JP2021524235A - Rna編集オリゴヌクレオチドの立体特異的結合 - Google Patents
Rna編集オリゴヌクレオチドの立体特異的結合 Download PDFInfo
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Abstract
Description
式I(Rp)および式II(Sp)
(式中、Xは、アルキル、アルコキシ、アリール、アルキルチオ、アシル、−NR1R1、アルケニルオキシ、アルキニルオキシ、アルケニルチオ、アルキニルチオ、−S−Z+、−Se−Z+、または−BH3−Z+であり、R1は、独立して、水素、アルキル、アルケニル、アルキニル、またはアリールであり、Z+は、アンモニウムイオン、アルキルアンモニウムイオン、ヘテロ芳香族イミニウムイオン、もしくはヘテロ環イミニウムイオンであり、そのいずれかが一級、二級、三級、もしくは四級であるか、または、Zは、一価の金属イオンである)
を有するヌクレオチド間結合に関する。
用語「アデニン」、「グアニン」、「シトシン」、「チミン」、「ウラシル」、および「ヒポキサンチン」(イノシンでの核酸塩基)とは、本明細書で使用される場合、それ自体で核酸塩基を指す。
コンピューターモデリングに基づく、一本鎖アンチセンス編集オリゴヌクレオチドの設計
本発明の発明者らは、モデリングデータが、標的RNAの編集を改善する(または編集の効率性を高める)ために編集オリゴヌクレオチド(EON)に組み込むことができる、構造的特徴の同定を支持し得ることを想定した。ADARの立体障害を回避し、さらにタンパク質をより効果的に動員するように、EONのヌクレオチドを化学修飾することにより、最適以下の配列状況に対処した。本プロセスを誘導するため、存在するRNA結合ADAR2構造を、開始点(構造テンプレート)として使用した。二本鎖RNAとの相互作用におけるADAR2デアミナーゼドメインの公表された構造(Matthews et al., Nature Structural and Molecular Biology, 2016)を解析し、新規の構造計算に必要な距離の分子内および分子間距離のネットワークを生成した。分子内および分子間距離の値に対して、上限値を規定した。分子内距離に対して、上限値は、RNA結合ADAR2デアミナーゼX線構造で観察される距離に相当する。分子間距離に対して、上限値は、結合界面での側鎖の適用を可能にする、観察された距離より大きい、1〜3Å間に設定した。ADAR2デアミナーゼドメインの二次構造エレメントに対して、上限距離および下限距離を挿入し、αらせんおよびβシートで古典的に検出される水素結合ネットワークを特徴付けた。二面角制限は、公表された構造から導かれた。この手法は、当業者に知られている、溶液中のタンパク質−RNA構造を解明するために使用される標準的な方法(核磁気共鳴分光法)に基づき、捻れ角ならびに分子動力学ステップを統合する。機能的に最適化されているEONに結合するADAR2デアミナーゼドメインの構造を、CYANA3.97(Herrmann et al., J. Mol. Biol., 2002)で計算し、選択した原子モデルを、ff99SB力場を使用する陰的水(implicit water)でのシミュレーテッドアニーリングにより、AMBER16(Case D.A. et al., J. Comput. Chem., 2005)のSANDERモジュールで精製した。インシリコでは、Idua RNA標的にアニールしたEONからなる二本鎖RNA複合体を使用した。このプロトコルは、タンパク質側鎖および二本鎖RNA−EONらせん間の相互作用の原子的な詳細の探索を可能にした。相互作用を、EONの酸素−リン酸骨格の化学修飾により調節した。
RNA編集におけるインシリコモデリングされたEONの使用
上記で概説した通り、許容および非許容の立体特異的ホスホロチオエート立体配置修飾のパターンを決定し、RNA編集実験においてこれをさらに実証するために、酵素的アッセイを行って、実験的に方法を確認する。これらのハーラー症候群モデル実験の手順は、国際公開第2017/220751号に記載される。第一の実験では、様々な位置での修飾を有するいくつかのEONを試験する。第二の実験では、立体特異的ホスホロチオエートRpおよび/またはSp修飾を、本明細書に概説したような原子スケールモデリング結果と一致した、EONでの特異的な位置で統合する。早期停止コドン(W392X)で改変したIdua遺伝子を過剰発現するMEF細胞におけるオリゴヌクレオチドのトランスフェクションの後、α−L−イズロニダーゼ(Idua遺伝子でコードされたタンパク質)の酵素的活性を、多数の対照に関して定量化する。EONをこれらのRNA標的に結合し、続いてADARで編集することで、酵素機能を復元する。
Claims (18)
- 細胞内の標的核酸分子と二本鎖複合体を形成することができ、ヌクレオチドデアミナーゼ活性を有する酵素を動員することができる、オリゴヌクレオチド組成物であって、前記標的核酸分子が、ヌクレオチド脱アミノ化活性を有する前記酵素による脱アミノ化のための標的ヌクレオチドを含み、前記オリゴヌクレオチドが、式
(式中、Xは、アルキル、アルコキシ、アリール、アルキルチオ、アシル、−NR1R1、アルケニルオキシ、アルキニルオキシ、アルケニルチオ、アルキニルチオ、−S−Z+、−Se−Z+、または−BH3−Z+であり、R1は、独立して、水素、アルキル、アルケニル、アルキニル、またはアリールであり、Z+は、アンモニウムイオン、アルキルアンモニウムイオン、ヘテロ芳香族イミニウムイオン、もしくはヘテロ環イミニウムイオンであり、そのいずれかが一級、二級、三級、もしくは四級であるか、またはZは、一価の金属イオンである)
によるRpまたはSp立体特異的立体配置が濃縮されている、少なくとも1つのヌクレオチド間結合を含むことを特徴とする、オリゴヌクレオチド組成物。 - 前記標的ヌクレオチドに対向し、前記標的ヌクレオチドとミスマッチする、ヌクレオチド位置0と称すヌクレオチドを含み、前記ヌクレオチド間結合の番号付けが、結合番号0がヌクレオチド位置0からの5’結合となるようにし、前記オリゴヌクレオチドでのヌクレオチド位置および結合位置がいずれも、5’末端および3’末端に向かってそれぞれ正(+)および負(−)に増分する、請求項1に記載のオリゴヌクレオチド。
- 主にRp立体配置を有する少なくとも1つの前記ヌクレオチド間結合が、結合位置+4、−1、−3、および/または−6にある、請求項2に記載のオリゴヌクレオチド組成物。
- 主にSp立体配置を有する少なくとも1つの前記ヌクレオチド間結合が、結合位置+10にある、請求項2または3に記載のオリゴヌクレオチド組成物。
- 前記オリゴヌクレオチドが、非修飾ホスホジエステルである少なくとも1つのヌクレオチド間結合を含む、請求項2から4のいずれか一項に記載のオリゴヌクレオチド組成物。
- 非修飾ホスホジエステルである少なくとも1つの前記ヌクレオチド間結合が、結合位置+5、+6、+7、+8、−4、および/または−5にある、請求項5に記載のオリゴヌクレオチド組成物。
- 前記オリゴヌクレオチドが、2’−O−メトキシエチル(2’−MOE)リボース修飾を含む1つまたは複数のヌクレオチドを含み、2’−MOEリボース修飾を含まない1つまたは複数のヌクレオチドを含む、請求項1から6のいずれか一項に記載のオリゴヌクレオチド組成物。
- 前記オリゴヌクレオチドが、2’−MOEリボース修飾を含まない位置で2’−O−メチル(2’−OMe)リボース修飾を含む、および/または前記オリゴヌクレオチドが、2’−MOEリボース修飾を含まない位置でデオキシヌクレオチドを含む、請求項1から7のいずれか一項に記載のオリゴヌクレオチド組成物。
- ヌクレオチドデアミナーゼ活性を有する前記酵素が、ADAR1またはADAR2などの、アデノシン脱アミノ化活性を有するデアミナーゼドメインを含む、請求項1から8のいずれか一項に記載のオリゴヌクレオチド組成物。
- ヌクレオチドデアミナーゼ活性を有する前記酵素が、天然に発現される真核アデノシン脱アミノ化酵素、好ましくはADAR2である、請求項1から8のいずれか一項に記載のオリゴヌクレオチド組成物。
- 前記オリゴヌクレオチドが、少なくとも10、11、12、13、14、15、16、または17ヌクレオチド長であり、100ヌクレオチドより短く、好ましくは60ヌクレオチドより短い、請求項1から10のいずれか一項に記載のオリゴヌクレオチド組成物。
- 前記標的ヌクレオチドが、イノシンに脱アミノ化するアデノシンである、請求項1から11のいずれか一項に記載のオリゴヌクレオチド組成物。
- 前記アデノシンが、UGAまたはUAG終止コドンに位置し、UGGコドンに編集される、請求項12に記載のオリゴヌクレオチド組成物。
- 請求項1から13のいずれか一項に記載のオリゴヌクレオチドおよび薬学的に許容される担体を含む医薬組成物。
- 嚢胞性線維症、ハーラー症候群、α−1−アンチトリプシン(A1AT)欠損症、パーキンソン病、アルツハイマー病、色素欠乏症、筋萎縮性側索硬化症、喘息、β−サラセミア、カダシル症候群、シャルコー−マリー−ツース症候群、慢性閉塞性肺疾患(COPD)、遠位脊髄性筋萎縮症(DSMA)、デュシェンヌ型/ベッカー型筋ジストロフィー、栄養障害性表皮水疱症、表皮水疱症、ファブリー病、第V因子ライデン関連障害、家族性腺腫性ポリポーシス、ガラクトース血症、ゴーシェ病、グルコース−6−リン酸脱水素酵素、血友病、遺伝性ヘモクロマトーシス、ハンター症候群、ハンチントン病、炎症性腸疾患(IBD)、先天性多凝集症候群、レーバー先天性黒内障、レッシュ−ナイハン症候群、リンチ症候群、マルファン症候群、ムコ多糖症、筋ジストロフィー、I型およびII型筋強直性ジストロフィー、神経線維腫症、ニーマン−ピック病A型、B型およびC型、NY−eso1関連がん、ポイツ−イェガース症候群、フェニルケトン尿症、ポンペ病、原発性線毛疾患、プロトロンビン突然変異関連障害(例えば、プロトロンビンG20210A突然変異)、肺高血圧症、色素性網膜炎、サンドホフ病、重症複合免疫不全症候群(SCID)、鎌状赤血球貧血、脊髄性筋萎縮症、スタルガルト病、テイサックス病、アッシャー症候群、X連鎖免疫不全、スタージ−ウェーバー症候群、ならびに、がんからなる群から好ましくは選択される、遺伝的障害の処置または予防での使用のための、請求項1から13のいずれか一項に記載のオリゴヌクレオチド組成物。
- 嚢胞性線維症、ハーラー症候群、α−1−アンチトリプシン(A1AT)欠損症、パーキンソン病、アルツハイマー病、色素欠乏症、筋萎縮性側索硬化症、喘息、β−サラセミア、カダシル症候群、シャルコー−マリー−ツース症候群、慢性閉塞性肺疾患(COPD)、遠位脊髄性筋萎縮症(DSMA)、デュシェンヌ型/ベッカー型筋ジストロフィー、栄養障害性表皮水疱症、表皮水疱症、ファブリー病、第V因子ライデン関連障害、家族性腺腫性ポリポーシス、ガラクトース血症、ゴーシェ病、グルコース−6−リン酸脱水素酵素、血友病、遺伝性ヘモクロマトーシス、ハンター症候群、ハンチントン病、炎症性腸疾患(IBD)、先天性多凝集症候群、レーバー先天性黒内障、レッシュ−ナイハン症候群、リンチ症候群、マルファン症候群、ムコ多糖症、筋ジストロフィー、I型およびII型筋強直性ジストロフィー、神経線維腫症、ニーマン−ピック病A型、B型およびC型、NY−eso1関連がん、ポイツ−イェガース症候群、フェニルケトン尿症、ポンペ病、原発性線毛疾患、プロトロンビン突然変異関連障害(例えば、プロトロンビンG20210A突然変異)、肺高血圧症、色素性網膜炎、サンドホフ病、重症複合免疫不全症候群(SCID)、鎌状赤血球貧血、脊髄性筋萎縮症、スタルガルト病、テイサックス病、アッシャー症候群、X連鎖免疫不全、スタージ−ウェーバー症候群、ならびに、がんからなる群から好ましくは選択される、遺伝的障害の処置または予防のための医薬の製造における、請求項1から13のいずれか一項に記載のオリゴヌクレオチド組成物の使用。
- 細胞内の標的核酸分子に存在する少なくとも1つの標的ヌクレオチドの脱アミノ化のための方法であって、
(i)前記細胞に、請求項1から13のいずれか一項に記載のオリゴヌクレオチド組成物を供給するステップ、
(ii)前記オリゴヌクレオチドの前記細胞による取込みを可能にするステップ、
(iii)前記標的核酸分子への前記オリゴヌクレオチドのアニーリングを可能にするステップ、
(iv)ヌクレオチドデアミナーゼ活性を有する哺乳動物酵素が、前記標的核酸分子中の前記標的ヌクレオチドを脱アミノ化することを可能にするステップ、および
(v)任意で、前記標的核酸中の脱アミノ化した前記ヌクレオチドの存在を同定するステップ
を含む方法。 - ステップ(v)が、
a)脱アミノ化した前記標的ヌクレオチドを含む、前記標的核酸分子の領域をシークエンシングすること、
b)前記標的ヌクレオチドが、UGAまたはUAG終止コドンに位置するアデノシンであり、脱アミノ化によってUGGコドンに編集される場合、機能性、伸長型、全長および/もしくは野生型タンパク質の存在を評価すること、
c)2つの標的アデノシンが、UAA終止コドンに位置し、両方の標的アデノシンの脱アミノ化によってUGGコドンに編集される場合、機能性、伸長型、全長および/もしくは野生型タンパク質の存在を評価すること、
d)前記標的核酸が、プレmRNAである場合、前記プレmRNAのスプライシングが、脱アミノ化により改変したかどうかを評価すること、または
e)機能的な読み出しを使用することであって、脱アミノ化後の前記標的核酸が、機能性、全長、伸長型および/もしく野生型タンパク質をコードする、こと
を含む、請求項17に記載の方法。
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US11827880B2 (en) | 2019-12-02 | 2023-11-28 | Shape Therapeutics Inc. | Therapeutic editing |
CA3158528A1 (en) | 2019-12-23 | 2021-07-01 | Jim SWILDENS | Antisense oligonucleotides for nucleotide deamination in the treatment of stargardt disease |
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