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NfκBin:一种基于机器学习的筛选肿瘤坏死因子-α诱导的核因子-κB抑制剂的方法。

NfκBin: a machine learning based method for screening TNF-α induced NF-κB inhibitors.

作者信息

Jain Shipra, Tomer Ritu, Patiyal Sumeet, Raghava Gajendra P S

机构信息

Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India.

Cancer and Data Science Laboratory (CDSL), National Cancer Institute, National Institutes of Health, Bethesda, MD, United States.

出版信息

Front Bioinform. 2025 Jul 17;5:1573744. doi: 10.3389/fbinf.2025.1573744. eCollection 2025.


DOI:10.3389/fbinf.2025.1573744
PMID:40746657
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12310657/
Abstract

INTRODUCTION: Nuclear Factor kappa B (NF-κB) is a transcription factor whose upregulation is associated in chronic inflammatory diseases, including rheumatoid arthritis, inflammatory bowel disease, and asthma. In order to develop therapeutic strategies targeting NF-κB-related diseases, we developed a computational approach to predict drugs capable of inhibiting TNF-α induced NF-κB signaling pathways. METHOD: We utilized a dataset comprising 1,149 inhibitors and 1,332 non-inhibitors retrieved from PubChem. Chemical descriptors were computed using the PaDEL software, and relevant features were selected using advanced feature selection techniques. RESULT: Initially, machine learning models were constructed using 2D descriptors, 3D descriptors, and molecular fingerprints, achieving maximum AUC values of 0.66, 0.56, and 0.66, respectively. To improve feature selection, we applied univariate analysis and SVC-L1 regularization to identify features that can effectively differentiate inhibitors from non-inhibitors. Using these selected features, we developed machine learning models, our support vector classifier achieved a highest AUC of 0.75 on the validation dataset. DISCUSSION: Finally, this best-performing model was employed to screen FDA-approved drugs for potential NF-κB inhibitors. Notably, most of the predicted inhibitors corresponded to drugs previously identified as inhibitors in experimental studies, underscoring the model's predictive reliability. Our best-performing models have been integrated into a standalone software and web server, NfκBin. (https://webs.iiitd.edu.in/raghava/nfkbin/).

摘要

引言:核因子κB(NF-κB)是一种转录因子,其上调与包括类风湿性关节炎、炎症性肠病和哮喘在内的慢性炎症性疾病相关。为了开发针对NF-κB相关疾病的治疗策略,我们开发了一种计算方法来预测能够抑制肿瘤坏死因子-α(TNF-α)诱导的NF-κB信号通路的药物。 方法:我们使用了一个包含从PubChem检索到的1149种抑制剂和1332种非抑制剂的数据集。使用PaDEL软件计算化学描述符,并使用先进的特征选择技术选择相关特征。 结果:最初,使用二维描述符、三维描述符和分子指纹构建机器学习模型,分别获得的最大曲线下面积(AUC)值为0.66、0.56和0.66。为了改进特征选择,我们应用单变量分析和支持向量分类器L1正则化来识别能够有效区分抑制剂和非抑制剂的特征。使用这些选定的特征,我们开发了机器学习模型,我们的支持向量分类器在验证数据集上获得的最高AUC为0.75。 讨论:最后,使用这个性能最佳的模型筛选美国食品药品监督管理局(FDA)批准的药物以寻找潜在的NF-κB抑制剂。值得注意的是,大多数预测的抑制剂对应于先前在实验研究中被确定为抑制剂的药物,这突出了该模型的预测可靠性。我们性能最佳的模型已被集成到一个独立的软件和网络服务器NfκBin(https://webs.iiitd.edu.in/raghava/nfkbin/)中。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e355/12310657/b473c84d911c/fbinf-05-1573744-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e355/12310657/4604753dc9f5/fbinf-05-1573744-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e355/12310657/c31010883317/fbinf-05-1573744-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e355/12310657/b473c84d911c/fbinf-05-1573744-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e355/12310657/4604753dc9f5/fbinf-05-1573744-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e355/12310657/c31010883317/fbinf-05-1573744-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e355/12310657/b473c84d911c/fbinf-05-1573744-g003.jpg

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本文引用的文献

[1]
Dual tobramycin and docosahexaenoic acid loaded nanoemulsions combating Pseudomonas aeruginosa-induced pulmonary infection.

Colloids Surf B Biointerfaces. 2024-10

[2]
Effectiveness of molecular fingerprints for exploring the chemical space of natural products.

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[3]
Synthesis and evaluation of the effects of solid lipid nanoparticles of ivermectin and ivermectin on cuprizone-induced demyelination via targeting the TRPA1/NF-kB/GFAP signaling pathway.

Iran J Basic Med Sci. 2023

[4]
Identification and mechanistic exploration of structural and conformational dynamics of NF-kB inhibitors: rationale insights from and studies.

J Biomol Struct Dyn. 2024

[5]
Anti-inflammatory actions of Pentosan polysulfate sodium in a mouse model of influenza virus A/PR8/34-induced pulmonary inflammation.

Front Immunol. 2023

[6]
Prediction of dual NF-κB/IκB inhibitors using an integrative approaches.

J Biomol Struct Dyn. 2023

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Drug Discov Today. 2022-11

[8]
Role of curcumin in the treatment of acute kidney injury: research challenges and opportunities.

Phytomedicine. 2022-9

[9]
ToxinPred2: an improved method for predicting toxicity of proteins.

Brief Bioinform. 2022-9-20

[10]
In Silico and In Vitro Screening of 50 Curcumin Compounds as EGFR and NF-κB Inhibitors.

Int J Mol Sci. 2022-4-2

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