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基于定制长短期记忆变分自动编码器深度学习架构的人类免疫缺陷病毒计算药物发现。

Computational drug discovery on human immunodeficiency virus with a customized long short-term memory variational autoencoder deep-learning architecture.

机构信息

Institute of Theoretical Physics and Astrophysics, Quantum Information Technology, University of Gdańsk, Gdańsk, Poland.

Faculty of Technology, Software Engineering, Fırat University, Elazig, Turkey.

出版信息

CPT Pharmacometrics Syst Pharmacol. 2024 Feb;13(2):308-316. doi: 10.1002/psp4.13085. Epub 2023 Dec 5.

Abstract

Despite attempts to control the spread of human immunodeficiency virus (HIV) through the use of anti-HIV medications, the absence of an effective vaccine continues to present a significant obstacle. In addition, the development of drug resistance by HIV underscores the necessity for computational drug discovery methods to identify novel therapies. This investigation specifically focused on employing a long short-term memory (LSTM) variational autoencoder deep-learning architecture for computational drug discovery in relation to HIV. Our data set comprised simplified molecular input line entry system (SMILES)-encoded compounds, which were used to train the LSTM autoencoder. Remarkably, our model achieved a training accuracy of 91%, with a data set containing 1377 compounds. Leveraging the generative model derived from the training phase, we generated potential new drugs for combating HIV and assessed their interaction with the virus using a previously developed artificial intelligence model. Lastly, we verified the drug likeliness of our computationally generated compounds in accordance with Lipinski's rule of five. Overall, our study presents a promising approach to computational drug discovery in the ongoing battle against HIV.

摘要

尽管人们试图通过使用抗 HIV 药物来控制人类免疫缺陷病毒 (HIV) 的传播,但缺乏有效的疫苗仍然是一个重大障碍。此外,HIV 产生耐药性突出表明需要计算药物发现方法来确定新的治疗方法。本研究专门针对使用长短期记忆 (LSTM) 变分自动编码器深度学习架构进行与 HIV 相关的计算药物发现。我们的数据集由简化分子输入行输入系统 (SMILES) 编码的化合物组成,用于训练 LSTM 自动编码器。值得注意的是,我们的模型在包含 1377 种化合物的数据集上实现了 91%的训练准确性。利用训练阶段得出的生成模型,我们生成了潜在的新的抗 HIV 药物,并使用之前开发的人工智能模型评估了它们与病毒的相互作用。最后,我们根据 Lipinski 的五规则验证了我们计算生成的化合物的药物相似性。总的来说,我们的研究为与 HIV 持续斗争中的计算药物发现提供了一种很有前途的方法。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/46a3/10864928/54dbe8b9fa4e/PSP4-13-308-g002.jpg

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