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Advances in machine learning for drug molecule structure optimization
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Xing-yu LI1, Tong WU1, Qi-lan XU1, Yi-wen WANG1, He-shui YU1, 2, 3, Shi-xin CEN1, 2, 3, *, Zheng LI1, 2, 3, 4, 5, *
Acta Pharmaceutica Sinica | 2025, 60(10) : 2963 - 2982
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Acta Pharmaceutica Sinica | 2025, 60(10): 2963-2982
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Advances in machine learning for drug molecule structure optimization
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Xing-yu LI1, Tong WU1, Qi-lan XU1, Yi-wen WANG1, He-shui YU1, 2, 3, Shi-xin CEN1, 2, 3, *, Zheng LI1, 2, 3, 4, 5, *
Affiliations
  • 1College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
  • 2State Key Laboratory of Component-based Chinese Medicine, Tianjin 301617, China
  • 3Tianjin Key Laboratory of Intelligent and Green Pharmaceuticals for Traditional Chinese Medicine, Tianjin 301617, China
  • 4Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
  • 5State Key Laboratory of Chinese Medicine Modernization, Tianjin 301617, China
Published: 2025-10-12 doi: 10.16438/j.0513-4870.2025-0412
Outline
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The optimization of drug molecular structure is a crucial step in enhancing the efficacy and safety of drugs. Its primary objective is to rationally adjust the molecular structure to meet the strict requirements for the comprehensive performance of drugs during the research and development process. However, the vast chemical space of drugs and the complex multi-objective optimization tasks pose significant challenges to this process. In recent years, machine learning techniques, represented by deep learning and reinforcement learning, have been widely applied in the optimization of drug molecular structures due to their powerful capabilities in information mining, feature extraction, and nonlinear fitting, providing new ideas and methods for drug design. This paper systematically reviews the latest research progress of machine learning in the optimization of drug molecular structures, deeply analyzes and compares their application advantages and characteristics in different structural optimization scenarios, summarizes the main challenges currently faced in the optimization of drug molecular structures, and provides a technical perspective on the possible research directions for future structural optimization.

drug structure design  /  molecular structure optimization  /  machine learn-ing  /  deep learning  /  reinforcement learning
李星雨, 武潼, 徐启兰, 王奕文, 余河水, 岑世欣, 李正. 机器学习在药物分子结构优化中的研究进展. 药学学报, 2025 , 60 (10) : 2963 -2982 . DOI: 10.16438/j.0513-4870.2025-0412
Xing-yu LI, Tong WU, Qi-lan XU, Yi-wen WANG, He-shui YU, Shi-xin CEN, Zheng LI. Advances in machine learning for drug molecule structure optimization[J]. Acta Pharmaceutica Sinica, 2025 , 60 (10) : 2963 -2982 . DOI: 10.16438/j.0513-4870.2025-0412
Year 2025 volume 60 Issue 10
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146
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Article Info
doi: 10.16438/j.0513-4870.2025-0412
  • Receive Date:2025-04-14
  • Online Date:2026-09-20
  • Published:2025-10-12
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History
  • Received:2025-04-14
  • Revised:2025-06-05
Affiliations
    1College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
    2State Key Laboratory of Component-based Chinese Medicine, Tianjin 301617, China
    3Tianjin Key Laboratory of Intelligent and Green Pharmaceuticals for Traditional Chinese Medicine, Tianjin 301617, China
    4Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
    5State Key Laboratory of Chinese Medicine Modernization, Tianjin 301617, China
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表12种不同金属材料的力学参数
科
Family
属数
Number of
genus
种数
Number of
species
占总种数比例
Percentage of
total species (%)
属
Genus
种数
Number of
species
占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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