JP2020510632A - セレブロンに対する小分子の親和性の測定方法 - Google Patents
セレブロンに対する小分子の親和性の測定方法 Download PDFInfo
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Abstract
Description
本願は、2017年2月3日に出願した米国特許仮出願第62/454,654号の優先権の権利を主張するものであり、この出願の内容は、参照により、その全体が本明細書に援用される。
本開示は広くは、セレブロンと2つの光感受性分子とを含む複合体と、セレブロンと化合物との親和性の測定方法と、治療効果を持つ可能性のある化合物を特定するために、上記の複合体を用いることに関するものである。
タンパク質のセレブロン(CRBN)には、少なくとも2つのアイソフォームが存在し、一方は442個のアミノ酸分の長さであり、もう一方は441個のアミノ酸分の長さであり、CRBNは、植物からヒトまで保存されている。ヒトでは、CRBN遺伝子は、常染色体劣性非症候群性精神遅滞(ARNSMR)の候補遺伝子として同定されている。Higgins,J.J.et al.,Neurology,2004,63:1927−1931を参照されたい。CRBNは当初、ラット脳内でカルシウム活性化カリウムチャネルタンパク質(SLO1)と相互作用するRGSを含有する新しいタンパク質として特徴付けられ、後に、網膜内でAMPK1及びDDB1とともに電位依存性塩素チャネル(CIC−2)と相互作用することが示された。Jo,S.et al.,J.Neurochem,2005,94:1212−1224、Hohberger B.et al.,FEBS Lett,2009,583:633−637、Angers S.et al.,Nature,2006,443:590−593を参照されたい。DDB1は元々、損傷DNA結合タンパク質2(DDB2)と会合するヌクレオチド除去修復タンパク質として同定された。その活性に異常があると、色素性乾皮症相補性E群(XPE)の患者で修復欠損を引き起こす。DDB1はまた、標的タンパク質のユビキチン化と、それに続くプロテアソーム分解を媒介する多数の異なるDCX(DDB1−CUL4−X−ボックス)E3ユビキチンタンパク質リガーゼ複合体の構成要素として機能すると見られる。CRBNもまた、大脳皮質の疾患に対する治療剤の開発の標的として同定されている。WO2010/137547A1を参照されたい。
一態様では、本発明で提供するのは、(i)そのCRBNのN末端にユウロピウム−抗His抗体を有するCRBNと、(ii)Cy5コンジュゲート小分子とを含む複合体であって、そのCy5コンジュゲート小分子が、そのCRBNと結合する複合体である。
様々ながんを治療するための免疫調節薬を含むいくつかの化合物は、CRL4(CUL4−RBX1−DDB1)ユビキチンリガーゼ複合体に対する基質レセプターであるセレブロン(CRBN)を標的とするとともに、このユビキチンリガーゼの基質特異性を変更して、がん細胞において臨床活性を誘導することが示されてきている。今では、いくつかの研究で、サリドマイドのような抗がん薬の作用機序には、タンパク質のCRBNへの結合が含まれることが示されているので、これらの薬物とCRBNとの結合について理解すれば有益であり、最終的には、治療効果の向上した新たな薬物を開発する助けとなる。
特許、出願、公開出願及びその他の刊行物はいずれも、参照により、本明細書に援用される。別段の定めのない限り、本明細書で使用するすべての技術用語と科学用語は、当業者によって一般的に理解される意味と同じ意味を有する。本明細書用語に複数の定義が存在する場合には、別段の記載のない限り、本項の定義を優先する。
本発明で提供するのは、例えば、E3ユビキチンリガーゼに結合する化合物をスクリーニングするか、または別段の形で特定する組成物、方法及びキットである。
一態様では、本発明で提供するのは、化合物がセレブロン(CRBN)に結合するかの判断方法であって、その化合物を複合体と接触させることを含み、その複合体が、(i)そのCRBNのN末端にユウロピウム−抗His抗体を有するCRBNと、(ii)Cy5コンジュゲート小分子とを含み、そのCy5コンジュゲート小分子がそのCRBNと結合する方法である。
下記の6.6項と6.7項に示されているように、細胞分解アッセイで示した場合、CRBNに対する生化学的な結合親和性が高い化合物ほど、細胞活性での効能の向上とよく相関する。したがって、本発明で提供する方法であって、CRBNに対する化合物の親和性の測定方法は、生物学的活性または治療効果を有する化合物の特定にも用いることができる。
特定の実施形態では、本開示における生物学的活性は、指定の細胞種カテゴリーに基づくものである。このような細胞としては、いずれかのタイプの細胞、例えば、幹細胞、血液細胞(例えば末梢血単核球)、リンパ球、B細胞、T細胞、単球、顆粒球、免疫細胞、腫瘍細胞またはがん細胞を挙げることができる。
本発明で提供する方法の特定の実施形態では、その方法は、本発明で提供する結合アッセイによって特定した化合物の特定の生物学的活性をアッセイして、例えば、その化合物の治療効果の可能性を検証することをさらに含む。
いくつかの実施形態では、本発明で提供する方法は、化合物とCRBNとの親和性を試験するためのものである。本発明で提供する各種方法のいくつかの実施形態では、その化合物は、いずれかのCRBN改変剤(すなわちCMA)であることができる。
また、本発明で提供するのは、CRBN介在性疾患の治療及び予防方法であって、本発明で提供する各種方法を用いて特定した化合物を患者に投与することを含む方法である。特定の実施形態では、このCRBN介在性疾患または障害は、がんである。特定の実施形態では、本発明で提供するのは、CRBN介在性疾患の治療及び予防方法で用いるものとして、本発明で提供する各種方法によって特定した化合物であって、その方法が、その化合物、またはそのエナンチオマー、そのエナンチオマーの混合物、その製薬学的に許容可能な塩、その溶媒和物、その水和物、その共結晶、その包接化合物もしくはその結晶多形を患者に投与することを含む化合物である。
6.実施例
6.1 3−[4−(4−モルホリン−4−イルメチル−ベンジルオキシ)−オキソ−1,3−ジヒドロ−イソインドール−2−イル]−ピペリジン−2,6−ジオン(化合物B)の調製
Matyskiela et al.,Nature 2016,535(7611),252−7で以前説明されたようにして、環化に備えてCRBN−DDB1の精製を行った。化合物BによるCRBN−DDB1の環化は、シッティングドロップ蒸気拡散法を用いて行った。1mMの化合物Bの存在下での30mg/mLのCRBN−DDB1と1:1で混合してから、20℃にて、200mMのフッ化ナトリウム及び20%PEG3350を含む母液に対して平衡化した。20%エチレングリコールを添加したリザーバー溶液において、結晶を凍結保護し、液体窒素下で冷却した。データをAdvance Photon SourceのビームラインLS−CAT21ID−Fで収集した。4TZ4のサーチモデルとともに、Phaserを用いて、分子置換法によって、複合体結晶構造を解明した(Chamberlian et al.,Nature structural & molecular biology 2014,21(9),803−9を参照されたい)。その後、Refmac5を用いて、Cootを用いたマニュアルモデル構築と精密化を行った(Emsley et al.,Acta crystallographica.Section D,Biological crystallography 2011,67(Pt4),355−67を参照されたい)。
トロンビン切断/オルトニッケル工程を除外する以外は、他の箇所に記載されているようにして、このアッセイで使用する、完全長ヒトDDB1に結合した6×Hisタグ化完全長ヒトCRBNを精製した。このアッセイでは、20mMのHEPES(pH7)、150mMのNaCl、0.005%のTween−20のアッセイバッファーにおいて、60nMの6×Hisタグ化CRBN−DDB1と、30nMのCy5コンジュゲートセレブロンモジュレーター及び3nMのLanthaScreen(登録商標)Eu−anti−His Tag Antibody(ThermoFisherカタログ番号PV5596)とを混ぜ合わせた。FRETは、340nmで励起して、615nmでの発光(Non−FRET発光)と665nmでの発光(FRET発光)をモニタリングすることによって観察し、Non−FRET発光に対するFRETの比率(665nm/615nm)によって、FRET効率を求める。競合するセレブロン調節化合物またはDMSO担体を滴定し、10分インキュベートしてから、ディレイが60マイクロ秒のプレートリーダーEnvisionでスキャンして、FRET効率の喪失を定量する。
化合物を事前に点着した384ウェルプレート(Corning#3712)に、セレブロン基質のIkaros、Aiolos及びGSPT1を発現しているDF15多発性骨髄腫細胞であって、ePLタグ(DiscoverX)に融合した細胞を分注した。化合物は、音響ディスペンサー(EDC BiosystemsのATS Acoustic Transfer System)によって、384ウェルプレートに、10点用量応答曲線で、3倍希釈を用いて、10μMで開始して0.0005μMまで低下させて分注した。1ウェルあたりに、5000個の細胞を含む25μLの培地(RPMI−1640+10%熱不活化FBS+25mMのHepes+1mMのピルビン酸ナトリウム+1×NEAA+0.1%Pluronic F−68+1×Pen Strep Glutamine)を分注した。アッセイプレートを37℃で、5%CO2とともに4時間インキュベートした。インキュベート後、25μlのInCELL Hunter(商標)Detection Reagent Working Solution(DiscoverX、カタログ番号96−0002、Fremont,CA)を各ウェルに加え、室温で30分、光から保護した状態でインキュベートした。30分後、発光を発光測定装置PHERAstar(Cary,NC)で計測した。化合物が所定の基質を分解するEC50値(50%効果濃度)を求めるために、4パラメーターロジスティックモデル(シグモイド型用量応答モデル)(FIT=(A+((B−A)/1+((C/x)^D))))(式中、Cは変曲点(EC50)、Dは相関係数、それぞれ、Aは適合度の下限、Bは適合度の上限である)を使用した。コントロール基質分解曲線の割合はいずれも、Activity Base(IDBS)を用いて処理及び評価した。
1×106個の細胞(DF15及びOPM2のいずれか)をレナリドマイド、ポマリドミドまたは化合物Bで5時間処理してから回収した。1×冷PBSで速やかにリンスした後、細胞溶解バッファー(Cell Signaling‘s Technologies)によって細胞を溶解した。10ugの全溶解液を各レーンに入れた。Bio−RadのTurbo Systemを用いて、タンパク質をニトロセルロース膜に転写した。ウェスタンで用いた抗体には、Ikaros(14859S、Cell Signaling Technologies)、Aiolos(15103S、Cell Signaling Technologies)、アクチン(A5316、Sigma)及びCRBN(Celgeneの自家作製抗体)が含まれていた。
レナリドマイドとポマリドミドのように、化合物Bは、セレブロンのトリTrpポケット内で結合するグルタルイミド環と、セレブロンと基質の両方と相互作用できるイソインドリノン環とを含む。加えて、化合物Bの化学構造は、レナリドマイドとポマリドミドよりも延伸されており、追加のフェニルとモルホリノ部分を含み、それにより、セレブロンまたは基質とのさらなる相互作用が可能になる(図3を参照)。レナリドマイドとポマリドミドと化合物Bとの相対的な結合親和性を判断するために、我々は、TR−FRETセレブロン結合アッセイ(上記の6.3項に説明されている)を用いて、これらの化合物のIC50値を求めた。このアッセイでは、CRBNのトリTrpポケットからのCy5コンジュゲートセレブロン調節化合物の変位をモニタリングする。これらのアッセイ条件下では、それぞれ、レナリドマイドのIC50値は1.5μMで、ポマリドミドのIC50値は1.2μMで、同程度であったが、化合物Bでは、これらよりも親和性が有意に高く、IC50は約60nmであった(図3を参照)。
化合物Bは、生化学的な結合親和性の向上と一致して、IkarosまたはAiolosのリガンド依存性枯渇を測定した細胞分解アッセイでの効能も高かった(図4のパートa)とb)を参照)。しかしながら、化合物Bは、GSPT1またはCK1αをあまり分解しない。細胞において、化合物による処理が、IkarosとAiolosの分解に及ぼす作用を測定するために、我々は、ePLタグを組み込んだタンパク質の化学発光シグナルを追跡する細胞ベースのアッセイを用いた。化合物Bによる処理によって、Ikarosタンパク質レベルが喪失し、EC50は、レナリドマイドでの67nMとポマリドミドでの24nMに対して、1nMとなることを我々は見出している。化合物Bは、Aiolosに対しても同様に強力であり、EC50は、レナリドマイドでの87nMとポマリドミドでの22nMに対して、0.5nMである。加えて、基質の枯渇度は、化合物Bの方が大きく、タンパク質の再合成速度よりも、基質分解の方が効率的であることが示されている。化合物Bの細胞分解能が高いことは、生化学的アッセイで観察された結合親和性の向上と一致することから、セレブロン親和性の向上が、細胞での効能の向上に寄与する可能性が高いことが示唆されている。これに対して、レナリドマイドよりも、ポマリドミドで観察された、細胞での効能が3〜4倍高いのは、基質親和性の変化のような他の要因によるものである可能性が高い。
化合物Bの方が、結合親和性が高くなる機序を調べるために、我々は、ヒトセレブロン(40〜442番目のアミノ酸)とヒトDDB1(完全長)に結合した化合物Bの三元複合体の結晶構造を3.1Aの分解能で求めた(図5のパートa)を参照)。全体構造は、以前我々が報告した、セレブロン−DDB1の構造によく似ており、セレブロンの面のうち、DDB1相互作用部位とは反対側の面に、セレブロンモジュレーターの結合部位を有していた。
Claims (35)
- (i)そのCRBNのN末端にユウロピウム−抗His抗体を有するCRBNと、(ii)Cy5コンジュゲート小分子とを含む複合体であって、前記Cy5コンジュゲート小分子が前記CRBNと結合する前記複合体。
- DDB1をさらに含む、請求項1に記載の複合体。
- 前記Cy5コンジュゲート小分子が、前記CRBNにおいてTrp380、Trp386及びTrp400によって形成された疎水性のトリトリプトファンポケット内で結合する、請求項1または2に記載の複合体。
- 化合物がセレブロン(CRBN)に結合するかの判断方法であって、前記化合物を複合体と接触させることを含み、前記複合体が、
(i)そのCRBNのN末端にユウロピウム−抗His抗体を有するCRBNと、
(ii)Cy5コンジュゲート小分子と、を含み、前記Cy5コンジュゲート小分子が前記CRBNと結合する前記方法。 - 前記複合体がDDB1をさらに含む、請求項5に記載の方法。
- 前記Cy5コンジュゲート小分子が、前記CRBNにおいてTrp380、Trp386及びTrp400によって形成された疎水性のトリトリプトファンポケット内で結合する、請求項5または6に記載の方法。
- 前記化合物を前記複合体と接触させた後に、蛍光共鳴エネルギー移動(FRET)を測定することをさらに含む、請求項5〜8のいずれか1項に記載の方法。
- 前記化合物を前記複合体と接触させる前に、FRETを測定することをさらに含む、請求項9に記載の方法。
- 前記化合物を前記複合体と接触させた後に、FRETが減少した場合に、前記化合物が前記CRBNに結合すると判断することをさらに含む、請求項9〜10のいずれか1項に記載の方法。
- 340nmで励起して、615nmでの発光(Non−FRET発光)と665nmでの発光(FRET発光)をモニタリングすることによってFRETを観察する、請求項9〜10のいずれか1項に記載の方法。
- 前記化合物を前記複合体と接触させる前に、第1のFRET効率を求め、前記化合物を前記複合体と接触させた後に、第2のFRET効率を求め、FRET効率が、615nmでのNon−FRET発光に対する665nmでのFRET発光の比率である、請求項12に記載の方法。
- 前記第2のFRET効率が、前記第1のFRET効率よりも低い場合に、前記化合物が前記CRBNに結合すると判断することをさらに含む、請求項13に記載の方法。
- セレブロン(CRBN)に対する化合物の親和性の測定方法であって、前記化合物を複合体と接触させることを含み、前記複合体が、
(i)そのCRBNのN末端にユウロピウム−抗His抗体を有するCRBNと、
(ii)Cy5コンジュゲート小分子と、を含み、前記Cy5コンジュゲート小分子が前記CRBNと結合する前記方法。 - 前記複合体が、DDB1をさらに含む、請求項15に記載の方法。
- 前記Cy5コンジュゲート小分子が、前記CRBNにおいてTrp380、Trp386及びTrp400によって形成された疎水性のトリトリプトファンポケット内で結合する、請求項15または16に記載の方法。
- 前記化合物を前記複合体と接触させた後に、蛍光共鳴エネルギー移動(FRET)を測定することをさらに含む、請求項15〜18のいずれか1項に記載の方法。
- 前記化合物を前記複合体と接触させる前に、FRETを測定することをさらに含む、請求項19に記載の方法。
- 340nmで励起して、615nmでの発光(Non−FRET発光)と665nmでの発光(FRET発光)をモニタリングすることによってFRETを観察する、請求項19〜20のいずれか1項に記載の方法。
- 前記化合物を前記複合体と接触させる前に、第1のFRET効率を求め、前記化合物を前記複合体と接触させた後に、第2のFRET効率を求め、FRET効率が、615nmでのNon−FRET発光に対する665nmでのFRET発光の比率である、請求項21に記載の方法。
- 前記第1のFRET効率と前記第2のFRET効率との差を測定することによって、CRBNに対する前記化合物の親和性を求める、請求項22に記載の方法。
- 疾患を治療するための化合物の特定方法であって、前記化合物を複合体と接触させることを含み、前記複合体が、
(i)そのCRBNのN末端にユウロピウム−抗His抗体を有するCRBNと、
(ii)Cy5コンジュゲート小分子と、を含み、前記Cy5コンジュゲート小分子が前記CRBNと結合する前記方法。 - 前記複合体がDDB1をさらに含む、請求項24に記載の方法。
- 前記Cy5コンジュゲート小分子が、前記CRBNにおいてTrp380、Trp386及びTrp400によって形成された疎水性のトリトリプトファンポケット内で結合する、請求項24または25に記載の方法。
- 前記化合物を前記複合体と接触させた後に、蛍光共鳴エネルギー移動(FRET)を測定することをさらに含む、請求項24〜27のいずれか1項に記載の方法。
- 前記化合物を前記複合体と接触させる前に、FRETを測定することをさらに含む、請求項28に記載の方法。
- 前記化合物を前記複合体と接触させた後に、FRETが減少した場合に、前記疾患の治療に、前記化合物を使用できる可能性があると判断することをさらに含む、請求項28〜29のいずれか1項に記載の方法。
- 340nmで励起して、615nmでの発光(Non−FRET発光)と665nmでの発光(FRET発光)をモニタリングすることによってFRETを観察する、請求項28〜29のいずれか1項に記載の方法。
- 前記化合物を前記複合体と接触させる前に、第1のFRET効率を求め、前記化合物を前記複合体と接触させた後に、第2のFRET効率を求め、FRET効率が、615nmでのNon−FRET発光に対する665nmでのFRET発光の比率である、請求項31に記載の方法。
- 前記第2のFRET効率が、前記第1のFRET効率よりも低い場合に、前記疾患の治療に、前記化合物を使用できる可能性があると判断することをさらに含む、請求項32に記載の方法。
- 前記疾患が、CRBN介在性疾患である、請求項24に記載の方法。
- 請求項1〜4のいずれか1項に記載の複合体を含む組成物。
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