US20170101432A1 - Crystalline 3',5'-cyclic diguanylic acid - Google Patents

Crystalline 3',5'-cyclic diguanylic acid Download PDF

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Publication number
US20170101432A1
US20170101432A1 US15/123,328 US201515123328A US2017101432A1 US 20170101432 A1 US20170101432 A1 US 20170101432A1 US 201515123328 A US201515123328 A US 201515123328A US 2017101432 A1 US2017101432 A1 US 2017101432A1
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crystal
cyclic diguanylic
acid
crystals
diguanylic acid
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Hisaki Tanaka
Kazuya Ishige
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Yamasa Corp
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Yamasa Corp
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
    • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
    • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
    • C07H19/16—Purine radicals
    • C07H19/20—Purine radicals with the saccharide radical esterified by phosphoric or polyphosphoric acids
    • C07H19/207—Purine radicals with the saccharide radical esterified by phosphoric or polyphosphoric acids the phosphoric or polyphosphoric acids being esterified by a further hydroxylic compound, e.g. flavine adenine dinucleotide or nicotinamide-adenine dinucleotide
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H1/00—Processes for the preparation of sugar derivatives
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
    • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
    • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
    • C07H19/16—Purine radicals
    • C07H19/20—Purine radicals with the saccharide radical esterified by phosphoric or polyphosphoric acids
    • C07H19/213—Purine radicals with the saccharide radical esterified by phosphoric or polyphosphoric acids containing cyclic phosphate

Definitions

  • the present invention is related to a crystal of 3′,5′-cyclic diguanylic acid deemed to be a useful substance as an adjuvant and to a manufacturing method of said crystal.
  • 3′,5′-Cyclic diguanylic acid is a signal transmitter involved in biofilm formation of bacteria or the like, and recently, expected in applications as an adjuvant, an antiviral agent, and an anticancer agent (Non-Patent Document 1).
  • Non-Patent Document 1 As a manufacturing method of 3′,5′-cyclic diguanylic acid, a synthetic method by an enzyme is known thus far, in which diguanylate cyclase from Genus Geobacillusis, for example, is used (Patent Document 1).
  • Non-Patent Documents 2 and 3 Conventionally, 3′,5′-cyclic diguanylic acid is obtained as a freeze-dried product or a co-crystal with a metal salt with cobalt or magnesium (Non-Patent Documents 2 and 3).
  • 3′,5′-cyclic diguanylic acid is provided as co-crystals containing a metal salt with cobalt or the like, and thus, in a case where the crystals are intended for utilization in a pharmaceutical raw material and the like, problems concerning safety or the like may arise.
  • crystals of free acid of 3′,5′-cyclic diguanylic acid that do not contain the metal salt nothing is conventionally known including methods of obtaining them.
  • all of conventional methods of obtaining crystals employ the vapor diffusion method, so that they are not suitable for obtaining a large amount of crystals in a short period of time, and thus, development of a method of obtaining a large amount of crystals easily has been desired.
  • the present inventors studied earnestly crystallization of 3′,5′-cyclic diguanylic acid and succeeded in obtaining crystals of the free acid of 3′,5′-cyclic diguanylic acid for the first time.
  • the crystals of 3′,5′-cyclic diguanylic acid obtained by the method of the present invention exhibit stability comparable to the existing crystals, and are very easy to handle in various applications, since no superfluous metal ions are included, and thus, useful as a raw material of pharmaceutical compositions and the like.
  • FIG. 1 shows a photograph of crystals of 3′,5′-cyclic diguanylic acid.
  • FIG. 2 shows a photograph of co-crystals of 3′,5′-cyclic diguanylic acid with magnesium.
  • FIG. 3 shows a photograph of co-crystals of 3′,5′-cyclic diguanylic acid with cobalt.
  • FIG. 4 shows a result of thermogravimetric measurement/differential thermal analysis of crystals of 3′,5′-cyclic diguanylic acid.
  • FIG. 5 shows a result of thermogravimetric measurement/differential thermal analysis of co-crystals of 3′,5′-cyclic diguanylic acid with magnesium.
  • FIG. 6 shows a result of thermogravimetric measurement/differential thermal analysis of co-crystals of 3′,5′-cyclic diguanylic acid with cobalt.
  • FIG. 7 shows an infrared absorption spectrum of crystals of 3′,5′-cyclic diguanylic acid.
  • FIG. 8 shows an infrared absorption spectrum of co-crystals of 3′,5′-cyclic diguanylic acid with magnesium.
  • FIG. 9 shows an infrared absorption spectrum of co-crystals of 3′,5′-cyclic diguanylic acid with cobalt.
  • FIG. 10 shows an X-ray diffraction spectrum of crystals of 3′,5′-cyclic diguanylic acid.
  • FIG. 11 shows an X-ray diffraction spectrum of co-crystals of 3′,5′-cyclic diguanylic acid with magnesium.
  • FIG. 12 shows an X-ray diffraction spectrum of co-crystals of 3′,5′-cyclic diguanylic acid with cobalt.
  • the present invention provides a crystal of 3′,5′-cyclic diguanylic acid represented by the following structural formula.
  • the crystal of 3′,5′-cyclic diguanylic acid of the present invention is a crystal of free acid containing no metal salt, which is obtained without utilizing a metal such as cobalt and magnesium at all in a crystalizing step.
  • a ‘crystal of 3’,5′-cyclic diguanylic acid′ in this description means a crystal of free acid containing none of said metal salts, unless specifically mentioned.
  • the crystal of 3′,5′-cyclic diguanylic acid of the present invention has purity of 97% or more or preferably 99% or more as purity-tested by the high-performance liquid chromatography method.
  • the crystal of 3′,5′-cyclic diguanylic acid of the present invention has water content of 9.3 to 13.9% as measured by the Karl Fischer method. That is, in the crystal of 3′,5′-cyclic diguanylic acid of the present invention, 4 to 6 molecules of water, more specifically, 3.9 to 6.2 molecules of water bond or attach to one molecule of 3′,5′-cyclic diguanylic acid.
  • the crystal of 3′,5′-cyclic diguanylic acid of the present invention has an endothermic peak at 213 to 217° C. as analyzed by a thermogravimetric measurement/differential thermal analysis (TG/DTA) apparatus (temperature elevation rate of 5° C./min). Said temperature is lower than those of the known co-crystals with a metal.
  • TG/DTA thermogravimetric measurement/differential thermal analysis
  • the crystal of 3′,5′-cyclic diguanylic acid of the present invention is obtained as a cubic crystal.
  • the conventionally known co-crystals with a metal are a hexagonal tabular crystal or a square bipyramidal crystal, and thus, the crystal of the present invention and the conventionally known co-crystals with a metal are different in structure.
  • the crystal of 3′,5′-cyclic diguanylic acid of the present invention has characteristic peaks around 3163, 1712, 1637, 1601, 1530, 1470, 1386 and 1339 (cm ⁇ 1 ) when an infrared absorption spectrum is measured.
  • an error range less than 2 (cm ⁇ 1 ) is sometimes included in measuring an infrared absorption spectrum, so that not only crystals whose peak positions in an infrared absorption spectrum coincide exactly with the values noted above but also crystals whose peak positions coincide within the error range less than 2 cm ⁇ 1 are included in the crystal of 3′,5′-cyclic diguanylic acid of the present invention.
  • characteristic peaks are observed at 3163 ⁇ 1.9, 1712 ⁇ 1.9, 1637 ⁇ 1.9, 1601 ⁇ 1.9, 1530 ⁇ 1.9, 1470 ⁇ 1.9, 1386 ⁇ 1.9 and 1339 ⁇ 1.9 (cm ⁇ 1 ).
  • the crystal of 3′,5′-cyclic diguanylic acid of the present invention has characteristic peaks in X-ray powder analysis, and, for example, when the crystal of the present invention is subjected to an analysis by an X-ray powder diffractometer using the Cu-K ⁇ ray, characteristic peaks are observed, as shown in Example below, around 8.1, 8.3, 10.8, 11.8, 16.9, 19.1, 19.5, 22.4, 25.0, 26.7, 27.0 and 27.7 (°) in diffraction angle (2 ⁇ ) (see FIG. 10 ).
  • the crystal of 3′,5′-cyclic diguanylic acid of the present invention has a decreasing rate of purity less than 1% as a value measured by high performance liquid chromatography after being stored at 50° C. for 167 days in a desiccator containing saturated saline, and thus, is a very stable crystal.
  • the crystal of 3′,5′-cyclic diguanylic acid of the present invention can be obtained by adding acid to an aqueous solution of 3′,5′-cyclic diguanylic acid so as to lower pH to 1 to 3.
  • 3′,5′-Cyclic diguanylic acid used in crystallization may be synthesized by a known method such as the enzymatic synthesis method or the chemical synthesis method, and one synthesized by the enzymatic synthesis method is preferable. Enzymatic synthesis may be performed following the known method, and, for example, the method described in Patent Document 1 may be used. After the reaction, 3′,5′-cyclic diguanylic acid generated in a reaction solution can be isolated and purified by the usual chromatography method using activated carbon, an ion-exchange resin or the like.
  • acid is added to an aqueous solution of 3′,5′-cyclic diguanylic acid so as to lower pH to 1 to 3, preferably, to 1.5 to 2.0.
  • the acid used are hydrochloric acid, sulfuric acid and nitric acid.
  • slow addition is preferable. Note that if a yield of crystals is low, second crystals may be obtained from the filtrate of said crystals by performing said process of crystal precipitation.
  • crystallization may be performed by a method comprising (1) a step of heating an aqueous solution of isolated and purified 3′,5′-cyclic diguanylic acid to 50 to 70° C., (2) a step of adding acid to said solution so as to lower pH to 1 to 3, preferably to 1.5 to 2.0, and (3) a step of cooling said solution until the solution reaches 1 to 10° C., preferably 4 to 8° C.
  • cooling in step (3) is performed slowly. Specifically, cooling with a temperature gradient of ⁇ 3 to ⁇ 11° C./hr is preferable.
  • steps (1) and (2) or steps (2) and (3) may be performed simultaneously.
  • the crystals of 3′,5′-cyclic diguanylic acid obtained by the manufacturing method described above may be collected by filtration and then dried at 30 to 70° C. for 1 to 10 hours, to be a product.
  • an appropriate method may be employed such as drying under reduced pressure.
  • 3′,5′-Cyclic diguanylic acid was synthesized enzymatically and purified according to a known method (Patent Document 1).
  • a 59.9 mM solution (191 mL) of 3′,5′-cyclic diguanylic acid obtained by purification was warmed to 60° C. in an incubator and 27.5 mL of 1 N hydrochloric acid solution was added while stirring over two hours so as to make pH at 1.9.
  • Co-crystals of 3′,5′-cyclic diguanylic acid with magnesium or cobalt were obtained in the following manner with reference to the descriptions of Non-Patent Documents 2 and 3.
  • the starting solution for crystallization was concentrated by an evaporator while being warmed at 55° C., filled up to 500 mL again at the time white turbidity was observed, and warmed at 55° C. for 30 minutes to achieve complete dissolution.
  • the solution was concentrated again, allowed to clarify, and left to stand overnight at 25° C., in which precipitation of hexagonal tabular crystals were observed, so that the crystals were grown sufficiently by the vapor diffusion method to obtain co-crystals with magnesium.
  • the starting solution for crystallization was concentrated by an evaporator while being warmed at 55° C. and left to stand overnight at 25° C., in which precipitation of square bipyramidal crystals were observed, so that the crystals were grown by the vapor diffusion method.
  • Detection method detection by UV 260 nm
  • FIGS. 1 to 3 Representative photographs of the crystals of 3′,5′-cyclic diguanylic acid prepared in Example 1 and the co-crystals of 3′,5′-cyclic diguanylic acid with magnesium and the co-crystals with cobalt prepared in Reference Examples are shown in FIGS. 1 to 3 .
  • the crystal of 3′,5′-cyclic diguanylic acid of the present invention is a cubic crystal
  • the co-crystal with magnesium is a hexagonal tabular crystal
  • the co-crystal with cobalt is a square bipyramidal crystal, and thus, the crystal of the present invention exhibited a completely different crystalline shape from those of the conventional crystals.
  • Water content of the crystals of 3′,5′-cyclic diguanylic acid prepared in Example 1 was measured by the Karl Fischer method and water content was found to be 9.3 to 13.9%. That is, it was revealed that, in the crystal of 3′,5′-cyclic diguanylic acid of the present invention, 4 to 6 molecules of water, more specifically, 3.9 to 6.2 molecules of water bonded or attached to one molecule of 3′,5′-cyclic diguanylic acid.
  • thermogravimetric measurement/differential thermal analysis (TG/DTA) apparatus temperature elevation rate of 5° C./min
  • the crystals of 3′,5′-cyclic diguanylic acid of the present invention showed a characteristic endothermic peak at 213 to 217° C.
  • the co-crystals of 3′,5′-cyclic diguanylic acid with magnesium showed a characteristic endothermic peak around 221° C.
  • co-crystals with cobalt showed a characteristic endothermic peak around 239° C. ( FIGS. 5 and 6 , respectively).
  • Infrared absorption spectrum was measured on each of the crystal of 3′,5′-cyclic diguanylic acid of the present invention, and the co-crystal of 3′,5′-cyclic diguanylic acid with magnesium and the co-crystal of 3′,5′-cyclic diguanylic acid with cobalt of Reference Examples using a Fourier transform infrared spectrophotometer, Spectrum One (product of PerkinElmer Co., Ltd.) by the ATR (Attenuated Total Reflectance) method.
  • the crystal of 3′,5′-cyclic diguanylic acid of the present invention had characteristic peaks around 3163, 1712, 1637, 1601, 1530, 1470, 1386 and 1339 (cm ⁇ 1 ).
  • the co-crystal with magnesium had characteristic peaks around 3226, 1702, 1634, 1597, 1531, 1477 and 1345 (cm ⁇ 1 ) and the co-crystal with cobalt had characteristic peaks around 3179, 1638, 1576, 1534, 1487 and 1383 (cm ⁇ 1 ).
  • X-ray diffraction spectra of the crystal of 3′,5′-cyclic diguanylic acid of the present invention, and the co-crystal of 3′,5′-cyclic diguanylic acid with cobalt and the co-crystal of 3′,5′-cyclic diguanylic acid with magnesium of Reference Examples were measured using an X-ray diffractometer X′Pert PRO MPD (product of Spectris Co., Ltd.) under the following measurement condition.
  • Scan range: 20 4.0 to 40.0°
  • Pretreatment Pulverization using an agate mortar
  • the crystal of 3′,5′-cyclic diguanylic acid of the present invention showed characteristic peaks around 8.1, 8.3, 10.8, 11.8, 16.9, 19.1, 19.5, 22.4, 25.0, 26.7, 27.0 and 27.7(°) in diffraction angle (2 ⁇ ).
  • the result of the co-crystal of 3′,5′-cyclic diguanylic acid with magnesium is shown in FIG. 11 and Table 3 and the result of the co-crystal of 3′,5′-cyclic diguanylic acid with cobalt in FIG. 12 and Table 4.
  • a decrease rate of HPLC purity of 3′,5′-cyclic diguanylic acid of the present invention is less than 1% after storing at 50° C. for 167 days, showing a very high stability. This value is comparable with those of the conventional co-crystals with a metal, meaning that practical use is possible.

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US15/123,328 2014-03-03 2015-02-27 Crystalline 3',5'-cyclic diguanylic acid Abandoned US20170101432A1 (en)

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JP2014040108 2014-03-03
JP2014-040108 2014-03-03
PCT/JP2015/055975 WO2015133411A1 (fr) 2014-03-03 2015-02-27 Acide diguanylique 3',5'-cyclique sous forme cristalline

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EP (1) EP3121188B1 (fr)
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Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10787479B2 (en) 2014-03-03 2020-09-29 Yamasa Corporation Crystalline 3′,5′-cyclic diguanylic acid
US10836783B2 (en) 2014-03-14 2020-11-17 Yamasa Corporation Inclusion compound of 3′ ,5′-cyclic diadenylic acid and manufacturing method thereof

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JPWO2005005450A1 (ja) * 2003-07-15 2006-08-24 三井化学株式会社 環状ビスジヌクレオチドの合成方法
EP1782826A1 (fr) 2005-11-08 2007-05-09 GBF Gesellschaft für Biotechnologische Forschung mbH PQS, c-diGMP et leurs conjugués utilisés comme adjuvants et leur emploi dans des compositions pharmaceutiques
WO2010101526A1 (fr) * 2009-03-02 2010-09-10 Nanyang Technological University Diguanylate cyclase, son procédé de production et son utilisation dans la fabrication de di-gmp cyclique et de ses analogues
CN102199183B (zh) * 2010-03-26 2013-12-18 北京大学 环二鸟苷酸及其类似物和制备方法
US9061048B2 (en) 2010-12-15 2015-06-23 The Regents Of The University Of California Cyclic di-AMP induction of type I interferon
US9650615B2 (en) 2012-02-29 2017-05-16 Yamasa Corporation Practical method for enzymatically synthesizing cyclic di-GMP
KR101946808B1 (ko) 2014-03-03 2019-02-12 야마사 쇼유 가부시키가이샤 결정성 3',5'-사이클릭 디구아닐산
JP6321135B2 (ja) 2014-03-14 2018-05-09 ヤマサ醤油株式会社 ３’，５’−サイクリックジアデニル酸の包接化合物、およびその製造法

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10787479B2 (en) 2014-03-03 2020-09-29 Yamasa Corporation Crystalline 3′,5′-cyclic diguanylic acid
US10836783B2 (en) 2014-03-14 2020-11-17 Yamasa Corporation Inclusion compound of 3′ ,5′-cyclic diadenylic acid and manufacturing method thereof

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KR101946808B1 (ko) 2019-02-12
JPWO2015133411A1 (ja) 2017-04-06
KR20160123379A (ko) 2016-10-25
US10787479B2 (en) 2020-09-29
CA2941353C (fr) 2019-08-20
JP6392320B2 (ja) 2018-09-19
CN106061988B (zh) 2019-12-10
WO2015133411A1 (fr) 2015-09-11
CA2941353A1 (fr) 2015-09-11
US20190315795A1 (en) 2019-10-17
EP3121188A4 (fr) 2017-02-22
EP3121188B1 (fr) 2021-12-29
EP3121188A1 (fr) 2017-01-25

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