Thursday, 12 February 2015

Takeda’s ixazomib soon to be filed for multiple myeloma


Takeda's ixazomib soon to be filed for multiple myeloma
Takeda’s flagship experimental cancer drug ixazomib is a giant leap closer to being filed with regulatory authorities around the globe for multiple myeloma, after turning in a solid performance in late-stage trials.

Takeda’s ixazomib soon to be filed for multiple myeloma

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CAS#:  1201902-80-8
Synonym:   Ixazomib; MLN-9708.
IUPAC/Chemical name: 
4-(carboxymethyl)-2-((R)-1-(2-(2,5-dichlorobenzamido)acetamido)-3-methylbutyl)-6-oxo-1,3,2-dioxaborinane-4-carboxylic acid
CAMBRIDGE, Mass., May 23, 2013 – Takeda Pharmaceutical Company Limited (TSE:4502)  today announced the initiation of an international phase 3 clinical trial evaluating once a week MLN9708 in combination with lenalidomide and dexamethasone in patients with  newly diagnosed multiple myeloma who are not candidates for transplant. The multi-center study with MLN9708, an investigational, oral proteasome inhibitor, will be conducted in Europe and North America.———————-READ MORE AT
Description of Ixazomib:  ixazomib is an orally bioavailable second generation proteasome inhibitor (PI) with potential antineoplastic activity. Ixazomib inhibits the activity of the proteasome, blocking the targeted proteolysis normally performed by the proteasome, which results in an accumulation of unwanted or misfolded proteins; disruption of various cell signaling pathways may follow, resulting in the induction of apoptosis. Compared to first generation PIs, second generation PIs may have an improved pharmacokinetic profile with increased potency and less toxicity. Proteasomes are large protease complexes that degrade unneeded or damaged proteins that have been ubiquinated
MLN9708 is an investigational proteasome inhibitor that, compared with bortezomib, has improved pharmacokinetics, pharmacodynamics, and antitumor activity in preclinical studies. MLN9708 rapidly hydrolyzes to MLN2238, the biologically active form. MLN9708 has a shorter proteasome dissociation half-life and improved pharmacokinetics, pharmacodynamics, and antitumor activity compared with bortezomib.MLN9708 has a larger blood volume distribution at steady state, and analysis of 20S proteasome inhibition and markers of the unfolded protein response confirmed that MLN9708 has greater pharmacodynamic effects in tissues than bortezomib. MLN9708 showed activity in both solid tumor and hematologic preclinical xenograft models, and we found a correlation between greater pharmacodynamic responses and improved antitumor activity. Moreover, antitumor activity was shown via multiple dosing routes, including oral gavage. Taken together, these data support the clinical development of MLN9708 for both hematologic and solid tumor indications. (source: Cancer Res. 2010 Mar 1;70(5):1970-80. Epub 2010 Feb 16.).
References
1: Mullard A. Next-generation proteasome blockers promise safer cancer therapy. Nat Med. 2012 Jan 6;18(1):7. doi: 10.1038/nm0112-7a. PubMed PMID: 22227650.
2: Anderson KC. The 39th David A. Karnofsky Lecture: bench-to-bedside translation of targeted therapies in multiple myeloma. J Clin Oncol. 2012 Feb 1;30(4):445-52. Epub 2012 Jan 3. PubMed PMID: 22215754.
3: Appel A. Drugs: More shots on target. Nature. 2011 Dec 14;480(7377):S40-2. doi: 10.1038/480S40a. PubMed PMID: 22169800.
4: Lee EC, Fitzgerald M, Bannerman B, Donelan J, Bano K, Terkelsen J, Bradley DP, Subakan O, Silva MD, Liu R, Pickard M, Li Z, Tayber O, Li P, Hales P, Carsillo M, Neppalli VT, Berger AJ, Kupperman E, Manfredi M, Bolen JB, Van Ness B, Janz S. Antitumor activity of the investigational proteasome inhibitor MLN9708 in mouse models of B-cell and plasma cell malignancies. Clin Cancer Res. 2011 Dec 1;17(23):7313-23. Epub 2011 Sep 8. PubMed PMID: 21903769.
5: Chauhan D, Tian Z, Zhou B, Kuhn D, Orlowski R, Raje N, Richardson P, Anderson KC. In vitro and in vivo selective antitumor activity of a novel orally bioavailable proteasome inhibitor MLN9708 against multiple myeloma cells. Clin Cancer Res. 2011 Aug 15;17(16):5311-21. doi: 10.1158/1078-0432.CCR-11-0476. Epub 2011 Jun 30. PubMed PMID: 21724551; PubMed Central PMCID: PMC3156932.
6: Kupperman E, Lee EC, Cao Y, Bannerman B, Fitzgerald M, Berger A, Yu J, Yang Y, Hales P, Bruzzese F, Liu J, Blank J, Garcia K, Tsu C, Dick L, Fleming P, Yu L, Manfredi M, Rolfe M, Bolen J. Evaluation of the proteasome inhibitor MLN9708 in preclinical models of human cancer. Cancer Res. 2010 Mar 1;70(5):1970-80. Epub 2010 Feb 16. Erratum in: Cancer Res. 2010 May 1;70(9):3853. Hales, Paul [added]. PubMed PMID: 20160034.
7: Dick LR, Fleming PE. Building on bortezomib: second-generation proteasome inhibitors as anti-cancer therapy. Drug Discov Today. 2010 Mar;15(5-6):243-9. Epub 2010 Jan 29. Review. PubMed PMID: 20116451.8: Marblestone JG. Ubiquitin Drug Discovery & Diagnostics 2009 – First Annual Conference. IDrugs. 2009 Dec;12(12):750-3. PubMed PMID: 19943215.
Chemical structure of ixazomib

Nasopharyngeal cancer is a sub-type of head and neck cancer that arises from the epithelial cells that cover the surface and line the nasopharynx. The incidence of nasopharyngeal cancer has been reported at approximately 0.5 to 2 new cases per year per 100,000 in Europe and the USA. Rottey et ah, Curr. Opin. Oncol., 23(3): 254-258 (201 1). There are three subtypes of nasopharyngeal cancer recognized in the World Health Organization (WHO) classification: (i) Type 1 – squamous cell carcinoma, typically found in the older adult population; (ii) Type 2 non-keratinizing carcinoma; and (iii) Type 3 – undifferentiated carcinoma. Treatment for nasopharyngeal cancer often involves radiotherapy and/or chemotherapy. There remains a continuing need for new and improved treatments for patients with nasopharyngeal cancer. There remains a further need to identify nasopharyngeal patients most likely to benefit from treatment with a proteasome inhibitor.
Proteasome inhibition represents an important new strategy in cancer treatment. King et al. , Science 274: 1652-1659 ( 1996), describes an essential role for the ubiquitin-proteasome pathway in regulating cell cycle, neoplastic growth and metastasis. The authors teach that a number of key regulatory proteins, including cyclins, and the cyclin-dependent kinases p21 and p27K,P ! , are temporally degraded during the cell cycle by the ubiquitin-proteasome pathway. The ordered degradation of these proteins is required for the cell to progress through the cell cycle and to undergo mitosis.
The proteasome inhibitor VELCADE© (bortezomib; N-2-pyrazinecarbonyl-L -phenylalanine -L- leucineboronic acid) is the first proteasome inhibitor to achieve regulatory approval. Mitsiades et ai, Current Drug Targets, 7: 1341 (2006), reviews the clinical studies leading to the approval of bortezomib for the treatment of multiple myeloma patients who have received at least one prior therapy. Fisher et ai , J. Clin. Oncol, 30:4867, describes an international multi-center Phase II study confirming the activity of bortezomib in patients with relapsed or refractory mantle cell lymphoma. Ishii et al, Anti-Cancer Agents in Medicinal Chemistry, 7:359 (2007), and Roccaro et al., Curr. Pharm. Biotech., 7: 1341 (2006), discuss a number of molecular mechanisms that may contribute to the antitumor activities of bortezomib. The proteasome inhibitorMLN9708 [2,2′-{2-[(lR)- l -( {[(2,5-dichlorobenzoyl)amino]acetyl}amino)-3- methylbutyl]-5-oxo-l,3,2-dioxaborolane-4,4-diyl}diacetic acid] is currently undergoing clinical evaluation for hematological and solid cancers. MLN9708 is a citrate ester which rapidly hydrolyzes to the active form [(lR)-l -({[(2,5-dichlorobenzoyl)amino]acetyl}amino)-3-methylbutyl]boronic acid (MLN2238) on exposure to aqueous solution or plasma. MLN9708 has demonstrated anti-tumor activity in a range of hematological and solid tumor xenograft models (Kupperman et al. (2010) Cancer Res. 70: 1970- 1980),
Summary
The invention relates to the discovery that patients with nasopharyngeal cancer respond to treatment with MLN9708. In one aspect, the invention relates to the discovery of the increased expression of Nuclear Factor Kappa-B RelA 65,000 dalton subunit (NFKB p65) in biological samples comprising cells obtained from patients with nasopharyngeal cancer and responsive toMLN9708.
Accordingly, the invention features treating nasopharyngeal cancer patients withMLN9708 if a sample from the patient demonstrates an elevated expression of NFKB p65.
…………………………………..

Figure imgf000013_0001
or a pharmaceutically acceptable salt or a pharmaceutical composition or a boronic acid anhydride thereof.
[048| The compound of formula (II), [( l R)-l -( } [(2,5-dichlorobenzoyl)amino]acetyl} amino)-3- methylbutyljboronic acid (MLN2238) is disclosed in Olhava and Danca, U .S. Patent No. 7,442,830, herein incorporated by reference in its entirety. [049] In some other embodiments, Z and Z together form a moiety derived from a compound having at least two hydroxyl groups separated by at least two connecting atoms in a chain or ring, said chain or ring comprising carbon atoms and, optionally, a heteroatom orheteroatoms which can be N, S, or O, wherein the atom attached to boron in each case is an oxygen atom.

In certain embodiments, wherein the alpha-hydroxy carboxylic acid or beta-hydroxy carboxylic acid is citric acid, the compound of formula (I) is characterized by formula (III-A) or (III-B):
Figure imgf000015_0001
(III-B), or a mixture thereof or a pharmaceutical composition thereof.
[054] In certain embodiments, wherein the alpha-hydroxy carboxylic acid orbeta-hydroxy carboxylic acid is citric acid, the compound of formula (I) is characterized by formula (III-A):
Figure imgf000015_0002
or a pharmaceutical composition thereof.
[055] The compound of formula (III-A), 2,2′- {2-[( l i?)- l -( { [(2,5-dichlorobenzoyl)amino]acetyl } amino)- 3-methylbutyl]-5-oxo- l ,3,2-dioxaborolane-4,4-diyl} diacetic acid (MLN9708) is disclosed in Elliott et al. , WO 09/ 154737, herein incorporated by reference in its entirety
…………………………………………
Example 1: Synthesis of 4-(/?,S)-(carboxymethyl)-2-( (R)-I -(2-(2,5- dichlorobenzamido)acetamido)-3-methylbutyl)-6-oxo-l,3,2-dioxaborinane-4- carboxylic acid (1-1)
Figure imgf000062_0001
Step l: 2,5-r(dichlorobenzoyI)aminolacetic acid
[0310] To a mixture of NaOH (12 g, 300 mmol) and glycine (18 g, 239 mmol) in water (120 mL) was added dropwise over 45 min a solution of 2,5-dichlorobenzoyl chloride (10 g, 48 mmol) in THF (15 mL) keeping the internal temperature below about 25 0C. After 1 h, the mixture was acidified with 2.0 M HCl (125 mL) keeping the internal temperature below about 5 0C. The resulting precipitate was collected by vacuum filtration. The crude product was recrystallized from water to give 2,5-[(dichlorobenzoyl)amino]acetic acid as a white, crystalline solid (6.1 g, 52%). mp 173.3 0C. 1H NMR (300 MHz, DMSOd6, δ): 12.72 (bs, IH), 8.89 (t, J = 6.0 Hz, IH), 7.54 (m, 2H), 7.48 (m, IH), 3.93 (d, J = 6.0 Hz). 13C NMR (75 MHz, DMSO-Ci6, δ): 41.6, 129.3, 129.6, 131.4, 132.2, 138.2, 171.4, 165.9. MS (ni/z): [M+H] calculated for C9H8Cl2NO3, 248.0; found, 248.0; [M+Na] calculated for C9H7Cl2NNaO3, 270.0; found 270.2.
[0311] 2,5-[(dichlorobenzoyl)amino]acetic acid was also be prepared via the following procedure: To a mixture of glycine (21.5 g, 286 mmol) in water (437 mL), was added 2.0 M NaOH (130 mL) and the resulting solution was cooled to 0 0C. A solution of 2,5-dichlorobenzoyl chloride (50.0 g, 239 mmol) in THF (75 mL) was added dropwise at such a rate that the internal temperature was maintained at 0 ± 1 0C. During the addition, the pH was controlled at 11.0 ± 0.2 using a pH controller titrated with 2.0 M NaOH. After complete addition, the mixture was stirred at 0 ± 1 0C for an additional 2 h. The mixture was then acidified with 2.0 M HCl (176 mL) to a final pH of 2.5. The resulting precipitate was collected by filtration, washed with cold water (125 mL), and dried at 45 0C in a vacuum oven to afford 2,5-[(dichlorobenzoyl)amino]acetic acid as a white solid (57.6 g, 97.3%). Step 2: 2,5-dichloro-N-f2-(( (lR’)-3-niethyl-l-r(3aS,4S.6S.7aR)-3a,5,5-trimethylhexahvdro-
4,6-methano-l,3,2-benzodioxaborol-2-yllbutyl }amino)-2-oxoethvπbenzamide
[0312] To a solution of 2,5-[(dichlorobenzoyl)amino]acetic acid (6.10 g, 24.6 mmol) and TBTU (8.34 g, 26.0 mmol) in DMF (40 mL) with an internal temperature below about 5 0C was added (IR)- 3-methyl-l-[(3aS,4S,6S,7aR)-3a,5,5-trimethylhexahydro-4,6-methano-l,3,2-benodioxaborol-2- yl]butan-l-amine»TFA (9.35 g, 24.7 mmol). DIPEA (13 mL, 75 mmol) was then added dropwise over 2 h keeping the internal temperature below about 5 0C. After 40 min, the mixture was diluted with EtOAc (90 mL), washed with 5% NaCl (150 mL), twice with 10% NaCl (2 x 40 mL), once with 2% K2CO3 (1 x 40 mL), once with 1% H3PO4 (1 x 40 mL), and once with 10% NaCl (1 x 40 mL). The resulting organic layer was concentrated to a thick oil, diluted with heptane (40 mL) and evaporated to yield 2,5-dichloro-N-[2-({ (lR)-3-methyl-l-[(3aS,4S,6S,7aR)-3a,5,5- trimethylhexahydro-4,6-methano-l ,3,2-benzodioxaborol-2-yl]butyl }amino)-2-oxoethyl]benzamide as a white solid which was used in the next step without purification.
Step 3: N,N\N’Wboroxin-2A6-triyltrisir(lR)-3-methylbutane-l J-diyllimino(2-oxoethane- 2,l-diyl)^ ^tris(2,5-dichlorobenzamide)
[0313] To a solution of 2,5-dichloro-N-[2-({(lR)-3-methyl-l-[(3aS,4S,6S,7aR)-3a,5,5- trimethylhexahydro-4,6-methano-l,3,2-benzodioxaborol-2-yl]butyl }amino)-2-oxoethyl]benzamide (12.2 g, 24.6 mmol) in methanol/hexane (1 :1) (250 mL) were added IN HCl (30 mL, 30 mmol) and (2-methylpropyl)boronic acid (6.5 g, 64 mmol). The reaction mixture was allowed to stir overnight. The phases were separated and the methanol layer was washed twice with additional heptane (2 x 55 mL). The resulting organic layer was concentrated to about 10 mL and partitioned between 2.0M NaOH (30 mL) and DCM (25 mL). The DCM layer was washed once with additional 2.0M NaOH (5 mL). The basic aqueous layers were then combined, washed twice with DCM (2 x 25 mL) and acidified with IM HCl (60 mL). The resulting mixture was diluted with DCM (40 mL), the layers were separated, and the resulting aqueous layer was washed three times with DCM (3 x 10 mL). The combined DCM extracts were dried over MgSO4 (25 g) and evaporated to a thick oil. The product was precipitated with heptane (50 mL) and collected by filtration to yield N,N’,N”-{boroxin-2,4,6- -riyltris[[(lR)-3-methylbutane-l,l-diyl]imino(2-oxoethane-2,l-diyl)] }tris(2,5-dichlorobenzamide) as a white solid (6.6 g, 74%). 1H NMR (300 MHz, DMSO-Cl6, δ): 8.93 (t, J – 6.0 Hz, IH), 8.68 (bs, IH), 7.63 (m, IH), 7.52 (m, 2H), 4.00 (d, J = 6.0 Hz, 2H), 2.62 (m, IH), 1.59 (m, IH), 1.33 (m, IH), 1.24 (m, IH), 0.81 (d, / = 5.9 Hz, 6H). 13C NMR (125 MHz, DMSO-Cl6, δ): 23.2, 25.8, 40.1, 40.7, 43.0, 129.0, 130.0, 131.0, 137.5, 165.0, 172.5. MS (m/z) in CH3CN: [M+H] calculated for C42H52B3Cl6N6O9, 1027.2; found, 1027.3; [M+Na] calculated for C42H51B3Cl6N6NaO9, 1049.2; found 1049.5.
Step 4: 4-(/?.S)-(carboxymethyl)-2-((/?)-l-(2-(2,5-dichlorobenzamido)acetamido)-3- methylbutyl)-6-oxo-l,3,2-dioxaborinane-4-carboxylic acid (1-1)
[0314] Form 1: To a solution of citric acid (2.75 g, 14.3 mmol) in EtOAc (85 mL) with an internal temperature of about 74 0C was added N,N’,N”-{boroxin-2,4,6-triyltris[[(lR)-3-methylbutane-l,l- diyl]imino(2-oxoethane-2,l-diyl)] }tris(2,5-dichlorobenzamide) (5.00 g, 4.87 mmol) as a solid. The solution was cooled uncontrolled until the internal temperature was about 25 0C and the mixture was stirred overnight. The resulting precipitate was collected by filtration to yield 2,2′-{2-[(lR)-l-({ [(2,5- dichlorobenzoyl)amino]acetyl }amino)-3-methylbutyl]-5-oxo-l,3,2-dioxaborolane-4,4-diyl}diacetic acid Form 1 as a crystalline solid (6.65 g, 88 %). 1H NMR (500 MHz, DMSOd6, δ 110 0C): 10.08 (s, IH), 8.69 (s, IH), 7.61 (s, IH), 7.52 (d, J = 1.3 Hz, 2H), 4.26 (d, J = 5.5 Hz, 2H), 2.70 (q, J = 14.5 Hz, 4H), 2.70 (bs, IH), 1.72 (sept, J – 6.5 Hz, IH), 1.42 (ddd, J = 5.2 Hz, J = 8.6 Hz, J = 13.9 Hz, IH), 1.28 (ddd, J = 5.3, J = 9.4 Hz, J = 14.3 Hz, IH), 0.91 (dd, J = 3.3 Hz, J = 6.6 Hz, 6H). MS (m/z) in CH3CN: [M+Na] calculated for C20H23BCl2N2NaO9, 539.1; found, 539.1.


Ixazomib citrate [USAN]
1,3,2-Dioxaborolane-4,4-diacetic acid, 2-[(1R)-1-[[2-[(2,5-dichlorobenzoyl)amino]acetyl]amino]-3-methylbutyl]-5-oxo- [ACD/Index Name]
1,3,2-Dioxaborolane-4,4-diacetic acid,2-[(1R)-1-[[2-[(2,5-dichlorobenzoyl)amino]acetyl]amino]-3-methylbutyl]-5-oxo-
1239908-20-3 [RN]
2,2′-{2-[(1R)-1-{[N-(2,5-Dichlorbenzoyl)glycyl]amino}-3-methylbutyl]-5-oxo-1,3,2-dioxaborolan-4,4-diyl}diessigsäure [German] [ACD/IUPAC Name]
2,2′-{2-[(1R)-1-{[N-(2,5-dichlorobenzoyl)glycyl]amino}-3-methylbutyl]-5-oxo-1,3,2-dioxaborolane-4,4-diyl}diacetic acid [ACD/IUPAC Name]
2-[(1R)-1-[[2-[(2,5-dichlorobenzoyl)amino]acetyl]amino]-3-methylbutyl]-5-oxo-1,3,2-dioxaborolane-4,4-diacetic acid
2-[4-(carboxymethyl)-2-[(1R)-1-[[2-[(2,5-dichlorobenzoyl)amino]acetyl]amino]-3-methyl-butyl]-5-oxo-1,3,2-dioxaborolan-4-yl]acetic acid
Acide 2,2′-{2-[(1R)-1-{[N-(2,5-dichlorobenzoyl)glycyl]amino}-3-méthylbutyl]-5-oxo-1,3,2-dioxaborolane-4,4-diyl}diacétique [French][ACD/IUPAC Name]
MLN9708

Thursday, 5 February 2015

Route Design in the 21st Century: The ICSYNTH Software Tool as an Idea Generator for Synthesis Prediction

Figure

The new computer-aided synthesis design tool ICSYNTH has been evaluated by comparing its performance in predicting new ideas for route design to that of historical brainstorm results on a series of commercial pharmaceutical targets, as well as literature data. Examples of its output as an idea generator are described, and the conclusion is that it adds appreciable value to the performance of the professional drug research and development chemist team.
 Chemical Development, AstraZeneca R&D, Silk Road Business Park, Macclesfield, SK10 2NA Cheshire, U.K.
 Chemnotia AB, Forskargatan 20 J, 151 36 Södertälje,Sweden
§ InfoChem GmbH, Landsberger Straße 408/V, D-81241 München, Germany
Org. Process Res. Dev., Article ASAP
DOI: 10.1021/op500373e
Publication Date (Web): January 22, 2015
Copyright © 2015 American Chemical Society
*(H.-J.F.) E-mail: Hans-Jurgen.Federsel@astrazeneca.com., *(M.G.H.) E-mail:mghutchings@infochem.de.
Currently, ICSYNTH has assumed a place as a unique predictive tool for route design in Chemical Development in AZ. While it is finding valuable commercial application in our own and others’ hands, it remains a work in progress.
ICsynthInfoChem’s powerful synthesis planning tool now in Version 2.0. Read more …
InfoChem will be represented at the forthcoming ACS Meeting in San Diego. You will find Dr. Josef Eiblmaier, Dr. Valentina Eigner Pitto, and Dr. Peter Loew …
ICSYNTH
InfoChem’s ICSYNTH is a powerful computer aided synthesis design tool that enables chemists to generate synthetic pathways for a target molecule. The benefit is that ICSYNTH can facilitate innovation by stimulating ideas for alternative or novel synthetic routes that otherwise may not be considered. This may lead to improved route design, for example shorter pathways or more economical reaction modifications.
After inputting the target, users can select different synthetic strategies depending on requirements. ICSYNTH then automatically generates a multistep interactive synthesis tree – each node on the tree representing a precursor. The advantages are that the suggested reactions are based on, and linked to, published reactions (or their analogs) and the precursor availability is automatically checked in commercial catalogs. Users can modify the synthesis tree or select precursors for further analysis.
At the heart of ICSYNTH is an algorithmic chemical knowledge base of transform libraries that are automatically generated from reaction databases. The number of transform libraries is only limited by the availability of validated reaction databases.
In addition to retro synthesis design, ICSYNTH has a forward reaction prediction module that offers reactivity mapping for the target molecule.Version 2.0 of ICSYNTH was launched in April 2014. The completely re-designed user interface (based on JavaScript) and major improvements in the algorithm responsible of the precursor search are the main enhancements of Version 2.0. In addition the forward reaction prediction algorithm has been optimized. Click here to see a complete version history.

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Saturday, 31 January 2015

Antimalarial Drug TCMDC 123812 and 123794




Synthesis of Analogs of Arylpyrrole Antimalarial Drug Leads

Abstract

Malaria continues to be one of the most widespread infectious diseases and with recent focus on global eradication and the continual evolution of drug resistant parasitic strains, the search for potent new antimalarials has gained momentum. In contrast to rational drug design approaches, the high-throughput screening of large compound libraries for potency against the parasite in whole cell assays has identified the Arylpyrrole series as a promising chemical lead. Before looking to comprehend the complex modes of biological action, the evaluation of analogs within this new drug class and the validation of their organic synthesis may act to identify specific compounds with increased potency or chemical moieties that lend themselves to the optimisation of the drug synthesis process. The collaborative efforts of open source drug discovery may help to identify potent compounds with a high-yielding and cost effective manufacturing process and thus accelerate the development of a promising candidate for integration into clinical practice.

Introduction

Malaria is a widespread tropical infectious disease caused by a number of species of the protozoan parasite of the genus plasmodium, most notably P. falciparum, which are transmitted through the saliva of the anopheles mosquito. Per year, more than 240 million people suffer from the disease and approximately 40% of the global population live in countries where Malaria is endemic.[1] As both a consequence of and a great contributor towards poverty, Malaria costs sub-Saharan Africa alone US$12 billion in productivity every year and while an approximate cost limitation for one antimalarial treatment is US $1[1], current estimates suggest that many may only be able to afford 10 cents per treatment.[2] Thus with the majority of sufferers of a poor socioeconomic background, drug design should focus on the cost-effective synthesis of highly potent compounds, in order to minimise the quantities administered.

Driven by a knowledge of the biology of the parasite, conventionally rational drug design deduces leads based on first identifying a possible molecular target and the potential mechanisms of drug action at that target. However through reversing this process, a high-throughput screening for potent compounds in whole cell assays can act to expedite the lead identification process.[3] By this approach a single compound may be applicable to many ambiguous or poorly understood, more complex biological targets, decreasing the chances of a parasitic strain evolving resistance mechanisms at every target. Ultimately this approach will allow the rapid identification of leads which, because of their capacity to act on complex targets, may result in more effective prophylactic or therapeutic drugs which retain their activity for longer.

Recently the data from the high-throughput screening of a two million compound library was released by GlaxoSmithKline (GSK), identifying 13, 533 compounds, which inhibited the intra-erythrocytic cycle of multidrug resistant strains of P. falciparum by more than 70%. This identified several promising classes of compounds which retained low cytotoxicity to human cell lines.[4] [5] Among these, the arylpyrrole series has been isolated and the resynthesis and validation of a number of lead compounds within this series are being conducted using open source science. Disseminating information over many online mediums has encouraged collaborative efforts within the international scientific community and this free exchange of data and ideas between organisations, individuals and academic institutions may stimulate faster optimisation and development of leads.

Initial validation of arylpyrrole leads involved the resynthesis of two known series compounds, that is TCMDC 123812 and TCMDC 123794, as high quality starting points for lead optimisation with reasonable druggability.[6] Following evaluation of two possible synthesis pathways to these final compounds, slight changes were introduced to the chemical substructures and synthesis re-evaluated. Based on knowledge of the in vivo functionality of certain moieties, analogs were identified that may influence synthesis or beneficially contribute to the overall drug profile and efficacy.

Modifications to the para-position of aryl ring were evaluated, with hydrogen, methyl and trifluoromethyl groups being chosen to substitute the fluorine present in the original compounds. The introduction of bonds weaker than the original carbon-fluorine bond at that position may influence metabolic stability, influencing the affinity of the drug to para-hydroxylation.[7] However, and especially in the instance of a hydrogen in that position, a null result may be invaluable in enabling the prioritisation of other more stable functional groups. Thus antiplasmodial activity and cytotoxicity may be impacted upon as variations may influence the modes of action, changing the in vivo efficacy of the drug. Resultant changes in the physical or chemical properties of analogs may affect the potential for developing high-yielding, efficient and cost effective synthesis strategies. However ramifications of these chemical modifications on the ease of organic synthesis are hard to predict and thus the viability of the synthesis of a range of analogs must be evaluated as primary steps in the lead optimisation process.

Two potential synthesis pathways were identified for obtaining the carboxylic acid which then undergoes the addition of an amide group through a coupling reaction to achieve the final compound.[6] The first relied on a Paal Knorr cyclisation reaction between a dicarbonyl compound and a para-substituted aniline resulting in the arylpyrrole core. A Vilsmeier-Haack reaction then employed the use of phosphoryl chloride and dimethylformamide to form a Vilsmeier reagent or chloroimminium ion, which when substituted onto the pyrrole ring acts as a formylating agent to produce an aldehyde, once hydrolysed at a low pH. A second synthesis pathway involved synthesis of an ester, initially involving alkylation using a reactive enolate ion to form an intermediate before continuing with a condensation reaction into the characteristic arylpyrrole core. This report will describe the synthesis of each analog via these two alternative synthesis pathways. (Fig. 1)
Figure 1: Synthesis Strategy initially proposed for lead compounds: TCMDC 123812 and  123794

Figure 1: Synthesis Strategy initially proposed for lead compounds: TCMDC 123812 and 123794

Materials and Methods

1. Paal Knorr Synthesis of 2,5-dimethyl-1H-phenyl-pyrrole
Figure 2: Paal Knorr Synthesis of 2,5-dimethyl-1H-phenyl-pyrrole

Figure 2: Paal Knorr Synthesis of 2,5-dimethyl-1H-phenyl-pyrrole

2. Paal Knorr synthesis of 2,5-dimethyl-1H-(p-tolyl)- pyrrole
Figure 3: Paal Knorr synthesis of 2,5-dimethyl-1H-(p-tolyl)- pyrrole

Figure 3: Paal Knorr synthesis of 2,5-dimethyl-1H-(p-tolyl)- pyrrole

3. Paal Knorr Synthesis of 2,5-dimethyl -1H-(p-trifluoromethyl)phenyl-pyrrole
Figure 4: Paal Knorr synthesis of 2,5-dimethyl -1H-(p-trifluoromethyl)phenyl-pyrrole

Figure 4: Paal Knorr synthesis of 2,5-dimethyl -1H-(p-trifluoromethyl)phenyl-pyrrole

4. Vilsmeier-Haack synthesis of 2,5-dimethyl-1H-phenyl pyrrole-3-carboxaldehyde
Figure 5: Vilsmeier-Haack synthesis of 2,5-dimethyl-1H-phenyl pyrrole-3-carboxaldehyde

Figure 5: Vilsmeier-Haack synthesis of 2,5-dimethyl-1H-phenyl pyrrole-3-carboxaldehyde

5. Vilsmeier-Haack Synthesis of 2,5-dimethyl-1H-(p-tolyl)-pyrrole-3-carboxaldehyde.
Figure 6: Vilsmeier-Haack synthesis of 2,5-dimethyl-1H-(p-tolyl)-pyrrole-3-carboxaldehyde

Figure 6: Vilsmeier-Haack synthesis of 2,5-dimethyl-1H-(p-tolyl)-pyrrole-3-carboxaldehyde

6. Synthesis of ethyl 2,5-dimethyl-1-(p-tolyl)-1H-pyrrole-3-carboxylate
Figure 7: Synthesis of ethyl 2,5-dimethyl-1-(p-tolyl)-1H-pyrrole-3-carboxylate

Figure 7: Synthesis of ethyl 2,5-dimethyl-1-(p-tolyl)-1H-pyrrole-3-carboxylate
7. Synthesis of ethyl 2,5-dimethyl-1-phenyl-1H-pyrrole-3-carboxylate
Figure 8: Synthesis of ethyl 2,5-dimethyl-1-phenyl-1H-pyrrole-3-carboxylate

Figure 8: Synthesis of ethyl 2,5-dimethyl-1-phenyl-1H-pyrrole-3-carboxylate

8. Synthesis of ethyl 2,5-dimethyl-1-[p-(trifluoromethyl)phenyl]-1H-pyrrole-3-carboxylate
Figure 9: Synthesis of ethyl 2,5-dimethyl-1-[p-(trifluoromethyl)phenyl]-1H-pyrrole-3-carboxylate

Figure 9: Synthesis of ethyl 2,5-dimethyl-1-[p-(trifluoromethyl)phenyl]-1H-pyrrole-3-carboxylate

General Reaction Mechanisms

Figure 10: Mechanism: Paal-Knorr cyclisation and Vilsmeier-Haack Synthesis to Aldehyde



Figure 10: Mechanism: Paal-Knorr cyclisation and Vilsmeier-Haack Synthesis to Aldehyde
Figure 11: Mechanism: Alkylation of ethyl acetoacetate with chloroacetone and condensation to Ester














Figure 11: Mechanism: Alkylation of ethyl acetoacetate with chloroacetone and condensation to Ester



Results

1. Paal-Knorr Synthesis of 2,5-dimethyl-1H-phenyl-pyrrole
Yield: 6.2 g (60.4%)
Comment: Product crystallised easily. Reasonably pure red brown granular substance after recrystallization.

2. Paal-Knorr synthesis of 2,5-dimethyl-1H-(p-tolyl)- pyrrole
Yield: 8.3 g (74.5%)
Comment: Crystallisation required use of activated charcoal. Recrystallisation produced ochre-coloured sand-like, relatively pure compound at a reasonable yield.

3. Paal-Knorr Synthesis of 2,5-dimethyl -1H-(p-trifluoromethyl)phenyl-pyrrole
Yield: 6.08g (60%)
Comment: Reaction took slightly longer. Recrystallisation produced a relatively pure red-brown sand-like compound.

4. Vilsmeier-Haack synthesis of 2,5-dimethyl-1H-phenyl pyrrole-3-carboxaldehyde
Yield: 407 mg (64%)
Comment: Vilsmeier reaction completed reasonably quickly. Pure compound that crystallised easily produced after recrystallization. (grey/beige free-flowing powder)

5. Vilsmeier-Haack Synthesis of 2,5-dimethyl-1H-(p-tolyl)-pyrrole-3-carboxaldehyde.
Yield: 423 mg (71%)
Comment: Recrystallised fairly easily producing a fairly pure grey/brown lumpy powder.

6. Synthesis of ethyl 2,5-dimethyl-1-(p-tolyl)-1H-pyrrole-3-carboxylate
Yield: 1.8 g (45.6%)
Comment: Upon the use of both activated charcoal and column chromatography, product crystallised easily to a relatively pure bright yellow powder.

7. Synthesis of ethyl 2,5-dimethyl-1-phenyl-1H-pyrrole-3-carboxylate
Yield: 952 mg (approximate yield 37%)
Comment: Lack of separation between product and impurity in column chromatography resulted in product not crystallising.

8. Synthesis of ethyl 2,5-dimethyl-1-[p-(trifluoromethyl)phenyl]-1H-pyrrole-3-carboxylate
Yield: 1.85 g (55%)
Comment: Crystallised easily following column chromatography to form a pale yellow powder.

Discussion

Synthesis via each reaction pathway was viable for most analogs however procedures need to be optimised and due to the nature of the corresponding reactions to the carboxylic acid, synthesis via the ester could be considered the most favourable.

The synthesis of the aldehyde via a Vilsmeier Haack synthesis following a Paal Knorr cyclisation was viable and the products synthesised achieved moderate yields and a reasonable level of purity with minimal purification steps. While viable, procedures could still be optimised further, however the oxidation of the aldehyde to obtain the carboxylic acid has proved problematic for the original resynthesis using the p-fluoro-phenyl-pyrrole-carbaldehyde. Unless a forgiving oxidation reaction becomes apparent, the simple base-hydrolysis via saponification necessary for the ester could prove a more favourable approach. For this reason only two aldehydes were synthesised with this strategy.

Although the ester exists in the correct oxidation state which acts to mitigate further issues with the synthesis of the carboxylic acid, complications in purification steps need to be overcome before the synthesis of analogs could be considered practical using this pathway. Potassium carbonate acts to remove a labile hydrogen off the alpha carbon of ethyl acetoacetate, which forms a reactive enolate ion. Sodium iodide substitutes the chlorine of the chloroacetone, which becomes susceptible to nucleophilic attack and an alkylation reaction follows to form a reactive intermediate. Enolate ion formation is susceptible to side reactions such as alkylation at the oxygen and while alkylation of the alpha carbon is preferential, the synthesis of the intermediate may need to be refined to ensure minimal side products and impurities. Additionally immediate condensation of the crude intermediate with the aniline derivatives may minimise formation of further side products. All three analogs required column chromatography, resulting in a significant amount of product loss and diminishing from the simplicity and practicality required for large-scale drug manufacture. It must be noted, however, this condensation reaction proved forgiving in the resynthesis of the original compounds, achieving a reasonable yield with minimal purification steps.[8] Thus appropriate optimisation of the synthesis procedures could affirm this as the most practical pathway for each analog.

Given synthesis complications and a likely propensity for para-hydroxylation, it may be unlikely that the N-phenyl analogs present promising drug leads, however further synthesis trials and testing against the parasite are required to conclusively determine this. Aqueous extraction of the final ester was problematic as a result of increased miscibility with dilute citric acid, and unsuccessful separation of product and impurity in column chromatography prevented crystallisation. It is unclear at this stage whether the parasubstituted methyl or trifluoromethyl groups retain any steric, inductive or other effects that contribute to any physicochemical properties that lend themselves to improving organic synthesis or in vivo drug targeting. The synthesis strategies require optimisation to eliminate time consuming and costly purification steps and the proceeding hydrolysis and coupling reactions need validation before testing the in vivo efficacy of the drugs in whole cell assays. Alternative reaction conditions, reagents, solvents or even new synthesis pathways should be tested to achieve optimisation as, irrespective of the drug’s antiplasmodial activity, it is crucial that cost-effective simple procedures be conserved so that large-scale production and distribution to impoverished nations remains possible.

Following the validation and testing of current analogs, additional analogs may be evaluated based on informed decisions of the potential advantages of specific chemical groups and the success of similar moieties. Once a promising lead has been identified and validated, the mode of action and how the drug acts to mediate host parasite-interactions on a molecular level may be researched and the drug tailored for that specific functionality. Mechanisms of action have already been postulated for related arylpyrroles, informing the choice of analogs and pursuit of specific lead compounds.[9]

Open source science has contributed significantly to the rapid identification of promising drug leads. Contributions from a variety of fields of expertise allow both synthetic and biological concerns for these lead compounds to be addressed, giving a more holistic view of the nature of drug design goals. Stimulating discussion and participation, this free exchange of ideas enables involvement of the wider scientific community, accelerating research and development so that it may be possible to find an effective solution to a devastating problem as soon as possible.

References

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  1. Wells T.N.C “Is the tide turning for New Malaria Medicines”, Science, 2010, Vol. 329 pp.1153-1154 
  1. Francisco-Javier, G., Sanz, LM., Jaume, V. “Thousands of chemical starting points for antimalarial lead identification”, Nature, 2010, Vol. 465, no. 7296, pp305-U56 
  1. Calderon, F., Barros, D., Beuno Jose, M. et al. “An Invitation to Open Innovation in Malaria Drug Discovery: 47 Quality Starting Points from the TCAMS”, ACS Chemistry Letters, 2011, Vol.2, no.10, pp741-746 
  1. The Synaptic Leap – Malaria Research Community (Updated 2011) 
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  1. Lee, BH., Lee, MJ., Park, S,. Oh, DC,. Elsasser, S,. Chen, PC,. Gartner, C,. Dimova, N,. Hanna, J,. Gygi, SP,. Wilson, SM,. King, RW,. Finley, D. “Enhancement of proteasome activity by a small-molecule inhibitor of USP14”, Nature, 2010, Vol. 467, pp179-184