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基于生成式人工智能的模型优化以增强分子设计

Generative artificial intelligence based models optimization towards molecule design enhancement.

作者信息

Khater Tarek, Alkhatib Sara Awni, AlShehhi Aamna, Pitsalidis Charalampos, Pappa Anna Maria, Ngo Son Tung, Chan Vincent, Truong Vi Khanh

机构信息

Department of Biomedical Engineering and Biotechnology, Khalifa University, P.O. Box 127788, Abu Dhabi, United Arab Emirates.

Center for Catalysis and Separations (CeCaS), Khalifa University, P.O. Box 127788, Abu Dhabi, United Arab Emirates.

出版信息

J Cheminform. 2025 Aug 4;17(1):116. doi: 10.1186/s13321-025-01059-4.


DOI:10.1186/s13321-025-01059-4
PMID:40759950
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12323263/
Abstract

Generative artificial intelligence (GenAI) models have emerged as a transformative tool for addressing the complex challenges of drug discovery, enabling the design of structurally diverse, chemically valid, and functionally relevant molecules. Despite significant advancements, the rapid expansion of GenAI applications still faces challenges related to prediction accuracy, molecular validity, and optimization for drug-like properties. This review provides a comprehensive analysis of recent techniques and strategies aimed at enhancing the performance of GenAI models in molecular design. We explore key generative architectures, including variational autoencoders, generative adversarial networks, and transformer-based models, highlighting their unique contributions to drug discovery. Additionally, we discuss critical advancements such as reinforcement learning, multi-objective optimization, and the integration of domain-specific chemical knowledge, which collectively enhance molecular validity, novelty, and drug-likeness. Also, the review examines persistent challenges, including data quality limitations, model interpretability, and the need for improved objective functions, while offering insights into future research directions. By mapping the evolving landscape of GenAI-driven molecular design and providing strategic guidance for overcoming existing limitations, this review serves as an essential resource for researchers leveraging GenAI in drug discovery.

摘要

生成式人工智能(GenAI)模型已成为应对药物发现复杂挑战的变革性工具,能够设计出结构多样、化学上合理且功能相关的分子。尽管取得了重大进展,但GenAI应用的快速扩展仍面临与预测准确性、分子有效性以及类药物性质优化相关的挑战。本综述对旨在提高GenAI模型在分子设计中性能的最新技术和策略进行了全面分析。我们探讨了关键的生成架构,包括变分自编码器、生成对抗网络和基于Transformer的模型,突出了它们对药物发现的独特贡献。此外,我们讨论了诸如强化学习、多目标优化以及特定领域化学知识的整合等关键进展,这些进展共同提高了分子的有效性、新颖性和类药物性。此外,本综述还审视了持续存在的挑战,包括数据质量限制、模型可解释性以及对改进目标函数的需求,同时提供了对未来研究方向的见解。通过描绘GenAI驱动的分子设计不断演变的格局并为克服现有局限性提供战略指导,本综述为在药物发现中利用GenAI的研究人员提供了重要资源。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a998/12323263/613f624738f5/13321_2025_1059_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a998/12323263/844fc0ba87c3/13321_2025_1059_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a998/12323263/92d398bcfe0f/13321_2025_1059_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a998/12323263/e76babc0cd0b/13321_2025_1059_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a998/12323263/d56cd5c5cc87/13321_2025_1059_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a998/12323263/6891001cd4de/13321_2025_1059_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a998/12323263/15b07d548a56/13321_2025_1059_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a998/12323263/098faa7549d4/13321_2025_1059_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a998/12323263/613f624738f5/13321_2025_1059_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a998/12323263/844fc0ba87c3/13321_2025_1059_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a998/12323263/92d398bcfe0f/13321_2025_1059_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a998/12323263/e76babc0cd0b/13321_2025_1059_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a998/12323263/d56cd5c5cc87/13321_2025_1059_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a998/12323263/6891001cd4de/13321_2025_1059_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a998/12323263/15b07d548a56/13321_2025_1059_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a998/12323263/098faa7549d4/13321_2025_1059_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a998/12323263/613f624738f5/13321_2025_1059_Fig8_HTML.jpg

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本文引用的文献

[1]
Crystal Structure Prediction Meets Artificial Intelligence.

J Phys Chem Lett. 2025-3-13

[2]
Text-guided small molecule generation via diffusion model.

iScience. 2024-9-19

[3]
AI-Guided Design of MALDI Matrices: Exploring the Electron Transfer Chemical Space for Mass Spectrometric Analysis of Low-Molecular-Weight Compounds.

J Am Soc Mass Spectrom. 2024-12-4

[4]
Geometry-complete diffusion for 3D molecule generation and optimization.

Commun Chem. 2024-7-3

[5]
Disentangled Representation Learning.

IEEE Trans Pattern Anal Mach Intell. 2024-12

[6]
Llamol: a dynamic multi-conditional generative transformer for de novo molecular design.

J Cheminform. 2024-6-21

[7]
Materials discovery with extreme properties reinforcement learning-guided combinatorial chemistry.

Chem Sci. 2024-4-24

[8]
Enhancing molecular design efficiency: Uniting language models and generative networks with genetic algorithms.

Patterns (N Y). 2024-3-14

[9]
RM-GPT: Enhance the comprehensive generative ability of molecular GPT model via LocalRNN and RealFormer.

Artif Intell Med. 2024-4

[10]
A dual diffusion model enables 3D molecule generation and lead optimization based on target pockets.

Nat Commun. 2024-3-26

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