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Drugit:非肽类VHL结合剂的众包分子设计

Drugit: crowd-sourcing molecular design of non-peptidic VHL binders.

作者信息

Scott Thomas, Smethurst Christian Alan Paul, Westermaier Yvonne, Mayer Moriz, Greb Peter, Kousek Roland, Biberger Tobias, Bader Gerd, Jandova Zuzana, Schmalhorst Philipp S, Fuchs Julian E, Magarkar Aniket, Hoenke Christoph, Gerstberger Thomas, Combs Steven A, Pape Richard, Phul Saksham, Kothiwale Sandeepkumar, Bergner Andreas, Waterson Alex G, Weinstabl Harald, McConnell Darryl B, Meiler Jens, Böttcher Jark, Moretti Rocco

机构信息

Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA.

Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240, USA.

出版信息

Nat Commun. 2025 Apr 14;16(1):3548. doi: 10.1038/s41467-025-58406-0.

DOI:10.1038/s41467-025-58406-0
PMID:40229246
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11997059/
Abstract

Building on the role of human intuition in small molecule drug design, we explored whether crowdsourcing could recruit citizen scientists to this task while in parallel building awareness for this scientific process. Here, we introduce Drugit ( https://drugit.org ), the small molecule design mode of the online citizen science game Foldit. We demonstrate its utility by identifying distinct binders to the von Hippel Lindau E3 ligase. Several thousand molecules were suggested by players in a series of ten puzzle rounds. The proposed molecules were further evaluated in silico and manually by an expert panel. Selected candidates were synthesized and tested. One of these molecules shows dose-dependent shift perturbations in protein-observed NMR experiments. The co-crystal structure in complex with the E3 ligase reveals that the observed binding mode matches the player's original idea. The completion of one full design cycle is a proof of concept for the Drugit approach and highlights the potential of involving citizen scientists in early drug discovery.

摘要

基于人类直觉在小分子药物设计中的作用,我们探讨了众包是否能够招募公民科学家参与这项任务,同时提升公众对这一科学过程的认知。在此,我们介绍Drugit(https://drugit.org),即在线公民科学游戏Foldit的小分子设计模式。我们通过识别与冯·希佩尔-林道E3连接酶不同的结合物来展示其效用。在一系列十轮解谜游戏中,玩家提出了数千种分子。提议的分子通过计算机模拟进一步评估,并由专家小组进行人工评估。选定的候选分子被合成并进行测试。其中一种分子在蛋白质观察核磁共振实验中显示出剂量依赖性的位移扰动。与E3连接酶形成的共晶体结构表明,观察到的结合模式与玩家最初的想法相符。完成一个完整的设计周期证明了Drugit方法的可行性,并突出了让公民科学家参与早期药物发现的潜力。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3dbb/11997059/6c9a9839d4db/41467_2025_58406_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3dbb/11997059/dfdb4cb4846d/41467_2025_58406_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3dbb/11997059/32ca0fef1c8e/41467_2025_58406_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3dbb/11997059/27572e27717a/41467_2025_58406_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3dbb/11997059/6c9a9839d4db/41467_2025_58406_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3dbb/11997059/dfdb4cb4846d/41467_2025_58406_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3dbb/11997059/32ca0fef1c8e/41467_2025_58406_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3dbb/11997059/27572e27717a/41467_2025_58406_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3dbb/11997059/6c9a9839d4db/41467_2025_58406_Fig4_HTML.jpg

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