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量子计算增强算法揭示潜在的KRAS抑制剂。

Quantum-computing-enhanced algorithm unveils potential KRAS inhibitors.

作者信息

Ghazi Vakili Mohammad, Gorgulla Christoph, Snider Jamie, Nigam AkshatKumar, Bezrukov Dmitry, Varoli Daniel, Aliper Alex, Polykovsky Daniil, Padmanabha Das Krishna M, Cox Iii Huel, Lyakisheva Anna, Hosseini Mansob Ardalan, Yao Zhong, Bitar Lela, Tahoulas Danielle, Čerina Dora, Radchenko Eugene, Ding Xiao, Liu Jinxin, Meng Fanye, Ren Feng, Cao Yudong, Stagljar Igor, Aspuru-Guzik Alán, Zhavoronkov Alex

机构信息

Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.

Department of Chemistry, University of Toronto, Toronto, Ontario, Canada.

出版信息

Nat Biotechnol. 2025 Jan 22. doi: 10.1038/s41587-024-02526-3.

DOI:10.1038/s41587-024-02526-3
PMID:39843581
Abstract

We introduce a quantum-classical generative model for small-molecule design, specifically targeting KRAS inhibitors for cancer therapy. We apply the method to design, select and synthesize 15 proposed molecules that could notably engage with KRAS for cancer therapy, with two holding promise for future development as inhibitors. This work showcases the potential of quantum computing to generate experimentally validated hits that compare favorably against classical models.

摘要

我们引入了一种用于小分子设计的量子-经典生成模型,特别针对用于癌症治疗的KRAS抑制剂。我们应用该方法设计、筛选并合成了15种拟议中的分子,这些分子有望与KRAS显著结合用于癌症治疗,其中有两种作为抑制剂具有未来开发的潜力。这项工作展示了量子计算在生成经实验验证的、与经典模型相比具有优势的命中分子方面的潜力。

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Quantum-computing-enhanced algorithm unveils potential KRAS inhibitors.量子计算增强算法揭示潜在的KRAS抑制剂。
Nat Biotechnol. 2025 Jan 22. doi: 10.1038/s41587-024-02526-3.
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Quantum Cardiovascular Medicine: From Hype to Hope-A Critical Review of Real-World Applications.量子心血管医学:从炒作到希望——对实际应用的批判性综述
J Clin Med. 2025 Aug 26;14(17):6029. doi: 10.3390/jcm14176029.
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ADMET-Guided Docking and GROMACS Molecular Dynamics of Phytochemicals Uncover Mutation-Agnostic Allosteric Stabilisers of the KRAS Switch-I/II Groove.基于ADMET的植物化学物质对接及GROMACS分子动力学研究揭示KRAS开关I/II结构域凹槽的非突变型别别构稳定剂
Pharmaceuticals (Basel). 2025 Jul 25;18(8):1110. doi: 10.3390/ph18081110.
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本文引用的文献

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Artificial design of organic emitters a genetic algorithm enhanced by a deep neural network.有机发光体的人工设计:一种由深度神经网络增强的遗传算法
Chem Sci. 2024 Jan 11;15(7):2618-2639. doi: 10.1039/d3sc05306g. eCollection 2024 Feb 14.
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Recent advances in the self-referencing embedded strings (SELFIES) library.自引用嵌入字符串(SELFIES)库的最新进展。
Digit Discov. 2023 Jul 1;2(4):897-908. doi: 10.1039/d3dd00044c. eCollection 2023 Aug 8.
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AlphaFold accelerates artificial intelligence powered drug discovery: efficient discovery of a novel CDK20 small molecule inhibitor.
用于从头药物设计的生成式深度学习——一场化学空间奥德赛。
J Chem Inf Model. 2025 Jul 28;65(14):7352-7372. doi: 10.1021/acs.jcim.5c00641. Epub 2025 Jul 9.
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Informatics at the Frontier of Cancer Research.癌症研究前沿的信息学
Cancer Res. 2025 Aug 15;85(16):2967-2986. doi: 10.1158/0008-5472.CAN-24-2829.
5
Targeting KRAS in Cancer Therapy: Beyond Inhibitors.癌症治疗中针对KRAS:超越抑制剂
MedComm (2020). 2025 Jun 25;6(7):e70267. doi: 10.1002/mco2.70267. eCollection 2025 Jul.
6
Quantum computing in surgery and urology - taking a quantum leap.外科与泌尿外科中的量子计算——实现巨大飞跃。
Nat Rev Urol. 2025 Jun 16. doi: 10.1038/s41585-025-01058-y.
7
Elucidating Ras protein as a dual therapeutic target for inflammation and cancer: a review.阐明Ras蛋白作为炎症和癌症的双重治疗靶点:综述
Discov Oncol. 2025 Jun 7;16(1):1029. doi: 10.1007/s12672-025-02783-x.
8
Quantum biological convergence: quantum computing accelerates KRAS inhibitor design.量子生物融合:量子计算加速KRAS抑制剂设计。
Signal Transduct Target Ther. 2025 May 14;10(1):152. doi: 10.1038/s41392-025-02239-2.
9
Response and Resistance to RAS Inhibition in Cancer.癌症中对RAS抑制的反应与抗性
Cancer Discov. 2025 Jul 3;15(7):1325-1349. doi: 10.1158/2159-8290.CD-25-0349.
AlphaFold加速人工智能驱动的药物发现:高效发现新型CDK20小分子抑制剂。
Chem Sci. 2023 Jan 10;14(6):1443-1452. doi: 10.1039/d2sc05709c. eCollection 2023 Feb 8.
4
Chemistry42: An AI-Driven Platform for Molecular Design and Optimization.Chemistry42:一个人工智能驱动的分子设计和优化平台。
J Chem Inf Model. 2023 Feb 13;63(3):695-701. doi: 10.1021/acs.jcim.2c01191. Epub 2023 Feb 2.
5
Drugging KRAS: current perspectives and state-of-art review.KRAS 靶向治疗:现状与展望。
J Hematol Oncol. 2022 Oct 25;15(1):152. doi: 10.1186/s13045-022-01375-4.
6
SELFIES and the future of molecular string representations.自拍与分子串表示法的未来。
Patterns (N Y). 2022 Oct 14;3(10):100588. doi: 10.1016/j.patter.2022.100588.
7
Parallel tempered genetic algorithm guided by deep neural networks for inverse molecular design.基于深度神经网络引导的并行回火遗传算法用于逆分子设计
Digit Discov. 2022 May 3;1(4):390-404. doi: 10.1039/d2dd00003b. eCollection 2022 Aug 8.
8
Why 90% of clinical drug development fails and how to improve it?为什么90%的临床药物研发会失败以及如何改进?
Acta Pharm Sin B. 2022 Jul;12(7):3049-3062. doi: 10.1016/j.apsb.2022.02.002. Epub 2022 Feb 11.
9
KRAS(G12D) can be targeted by potent inhibitors via formation of salt bridge.KRAS(G12D)可通过形成盐桥被强效抑制剂靶向。
Cell Discov. 2022 Jan 25;8(1):5. doi: 10.1038/s41421-021-00368-w.
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The path to the clinic: a comprehensive review on direct KRAS inhibitors.通往临床的道路:直接 KRAS 抑制剂的全面综述。
J Exp Clin Cancer Res. 2022 Jan 19;41(1):27. doi: 10.1186/s13046-021-02225-w.