A systematic exploration of boceprevir-based main protease inhibitors as SARS-CoV-2 antivirals.
A systematic exploration of boceprevir-based main protease inhibitors as SARS-CoV-2 antivirals.
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DOI：
10.1016/j.ejmech.2022.114596
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发表时间：
2022-10-05
影响因子：
6.7
通讯作者：
Liu, Wenshe Ray
中科院分区：
文献类型：
--
作者：
Alugubelli, Yugendar R.;Geng, Zhi Zachary;Yang, Kai S.;Shaabani, Namir;Khatua, Kaustav;Ma, Xinyu R.;Vatansever, Erol C.;Cho, Chia-Chuan;Ma, Yuying;Xiao, Jing;Blankenship, Lauren R.;Yu, Ge;Sankaran, Banumathi;Li, Pingwei;Allen, Robert;Ji, Henry;Xu, Shiqing;Liu, Wenshe Ray
Boceprevir是一种HCV NSP 3抑制剂，被探索作为治疗COVID-19的重新用途药物。它抑制SARS-CoV-2主要蛋白酶（MPro），含有α-酮酰胺弹头、P1 β-环丁基丙氨酰部分、P2二甲基环丙基脯氨酸、P3叔丁基甘氨酸和P4 N-末端叔丁基脲。通过在所有四个位置引入修饰，我们合成了包括PF-07321332在内的20种基于boceprevir的MPro抑制剂，并在试管（体外）和293 T细胞（细胞内）中表征了其MPro抑制效力。对10种抑制剂结合MPro的晶体结构和4种抑制剂的细胞毒性和抗病毒活性进行了表征。用β-（S-2-氧代吡咯烷-3-基）-丙氨酰（Opal）残基替换P1位点，并用醛替换弹头，导致高体外效力。博赛泼维中P2、P3和P4 N-末端帽位置处的原始部分比其他测试的化学部分更好地获得高体外效力。在晶体结构中，所有抑制剂与MPro活性位点半胱氨酸形成共价加合物。P1蛋白石残基，P2二甲基环丙基脯氨酸和P4 N-末端叔丁基脲与MPro产生强疏水相互作用，解释了含有这些部分的抑制剂的高体外效力。用含有P4 N-末端异戊酰胺的抑制剂进行了独特的观察。在其MPro复合物结构中，P4 N-末端异戊酰胺深深地隐藏在MPro的小口袋中，该小口袋最初识别底物中的P4丙氨酸侧链。尽管所有抑制剂都显示出高的体外效力，但它们在抑制人293 T细胞中异位表达的MPro的细胞效力方面有显著差异。通常，具有P4 N-末端脲或酰胺的抑制剂具有低的细胞效力。当P4 N-末端帽变为氨基甲酸酯时，这种趋势逆转。P3 O-叔丁基-苏氨酸的安装改善了纤维素效力。三种含有P4 N-末端氨基甲酸酯的分子进行了293 T细胞的细胞毒性试验和三种SARS-CoV-2变体的抗病毒效力试验。它们都具有相对较低的细胞毒性和较高的抗病毒效力，EC 50值约为1 μM。具有腈弹头和P4 N-末端酰胺的对照化合物具有不可检测的抗病毒效力。基于所有的观察，我们得出结论，在boceprevir衍生物中的P4 N-末端氨基甲酸酯是针对SARS-CoV-2的高抗病毒效力的关键。
Boceprevir is an HCV NSP3 inhibitor that was explored as a repurposed drug for COVID-19. It inhibits the SARS-CoV-2 main protease (MPro) and contains an α-ketoamide warhead, a P1 β-cyclobutylalanyl moiety, a P2 dimethylcyclopropylproline, a P3 tert-butylglycine, and a P4 N-terminal tert-butylcarbamide. By introducing modifications at all four positions, we synthesized 20 boceprevir-based MPro inhibitors including PF-07321332 and characterized their MPro inhibition potency in test tubes (in vitro) and 293T cells (in cellulo). Crystal structures of MPro bound with 10 inhibitors and cytotoxicity and antiviral potency of 4 inhibitors were characterized as well. Replacing the P1 site with a β-(S-2-oxopyrrolidin-3-yl)-alanyl (Opal) residue and the warhead with an aldehyde leads to high in vitro potency. The original moieties at P2, P3 and the P4 N-terminal cap positions in boceprevir are better than other tested chemical moieties for high in vitro potency. In crystal structures, all inhibitors form a covalent adduct with the MPro active site cysteine. The P1 Opal residue, P2 dimethylcyclopropylproline and P4 N-terminal tert-butylcarbamide make strong hydrophobic interactions with MPro, explaining high in vitro potency of inhibitors that contain these moieties. A unique observation was made with an inhibitor that contains a P4 N-terminal isovaleramide. In its MPro complex structure, the P4 N-terminal isovaleramide is tucked deep in a small pocket of MPro that originally recognizes a P4 alanine side chain in a substrate. Although all inhibitors show high in vitro potency, they have drastically different in cellulo potency to inhibit ectopically expressed MPro in human 293T cells. In general, inhibitors with a P4 N-terminal carbamide or amide have low in cellulo potency. This trend is reversed when the P4 N-terminal cap is changed to a carbamate. The installation of a P3 O-tert-butyl-threonine improves in cellulo potency. Three molecules that contain a P4 N-terminal carbamate were advanced to cytotoxicity tests on 293T cells and antiviral potency tests on three SARS-CoV-2 variants. They all have relatively low cytotoxicity and high antiviral potency with EC50 values around 1 μM. A control compound with a nitrile warhead and a P4 N-terminal amide has undetectable antiviral potency. Based on all observations, we conclude that a P4 N-terminal carbamate in a boceprevir derivative is key for high antiviral potency against SARS-CoV-2.
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影响因子：
16.8
作者：
Jin, Zhenming;Zhao, Yao;Rao, Zihe
通讯作者：
Rao, Zihe
影响因子：
16.6
作者：
Douangamath A;Fearon D;Gehrtz P;Krojer T;Lukacik P;Owen CD;Resnick E;Strain-Damerell C;Aimon A;Ábrányi-Balogh P;Brandão-Neto J;Carbery A;Davison G;Dias A;Downes TD;Dunnett L;Fairhead M;Firth JD;Jones SP;Keeley A;Keserü GM;Klein HF;Martin MP;Noble MEM;O'Brien P;Powell A;Reddi RN;Skyner R;Snee M;Waring MJ;Wild C;London N;von Delft F;Walsh MA
通讯作者：
Walsh MA
影响因子：
56.9
作者：
Dai, Wenhao;Zhang, Bing;Liu, Hong
通讯作者：
Liu, Hong
影响因子：
64.8
作者：
Gordon, David E.;Jang, Gwendolyn M.;Krogan, Nevan J.
通讯作者：
Krogan, Nevan J.
DOI：
10.1126/science.abf7945
发表时间：
2021-05-07
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Günther S;Reinke PYA;Fernández-García Y;Lieske J;Lane TJ;Ginn HM;Koua FHM;Ehrt C;Ewert W;Oberthuer D;Yefanov O;Meier S;Lorenzen K;Krichel B;Kopicki JD;Gelisio L;Brehm W;Dunkel I;Seychell B;Gieseler H;Norton-Baker B;Escudero-Pérez B;Domaracky M;Saouane S;Tolstikova A;White TA;Hänle A;Groessler M;Fleckenstein H;Trost F;Galchenkova M;Gevorkov Y;Li C;Awel S;Peck A;Barthelmess M;Schlünzen F;Lourdu Xavier P;Werner N;Andaleeb H;Ullah N;Falke S;Srinivasan V;França BA;Schwinzer M;Brognaro H;Rogers C;Melo D;Zaitseva-Kinneberg JI;Knoska J;Peña-Murillo GE;Mashhour AR;Hennicke V;Fischer P;Hakanpää J;Meyer J;Gribbon P;Ellinger B;Kuzikov M;Wolf M;Beccari AR;Bourenkov G;von Stetten D;Pompidor G;Bento I;Panneerselvam S;Karpics I;Schneider TR;Garcia-Alai MM;Niebling S;Günther C;Schmidt C;Schubert R;Han H;Boger J;Monteiro DCF;Zhang L;Sun X;Pletzer-Zelgert J;Wollenhaupt J;Feiler CG;Weiss MS;Schulz EC;Mehrabi P;Karničar K;Usenik A;Loboda J;Tidow H;Chari A;Hilgenfeld R;Uetrecht C;Cox R;Zaliani A;Beck T;Rarey M;Günther S;Turk D;Hinrichs W;Chapman HN;Pearson AR;Betzel C;Meents A
通讯作者：
Meents A