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Zheng L, Shi F, Peng C, Xu M, Fan F, Li Y, Zhang L, Du J, Wang Z, Lin Z, Sun Y, Deng C, Duan X, Wei L, Zhao C, Fang L, Zhang P, Ma S, Lai L, Yang M. Application scenario-oriented molecule generation platform developed for drug discovery. Methods 2024; 222:112-121. [PMID: 38215898 DOI: 10.1016/j.ymeth.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/22/2023] [Accepted: 12/23/2023] [Indexed: 01/14/2024] Open
Abstract
Design of molecules for candidate compound selection is one of the central challenges in drug discovery due to the complexity of chemical space and requirement of multi-parameter optimization. Here we present an application scenario-oriented platform (ID4Idea) for molecule generation in different scenarios of drug discovery. This platform utilizes both library or rule based and generative based algorithms (VAE, RNN, GAN, etc.), in combination with various AI learning types (pre-training, transfer learning, reinforcement learning, active learning, etc.) and input representations (1D SMILES, 2D graph, 3D shape, binding site, pharmacophore, etc.), to enable customized solutions for a given molecular design scenario. Besides the usual generation followed screening protocol, goal-directed molecule generation can also be conducted towards predefined goals, enhancing the efficiency of hit identification, lead finding, and lead optimization. We demonstrate the effectiveness of ID4Idea platform through case studies, showcasing customized solutions for different design tasks using various input information, such as binding pockets, pharmacophores, and compound representations. In addition, remaining challenges are discussed to unlock the full potential of AI models in drug discovery and pave the way for the development of novel therapeutics.
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Affiliation(s)
- Lianjun Zheng
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Fangjun Shi
- XtalPi Innovation Center, XtalPi Inc., Beijing, China
| | - Chunwang Peng
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Min Xu
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Fangda Fan
- XtalPi Innovation Center, XtalPi Inc., Beijing, China
| | - Yuanpeng Li
- XtalPi Innovation Center, XtalPi Inc., Beijing, China
| | - Lin Zhang
- XtalPi Innovation Center, XtalPi Inc., Beijing, China
| | - Jiewen Du
- XtalPi Innovation Center, XtalPi Inc., Beijing, China
| | - Zonghu Wang
- XtalPi Innovation Center, XtalPi Inc., Beijing, China
| | - Zhixiong Lin
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Yina Sun
- XtalPi Innovation Center, XtalPi Inc., Beijing, China
| | - Chenglong Deng
- Jingtai Zhiyao Technology (Shanghai) Co., Ltd. (XtalPi), No. 207 Huanqiao Road, Pudong New Area, Shanghai 201315, China
| | - Xinli Duan
- XtalPi Innovation Center, XtalPi Inc., Beijing, China
| | - Lin Wei
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | | | - Lei Fang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Peiyu Zhang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Songling Ma
- XtalPi Innovation Center, XtalPi Inc., Beijing, China.
| | - Lipeng Lai
- XtalPi Innovation Center, XtalPi Inc., Beijing, China.
| | - Mingjun Yang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China.
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