclines); Springer, Boston, MA, 2012).

[0011] The expression of tetracycline-specific efflux pumps and significant class-based resistance due to ribosome protection mechanisms have reduced the effectiveness of tetracyclines. In 1999, tigecycline (compound 4, formula 2), a minocycline derivative of the glycylcycline subclass, emerged as a broad-spectrum tetracycline that can circumvent ribosome protection and active efflux resistance mechanisms with activity against drug-resistant Gram-negative and Gram-positive bacteria (Glycylcyclines: Third-Generation Tetracycline Antibiotics Ian Chopra. 2001, 464-469; Bush, K. Improving Known Classes of Antibiotics: An Optimistic Approach for the Future. Curr. Opin. Pharmacol. 2012, 12(5), 527-534). In 2005, it was approved for the treatment of complicated skin and soft tissue and complicated intra-abdominal infections (Babinchak, T.; Ellis-Grosse, E.; Dartois, N.; Rose, G.; Loh, E. The Efficacy and Safety of Tigecycline for the Treatment of Complicated Intra-Abdominal Infections: Analysis of Pooled Clinical Trial Data. Clin. Infect. Dis. 2005, 41(s5), S354-S367). In 2008, it was approved by the FDA for the treatment of community-acquired bacterial respiratory infections (Stein, GE; Babinchak, T. Tigecycline: An Update. Diagn. Microbiol. Infect. Dis. 2013, 75(4), 331-336). However, it is an intravenous drug only.It causes significantly more nausea and vomiting than other tetracyclines (Shen, F.; Han, Q.; Xie, D.; Fang, M.; Zeng, H.; Deng, Y.; Efficacy and Safety of Tigecycline for the Treatment of Severe Infectious Diseases: An Updated Meta-Analysis of RCTs. International Journal of Infectious Diseases. 2015, pp 25-33) and may cause mutations in gram-negative efflux pumps during treatment (Pournaras, S.; Koumaki, V.; Spanakis, N.; Gennimata, V. Current Perspectives on Tigecycline Resistance in Enterobacteriaceae Susceptibility Testing Issues and Mechanisms of Resistance. Int. J. Antimicrob. Agents 2016, 48, 11-18). More recently, a new generation of tetracyclines, namely omadacycline (5), eravacycline (6) and sarecycline (7)-formula 2, has emerged to overcome the toxicity of tigecycline.

[0012] Omadacycline from Paratek Pharmaceuticals, known as Nuzyra™, is a novel aminomethyl-substituted derivative of minocycline (compound 8, form 2). Nuzyra™ was approved by the FDA in October 2018 (https: / / www.accessdata.fda.gov / scripts / cder / ob / results_product.cfm?Appl_Type=N&Appl_No=209817) in tablet form (NDA209816) and powder form (NDA209817) for community-acquired bacterial pneumonia (CABP) and acute bacterial skin and skin structure infections (ABSSSI) (Paratek Pharmaceuticals. Full Prescribing Information NUZYRA(omadacycline)Paratek Pharmaceuticals,Inc 2018).

[0013] [ka]

[0014] Omadacycline Omadacycline is a novel first-in-class aminomethylcycline and semisynthetic derivative of minocycline (Honeyman, L.; Ismail, M.; Nelson, ML; Bhatia, B.; Bowser, TE; Chen, J.; Mechiche, R.; Ohemeng, K.; Verma, AK; Cannon, EP; Macone, A.; Tanaka, SK; Levy, S. Structure-Activity Relationship of the Aminomethylcyclines and the Discovery of Omadacycline. Antimicrob. Agents Chemother. 2015, 59(11), 7044-7053). It is characterized by an aminomethyl substituent at the C9 position of the tetracycline D ring according to formula 1 (US Pat. No. 9,365,500). Modifications at this position resulted in enhanced activity against Gram-positive and Gram-negative bacteria and overcame resistance mechanisms (i.e., efflux and ribosome protection) known to affect older generation tetracyclines. (Chopra, I.; Roberts, M. Tetracycline Antibiotics: Mode of Action, Applications, Molecular Biology, and Epidemiology of Bacterial Resistance. Microbiol. Mol. Biol. Rev. 2001, 65(2), 232-260; Gotfried, MH; Horn, K.; Garrity-Ryan, L.; Villano, S.; Tzanis, E.; Chitra, S.; Manley, A.; Tanaka, SK; Rodvoldb, KAComparison of omadacycline and tigecycline pharmacokinetics in the Plasma, Epithelial Lining Fluid, and Alveolar Cells of Healthy Adults Subjects.Antimicrob.Agents Chemother.2017,61(9),1-13)).

[0015] The main effect of omadacycline is its great potency in inhibiting bacterial protein synthesis. (Draper, MP; Weir, S.; Macone, A.; Donatelli, J.; Trieber, CA; Tanaka, SK; Levy, SB Mechanism of Action of the Novel Aminomethylcycline Antibiotic Omadacycline. Antimicrob. Agents Chemother. 2014, 58(3), 1279-1283). It acts by binding to the 30S ribosomal subunit in the bacterial mRNA translation complex and inhibiting the binding of aminoacyl-tRNA to the mRNA-ribosomal complex, thereby inhibiting protein expression. (Gotfried, MH; Horn, K.; Garrity-Ryan, L.; Villano, S.; Tzanis, E.; Chitra, S.; Manley, A.; Tanaka, SK; Rodvoldb, KA Comparison of omadacycline and Tigecycline Pharmacokinetics in the Plasma, Epithelial Lining Fluid, and Alveolar Cells of Healthy Adult Subjects.Antimicrob.Agents Chemother.2017,61(9),1-13)

[0016] In January 2013, the FDA designated omadacycline as a QIDP for both IV and oral formulations in the treatment of acute bacterial skin and skin structure infections (ABSSSIs) and community-acquired bacterial pneumonia (CABP). (Liapikou, A.; Cilloniz, C.; Mensa, J.; Torres, A. Pulmonary Pharmacology & Therapeutics New Antimicrobial Approaches to Gram Positive Respiratory Infections. Pulm. Pharmacol. Ther. 2015, 32, 137-143; Berg, JK; Tzanis, E.; Garrity-Ryan, L.; Bai, S.; Chitra, S.; Manley, A.; Villano, S. Pharmacokinetics and Safety of omadacycline in Subjects with Impaired Renal Function. Antimicrob. Agents Chemother. 2018, 62(2), 1-9). ABSSSIs include cellulitis / erysipelas, wound infections, and major skin abscesses. (FDA Acute Bacterial Skin and Skin Structure Infections: Developing Drugs for Treatment; 2013). CABP is a common disease in adults with 5.16-7.06 cases per 1000 people per year (Marrie, TJ; Huang, JQ Epidemiology of Community-Acquired Pneumonia in Edmonton, Alberta: An Emergency Department-Based Study. Can. Respir. J. 2005, 12(3), 139-143).

[0017] In October 2018, omadacycline was approved by the FDA for the treatment of severe skin and soft tissue infections and community-acquired bacterial pneumonia (CAPB) (Paratek Pharmaceuticals. Full Prescribing Information NUZYRA (omadacycline) Paratek Pharmaceuticals,Inc 2018; FDA Omadacycline Injection and Oral Products https: / / www.fda.gov / drugs / development-resources / omadacycline-injection-and-oral-products (accessed March 1, 2021)). (O'Riordan,W.;Green,S.;Overcash,JS;Puljiz,I.;Metallidis,S.;Gardovskis,J.;Garrity-Ryan,L.;Das,AF;Tzanis,E.;Eckburg,PB;Manley,A.;Villano,SA;Steenbergen,JN;Loh,E.omadacycline for Acute Bacterial Skin and Skin-Structure Infections.N.Engl.J.Med.2019,380(6),528-538;Stets,R.;Popescu,M.;Gonong,JR;Mitha,I.;Nseir,W.;Madej,A.;Kirs ch,C.;Das,AF;Garrity-Ryan,L.;Steenbergen,JN;Manley,A.;Eckburg,PB;Tzanis,E.;McGovern,PC;Loh,E.omadacycline for Community-Acquired Bacterial Pneumonia.N.Engl.J.Med.2019,380(6),517-527;Chopra,T.;Sandhu,A.;Theriault,N.;Meehan,J.;Tillotson,G.Omadacycline: A Therapeutic Review of Use in Community-Acquired Bacterial Pneumonia and Acute Bacterial Skin and Skin Structure Infections. Future Microbiol. 2020, 15(14), 1319-1333; Lakota, EA; Van Wart, SA; Trang, M.; Tzanis, E.; Bhavnani, SM; Safir, MC; Friedrich, L.; Steenbergen, JN; Ambrose, PG; Rubino, CMP Population Pharmacokinetic Analyses for Omadacycline Using Phase 1 and 3 Data. Antimicrob. Agents Chemother. 2020, 64(7), 1-10; U.S. Patent Application Publication No. 2018 / 0153908).

[0018] Omadacycline can be administered intravenously or orally. Its broad spectrum of activity is comparable to that of doxycycline (Draper, MP; Weir, S.; Macone, A.; Donatelli, J.; Trieber, CA; Tanaka, SK; Levy, SBMechanism of Action of the Novel Aminomethylcycline Antibiotic Omadacycline. Antimicrob. Agents Chemother. 2014, 58(3), 1279-1283), minocycline, clindamycin, and linezolid (O'Riordan, W.; Cardenas, C.; Shin, E.; Sirbu, A.; Garrity-Ryan, L.; Das, AF; Eckburg, PB; Manley, A.; Steenbergen, JN; Tzanis, E.; McGovern, PC; Loh, E.Once-Daily Oral Omadacycline versus Twice-Daily Oral Linezolid for Acute Bacterial Skin and Skin Structure Infections (OASIS-2):A Phase 3,Double-Blind,Multicentre,Randomised,Controlled,Non-Inferiority Trial.Lancet Infect.Dis.2019,19(10),1080-1090;Noel,GJ;Draper,MP;Hait,H.;Tanaka,SK;Arbeit,RDA Randomized,Evaluator-Blind,Phase 2 Study Comparing the Safety and Efficacy of Omadacycline to Those of Linezolid for Treatment of Complicated Skin and Skin Structure Infections.2012,56(11),5650-5654) or vancomycin.(Macone, AB; Caruso, BK; Leahy, RG; Donatelli, J.; Weir, S.; Draper, MP; Tanaka, SK; Levy, SB. It has potent bacteriostatic activity against gram-positive methicillin-resistant Staphylococcus Aureus (MRSA), multidrug-resistant S. pneumoniae, vancomycin-resistant enterococci, E. faecalis or E. faecium, as well as penicillin- and multidrug-resistant strains and S. pneumoniae strains, including anaerobic Clostridium difficille (WO 2017 / 165729, 2016). The same is true for gram-negative Haemophilus influenzae, E. coli and Legionella (Huband, MD; Pfaller, MA; Shortridge, D.; Flamm, R.K. Surveillance of omadacycline Activity Tested against Clinical Isolates from the United States and Europe: Results from the SENTRY Antimicrobial Surveillance Programme, 2017. J. Glob. Antimicrob. Resist. 2019, 19, 56-63; U.S. Patent No. 9,724,358).Consequently, omadacycline may be an important and desirable treatment option for patients with infections where epidemiology suggests a problematic prevalence of resistant pathogens (Macone, AB; Caruso, BK; Leahy, RG; Donatelli, J.; Weir, S.; Draper, MP; Tanaka, SK; Levy, SB In Vitro and in Vivo Antibacterial Activities of omadacycline, a Novel Aminomethylcycline. Antimicrob. Agents Chemother. 2014, 58(2), 1127-1135). Methods of treatment using omadacycline for urinary tract infections (UTIs), bacterial infections caused by biological weapons, and modulating gene expression have also been described (U.S. Pat. No. 9,724,358; Bal, A. M.; David, M. Z.; Garau, J.; Gottlieb, T.; Mazzei, T.; Scaglione, F.; Tattevin, P.; Gould, I.M. Future Trends in the Treatment of Methicillin-Resistant Staphylococcus Aureus (MRSA) Infection: An in-Depth Review of Newer Antibiotics Active against an Enduring Antibiotic). Pathogen. J. Glob. Antimicrob. Resist. 2017, 10, 295-303; WO 2017 / 192516; WO 2016 / 154332; WO 2007 / 133798; WO 2018 / 026987; U.S. Patent No. 9078811; WO 2009 / 120389). Phase 1 clinical trials are ongoing for tissue penetration in diabetic patients with hemodialysis wound infections (NCT04144374) and for the treatment of diabetic foot infections (NCT04714411).Phase 2 clinical trials have been completed for the treatment of acute pyelonephritis in adults (NCT03757234) and for the oral treatment of acute cystitis in women (NCT03425396) (Overcash, J.S.; Bhiwandi, P.; Garrity-ryan, L.; Steenbergen, J.; Bai, S.; Chitra, S.; Manley, A.; Tzanis, E. Pharmacokinetics, Safety, and Clinical Outcomes of omadacycline in Women with Cystitis: Results from a Phase 1b Study. Antimicrob. Agents Chemother. 2019, 63(5), 1-10).

[0019] In 2019, Paratek Pharmaceuticals Inc. signed a five-year BARDA Project BioShield contract worth up to $285 million to support the development of Paratek's NUZYRA® (omadacycline) for the treatment of pulmonary anthrax with an option to procure up to 10,000 treatment courses of NUZYRA® for the Strategic National Stockpile (SNS) for use against a potential biopharmaceutical (Paratek Pharmaceuticals.Paratek Awarded BARDA Project BioShield Contract for NUZYRA®https: / / www.globenewswire.com / news-release / 2019 / 12 / 18 / 1962517 / 0 / en / Paratek-Awarded-BARDA-Project-BioShield-Contract-for-NUZYRA.html(accessed March 5, 2021)).

[0020] The current synthesis of omadacycline, shown in Scheme 1, has been used for multi-kilogram preparations and is described in U.S. Pat. No. 9,434,680 (which also discloses 9-aminomethyltetracycline compounds other than omadacycline).

[0021] [ka]

[0022] Minocycline has several reactive functional groups, with the C2 primary amide being more reactive towards electrophiles than the C9 or C10 (Equation 1). Due to this fact, the first step of Scheme 1 requires approximately 3 equivalents of N'-(hydroxymethyl)-phthalimide in trifluoromethanesulfonic acid resulting in the bis-substituted aminomethyl-phthalimide tetracycline compound. In the second step of Scheme 1, the phthalimide is deprotected with a large excess of methylamine in an alcoholic solution to give the bis-substituted aminomethyl tetracycline intermediate. In the third step of Scheme 1, the resulting intermediate is reacted with hydrogen under hydrogenation conditions to form the C9-substituted aminomethyl tetracycline intermediate. In the fourth step of Scheme 1, the formed compound is reacted with pivaldehyde under hydrogenation conditions to give omadacycline. After reverse phase chromatography purification, pH adjustment and precipitation, the desired product is obtained as an amorphous unstable solid. For a long-term manufacturing route, the challenges of the instability of the aminomethyl intermediate and the chromatographic column purification step must be overcome.

[0023] We describe a three-step synthesis of omadacycline via an electronically tuned monochloroacyliminium Friedel-Crafts reaction (Tscherniac-Einhorn reaction) using acyliminium ions as starting materials in 15-18% overall yields (see Scheme 2 and Chung, JYL; Hartner, FW; Cvetovich, RJ Synthesis Development of an Aminomethylcycline Antibiotic via an Electronically Tuned Acyliminium Friedel-Crafts Reaction. Tetrahedron Lett. 2008, 49(42), 6095-6100).

[0024]

change

[0025] Acyliminium reagents are prepared from neopentylamine and paraformaldehyde to give triazans, followed by treatment with anhydrides. (Chung, JYL; Hartner, FW; Cvetovich, RJ Synthesis Development of an Aminomethylcycline Antibiotic via an Electronically Tuned Acyliminium Friedel-Crafts Reaction. Tetrahedron Lett. 2008, 49(42), 6095-6100; Taguchi, M.; Aikawa, N.; Tsukamoto, G. Reaction of Rifamycin S with Hexahydro-1,3,5-Triazines Prepared from Formaldehyde and Primary Aliphatic Amines. Bull Chem Soc Jpn 1988, 61, 2431-2436; Anderson, J.; Casarini, D.; Ijeh, A. Eclipsed Conformation for Both Axial and Equatorial N-CH2 Bonds in N,N',N"-Tris(Neopentyl)-1,3,5-Triazane. J. Am. Chem. Soc. 1995, 117(11), 3054-3056). According to Chung J. et.al, trifluoromethanesulfonic acid is the solvent used because a solution of minocycline in trifluoromethanesulfonic acid is stable against air oxidation, C4 epimerization and other modes of decomposition. In the first step of Scheme 2, the optimized yield is 83% using 5 equivalents of acyliminium at 35 / 40°C for 24 hours. The second step removes the chloroacetyl group and converts the chloroacetyl intermediate to 3N The reverse epimerization consists of heating in HCl at 70° C. for 20 hours. Reverse epimerization is carried out by heating a racemic mixture of omadacycline (crude) in aqueous n-butanol in the presence of calcium chloride and ethanolamine at 105° C. The resulting amorphous solid is unstable at temperatures above 0° C. and when exposed to air, so a stable salt must be prepared.The crystalline salts of omadacycline (monotosylate, bis-HCl, and mesylate) are stable at 25° C. (US Patent Publication No. 2018 / 0104262). However, the synthesis requires a purification step to be adapted from a chromatography system to make kilogram-scale operations viable.

[0026] US 9365500 describes a synthetic route for omadacycline based on the Tscherniac-Einhorn reaction and is depicted in Scheme 3. In the first step of Scheme 3, an aminomethyl intermediate can be synthesized using N'-(hydroxymethyl)benzylcarbamate in acidic medium at 25°C for 24 hours using minocycline as a substrate. The second step consists of reductive amination of the intermediate to give omadacycline (US 9365500).

[0027] [ka]

[0028] In 1983, Baillargeon et al (Baillargeon, V.; Stille, J. Direct Conversion of Organic Halides to Aldehydes with Carbon Monoxide and Tin Hydride Catalyzed by Palladium. J. Am. Chem. Soc. 1983, 105, 7175) described palladium-catalyzed formylation of organic halide substrates in the presence of carbon monoxide to give aldehydes in high yields. Seyedi F. et al., described in U.S. Pat. No. 9,522,872, performed this procedure for the preparation of 9-iodominocycline and subsequently 9-formylminocycline in 99% yield. The resulting intermediate is reacted with sodium borohydride triacetate to give omadacycline.

[0029] [ka] Summary of the Invention

[0030] Although omadacycline has been proven to be safe and highly effective against multidrug-resistant Gram-positive and Gram-negative bacteria, to the best of our knowledge, all described methods for synthesizing 9-aminomethyltetracycline compounds have low yields, low selectivity, and very difficult purification steps. Industrial-scale synthesis methods still require optimization to reduce impurities and achieve better yields when preparing this type of compound. The present invention provides a new method that uses an innovative chemical strategy. Utilizing continuous flow technology, we have used process intensification (e.g., high temperature and pressure) and improved mass and heat transfer to increase selectivity and overcome the challenges of purification, low yields, and isolation of unstable intermediates. Furthermore, with the concept of green chemistry in mind, we have developed a method to select solvents and reagents that are as environmentally friendly as possible.

[0031] The present inventors seek to develop new, greener, cheaper and better methods for synthesizing 9-aminomethyltetracycline compounds, particularly omadacycline, which may ultimately benefit patients, industry and the environment. The present invention meets such objectives as it provides a method that reduces or eliminates one or more of the problems associated with known methods outlined above.

[0032] According to the present invention, the inventors have developed a method that can be operated as a semi-continuous or continuous process, which is used to prepare amino-alkyl tetracycline compounds, such as 9-aminomethyl minocycline, in the most ecologically clean way possible, reducing time and waste. The inventors have found that by using flow chemistry techniques, it is possible to use environmentally friendly solvents, avoid degradation of sensitive intermediates, and control the formation of epimers, which makes it possible to obtain aminomethyl tetracycline compounds with a purity of more than 50%, preferably 70-80%, more preferably 81-100%. Furthermore, with an overall yield (also known as cumulative yield) of more than 30%, preferably 50-70%, more preferably 71-100%. One example of an aminomethyl tetracycline compound that can be prepared by the method of the present invention is omadacycline. [Brief description of the drawings]

[0033] [Figure 1] FIG. 1 shows the synthetic sequence of omadacycline. [Diagram 2] FIG. 1 illustrates a continuous flow setup. [Diagram 3] FIG. 1 illustrates a continuous flow setup. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0034] According to one aspect of the invention, there is provided a method of synthesizing a 9-aminomethyltetracycline compound according to formula 3, wherein R is hydrogen or a C1-C10 straight chain alkyl group, a C3-C20 branched chain alkyl group, a substituted alkyl group (optionally substituted with at least one of halogen, hydroxyl group, ketone and ether), a C3-C10 or C6-C10 aryl group, a substituted C3-C10 or C6-C10 aryl group (optionally substituted with at least one of halogen, hydroxyl group, ketone and ether), or a C3-C10 heteroaryl group containing at least one oxygen, nitrogen, sulfur or phosphorus atom; [ka] Such a method comprises: a) reacting minocycline and a hydroxymethylamide derivative to form 2,9-(methylamide substituted) minocycline and 2-(methylamide substituted) minocycline; b) reacting the 2,9-(methylamide substituted) minocycline from step a) with an amine or diamine to form a 9-aminomethyltetracycline intermediate; and c) reacting the 9-aminomethyltetracycline intermediate from step b) with an aldehyde in the presence of a reducing agent to form a 9-aminomethyltetracycline compound; or d) reacting the 9-aminomethyltetracycline intermediate from step b) with an alkyl halide or alkyl reagent to form a 9-aminomethyltetracycline compound. Includes.

[0035] The method of the present invention is a multi-step process using electrophilic aromatic substitution between minocycline and a hydroxymethylamide derivative in step a) to obtain 2,9-(methylamide substituted) minocycline, aminolysis reaction between 2,9-(methylamide substituted) minocycline and an amine or diamine in step b) to obtain a 9-aminomethyltetracycline intermediate, and either a reductive amination reaction between the 9-aminomethyl intermediate and an aldehyde in step c) or N'-alkylation between the 9-aminomethyl intermediate and an alkyl halide or alkyl reagent in step d) to form the desired 9-aminomethyltetracycline compound. As used herein, the term "multi-step chemical synthesis" generally refers to a synthetic method that includes multiple chemical reactions. The term is not intended to encompass synthetic methods in which a single chemical reaction may be carried out over multiple steps.

[0036] The hydroxymethylamide derivative used in step a) may be according to formula 4, [ka] In the formula, R1 is selected from the group consisting of a C1-C10 linear alkyl group, a C3-C20 branched alkyl group, a C2-C10 linear alkenyl group, a C3-C20 branched alkenyl group, a C2-C10 linear alkynyl group, a C3-C20 branched alkynyl group, a C3-C10 or C6-C10 aryl group, a C3-C10 heteroaryl group containing at least one oxygen, nitrogen, sulfur or phosphorus atom, or chlorine, bromine and iodine. and R2 is a C1-C10 linear alkyl group, a C3-C20 branched alkyl group, a C2-C10 linear alkenyl group, a C3-C20 branched alkenyl group, a C2-C10 linear alkynyl group, a C3-C20 branched alkynyl group, a C3-C10 or C6-C10 aryl group, or a C3-C10 heteroaryl group containing at least one oxygen, nitrogen, sulfur or phosphorus atom. R2 is optionally linked to R1 to form a 4-8 membered ring, which may be optionally substituted with other functional groups such as halogens, hydroxyl groups, ketones, ethers, esters and amides, and contains carbon atoms and / or heteroatoms such as oxygen, nitrogen and sulfur. The hydroxymethylamide derivative in step a) may be N'-hydroxymethyl-phthalimide.

[0037] The term alkyl, as used herein, is a general term that refers to a group derived from an alkane by removing a hydrogen atom from any carbon atom of the alkane, and includes saturated aliphatic groups, including straight chain alkyl groups (e.g., methyl, ethyl, propyl, butyl, pentyl, etc.), branched chain alkyl groups (e.g., isopropyl, tert-butyl, isobutyl, etc.), and cycloalkyl groups (e.g., cyclopropyl, cyclopentyl, etc.). The term alkyl further includes alkyl groups that may further include oxygen, nitrogen, sulfur, or phosphorus atoms.

[0038] The term aryl, as used herein, is a general term that refers to any aromatic group derived from an arene (also known as an aromatic hydrocarbon) by removing a hydrogen atom from any carbon atom of the aromatic ring.

[0039] The amine or diamine used in step b) may be according to formula 5, NHR3R4 formula 5 In the formula, R3 and R4 are hydrogen atoms, C1-C10 straight chain alkyl groups, C3-C20 branched chain alkyl groups, or substituted alkyl groups (optionally substituted with alcohol or ether). Preferably, R3 and R4 are selected from C1-C4 straight chain alkyl groups, C3-C4 branched chain alkyl groups, or substituted alkyl groups. Optionally, the amine or diamine in step b) is selected from methylamine, ethanolamine, and n-propylamine.

[0040] An excess of amine or diamine may be used in step b), optionally being continuously removed prior to steps c) or d).

[0041] In contrast to some prior art processes, step b) can be operated in the absence of a hydrogenation reaction, i.e., reacting 2,9-(methylamide substituted) minocycline with an amine or diamine directly forms the 9-aminomethyltetracycline intermediate without the need to hydrogenate the compound to form the intermediate.

[0042] The aldehyde used in step c) may be according to formula 6, R5COH formula 6 wherein R5 is hydrogen, a C1-C10 straight chain alkyl group, a C3-C20 branched chain alkyl group, a substituted alkyl group (optionally substituted with an alcohol, amide or ether), a C3-C10 or C6-C10 aryl group, a substituted C3-C10 or C6-C10 aryl group, or a C3-C10 heteroaryl group containing at least one oxygen, nitrogen, sulfur or phosphorus atom. Optionally, the aldehyde used in step c) is selected from pivaldehyde, acetaldehyde and benzaldehyde.

[0043] The reducing agent used in step c) may be an immobilized reducing agent, optionally immobilized sodium cyanoborohydride.

[0044] When an alkyl halide is used in step d), the alkyl halide may be according to formula 7: R6X formula 7 wherein R6 can be a C1-C10 straight chain alkyl group, a C3-C20 branched chain alkyl group, a substituted alkyl group, a C3-C10 or C6-C10 aryl group, a substituted C3-C10 or C6-C10 aryl group, or a C3-C10 heteroaryl group containing at least one oxygen, nitrogen, sulfur, or phosphorus atom, and X is a halogen selected from chlorine, bromine, and iodine. The alkyl halide used in step d) may include 1-chloro-2,2-dimethylpropane, 1-bromo-2,2-dimethylpropane, or 1-iodo-2,2-dimethylpropane.

[0045] When an alkylating reagent is used in step d), the alkylating reagent may have a good leaving group such as mesyl or tosyl. Optionally, the alkylating reagent is neopentyl 4-methylbenzenesulfonate, neopentyl methanesulfonate or a mixture thereof.

[0046] The reaction of step c) or d) may be carried out in the presence of a proton acceptor, optionally selected from triethylamine, ammonia and 4-dimethylaminopyridine.

[0047] The reaction in step c) may be carried out in the presence of an organic acid, such as formic acid or acetic acid, an inorganic acid, or a mixture thereof.

[0048] The ratio of reactants used in each of steps a), b) and c) or d) may vary from 1:1 to 1:30.

[0049] A method can be defined as a continuous flow process where there is a continuous feed of reagents / starting materials into the reactor and a continuous product flow exiting the reactor. A continuous flow process utilizes equipment, materials and conditions that allow chemical synthesis to be carried out in a continuous mode using a flow reactor. As used herein, continuous flow procedures do not include the conventional procedures of chemical synthesis in batches.

[0050] The method of the present invention can be a semi-continuous or continuous flow process. Thus, in a continuous flow process, the entire synthetic sequence of the method of the present invention can be carried out from the minocycline reacted in step a) to the 9-aminomethyltetracycline compound formed in step d) in the absence of a hydrogenation reaction before step c) or d) without the use of a batch reactor and without the need to isolate the 9-aminomethyltetracycline intermediate formed in step b). Alternatively, in a semi-continuous flow process, two of steps a), b) and c) or d) can be carried out without the use of a batch reactor and without the need to isolate the intermediate product between the reaction steps. Steps a) and b) of the method of the present invention can be operated continuously, steps b) and c) of the method of the present invention can be operated continuously, or steps b) and d) of the method of the present invention can be operated continuously. When steps b) and c) or steps b) and d) are operated continuously, the 9-aminomethyltetracycline intermediate formed in step b) can be used directly in step c) or d).

[0051] In a semi-continuous flow process, some, but not all, of the reaction steps of the present invention may be carried out in a continuous flow reactor. In a continuous flow process, all of the reaction steps of the present invention may be carried out in a single continuous flow reactor or in multiple continuous flow reactors in fluid communication with each other.

[0052] Step a) of the process of the present invention may comprise continuously feeding a solution or suspension containing minocycline and a solution or suspension containing a hydroxymethylamide derivative in a suitable solvent or solvent mixture to a flow reactor which continuously produces at its outlet a solution or suspension containing a variable amount of a 2-(methylamide substituted) minocycline compound. Step b) of the process of the present invention may comprise feeding a solution or suspension of a 2,9-(methylamide substituted) minocycline compound and a solution or suspension containing an amine or diamine in a suitable solvent to a flow reactor which continuously produces at its outlet a solution or suspension containing a variable amount of a 9-aminomethyltetracycline intermediate. Step c) of the process of the present invention may comprise feeding a solution or suspension of the 9-aminomethyltetracycline intermediate, a solution or suspension of an aldehyde in a suitable solvent to a flow reactor containing a reducing agent which continuously produces at its outlet a solution or suspension containing the desired 9-aminomethyltetracycline compound. Alternatively, step d) of the process of the invention may comprise feeding a solution or suspension of the 9-aminomethyltetracycline intermediate, a solution or suspension of the alkyl halide or alkyl reagent in a suitable solvent to a flow reactor which continuously produces a solution or suspension containing the desired 9-aminomethyltetracycline compound at its outlet. Omadacycline is an antibiotic that may be produced by the synthetic sequence shown in Figure 1.

[0053] Surprisingly, it has been found that it is possible to synthesize 9-aminomethyltetracycline intermediates directly from 2,9-(methylamide substituted) minocycline compounds by using higher temperatures that are only feasible by using flow chemistry techniques at low residence times.

[0054] The residence time of the reaction in steps a), b) and c) or d) can be from 12 seconds to 2 hours, optionally from 12 seconds to 30 minutes. The residence time of each reaction step may be different from the residence time of the other reaction steps.

[0055] The residence times of reagents along a selected distance of the continuous flow reactor associated with the electrophilic aromatic substitution reaction in step a), the aminolysis reaction in step b), the reductive amination reaction in step c) and the N'-alkylation reaction in step d) may vary from 1 minute to 2 hours. The yield of each reaction step may be about 5% or more, preferably 50% or more, more preferably 80% or more. The chromatographic purity of the reaction crude product obtained from step a) or b) may be about 50% or more, more preferably 80% or more.

[0056] The solvents used in the process of the invention may be common organic solvents, aqueous solvents, aqueous-based solvents, water or mixtures thereof. Any compatible solvent or solvent system may be used. The solvent system used may include colloidal suspensions or emulsions. The solvent system used may include alcohol, water, or a mixture of both. The solvent systems may include mixtures of water-miscible organic solvents and water. They may also include water-immiscible organic solvents in contact or not in contact with water. Any particular combination of the solvents listed above may be used. The process steps of the invention may not be optimally performed in the same solvent or solvent system, and the preparation of the solvent / solvent composition or solvent switch may be performed continuously, if desired, for example without the need to isolate or purify intermediates.

[0057] The minocycline used in step a) may be in solution or suspension, optionally with a solvent selected from organic or mineral acids such as sulfuric acid, methanesulfonic acid, trifluoromethanesulfonic acid, sulfuric acid fuming 65% SO3 or mixtures thereof. Optionally, a solution or suspension of minocycline in sulfuric acid at a concentration of 130-230 mg / mL may be used in step a). The hydroxymethylamide derivative used in step a) may be in solution or suspension, optionally with a solvent selected from organic or mineral acids such as sulfuric acid, methanesulfonic acid, trifluoromethanesulfonic acid, sulfuric acid fuming 65% SO3 or mixtures thereof. Optionally, a solution or suspension of hydroxymethylamide derivative in sulfuric acid at a concentration of 100-160 mg / mL may be used in step a). Thus, minocycline and hydroxymethylamide derivative may react together when both are in solution, when one is in solution and the other is in suspension, or when both are in suspension. Additionally, the minocycline and the hydroxymethylamide derivative may be in a solution or suspension comprising the same solvent or mixture of solvents, or different solvents, or different combinations of solvents. Additionally, the minocycline and the hydroxymethylamide derivative may be in a solution or suspension at the same or different concentrations.

[0058] The 2,9-(methylamido-substituted) minocycline used in step b) may be in solution or suspension, optionally comprising a solvent selected from an alcohol such as benzyl alcohol, a polar aprotic solvent such as dimethylsulfoxide, dimethylformamide or dichloromethane, or a mixture thereof. Optionally, a solution or suspension of 2,9-(methylamido-substituted) minocycline at a concentration of 50-200 mg / mL may be used in step b). The amine or diamine used in step b) may be in solution or suspension, optionally comprising a solvent selected from an alcohol such as benzyl alcohol, a polar aprotic solvent such as dimethylsulfoxide, dimethylformamide or dichloromethane, or a mixture thereof. Optionally, a solution or suspension of amine or diamine at a concentration of 50-200 mg / mL may be used in step b). Thus, the 2,9-(methylamido-substituted) minocycline and the amine or diamine may react together when both are in solution, when one is in solution and the other is in suspension, or when both are in suspension. Additionally, the 2,9-(methylamido-substituted) minocycline and the amine or diamine may be in a solution or suspension that includes the same solvent or mixture of solvents, or different solvents, or different combinations of solvents. Additionally, the 2,9-(methylamido-substituted) minocycline and the amine or diamine may be in a solution or suspension that is the same or different concentrations.

[0059] The 9-aminomethyltetracycline intermediate used in step c) or d) may be in solution or suspension, optionally comprising a solvent selected from alcohols such as benzyl alcohol, ethanol or methanol, polar aprotic solvents such as dimethylsulfoxide, dimethylformamide or dichloromethane, or mixtures thereof. Optionally, a solution or suspension of the 9-aminomethyltetracycline intermediate at a concentration of 20-100 mg / mL may be used in step c) or d). The aldehyde used in step c) may be in solution or suspension, optionally comprising a solvent selected from alcohols such as benzyl alcohol, ethanol or methanol, polar aprotic solvents such as dimethylsulfoxide, dimethylformamide or dichloromethane, or mixtures thereof. Optionally, a solution or suspension of the aldehyde at a concentration of 5-100 mg / mL may be used in step c). Thus, the 9-aminomethyltetracycline intermediate and the aldehyde may react together when both are in solution, when one is in solution and the other is in suspension, or when both are in suspension. Furthermore, the 9-aminomethyltetracycline intermediate and the aldehyde may be in a solution or suspension that includes the same solvent or mixture of solvents, or different solvents, or different combinations of solvents. Furthermore, the 9-aminomethyltetracycline intermediate and the aldehyde may be in a solution or suspension at the same concentration or different concentrations.

[0060] The concentration of the solutions or suspensions used in each step of the method of the present invention depends on the solubility of the reactants used.

[0061] One advantage of carrying out the methods of the present invention as a continuous process in a continuous flow reactor, such as a pipe reactor, is that the volume of solvent is greatly reduced compared to that used in a batch reactor, which results in a reduction in subsequent effluents, thus making these methods more environmentally friendly.

[0062] The use of continuous flow processes can provide the ability to perform chemical reactions with improved selectivity, reaction yields and product purity profiles, which is an environmentally friendly way to perform chemical synthesis, and reduces waste. In many cases, continuous flow reactors allow for process intensification (e.g., high temperatures and pressures) and can therefore be utilized to further reduce the time and cost required to synthesize a desired product. For example, a continuous flow process can include flowing a fluid sample containing one or more precursor species through a flow-through system and carrying out chemical reactions within the piping of such a system to convert the precursor species to a desired product.

[0063] The use of continuous flow reactors may offer the ability to employ temperatures and pressures not easily achievable in batch processes. The use of high temperatures and pressures may facilitate the conversion of precursor species to reaction products without the need for additives or promoter species.

[0064] Optionally, the reactions in steps a), b) and c) or d) are carried out at a temperature of at least 10°C, at least 20°C, at least 75°C, at least 100°C, at least 125°C, at least 150°C, at least 175°C, at least 200°C, at least 225°C, at least 250°C, at least 275°C, at least 300°C, or optionally higher. Optionally, the chemical reactions in steps a), b) and c) or d) are carried out at a temperature of 20°C to 150°C, preferably 20°C to 120°C. Optionally, the reaction in step a) is carried out at a temperature of 25°C to 200°C or 25°C to 50°C. Optionally, the reaction in step b) is carried out at a temperature of 25°C to 200°C or 100°C to 200°C. Optionally, the reaction in step c) is carried out at a temperature of at least 10°C or 20°C to 80°C. Optionally, the reaction of step d) is carried out at a temperature between 25°C and 200°C or between 20°C and 50°C.

[0065] Optionally, the reactions in steps a), b) and c) or d) are carried out at a pressure of at least 100 psi (689 KPa), at least 125 psi (862 KPa), at least 150 psi (1034175 KPa), at least 175 psi (1207 KPa), at least 200 psi (1379 KPa), at least 225 psi (1551 KPa), at least 250 psi (1724 KPa), at least 275 psi (1896 KPa), at least 300 psi (2068 KPa), at least 400 psi (2758 KPa), at least 500 psi (3447 KPa), or even more. Optionally, the reactions in steps a), b) and c) or d) are carried out at a pressure of from 100 to 2000 KPa. Optionally, the reaction in step b) is carried out at a pressure of at least 300 KPa, for example at a pressure of from 300 to 2000 KPa.

[0066] The term "flow-through system" is used to refer to a system that includes one or more reactors that allow a chemical reaction to occur in a continuous flow. The method of the present invention can be carried out in a pipe reactor, a plug flow reactor, a coil reactor, a tube reactor, a microchip, a continuous plate reactor, a packed bed reactor, a continuous stirred tank reactor (CSTR), or another commercially available continuous flow reactor, or a combination of two or more such reactors to form a flow-through system. Flow-through systems can be designed and manufactured to be able to withstand a wide range of solvent and chemical conditions, including high temperatures, high pressures, exposure to various solvents and reagents, and the like.

[0067] The continuous flow reactor can be made of any suitable compatible material, including glass, different types of polymers (PFA, ETFE, PEEK, etc.), Hastelloy®, silicon carbide, stainless steel, and / or one or more high performance alloys. The continuous flow reactor can include a static mixing device. The continuous flow reactor can handle slurries, be suitable for exposure to a temperature or temperature range, and / or be suitable for exposure to pressure. When one or more of the same continuous flow reactors or a combination of different continuous flow reactors listed above are used, the reactors may be connected to each other such that they are in fluid communication. With regard to the term "connected", this should be understood to mean that the continuous flow reactors do not necessarily have to be directly attached to each other, but that the reactors should be in fluid communication with at least one other reactor. However, if desired, the reactors may be directly attached to each other.

[0068] One advantage of using a packed bed reactor is that this type of reactor provides a higher effective molar concentration of any immobilized reagent, thereby reducing the reaction time. Furthermore, any immobilized reagent is contained in the matrix, so that there is no need to separate the reaction mixture from such reagent.

[0069] In some cases, the reaction profile (e.g., reaction time, overall yield, distribution of reaction products, etc.) may be substantially independent of the volume of the fluid sample, such that the chemical reaction can be carried out on a larger scale without substantially changing the reaction profile.

[0070] The method of the present invention may comprise at least one chemical reaction step carried out continuously with isolation of the product. Furthermore, the method of the present invention may comprise at least two chemical reaction steps carried out in a continuous telescope mode without isolation of reaction products / process intermediates, only a change of solvent, and / or without removal of excess reagents between reaction steps. Furthermore, the product of reaction step b) is an intermediate that is used as a reactant in reaction step c) to prepare the desired product.

[0071] Optionally, the methods of the invention can include one or more additional steps, which can include one or more washing steps, one or more purification steps, one or more isolation steps, or a combination thereof.

[0072] When continuous flow reactors are used, the conditions in one or more continuous flow reactors can be controlled. This can be done, for example, to allow a particular reaction to occur or to obtain a desired reaction rate. Controlling the conditions in one or more continuous flow reactors can include adjusting or changing one or more of the following: temperature in the continuous flow reactor(s); pressure in the continuous flow reactor(s); solvent or solvent system in the flow reactor(s); flow rate in the continuous flow reactor(s). The concentration of each of the solutions or suspensions used in each of steps a), b) and c) or d) affects the flow rate, residence time and ratio of reactants. Thus, adjusting or changing the concentration of each of the solutions or suspensions used in each of steps a), b) and c) or d) can also help control the conditions in one or more continuous flow reactors.

[0073] The flow rates of reagents through the continuous flow reactor can be controlled, altered, or regulated depending on the reaction taking place in the reactor. The flow rates of reagents may be different along one or more selected distances of the continuous flow reactor. The flow rates of reagents associated with a reaction step may affect the flow rates associated with a subsequent reaction step. Reagents may travel along selected distances of the continuous flow reactor at different flow rates. The flow rates of reagents through the continuous flow reactor can be controlled, altered, or regulated using pumps.

[0074] As used herein, the term "reaction" refers to the formation of one or more bonds between two or more components to produce a stable, isolatable compound (an intermolecular reaction), or the formation of one or more bonds between two or more parts of the same molecule to form a stable, isolatable compound (an intramolecular reaction). That is, the term "reaction" does not refer to the interaction of solvents, catalysts, bases, ligands, or other materials that may serve to facilitate the occurrence of the reaction with the component(s).

[0075] Each reaction takes place in a heterogeneous or homogeneous environment. The continuous flow reactor can be adapted to carry out reactions in heterogeneous and / or homogeneous environments. In particular, one or more continuous flow reactors may be adapted to carry out heterogeneous and / or homogeneous reactions. For example, the continuous flow reactors may contain one or more reagents or catalysts therein (e.g., within their bores). The catalysts may be homogeneous or heterogeneous with respect to the reactants, reagents and / or solvents.

[0076] The reaction rates of each individual reaction step, the flow rates through each flow-through system, and the rates of solvent change can be adjusted so that the flows through the entire system used to carry out the methods of the invention do not require the use of holding tanks at intermediate stages, although under certain circumstances the use of holding tanks in downstream operations may be an option.

[0077] When continuous flow reactors are used, the output of one or more continuous flow reactors can be carefully controlled so that the composition of intermediates, reactants, impurities, solvents, etc. is appropriate to feed the subsequent continuous flow reactor to enable optimal reaction conditions.

[0078] When a flow-through system is used, the conditions of the flow-through system (e.g., a system including multiple tubular reactors) can vary over a wide range. In particular, the conditions can vary from homogeneous reaction conditions to heterogeneous conditions. For example, a heterogeneous reaction can be used in the reductive amination reaction of step c) in which a continuous flow reactor, such as a tubular reactor, is filled with a heterogeneous catalyst. The heterogeneous catalyst can be, for example, a reducing agent.

[0079] Also, successive solvent extraction / washing steps or membrane purification can be applied to remove impurities, excess reagents, or other undesirable materials that may be detrimental to subsequent chemical reactions or the purity of the final product. The pressure within each reactor in the flow-through system may be atmospheric or superatmospheric, and the temperature may vary from subambient to greater than 200°C.

[0080] Purification, isolation and drying of the final product can also be carried out in a continuous manner using successive extraction, membrane, crystallization, filtration and drying processes, if desired. EXAMPLES

[0081] Example 1 Flow experiments were performed using the continuous flow setup shown in FIG. 2, where "TI" means temperature instrument, coil reactor #1 is the reaction coil, and coil reactor #2 is the cooling coil. Solution A was prepared by dissolving minocycline (10.00 g) in sulfuric acid (50 mL). Solution B was prepared by dissolving N'-(hydroxymethyl)phthalimide (7.75 g) in sulfuric acid (50 mL). Solutions A and B were pumped in a 2:1 ratio and allowed to reside in the coil reactor (504 μL) at 80° C. for 5 minutes. The resulting solution showed 100% conversion of the starting material, resulting in 50% 2,9-methylphthalimido minocycline and 50% 2-methylphthalimido minocycline.

[0082] Example 2 Flow experiments were performed using a continuous flow setup, shown as Error! Reference source not found. Figure 3 (where "TI" means temperature instrument, "PI" means pressure instrument, "BPR" means back pressure regulator, "HPLC pump" means high performance liquid chromatography pump, coil reactor #1 is the reaction coil, and coil reactor #2 is the cooling coil). Solution A was prepared by dissolving 2,9-methylphthalimido minocycline (15.00 g) in benzyl alcohol (150 mL). Solution B was prepared by mixing methylamine ethanol solution (33%) (41.85 g) with benzyl alcohol (94.65 mL). Solutions A and B were pumped in a 1:1 ratio to achieve a residence time of 6 minutes in the coil reactor (10 mL) at 115 °C and 7 bar (700 KPa) back pressure. The product stream was collected at the outlet in a round bottom flask containing absolute ethanol (200 mL) at 30 °C. The mixture was distilled to obtain a solution containing residual amounts of methylamine (Solution C). Solution D was prepared by mixing pivaldehyde (4.90 mL), triethylamine (2.52 mL) and benzyl alcohol (292.6 mL). Solutions C and D were pumped in a 1:1 ratio and mixed thoroughly to achieve a residence time of 30 minutes at a temperature of 25° C. in a packed bed reactor containing immobilized sodium cyanoborohydride (25 g). Once steady state was achieved, fractions were collected and appropriately diluted for HPLC analysis. The resulting solution showed 78% conversion.

[0083] Example 3 Flow experiments were performed using the continuous flow setup shown in Figure 3. Solution A was prepared by dissolving (4S,12aS)-9-(aminomethyl)-4,7-bis(dimethylamino)-3,10,12,12a-tetrahydroxy-1,11-dioxo-4a,5,5a,6-tetrahydro-4H-tetracene-2-carboxamide (0.50 g, 1 mmol) in dichloromethane (3 mL). Solution B was prepared by mixing triethylamine (0.21 g, 2.1 mmol) and 1-chloro-2,2-dimethyl-propane (0.22 g, 2.1 mmol) in dichloromethane (3 mL). Solutions A and B were pumped in a 1:1 ratio to achieve a residence time of 1 h in a coil reactor (1 mL) at 35 °C and 2 bar back pressure. Quantitative yields of raw materials were obtained.

[0084] Example 4 A laboratory-scale nanofiltration device (MetCell Cross Flow System) was used for the separation of methylamine, reaction by-products and 9-aminomethyltetracycline intermediates. Membrane disks were prepared according to the diameter of the filtration cell and the system was assembled with matching O-rings. The crude solution of 9-aminomethyltetracycline intermediates was added to the METCell tank base and recirculated for 10 min. A pressure of 30 bar (3000 KPa) was applied to the system and the permeate flow rate was calculated by chronometer (Qperm=0.133 mL / min). A fresh solution of ethanol was fed to the system at a constant flow rate of 0.2 mL / min for 5 h. The permeate samples and the final retentate were analyzed by HPLC and GC. 200 mL of retentate was obtained (45 wt.% BnOH, 5 wt.% methylamine, 43% EtOH, 8 wt.% solutes). The membrane rejection of 9-aminomethyltetracycline intermediates during this operation step was 99%.

[0085] Example 5 Feed 1 contained the 9-aminomethyltetracycline intermediate in benzyl alcohol solution (3.3 mmol, 55 mL) and Feed 2 contained pivaldehyde (1.08 mL), triethylamine (0.46 mL) and benzyl alcohol to reach 55 mL. Both streams were pumped using two high pressure liquid pumps (P1 and P2, Knauer) at 0.1 mL / min each. The two liquid streams were combined in a T-mixer and mixed in a Uniqsis glass static mixer (578 μL, T: 175 s) before entering a packed bed reactor (T: 30 min) containing immobilized sodium cyanoborohydride (5.33 g, 84.8 mmol). The packed bed was placed on a HPLC oven heated to 25 °C. The HPLC pump flow rate and pressure were measured and monitored by the control platform of the pump system. Once steady state was achieved, fractions were collected and appropriately diluted for HPLC analysis. The conversion and yield were determined by HPLC, and the combined fractions measured 75.53% conversion.

[0086] Example 6 The reaction solution was slowly added to a flask containing a mixture of methyl tert-butyl ether (MTBE) and n-heptane. The solid was filtered, washed with MTBE, and dried in an oven at a temperature below 30° C. and with a nitrogen sweep until a constant weight was reached. The solid was resuspended in i-PrOH (70 mL, 7 mL / g) and p-toluenesulfonic acid was added and stirred at 550 rpm at room temperature under a nitrogen atmosphere for 24 hours. Omadacycline tosylate was obtained in 77.08% molar yield.

Claims

1. Formula 3's 9-aminomethyltetracycline compound 【Chemistry 1】 In the formula, R is a C1-C10 linear alkyl group substituted with at least one of a C1-C10 linear alkyl group, a C3-C20 branched alkyl group, a halogen, a hydroxyl group, a ketone, and an ether, a C3-C20 branched alkyl group substituted with at least one of a halogen, a hydroxyl group, a ketone, and an ether, a C6-C10 aryl group substituted with at least one of a halogen, a hydroxyl group, a ketone, and an ether, or a C3-C10 heteroaryl group containing at least one oxygen, nitrogen, or sulfur atom. A method for synthesizing, a) A step of reacting minocycline and a hydroxymethylamide derivative at a temperature of 20°C to 120°C to form 2,9-(methylamide-substituted)minocycline and 2-(methylamide-substituted)minocycline. b) A step in which the 2,9-(methylamide-substituted)minocycline from step a) is reacted with an amine at a temperature of 100°C to 200°C to form a 9-aminomethyltetracycline intermediate, wherein the amine is of formula 5 NHR ３ R ４ Formula 5 In the formula, R ３ and R ４ The steps are: a C1-C10 linear alkyl group substituted with at least one of a hydrogen atom, a C1-C10 linear alkyl group, a C3-C20 branched alkyl group, a halogen, a hydroxyl group, a ketone, and an ether, or a C3-C20 branched alkyl group substituted with at least one of a halogen, a hydroxyl group, a ketone, and an ether, and c) The step of reacting the 9-aminomethyltetracycline intermediate from step b) with an aldehyde in the presence of a reducing agent at a temperature of 20°C to 80°C to form a 9-aminomethyltetracycline compound, or d) The 9-aminomethyltetracycline intermediate from step b) and the halogen of formula 7 R ６ X-type 7 In the formula, R ６ X is a C1-C10 linear alkyl group, a C3-C20 branched alkyl group, a C1-C10 linear alkyl group substituted with at least one of a halogen, a hydroxyl group, a ketone, and an ether, a C3-C20 branched alkyl group substituted with at least one of a halogen, a hydroxyl group, a ketone, and an ether, a C6-C10 aryl group, a C6-C10 aryl group substituted with at least one of a halogen, a hydroxyl group, a ketone, and an ether, or a C3-C10 heteroaryl group containing at least one oxygen, nitrogen, or sulfur atom, where X is a halogen selected from chlorine, bromine, and iodine. Alternatively, the step of reacting an alkylating reagent selected from neopentyl 4-methylbenzenesulfonate, neopentylmethanesulfonate, or a mixture thereof at a temperature of 20°C to 50°C to form a 9-aminomethyltetracycline compound. Includes, The reaction in steps a), b) and c) or d) is carried out in a pipe reactor, plug flow reactor, coil reactor, tube reactor, microchip, continuous plate reactor, packed bed reactor, continuous stirred tank reactor (CSTR), or another commercially available continuous flow reactor, or a combination of two or more such reactors. A method wherein the method is a semi-continuous or continuous flow process.

2. The method according to claim 1, wherein R is a C6-C10 aryl group or a substituted C6-C10 aryl group.

3. The method according to claim 1, wherein step b) is carried out in the absence of a hydrogenation reaction.

4. (i) Steps a) and b) of the method of the present invention are carried out in succession. (ii) Steps b) and c) of the method of the present invention are carried out sequentially, or (iii) Steps b) and d) of the method of the present invention are carried out sequentially. The method according to claim 1, 2, or 3.

5. The method according to claim 1, 2, or 3, wherein the residence time of the reaction in step a), b) and c) or d) is 12 seconds to 30 minutes.

6. Step a) The minocycline is in a solution or suspension, and optionally the solution or suspension contains sulfuric acid, methanesulfonic acid, trifluoromethanesulfonic acid, 65% SO ３ The method according to claim 1, 2, or 3, comprising a solvent selected from organic acids or mineral acids, such as fuming sulfuric acid or mixtures thereof.

7. In step a), the hydroxymethylamide derivative is in a solution or suspension, and optionally the solution or suspension contains sulfuric acid, methanesulfonic acid, trifluoromethanesulfonic acid, 65% SO ３ The method according to claim 1, 2, or 3, comprising a solvent selected from organic acids such as sulfuric acid or mineral acids that fume.

8. The hydroxymethylamide derivative in step a) is of formula 4 【Chemistry 2】 wherein, R １ is a C1-C10 linear alkyl group, a C3-C20 branched alkyl group, a C2-C10 linear alkenyl group, a C3-C20 branched alkenyl group, a C2-C10 linear alkynyl group, a C3-C20 branched alkynyl group, a C3-C10 aryl group, a C3-C10 heteroaryl group containing at least one oxygen, nitrogen or sulfur atom, or a halogen selected from chlorine, bromine and iodine, R ２ The C1-C10 linear alkyl group, the C3-C20 branched alkyl group, the C2-C10 linear alkenyl group, the C3-C20 branched alkenyl group, the C2-C10 linear alkynyl group, the C3-C20 branched alkynyl group, the C3-C10 aryl group, or the C3-C10 heteroaryl group containing at least one oxygen, nitrogen, or sulfur atom, and optionally R ２ R １ Linked to form a 4-8 membered ring, the ring may be substituted and may contain carbon atoms and / or heteroatoms such as oxygen, nitrogen, and sulfur. The method according to claim 1, 2, or 3, as represented by the following:

9. The method according to claim 1, 2, or 3, wherein the hydroxymethylamide derivative in step a) is N'-hydroxymethyl-phthalimide.

10. The method according to claim 1, 2, or 3, wherein the 2,9-(methylamide-substituted) minocycline in step b) is in a solution or suspension, and optionally the solution or suspension comprises a solvent selected from an alcohol such as benzyl alcohol, a polar aprotic solvent such as dimethyl sulfoxide, dimethylformamide, or dichloromethane, or a mixture thereof.

11. The method according to claim 1, 2, or 3, wherein the amine in step b) is in a solution or suspension, and optionally the solution or suspension comprises a solvent selected from an alcohol such as benzyl alcohol, a polar aprotic solvent such as dimethyl sulfoxide, dimethylformamide, or dichloromethane, or a mixture thereof.

12. The R of the amine ３ and R ４ The method according to claim 1, 2, or 3, wherein the C1-C4 linear alkyl group is selected from a C1-C4 linear alkyl group, a C3-C4 branched alkyl group, a substituted C1-C4 linear alkyl group, or a substituted C3-C4 branched alkyl group.

13. The method according to claim 1, 2, or 3, wherein the amine in step b) is selected from methylamine, ethanolamine, and n-propylamine.

14. The method according to claim 1, 2, or 3, wherein an excess amount of amine is used in step b).

15. The method according to claim 14, wherein the excess amine is successively removed before step c) or d).

16. The method according to claim 1, 2, or 3, wherein the 9-aminomethyltetracycline intermediate in step c) or d) is in a solution or suspension, and optionally the solution or suspension comprises a solvent selected from an alcohol such as benzyl alcohol, ethanol or methanol, a polar aprotic solvent such as dimethyl sulfoxide, dimethylformamide or dichloromethane, or a mixture thereof.

17. The method according to claim 1, 2, or 3, wherein the aldehyde in step c) is in a solution or suspension, and optionally the solution or suspension comprises a solvent selected from an alcohol such as benzyl alcohol, ethanol or methanol, a polar aprotic solvent such as dimethyl sulfoxide, dimethylformamide or dichloromethane, or a mixture thereof.

18. The aldehyde in step c) is, Formula 6 R ５ COH Formula 6 In the formula, R ５ However, it is a C1-C10 linear alkyl group substituted with at least one of hydrogen, a C1-C10 linear alkyl group, a C3-C20 branched alkyl group, a halogen, a hydroxyl group, a ketone, and an ether, a C3-C20 branched alkyl group substituted with at least one of a halogen, a hydroxyl group, a ketone, and an ether, a C6-C10 aryl group substituted with at least one of a halogen, a hydroxyl group, a ketone, and an ether, or a C3-C10 heteroaryl group containing at least one oxygen, nitrogen, or sulfur atom. The method according to claim 1, 2, or 3, as represented by the following:

19. The method according to claim 1, 2, or 3, wherein the aldehyde in step c) is selected from pivaldehyde, acetaldehyde, and benzaldehyde.

20. The method according to claim 1, 2, or 3, wherein the reducing agent in step c) is an immobilized reducing agent.

21. The method according to claim 20, wherein the immobilized reducing agent is immobilized sodium cyanoborohydride.

22. The method according to claim 1, 2, or 3, wherein the halogen is selected from 1-chloro-2,2-dimethylpropane, 1-bromo-2,2-dimethylpropane, and 1-iodo-2,2-dimethylpropane.

23. The method according to claim 1, 2, or 3, wherein reaction step c) or d) is carried out in the presence of a proton receptor.

24. The method according to claim 23, wherein the proton acceptor is selected from triethylamine, ammonia, and 4-dimethylaminopyridine.

25. The method according to claim 1, 2, or 3, wherein reaction step c) or d) is carried out in the presence of an organic acid such as formic acid or acetic acid, an inorganic acid, or a mixture thereof.

26. The method according to claim 1, 2, or 3, wherein the reaction in step a), b), c) and / or d) is carried out at a pressure of 100 to 2000 kPa.

27. The method according to claim 1, 2, or 3, wherein the 9-aminomethyltetracycline compound formed in step c) or d) is omadacycline.

28. The method according to claim 1, 2, or 3, wherein, following step c) or d), counterion exchange is performed to form an omadacycline salt.

29. The method according to claim 27, wherein the formed omadacycline has a purity of more than 50%, and optionally 70-80% or 81-100%.

30. The method according to claim 27, wherein the formed omadacycline has an epimer content of less than 10%, and optionally less than 2%.

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