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 a novel and improved process for producing 9-aminomethyltetracycline compounds known from the prior art (U.S. Patent No. 9365500), including but not limited to omadacycline.

Background Art

[0002] Antibiotics are indispensable drugs for protecting lives that have revolutionized medicine, starting from 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 the treatment of infections caused by Gram-positive and Gram-negative bacteria, while others are only effective against Gram-positive bacteria. An ideal antibiotic is 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 intestinal / skin flora. In any case, ideal or not, antibiotics do not remain permanently effective mainly due to over-prescription or inappropriate prescription, which has led to the increased emergence and 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 surgeries. As highlighted in the EU One Health Action Plan against Antimicrobial Resistance (AMR) (European Commission, 2017) and the US Department of Health and Human Services' report on the threat of antibiotic resistance (Antibiotic Resistance Threats in the United States - Report 2019), it is a global concern with serious health and economic consequences. A major challenge is the excessive and inappropriate use of antimicrobial agents in animal and human medicine, leading to the development of resistance, which is estimated to cause 33,000 deaths annually in the EU / EEA and over 35,000 deaths in the United States (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 a person dies every 1 minute and 23 seconds due to drug-resistant infections, and by 2050, if research and development of new drugs and treatments continue at this pace, the number of deaths could reach a staggering one every 3 seconds (O'Neill, J. Tackling Drug-Resistant Infections Globally: Final Report and Recommendations; 2016). Current incentive models do not offer sustainable solutions, and new business approaches are needed, including new incentives and pricing systems for developing antimicrobial agents.

[0004] Investment in research and development for innovative medicines and treatments is essential for advancing disease prevention and treatment. Access to safe, high-quality, and effective medicines is a critical element of social well-being (European Commission. Pharmaceutical Strategy for Europe 2020; 2020). The continuous development of new antimicrobial agents is recognized as extremely important for human health. Faced with increasing resistance, there is a need for new antimicrobial agents that are suitable for treating patients' infections. Furthermore, in recent years, there have been efforts to re-evaluate the dosage regimens of some approved drugs in order to maximize the effectiveness of several approved drugs 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, due to a lack of commercial interest, few new antibiotics have been brought to market (Wright, GDPerspective Antibiotics: A New Hope. Chem. Biol. 2012, 19(1), 3-10). Currently, due to a lack of commercial interest or scientific limitations, investment is not necessarily focused on the greatest unmet needs. For example, there is a lack of development of new antimicrobial agents, treatments, or vaccines against emerging health threats (including 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 treatment for specific populations such as pregnant and breastfeeding women and the elderly. Given the lack of treatment options to address AMR, the development of novel antimicrobial agents or alternatives is a prime example of an unmet medical need. Identifying new biochemical targets for creating different classes of drugs is complex and, in that case, presents economic challenges associated with low returns on investment.Because new antibiotics are entering the market without bacterial resistance, guidelines dictate that these drugs should be reserved as a last resort when all other treatment options fail, thus limiting their sales. To complement this issue, many antibiotics, including low-cost generic drugs, are already available in clinics (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 U.S. Food and Drug Administration's Safety and Innovation Act. It created incentives for sponsors to bring antimicrobial and antifungal drugs (known as QIDPs - Qualified Infectious Disease Products) to market for the treatment of serious or life-threatening infections. Sponsors may request GAIN for their drugs, and the FDA reviews the requests and responds within 60 days of submission (FDA Generating Antibiotics Incentive Now; 2017).

[0006] Sponsors developing and submitting QIDP applications may be eligible to receive incentives through GAIN. The main incentive included in GAIN is that being designated as a QIDP qualifies for five years of marketing exclusivity in addition to certain exclusivity already provided by the Food, Drug, and Cosmetic Act. GAIN also manufactures pharmaceuticals designated as QIDPs that qualify for fast track designation. Finally, GAIN requests the FDA to grant priority examination to the first application submitted for QIDP approval.

[0007] tetracycline Tetracyclines, broad-spectrum antibiotics, inhibit bacterial growth by inhibiting protein synthesis. Generally, they bind to the bacterial 30S ribosome subunit, preventing the addition of amino acids to growing polypeptide chains. (U.S. Patent No. 9,365,500, Bradford, P.; Jones, C. Antibiotic Discovery and Development - Chapter 5 (Tetracyclines); Springer, Boston, MA, 2012). Since the discovery of the first tetracycline, it has 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. NYAcad. Sci. 1948, 51, 177-181) that 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 (ultimately, 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, Pfizer chemists modified 7-chlorotetracycline to create a molecule known as tetracycline (compound 3, formula 2). 2) Furthermore, we manufactured antibiotics with even higher activity (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, efforts to discover and develop novel and modified antimicrobial agents that are not affected by common bacterial tetracycline resistance mechanisms have declined over the past decade (Bradford, P.; Jones, C. Antibiotic Discovery and Development - Chapter 5 (Tetracyclines); Springer, Boston, MA, 2012).

[0011] Significant class-based resistance due to the expression of tetracycline-specific efflux pumps and ribosome protection mechanisms reduces the efficacy of tetracycline. In 1999, tigecycline (compound 4, formula 2), a minocycline derivative of a glycylcycline subclass, emerged as a broad-spectrum tetracycline that could evade active efflux resistance mechanisms that provide ribosome protection and 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 cutaneous and soft tissue infections 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 only available for intravenous administration.This can cause 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 the Gram-negative efflux pump 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), ellabacycline (6), and thalecycline (7)-Equation 2, have been identified to overcome the toxicity of tigecycline.

[0012] Omadacycline from Paratek Pharmaceuticals, known as Nuzyra (trademark), is a novel aminomethyl-substituted derivative of minocycline. Compound 5, formula 2Nuzyra® 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) for community-acquired bacterial pneumonia (CABP) and acute bacterial skin and cutaneous structural infections (ABSSSI) in tablet form (NDA209816) and powder form (NDA209817) (Paratek Pharmaceuticals. Full Prescribing Information NUZYRA(omadacycline)Paratek Pharmaceuticals, Inc 2018).

[0013] [ka]

[0014] Omada Cyclone Omadacycline is a novel, first-in-class, semi-synthetic derivative of aminomethylcycline and 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 (U.S. Patent No. 9,365,500). Modification at this location resulted in enhanced activity against Gram-positive and Gram-negative bacteria and overcame resistance mechanisms (i.e., elution and ribosome protection) known to affect older generations of tetracycline. ((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, 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)).

[0015] The primary effect of omadacycline is its strong efficacy in inhibiting bacterial protein synthesis. (Draper, MP; Weir, S.; Macone, A.; Donatelli, J.; Trieber, CA; Tanaka, SK; Levy, S.B. Mechanism of Action of the Novel Aminomethylcycline Antibiotic omadacycline. Antimicrob. Agents Chemother. 2014, 58(3), 1279-1283). It acts by binding to the 30S ribosome subunit in bacterial mRNA translation complexes, inhibiting the binding of aminoacyl-tRNA to the mRNA-ribosome complex, and consequently 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 (Quick Infectious Disease) in both IV and oral formulations for the treatment of acute bacterial skin and cutaneous structural infections (ABSSSI) 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). ABSSSI includes 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 received FDA approval 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. 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 activity spectrum includes doxycycline (Draper, MP; Weir, S.; Macone, A.; Donatelli, J.; Trieber, CA; Tanaka, SK; Levy, S. Mechanism 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, Randomized, 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 Streptococcus pneumoniae (S. pneumonia), vancomycin-resistant enterococci, E. faecalis or E. faecium, as well as penicillin and multidrug-resistant strains and Streptococcus pneumoniae strains, including anaerobic Clostridioides (Clostridium difficille) (International Publication No. 2017 / 165729, 2016). The same applies to Gram-negative Haemophilus influenzae, Escherichia coli (E. coli), and Legionella (Huband, MD; Pfaller, MA; Shortridge, D.; Flamm, RKS; 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. 9724358).As a result, omadacycline may be an important and desirable treatment option for patients with infections in which epidemiology suggests a high prevalence of drug-resistant pathogens (Macone, AB; Caruso, BK; Leahy, RG; Donatelli, J.; Weir, S.; Draper, MP; Tanaka, SK; Levy, SBC In Vitro and in Vivo Antibacterial Activities of omadacycline, a Novel Aminomethylcycline. Antimicrob. Agents Chemother. 2014, 58(2), 1127-1135). The report also describes treatments for urinary tract infections (UTIs), bacterial infections caused by biological weapons, and the use of omadacycline to regulate gene expression (U.S. Patent No. 9724358; Bal, AM; David, MZ; Garau, J.; Gottlieb, T.; Mazzei, T.; Scaglione, F.; Tattevin, P.; Gould, I. Future Trends in the Treatment of Methicillin-Resistant Staphylococcus Aureus (MRSA) Infection: An in-Depth Review of Newer Antibiotics Active against an Enduring Pathogen.J.Glob.Antimicrob.Resist.2017,10,295-303;International Publication No. 2017 / 192516;International Publication No. 2016 / 154332;International Publication No. 2007 / 133798;International Publication No. 2018 / 026987;U.S. Patent No. 9078811;International Publication No. 2009 / 120389). Phase 1 clinical trials are ongoing for tissue penetration (NCT04144374) and treatment of diabetic foot infections (NCT04714411) in diabetic patients with hemodialysis-induced wound infections.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, JS; 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. entered into 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 and to obtain the option to procure up to 10,000 treatment courses of NUZYRA® for use in the Strategic National Stockpile (SNS) for use against potential biopharmaceuticals (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 is used for multi-kilogram preparations and is described in U.S. Patent No. 9,434,680. (U.S. Patent No. 9,434,680 also discloses 9-aminomethyltetracycline compounds other than omadacycline).

[0021]

Chem.

[0022] Minocycline has several reactive functional groups, and the primary amide at C2 exhibits higher reactivity toward electrophiles than C9 or C10 (Formula 1). Due to this fact, the first step of Scheme 1 requires approximately 3 equivalents of N'-(hydroxymethyl)-phthalimide in trifluoromethanesulfonic acid to yield a 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 alcohol solution to obtain a bis-substituted aminomethyl tetracycline intermediate. In the third step of Scheme 1, the resulting intermediate is reacted with hydrogen under hydrogenation conditions to form a C9-substituted aminomethyl tetracycline intermediate. In the fourth step of Scheme 1, the formed compound is reacted with pivalaldehyde under hydrogenation conditions to obtain omadacycline. After reverse phase chromatography purification, pH adjustment and precipitation, the desired product is obtained as an amorphous unstable solid. For long-term manufacturing routes, the instability of the aminomethyl intermediate and the challenges of the chromatography column purification step must be overcome.

[0023] A three-step synthesis of omadacycline is described with an overall yield of 15 to 18%, starting from an acyliminium ion via the Friedel-Crafts reaction of electronically tuned monochloroacyliminium (Tscherniac-Einhorn reaction) (see Scheme 2 and Chung, J.Y.L.; Hartner, F.W.; Cvetovich, R.J. 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 obtain triazanes, which are then treated with anhydrous compounds. (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 decomposition modes. In the first step of Scheme 2, 5 equivalents of acyliminium are used at 35 / 40°C for 24 hours, and the optimized yield is 83%. In the second step, the chloroacetyl group is removed, and the chloroacetyl intermediate is 3N The process involves heating in HCl at 70°C for 20 hours. Reverse epimerization is carried out by heating a racemic mixture of crude omadacycline in an aqueous solution of n-butanol at 105°C in the presence of calcium chloride and ethanolamine. The resulting amorphous solid is unstable when exposed to temperatures above 0°C and air, so it is necessary to prepare a stable salt.The crystalline salts of omadacycline (monotosilate, bisHCl, and mesylate) are stable at 25°C (U.S. Patent Application Publication No. 2018 / 0104262). However, in this synthesis, the purification step must be changed from a chromatographic system to a kilogram-scale, maneuverable operation.

[0026] U.S. Patent No. 9,365,500 describes a synthetic route for omadacycline based on the Tscherniac-Einhorn reaction, as shown in Scheme 3. In the first step of Scheme 3, using minocycline as the substrate, an aminomethyl intermediate can be synthesized using N'-(hydroxymethyl)benzylcarbamate in an acidic medium at 25°C for 24 hours. The second step consists of reductive amination of the intermediate to obtain omadacycline (U.S. Patent No. 9,365,500).

[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 the palladium-catalyzed formylation of organic halide substrates in the presence of carbon monoxide, yielding aldehydes in high yield. Seyedi F. et al., in U.S. Patent No. 9522872, carried out this procedure for the preparation of 9-iodominocycline and subsequently 9-formylminocycline in 99% yield. The resulting intermediate was reacted with sodium borohydride triacetate to obtain omadacycline.

[0029] [ka] [Overview of the project]

[0030] Omadacycline is safe and has proven highly effective against multidrug-resistant Gram-positive and Gram-negative bacteria. However, to the best of our knowledge, all described methods for synthesizing 9-aminomethyltetracycline compounds have low yields, low selectivity, and extremely difficult purification steps. Industrial-scale synthesis methods still require optimization to reduce impurities and achieve better yields when preparing these types of compounds. This invention provides a novel method using an innovative chemical strategy. Utilizing continuous flow technology, we have overcome the challenges of purification, low yields, and isolation of unstable intermediates by utilizing process enhancements (e.g., high temperature and high pressure) and improvements in mass and heat transfer to increase selectivity. Furthermore, with the concept of green chemistry in mind, we have developed a method for selecting solvents and reagents that are as environmentally friendly as possible.

[0031] The inventors are seeking to develop a new, more environmentally friendly, less expensive, and superior method for synthesizing 9-aminomethyltetracycline compounds, particularly omadacycline, a method that could ultimately benefit patients, businesses, and the environment. The present invention satisfies such objectives by providing a method to reduce or eliminate one or more of the problems of the 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-alkyltetracycline compounds such as 9-aminomethylminocycline in the most ecologically clean manner possible, reducing time and waste. The inventors have found that by using flow chemistry techniques, it is possible to use environmentally friendly solvents, avoid the decomposition of sensitive intermediates, and control the formation of epimers, thereby making it possible to obtain aminomethyltetracycline compounds with a purity of over 50%, preferably 70-80%, and more preferably 81-100%. Furthermore, the overall yield (also known as cumulative yield) is over 30%, preferably 50-70%, and more preferably 71-100%. An example of an aminomethyltetracycline compound that can be prepared by the method of the present invention is omadacycline. [Brief explanation of the drawing]

[0033] [Figure 1] This diagram shows the synthesis sequence of omadacycline. [Figure 2] This is a diagram showing the continuous flow setting. [Figure 3] This is a diagram showing the continuous flow setting. [Modes for carrying out the invention]

[0034] According to one aspect of the present invention, a method is provided for synthesizing a 9-aminomethyltetracycline compound according to formula 3, wherein R is hydrogen, a C1-C10 linear alkyl group, a C3-C20 branched alkyl group, a substituted alkyl group (which may be substituted with at least one of a halogen, a hydroxyl group, a ketone, and an ether), a C3-C10 or C6-C10 aryl group, a substituted C3-C10 or C6-C10 aryl group (which may be 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, sulfur, or phosphorus atom. [ka] This method is, a) A step of reacting minocycline with a hydroxymethylamide derivative to form 2,9-(methylamide-substituted)minocycline and 2-(methylamide-substituted)minocycline, b) The step of reacting 2,9-(methylamide-substituted)minocycline from step a) with an amine or diamine to form a 9-aminomethyltetracycline intermediate, and c) A step in which the 9-aminomethyltetracycline intermediate from step b) is reacted with an aldehyde in the presence of a reducing agent to form a 9-aminomethyltetracycline compound, or d) The step of reacting the 9-aminomethyltetracycline intermediate from step b) with an alkyl halide or alkyl reagent to form a 9-aminomethyltetracycline compound. Includes.

[0035] The present invention is a multi-step method for obtaining 2,9-(methylamide-substituted)minocycline by electrophilic aromatic substitution between minocycline and a hydroxymethylamide derivative in step a), obtaining a 9-aminomethyltetracycline intermediate by aminolysis reaction between 2,9-(methylamide-substituted)minocycline and an amine or diamine in step b), and forming the desired 9-aminomethyltetracycline compound by either reductive amination 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). As used herein, the term “multi-step chemical synthesis” generally refers to a synthetic method involving multiple chemical reactions. This term is not intended to encompass synthetic methods in which only one chemical reaction may occur over multiple steps.

[0036] The hydroxymethylamide derivative used in step a) may be one that conforms to formula 4. [ka] In the formula, R1 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, a C3-C10 heteroaryl group containing at least one oxygen, nitrogen, sulfur, or phosphorus atom, or chlorine, bromine, and iodine. The selected halogen 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 may optionally be linked to R1 to form a 4- to 8-membered ring, which may optionally be substituted with other functional groups, such as halogens, hydroxyl groups, ketones, ethers, esters, and amides, and may contain carbon atoms and / or heteroatoms, such as oxygen, nitrogen, and sulfur. The hydroxymethylamide derivative of step a) may also be N'-hydroxymethyl-phthalimide.

[0037] As used herein, the term alkyl is a general term referring 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 linear alkyl groups (e.g., methyl, ethyl, propyl, butyl, pentyl, etc.), branched alkyl groups (e.g., isopropyl, tert-butyl, isobutyl, etc.), and cycloalkyl groups (e.g., cyclopropyl, cyclopentyl, etc.). The term alkyl further includes alkyl groups which may further contain oxygen, nitrogen, sulfur, or phosphorus atoms.

[0038] As used herein, the term aryl is a general term referring 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 one that conforms to formula 5. NHR3R4 formula 5 In the formula, R3 and R4 are a hydrogen atom, a C1-C10 linear alkyl group, a C3-C20 branched alkyl group, or a substituted alkyl group (which may be substituted with an alcohol or ether). Preferably, R3 and R4 are selected from a C1-C4 linear alkyl group, a C3-C4 branched alkyl group, or a substituted alkyl group. Optionally, the amine or diamine in step b) is selected from methylamine, ethanolamine, and n-propylamine.

[0040] Excess amine or diamine may be used in step b). If applicable, the excess amine or diamine may be successively removed before step c) or d).

[0041] In contrast to some conventional methods, step b) can be carried out in the absence of a hydrogenation reaction. That is, when 2,9-(methylamide-substituted)minocycline is reacted with an amine or diamine, the 9-aminomethyltetracycline intermediate is directly formed without the need to hydrogenate the compound to form an intermediate.

[0042] The aldehyde used in step c) may be the one given by formula 6. R5COH formula 6 In the formula, R5 is hydrogen, a C1-C10 linear alkyl group, a C3-C20 branched alkyl group, a substituted alkyl group (which may be 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, and optionally immobilized sodium cyanoborohydride.

[0044] When an alkyl halide is used in step d), the alkyl halide may be one that conforms to formula 7. R6 X formula 7 In the formula, R6 may be a C1-C10 linear alkyl group, a C3-C20 branched 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 of oxygen, nitrogen, sulfur, or phosphorus atoms, where 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 alkyl reagent is used in step d), the alkyl reagent may have a good leaving group such as mesyl or tosyl. In some cases, the alkyl reagent is neopentyl 4-methylbenzenesulfonate, neopentylmethanesulfonate, or a mixture thereof.

[0046] The reaction in 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) can vary from 1:1 to 1:30.

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

[0050] The method of the present invention may be a semi-continuous or continuous flow process. Therefore, in a continuous flow process, the total 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, 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. Steps a) and b) of the method of the present invention may be operated continuously, steps b) and c) may be operated continuously, or steps b) and d) may be operated continuously. When steps b) and c) or steps b) and d) are operated continuously, the 9-aminomethyltetracycline intermediate formed in step b) may 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 that are in fluid communication with one another.

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

[0053] Surprisingly, it was discovered that it is possible to directly synthesize the 9-aminomethyltetracycline intermediate from 2,9-(methylamide-substituted)minocycline compounds by using higher temperatures that are only achievable by employing flow chemistry techniques with low residence times.

[0054] The residence times for the reactions in steps a), b), and c) or d) may be 12 seconds to 2 hours, and possibly 12 seconds to 30 minutes. The residence times for each reaction step may differ from those for the other reaction steps.

[0055] The residence times of the reagents along a selected distance in a continuous flow reactor related to 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 in step d) can vary from 1 minute to 2 hours. The yield of each reaction step may be about 5% or more, preferably 50% or more, and more preferably 80% or more. The chromatographic purity of the crude reaction product obtained from step a) or b) may be about 50% or more, more preferably 80% or more.

[0056] The solvent used in the method of the present invention may be a common organic solvent, an aqueous solvent, an aqueous solvent system, water, or a mixture thereof. Any suitable solvent or solvent system may be used. The solvent system used may include a colloidal suspension or emulsion. The solvent system used may include an alcohol, water, or a mixture of both. The solvent system may include a mixture of a water-miscible organic solvent and water. They may also include water-immiscible organic solvents that are in contact with or not in contact with water. Any specific combination of the solvents listed above may be used. The method steps of the present invention do not necessarily have to be optimally carried out with the same solvent or solvent system, and the preparation of solvent / solvent compositions or solvent switches may be carried out sequentially as needed, for example, without the need to isolate or purify intermediates.

[0057] The minocycline used in step a) may be in solution or suspension, and optionally the solution or suspension may contain a solvent selected from organic acids or mineral acids such as sulfuric acid, methanesulfonic acid, trifluoromethanesulfonic acid, sulfuric acid that fumes 65% SO3, or mixtures thereof. Optionally, a sulfuric acid solution or suspension of minocycline 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, and optionally the solution or suspension may contain a solvent selected from organic acids or mineral acids such as sulfuric acid, methanesulfonic acid, trifluoromethanesulfonic acid, sulfuric acid that fumes 65% SO3, or mixtures thereof. Optionally, a solution or suspension of the hydroxymethylamide derivative in sulfuric acid at a concentration of 100-160 mg / mL may be used in step a). Therefore, minocycline and the hydroxymethylamide derivative can 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, minocycline and hydroxymethylamide derivatives may be present in solutions or suspensions containing the same solvent or a mixture of solvents, or different solvents or different combinations of solvents. Additionally, minocycline and hydroxymethylamide derivatives may be present in solutions or suspensions of the same or different concentrations.

[0058] The 2,9-(methylamide-substituted) minocycline used in step b) may be in solution or suspension, and the solution or suspension may contain a solvent selected from alcohols such as benzyl alcohol, polar aprotic solvents such as dimethyl sulfoxide, dimethylformamide, or dichloromethane, or mixtures thereof. A solution or suspension of 2,9-(methylamide-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, and the solution or suspension may contain a solvent selected from alcohols such as benzyl alcohol, polar aprotic solvents such as dimethyl sulfoxide, dimethylformamide, or dichloromethane, or mixtures thereof. A solution or suspension of amine or diamine at a concentration of 50-200 mg / mL may be used in step b). Therefore, 2,9-(methylamide-substituted)minocycline and amines or diamines can 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, 2,9-(methylamide-substituted)minocycline and amines or diamines may be in solutions or suspensions containing the same solvent or a mixture of solvents, or different solvents or different combinations of solvents. Furthermore, 2,9-(methylamide-substituted)minocycline and amines or diamines may be in solutions or suspensions of the same or different concentrations.

[0059] The 9-aminomethyltetracycline intermediate used in step c) or d) may be in solution or suspension, and optionally the solution or suspension may contain a solvent selected from alcohols such as benzyl alcohol, ethanol or methanol, polar aprotic solvents such as dimethyl sulfoxide, 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, and optionally the solution or suspension may contain a solvent selected from alcohols such as benzyl alcohol, ethanol or methanol, polar aprotic solvents such as dimethyl sulfoxide, 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). Therefore, the 9-aminomethyltetracycline intermediate and the aldehyde can 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 solutions or suspensions containing the same solvent or a mixture of solvents, or different solvents or different combinations of solvents. Moreover, the 9-aminomethyltetracycline intermediate and the aldehyde may be present in solutions or suspensions at the same or different concentrations.

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

[0061] One advantage of implementing the method 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 significantly reduced compared to that used in a batch reactor. This results in a reduction in subsequent effluent, and therefore makes these methods more environmentally friendly.

[0062] The use of continuous flow processes is an environmentally friendly method for carrying out chemical synthesis, can provide the ability to carry out chemical reactions with improved selectivity, reaction yield, and product purity profiles, and reduces waste. In many cases, continuous flow reactors can be used to further reduce the time and cost required to synthesize the desired product, as they allow for process enhancements (e.g., high temperature and high pressure). For example, a continuous flow process may involve flowing a fluid sample containing one or more precursor species through a flow-through system and carrying out a chemical reaction within the piping of such a system to convert the precursor species into the desired product.

[0063] The use of continuous flow reactors can provide the ability to utilize temperatures and pressures that are not readily achievable in batch processes. The use of high temperatures and pressures can accelerate the conversion of precursor species to reaction products without the need for additives or accelerators.

[0064] In some cases, the reactions in steps a), b), and c) or d) are carried out at temperatures 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 possibly higher. In some cases, the chemical reactions in steps a), b), and c) or d) are carried out at temperatures of 20°C to 150°C, preferably 20°C to 120°C. In some cases, the reaction in step a) is carried out at temperatures of 25°C to 200°C or 25°C to 50°C. In some cases, the reaction in step b) is carried out at temperatures of 25°C to 200°C or 100°C to 200°C. In some cases, the reaction in step c) is carried out at temperatures of at least 10°C or 20°C to 80°C. Depending on the circumstances, the reaction in step d) may be carried out at a temperature of 25°C to 200°C or 20°C to 50°C.

[0065] In some cases, 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 possibly higher. In some cases, the reactions in steps a), b) and c) or d) are carried out at a pressure of 100 to 2000 kPa. In some cases, the reaction in step b) is carried out at a pressure of at least 300 kPa, for example, 300 to 2000 kPa.

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

[0067] Continuous flow reactors can be made of any suitable material, including glass, different types of polymers (PFA, ETFE, PEEK, etc.), Hastelloy®, silicon carbide, stainless steel, and / or one or more high-performance alloys. Continuous flow reactors may include static mixing devices. Continuous flow reactors can handle slurries and are suitable for exposure to temperature or temperature ranges and / or pressure. When one or more identical continuous flow reactors or combinations of different continuous flow reactors listed above are used, the reactors may be connected to each other so that fluid communication is possible. With respect to the term “connected,” this should be understood to mean that continuous flow reactors do not necessarily have to be directly mounted to each other, and that reactors should be in fluid communication with at least one other reactor. However, if necessary, reactors may be directly mounted 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 shortening the reaction time. Furthermore, any immobilized reagent is contained within the matrix, and as a result, the reaction mixture does not need to be separated from such reagents.

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

[0070] The method of the present invention may comprise at least one chemical reaction step carried out sequentially with the 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 changes of solvent, and / or removal of excess reagents between reaction steps. Furthermore, the product of reaction step b) is an intermediate used as a reactant in reaction step c) to prepare the desired product.

[0071] If necessary, the method of the present invention may include one or more additional steps. The additional steps may 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 within one or more continuous flow reactors can be controlled. This may be done, for example, to allow a particular reaction to occur or to obtain a desired reaction rate. Controlling the conditions within one or more continuous flow reactors may involve adjusting or changing one or more of the following: temperature within the continuous flow reactor(s); pressure within the continuous flow reactor(s); solvent or solvent system within the flow reactor(s); flow rate within the continuous flow reactor(s). The concentration of each solution or suspension used in each of steps a), b), and c) or d) affects the flow rate, residence time, and reactant ratio. Therefore, adjusting or changing the concentration of each solution or suspension used in each of steps a), b), and c) or d) may also help control the conditions within one or more continuous flow reactors.

[0073] The flow rate of reagents through a continuous flow reactor can be controlled, modified, or adjusted depending on the reaction taking place in the reactor. The reagent flow rate may differ along one or more selected distances of the continuous flow reactor. The reagent flow rate associated with a reaction step may affect the flow rate associated with subsequent reaction steps. Reagents can be moved along selected distances of the continuous flow reactor at different flow rates. The flow rate of reagents through the continuous flow reactor can be controlled, adjusted, or modified using a pump.

[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, isolable compound (intermolecular reaction), or the formation of one or more bonds between two or more parts of the same molecule to produce a stable, isolable compound (intramolecular reaction). In other words, the term “reaction” does not refer to the interaction of solvents, catalysts, bases, ligands, or other materials that may help facilitate the occurrence of a reaction with the component(s).

[0075] Each reaction is carried out in a heterogeneous or homogeneous environment. Continuous flow reactors 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, a continuous flow reactor may contain one or more reagents or catalysts within it (e.g., within its bores). The catalyst may be homogeneous or heterogeneous with respect to the reactants, reagents, and / or solvents.

[0076] The reaction rate of each individual reaction step, the flow rate through each flow-through system, and the rate of change of solvent can be adjusted so that the flow through the entire system used to carry out the method of the present invention does not require the use of a holding tank at an intermediate stage. However, under certain circumstances, the use of a holding tank in the downstream operation may be an option.

[0077] When continuous flow reactors are used, the output of one or more continuous flow reactors can be carefully controlled to ensure that the composition of intermediates, reactants, impurities, and solvents is suitable for supplying to subsequent continuous flow reactors 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 to heterogeneous. For example, heterogeneous reactions can be used in the reductive amination reaction of step c), where a continuous flow reactor, such as a tubular reactor, is filled with a heterogeneous catalyst. The heterogeneous catalyst may be, for example, a reducing agent.

[0079] Furthermore, continuous solvent extraction / washing steps or membrane purification can be applied to remove impurities, excess reagents, or other undesirable substances, which may be detrimental to subsequent chemical reactions or the purity of the final product. The pressure in each reactor within the flow-through system may be atmospheric pressure or higher, and the temperature may vary from below ambient temperature to above 200°C.

[0080] The purification, isolation, and drying of the final product can also be carried out in a continuous manner using continuous extraction, membrane, crystallization, filtration, and drying processes, if necessary. [Examples]

[0081] Example 1 Flow experiments were conducted using the continuous flow setup shown in Figure 2 (wherein "TI" represents a 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 retained in a coil reactor (504 μL) at 80°C for 5 minutes. The resulting solutions showed 100% conversion of the starting materials, yielding 50% 2,9-methylphthalimidominocycline and 50% 2-methylphthalimidominocycline.

[0082] Example 2 The flow experiment was performed using a continuous flow setup shown in Figure 3 (where "TI" means temperature equipment, "PI" means pressure equipment, "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-methylphthalimidominocycline (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 and a residence time of 6 minutes was achieved in a coil reactor (10 mL) at 115 °C and a back pressure of 7 bar (700 kPa). The product stream was collected at the outlet in a round-bottom flask containing anhydrous ethanol (200 mL) at 30 °C. The mixture was distilled to obtain a solution (Solution C) containing the remaining amount of methylamine. Solution D was prepared by mixing pivaldihyde (4.90 mL), triethylamine (2.52 mL), and benzyl alcohol (292.6 mL). Solutions C and D were pumped in a 1:1 ratio, thoroughly mixed, and then subjected to a 30-minute residence time at 25°C in a packed-bed reactor containing immobilized sodium borohydride (25 g). Once a steady state was achieved, the fraction was collected and appropriately diluted for HPLC analysis. The resulting solution showed a 78% conversion.

[0083] Example 3 Flow experiments were conducted 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 and a residence time of 1 hour was achieved in a coil reactor (1 mL) at 35°C and a back pressure of 2 bar. Quantitative yields of the raw materials were obtained.

[0084] Example 4 A laboratory-scale nanofiltration system (MetCell Cross Flow System) was used to separate methylamine, reaction by-products, and the 9-aminomethyltetracycline intermediate. Membrane disks were prepared according to the diameter of the filtration cell, and the system was assembled using appropriate O-rings. A crude solution of the 9-aminomethyltetracycline intermediate was added to the METCell tank base and recirculated for 10 minutes. A pressure of 30 bar (3000 kPa) was applied to the system, and the permeate flow rate was calculated using a chronometer (Qperm = 0.133 mL / min). A fresh solution of ethanol was supplied to the system at a constant flow rate of 0.2 mL / min for 5 hours. The permeate sample and final retained solution were analyzed by HPLC and GC. 200 mL of retained solution was obtained (45 wt% BnOH, 5 wt% methylamine, 43% EtOH, 8 wt% solute). The membrane exclusion rate of the 9-aminomethyltetracycline intermediate during this procedure was 99%.

[0085] Example 5 Feed 1 contained a benzyl alcohol solution of the 9-aminomethyltetracycline intermediate (3.3 mmol, 55 mL), and Feed 2 contained pivaldihyde (1.08 mL), triethylamine (0.46 mL), and benzyl alcohol, reaching 55 mL. Both flows were pumped at 0.1 mL / min each using two high-pressure liquid pumps (P1 and P2, Knauer). The two liquid flows were combined in a T-mixer and mixed in a Uniqsis glass static mixer (578 μL, T: 175 sec) before entering a packed bed reactor (T: 30 min) containing immobilized sodium borohydride (5.33 g, 84.8 mmol). The packed bed was placed on an HPLC oven heated to 25°C. HPLC pump flow rates and pressures were measured and monitored by the pump system's control platform. Once steady state was achieved, fractions were collected and appropriately diluted for HPLC analysis. The conversion rate and yield were determined by HPLC. The combined fraction showed a conversion rate of 75.53%.

[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 a drying oven at a temperature below 30°C and under nitrogen sweep until a constant weight was reached. The solid was resuspended in i-PrOH (70 mL, 7 mL / g), p-toluenesulfonic acid was added, and the mixture was stirred at 550 rpm at room temperature under a nitrogen atmosphere for 24 hours. Omadacyclin silate was obtained in 77.08% mol 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】 In the formula, 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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