JP2020508048A - Prmt5阻害剤による治療に応答する癌患者の同定におけるバイオマーカーの使用 - Google Patents
Prmt5阻害剤による治療に応答する癌患者の同定におけるバイオマーカーの使用 Download PDFInfo
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Abstract
Description
・PIC3CA活性化変異、
・スプライソソームの改変、
・サイクリンD1経路の増幅、および/または
・WNT経路の改変
のいずれかの存在について患者からの生物学的試料を評価することを含む方法を含み、ここで、任意の前記変異または改変の存在は、任意の前記変異または改変が存在しない場合よりも、前記患者が前記PRMT5阻害剤による治療に応答する可能性が高いことを示す。
いくつかの実施形態では、ハイスループット、大規模並行シーケンシングは、可逆的ダイターミネーターを用いた合成によるシーケンシングを用いる。他の実施形態では、シーケンシングは、ライゲーションによるシーケンシングにより行われる。さらに他の実施形態では、シーケンシングは、単一分子シーケンシングである。次世代シーケンシング手法の例としては、パイロシーケンシング、可逆的ダイターミネーターシーケンシング、SOLiDシーケンシング、イオン半導体シーケンシング、Helioscope単一分子シーケンシングなどが挙げられるが、これらに限定されない。
当業者は、核酸の増幅には、増幅が求められる領域に隣接する核酸鎖の5’および3’領域に相補的であり、それに結合するプライマーが必要であることを知っている。本明細書では、「プライマー対」は、増幅工程で使用される順方向および逆方向プライマーを指す。
機能的ゲノミクスおよび転写解析は、標準的な手法およびプロトコルを使用して、経路および遺伝子の増幅を解析するために使用することができる。
本明細書では、開示の方法で使用するのに好適なPRMT5阻害剤が提供される。いくつかの実施形態では、PIC3CA活性化変異、スプライソソームの改変、サイクリンD1経路増幅および/またはWNT経路の改変を含む1つ以上の変異または増幅が試料中に存在する場合、PCT/欧州特許出願公開第2016/070097号明細書(参照により本明細書に組み込まれる)で開示されたPRMT5阻害剤(その任意の互変異性体または立体化学的異性形態を含む)およびそのN−オキシド、その薬学的に許容される塩またはその溶媒和物(好適なR基もPCT/欧州特許出願公開第2016/070097号明細書に開示されている)により患者を治療することができる。例えば、いくつかの態様では、化合物2または化合物80(その任意の互変異性体または立体化学異性形態を含む)およびそのN−オキシド、その薬学的に許容される塩またはその溶媒和物で患者を治療することができる。いくつかの態様では、薬学的に許容される塩は、HCl塩である。
本明細書では、PIC3CA活性化変異、スプライソソームの改変、サイクリンD1経路増幅および/またはWNT経路の改変を含む1つ以上の変異または増幅の存在について患者の生物学的試料を評価することと、PIC3CA活性化変異、スプライソソームの改変、サイクリンD1経路増幅および/またはWNT経路の改変を含む1つ以上の変異または増幅が試料中に存在する場合、PRMT5阻害剤で患者を治療することとを含む、患者の癌を治療する方法が開示される。
変異または改変遺伝子の存在を同定するキット
生物学的試料の、PIC3CA活性化変異、スプライソソームの改変、サイクリンD1経路増幅および/またはWNT経路の改変を含む1つ以上の変異または増幅の存在を同定するためのキットであって、それらの組み合わせの配列を有するプライマー対と、PIC3CA活性化変異、スプライソソームの改変、サイクリンD1経路増幅および/またはWNT経路の改変を含む1つ以上の変異または増幅を検出するためのアッセイを実施するための使用説明書とを含むキットがさらに開示される。
アセトン(330mL)中の6−クロロ−7−デアザプリンベータ−d−リボシド(25.0g、87.5mmol)の混合物に2,2−ジメトキシプロパン(18.2g、175mmol)および4−メチルベンゼンスルホン酸(TosOH)(1.51g、8.75mmol)をN2下、25℃で一度に加えた。この混合物を60℃で2時間撹拌した。混合物を25℃に冷却した。飽和NaHCO3(100mL)をゆっくりと加えて反応を停止させ、その後、酢酸エチル(125mL×5)で抽出した。有機相をまとめて飽和塩水(120mL)で洗浄し、無水MgSO4で乾燥させ、ろ過し、真空中で濃縮した。残留物をシリカゲルクロマトグラフィー(勾配溶離:DCM/酢酸エチル(1:0〜2:1))により精製して、粗中間体1(38.0g)を淡黄色ガムとして得た。
アゾジカルボン酸ジイソプロピル(0.221mL、1.125mmol)を中間体1(0.27g、0.80mmol)、3−ブロモキノリン−7−オール(0.18g、0.80mmol)およびトリフェニルホスフィン樹脂(0.375g、3mmol/g、1.125mmol)のTHF(8ml)懸濁液に撹拌しながら室温で滴下した。添加後、反応混合物を18時間撹拌した。反応混合物をDicalite(登録商標)パッドでろ過した。残留物をメタノールで洗浄した。ろ液の溶媒を蒸発させた。残留物をそのまま次の工程で使用した。
粗中間体59(q.s.、理論的には0.83mmol)をMeOH(20mL、7M、140mmol)中、7MのNH3に溶解した。得られた溶液を撹拌し、マイクロ波照射を用いて130℃で2時間加熱した。溶媒を蒸発させた。残渣をジクロロメタンに溶解し、Grace Reveleris SRC型、12g、Si 40のSiO2カラム上、Grace Reveleris X2精製システムにより、ジクロロメタンおよびメタノールを溶離液として用い、100%DCMでの20カラム容量から出発し、20%MeOHおよび80%DCMでの20カラム超の容量までの勾配で精製した。生成物を含有する画分を一緒にし、溶媒を蒸発させて、粗中間体105(175mg)を得、これをそのまま次の反応工程で使用した。
ジオキサン(0.7mL、2.9mmol)中、4MのHClを中間体105(175.1mg、粗生成物、≒0.29mmol)のMeOH(10mL)溶液に撹拌しながら室温で加えた。この反応混合物を室温で18時間撹拌した。MeOH中、7NのNH3溶液1.5mLを加えて反応を停止させた。溶媒を蒸発させた。残渣をDCMに溶解した。沈殿物をろ別した。Grace Reveleris SRC型、12g、Si 40のSiO2カラム上、Armen Spot II Ultimate精製システムにより、DCMおよびMeOHを溶離液として用い、100%DCMから開始し、40%MeOHおよび60%DCMで終了する勾配でろ液を精製した。生成物を含有する画分を一緒にし、溶媒を蒸発させて24.5mgの化合物2を得た。
プロパン−2−オール/H2O(208mL、7:1)中の4,6−ジクロロ−5−(2,2−ジエトキシエチル)ピリミジン(14.0g、52.8mmol)および(1R,2S,3R,5R)−3−アミノ−5−(ヒドロキシメチル)シクロペンタン−1,2−ジオール塩酸塩(10.7g、58.1mmol)の混合物にEt3N(13.4g、132mmol)をN2下、25℃で一度に加えた。この混合物を90℃で23時間撹拌した。混合物を50℃に冷却し、4MのHCl(24mL、106mmol)をゆっくりと加えた。続いて、残渣を50℃で2時間撹拌した。反応混合物を25℃に冷却し、NaHCO3(14g、100mmol)をゆっくりと加えた。酢酸エチル(230mL)を加えた後、半飽和NaHCO3溶液(q.s.)を加えた。有機相を単離し、水相を酢酸エチルで抽出した(230mL×2)。有機相をまとめて無水MgSO4で乾燥させ、ろ過し、真空中で濃縮して、黄色固体として中間体9(17.4g、2工程の定量的収量)を得た。粗生成物をさらに精製することなくそのまま次の反応工程で直接使用した。
アセトン(250mL)中の中間体9(17.4g、≒52.7ミリモル)の混合物に2,2−ジメトキシプロパン(11.0g、105ミリモル)およびTsOH・H2O(908mg、5.27ミリモル)をN2下、25℃で一度に加えた。この混合物を60℃で2時間撹拌した。この混合物を25℃に冷却し、溶液を真空中で濃縮し、飽和NaHCO3(100mL)でゆっくりと反応を停止させ、その後、酢酸エチル(100mL×3)で抽出した。有機相をまとめて飽和塩水(100mL)で洗浄し、無水MgSO4で乾燥させ、ろ過し、真空中で濃縮した。残渣をシリカゲルフラッシュクロマトグラフィー(勾配溶離:DCM/酢酸エチル(1/0〜2/1))により精製して、中間体10(15.5g、収率89%)を淡黄色ガムとして得た。
DCM(40mL)中の中間体1(2.00g、理論的には6.18mmol)の混合物にデス−マーチンペルヨージナン(5.24g、12.36mmol)をN2下、0℃で一度に加えた。この混合物を0℃で3時間撹拌した。この混合物に飽和NaHCO3(20mL)中のNa2S2O3(4g)を加え、10min間撹拌した。水相をDCM(20mL×3)で抽出した。有機相をまとめて飽和塩水(20mL×2)で洗浄し、無水MgSO4で乾燥させ、ろ過し、真空中で濃縮し、淡黄色ガムとして中間体33(1.80g、粗製)を得た。粗生成物をさらに精製することなくそのまま次の反応工程で直接使用した。
方法1
THF(500mL)中のメチルトリフェニルホスホニウムブロミド(4.87g、13.62mmol)の混合物にt−BuOK(11.4mL、THF中1M、1.27g、11.35mmol)をN2下、0℃で滴下した。懸濁液は、鮮黄色に変化し、それを0℃で0.5h撹拌し、その後、0.5hで25℃にまで加温した。混合物を−40℃に冷却した。中間体35(1.46g、理論的に4.54mmol)のTHF(130.0mL)溶液を滴下し、次いで−20℃で1h撹拌し、その後、混合物を2hで25℃にまで加温した。この混合物に飽和NH4Cl(300ml)を加え、10min間撹拌した。層を分離し、水相をDCM(300mL×2)で抽出した。有機相をまとめて飽和塩水(500mL)で洗浄し、無水MgSO4で乾燥させ、ろ過し、真空中で濃縮した。残渣をシリカゲルクロマトグラフィー(ISCO(登録商標);80g SepaFlash(登録商標)シリカフラッシュカラム、勾配溶離:0%から15%の酢酸エチル/石油エーテル)により精製した。所望の画分を回収し、溶媒を蒸発させた。オフホワイトの固体として中間体38を得た(530mg、収率36%)。
中間体38
中間体35(10.0g、理論的に31.1mmol)のTHF(100mL)溶液をN2下、30分間にわたってビス(ヨードジンシオ)メタンのTHF(180mL、0.31M、55.9mmol、Tetrahedron 2002,58,8255〜8262に記載の手順に従って調製した)溶液に滴下し、完全に転化するまで(約2時間)撹拌を続けた。飽和NH4Cl水溶液をゆっくりと加えて反応混合物の反応を停止させ、その間、塩の生成が観察された。抽出(EtOAc、2×200mL)前に塩をアンモニア水溶液(25%)の添加によって再度溶解させた。有機相をまとめて亜硫酸水素ナトリウム水溶液および塩水で洗浄し、無水MgSO4で乾燥させ、ろ過し、真空中で濃縮した。残渣をシリカゲルクロマトグラフィー(溶離液:ジクロロメタン/EtOAc 95/5)により精製して、オフホワイトの固体として中間体38を得た(6.9g、66%)。
3−ブロモ−7−ヨード−キノリン(5.99g、17.7mmol)をジクロロメタン(60mL)に溶解し、次いでm−CPBA(4.57g、26.5mmol)を何回かに分けて加えた。この混合物を室温で4日間撹拌した。飽和Na2S2O3水溶液(40mL)および飽和NaHCO3水溶液(PH6〜7へ)によって混合物の反応を停止させ、次いでジクロロメタン(50mL×3)で抽出した。有機相をH2O(50mL)で洗浄し、無水Na2SO4で乾燥させ、減圧下で蒸発させた。残渣をシリカゲルカラム(溶離液:石油エーテル/酢酸エチル=10/1〜1/1)で精製し、所望の生成物中間体174(1.9g、収率14.1%)を黄色固体として得た。
中間体174(2.9g、8.29mmol)のクロロホルム(60mL)溶液にリン酸トリクロリド(8.3g、54.1mmol)を加えた。混合物を80℃で12h撹拌した。混合物を減圧下で蒸発させて、粗生成物を得た。粗生成物をクロマトグラフィーカラム(溶離液:石油エーテル/酢酸エチル=10/1〜1/1)により精製した。所望の画分を回収し、濃縮して、白色固体として生成物中間体175(1.3g、収率41.5%)を得た。
4−メトキシベンジルアミン(1.34g、9.78mmol)をエタノール(10ml)中の中間体175混合物(0.8g、≒1.95mmol)に加えた。密封管中、100℃で12h、混合物を加熱した。混合物を真空下で蒸発させて、粗生成物を得た。これをクロマトグラフィーカラム(勾配溶離液:酢酸エチル/石油エーテル=0/1〜1/10)により精製した。所望の画分を回収し、濃縮して、油として生成物中間体176(600mg、収率51.6%)を得た。
9−BBN(1.3ml、0.69mmol、THF中0.5M)中の中間体38(44mg、0.138mmol)の混合物をN2下で1h還流した。混合物を室温に冷却し、次いでH2O(1mL)中のK3PO4(87mg、0.413mmol)を加え、続いてTHF(5ml)、中間体176(122.727mg、≒0.206mmol)および[1,1’−ビス(ジフェニルホスフィノ)フェロセン]ジクロロパラジウム(II)(4.48mg、0.007mmol)を加えた。反応混合物を3時間還流した。混合物を濃縮した。残渣を酢酸エチル(40ml)に溶解し、水(6ml)、塩水(6ml)で洗浄した。有機相をNa2SO4上で乾燥させ、ろ過し、濃縮して、粗中間体177画分1(120mg、収率71.5%)を得た。
ジオキサン(10ml)中の中間体177(300mg、≒0.446mmol)およびNH3・H2O(10ml)の混合物を密封管中において120℃で14h撹拌した。この反応物を真空下で蒸発させて、油として中間体178(250mg、収率87.1%)を得た。
TFA(5ml)中の中間体178(250mg、≒0.388mmol)の混合物を50℃で1h撹拌した。この混合物を真空下で蒸発させて、油として中間体179(350mg、収率63.4%)を得た。
メタノール(3mL)中の中間体179(350mg)およびK2CO3(102mg、0.74mmol)の混合物を60℃で1h撹拌した。混合物をろ過し、真空下で蒸発させて、粗生成物を得た。粗生成物を分取−HPLC(カラム:Waters Xbridge Prep OBD C18 150×30mm、5μm、条件:勾配 水(0.05%水酸化アンモニアv/v)−ACN)で精製した。所望の画分を回収し、溶媒を蒸発させて、白色固体として化合物80(113.3mg、収率94.9%)を得た。
NMR
多くの化合物について、360MHzで稼働させたBruker DPX−360、600MHzで稼働させたBruker Avance 600、400MHzで稼働させたBruker Avance 400または400MHzで稼働させたVarian 400MR分光計で1H NMRスペクトルを記録した。溶媒として、クロロホルム−d(重水素化クロロホルム、CDCl3)、メタノール−d4またはDMSO−d6(重水素化DMSO、ジメチル−d6スルホキシド)を使用した。化学シフト(δ)は、内部標準として使用したテトラメチルシラン(TMS)に対する百万分率(ppm)で報告する。
Co.80:1H NMR(600MHz,DMSO−d6)δ ppm 1.50−1.56(m,1H)1.68−1.75(m,1H)1.85−1.92(m,1H)1.96(ddt,J=13.0,9.0,6.5,6.5Hz,1H)2.25(dt,J=12.7,7.9Hz,1H)2.69−2.80(m,2H)3.76(br t,J=4.7Hz,1H)4.21(dd,J=7.6,6.0Hz,1H)4.57(br s,1H)4.72(br s,1H)4.80(dt,J=10.5,7.9Hz,1H)6.50(br s,2H)6.59(d,J=3.5Hz,1H)7.07(br s,2H)7.12(dd,J=8.2,1.6Hz,1H)7.29(d,J=3.6Hz,1H)7.34(s,1H)7.58(d,J=8.1Hz,1H)8.07(s,1H)8.31(s,1H).
試薬。
PRMT5−MEP50酵素は、Charles River(Argenta)から購入した。酵素複合体は、2種のバキュロウイルスを同時に感染させた昆虫細胞(Sf9)で産生した。1つのウイルスは、N末端にFlagタグを有する完全長ヒトPRMT5を発現し、第2のウイルスは、N末端にHis6−TEV切断を有する完全長MEP50を発現する。3×FLAGペプチドで溶出される抗Flag(M2)ビーズ、続いて0.5Mのイミダゾールで溶出されるHis−Selectを用いてタンパク質をアフィニティー精製した。続いて、溶出したタンパク質を、20%グリセロールおよび3mMジチオトレイトール(DTT)を含有するトリス緩衝化生理塩水(TBS)(pH8.0)に対して透析した。
PRMT5は、補基質S−アデノシル−L−メチオニン(AdoMet、SAM)を用いてタンパク質内のアルギニン残基のグアニジン基上の末端窒素原子の連続的メチル化を触媒して、モノメチル(MMA)、対称性ジメチルアルギニン(sDMA)およびS−アデノシル−L−ホモシステイン(AdoHcy、SAH)を生成する。ハイスループット質量分析(Sciex 4000シリーズQTrap(登録商標)triple−quad MS/MSに接続したAgilent Rapidfire 300 System)を用いて、生成物のSAH生成を追跡することにより酵素活性を決定した。反応緩衝液は、20mMトリス−HCl、pH8.5、50mM NaCl、5mM MgCl2および1mM DTTであった。1%ギ酸(最終濃度)を用いて反応活性を停止させた。
Y=Bottom+(Top−Bottom)/(1+10^((log IC50−X)*h))
式中、IC50は、50%阻害時の阻害濃度(Xと同じ単位)であり、hは、ヒル勾配である。Yは、阻害率であり、Xは、化合物濃度の対数である。BottomおよびTopは、Yと同じ単位のプラトーである。
化合物2の細胞感受性プロファイルを広範な肺癌細胞株パネルのSCLCサブ分類で評価した。驚くべきことに、最も感受性の高い細胞株のいくつかは、PIK3Cα遺伝子で異なる機能獲得変異を有し、それらは、表2で言及されている。標準治療(シスプラチン)または最新のPARP阻害剤生成のような標的薬剤に対する腫瘍応答としてのPI3Kα経路(機能獲得変異または経路刺激)の活性化は、治療後のSCLC患者の低い全生存と関連し得る耐性の過程での重要な役割を示唆する。
癌特異的スプライシングイベントは、悪性腫瘍を開始し、疾患進行にも寄与することが知られている。これまでのところ、スプライシングに関与する2つのタンパク質、U2AF1およびRBM10がNSCLCにおいて誤調節的であると記載されている。
G1サイクリンファミリーの増幅および/または発現の増加は、NSCLCを含む複数の癌で報告されている。PRMT5と、サイクリンD1、CDK4およびCDK6を含む細胞周期のモジュレーターの発現との間に相関が観察されており、PRMT5がG1期に調節効果を有し得ることを示唆している。化合物2処理した肺細胞株パネルの分析は、サイクリンD1/CDK4/CDK6増幅とPRMT5i感受性との間の有意な関連を明らかにし、サイクリン経路異常が患者選択のためのマーカーとして使用できることを示した。表4は、そうしたサイクリンD1/CDK4/CDK6増幅を有するNSCLC細胞株が化合物2での治療に対して感受性を有することを示す。
β−カテニンおよびAPCを含む重要なWntシグナル伝達遺伝子に変異を有する細胞株は、表5に示すように、PRMT5i治療に対して感受性を示す。
Claims (7)
- タンパク質アルギニンN−メチルトランスフェラーゼ5(PRMT5)阻害剤による治療に応答する可能性がある患者を同定する方法であって、スプライソソームの改変の存在について前記患者からの生物学的試料を評価することを含み、任意の前記改変の存在は、任意の前記改変が存在しない場合よりも、前記患者が前記PRMT5阻害剤による治療に応答する可能性が高いことを示す、方法。
- 前記スプライソソームの改変は、U2AF1、RBM10およびKIAA1429からなる群から選択される遺伝子における変異を含む、請求項1に記載の方法。
- 前記遺伝子は、U2AF1であり、および前記変異は、S34Fである、請求項2に記載の方法。
- 前記遺伝子は、RBM10であり、および前記変異は、I696fs、I348N、G840fsからなる群から選択される、請求項2に記載の方法。
- 前記遺伝子は、KIAA1429であり、および前記変異は、L837V、F1260L、D251if、T1333M、V1548L、G397AおよびQ962Eからなる群から選択される、請求項2に記載の方法。
- 前記生物学的試料は、スプライソソームの改変を含み、および前記患者は、NSCLCを有する、請求項1〜5のいずれか一項に記載の方法。
- 前記PRMT5阻害剤は、化合物2または化合物80である、請求項1〜6のいずれか一項に記載の方法。
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JOP20190199B1 (ar) | 2023-09-17 |
EP3585904A1 (en) | 2020-01-01 |
KR20190122677A (ko) | 2019-10-30 |
TN2019000212A1 (en) | 2021-01-07 |
JOP20190199A1 (ar) | 2019-08-27 |
CL2019002438A1 (es) | 2019-11-29 |
EA201992026A1 (ru) | 2020-01-24 |
EP3585904C0 (en) | 2023-11-29 |
MA47594A (fr) | 2020-01-01 |
PH12019501942A1 (en) | 2020-06-29 |
US20200010881A1 (en) | 2020-01-09 |
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