Tracking protein kinase targeting advances: integrating QSAR into machine learning for kinase-targeted drug discovery
Creators: name: Shahin, Rand
name: Jaafreh, Sawsan
name: Azzam, Yusra
Publisher: name: Taylor & Francis
Year: 2025
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Astronomical and Space Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Plant Biology
subject: FOS: Biological sciences
subject: Virology
subject: Computational Biology

description: Protein kinases are vital drug targets, yet designing selective inhibitors is challenging, compounded by resistance and kinome complexity. This review explores Quantitative Structure-Activity Relationship (QSAR) modeling for kinase drug discovery, focusing on integrating traditional QSAR with machine learning (ML)—CNNs, RNNs—and structural data. Methods include structural databases, docking, and deep learning QSAR. Key findings show ML-integrated QSAR significantly improves selective inhibitor design for CDKs, JAKs, PIM kinases. The IDG-DREAM challenge exemplifies ML’s potential for accurate kinase-inhibitor interaction prediction, outperforming traditional methods and enabling inhibitors with enhanced selectivity, efficacy, and resistance mitigation. QSAR combined with advanced computation and experimental data accelerates kinase drug discovery, offering transformative precision medicine potential. This review highlights deep learning-enhanced QSAR’s novelty in automating feature extraction and capturing complex relationships, surpassing traditional QSAR, while emphasizing interpretability and experimental validation for clinical translation. <b><i>Kinase biology and therapeutics</i></b>Kinases regulate cellular functions and cell cycle progression, with their dysregulation linked to diseases like cancer and autoimmune disorders.Understanding kinase structure and binding pockets have facilitated drug discovery efforts, leading to over 80 FDA-approved inhibitors. Kinases regulate cellular functions and cell cycle progression, with their dysregulation linked to diseases like cancer and autoimmune disorders. Understanding kinase structure and binding pockets have facilitated drug discovery efforts, leading to over 80 FDA-approved inhibitors. <b><i>Quantitative structure-activity relationship (QSAR) in drug design</i></b>QSAR modeling provides a framework to predict biological activity based on molecular features.Traditional QSAR methods, including CoMFA, CoMSIA, and 3D-QSAR, have been pivotal in optimizing kinase inhibitors. QSAR modeling provides a framework to predict biological activity based on molecular features. Traditional QSAR methods, including CoMFA, CoMSIA, and 3D-QSAR, have been pivotal in optimizing kinase inhibitors. <b><i>The role of machine learning in QSAR</i></b>Machine learning techniques such as Convolutional Neural Networks (CNNs) and Recurrent Neural Networks (RNNs) have revolutionized QSAR, uncovering complex molecular relationships.Deep QSAR enhances predictive power, facilitating the identification of active kinase inhibitors from vast virtual libraries. Machine learning techniques such as Convolutional Neural Networks (CNNs) and Recurrent Neural Networks (RNNs) have revolutionized QSAR, uncovering complex molecular relationships. Deep QSAR enhances predictive power, facilitating the identification of active kinase inhibitors from vast virtual libraries. <b><i>Case studies and applications</i></b>QSAR has been involved in understanding ligand-target interactions in kinases like CDKs, JAKs, and PIM kinases. QSAR has been involved in understanding ligand-target interactions in kinases like CDKs, JAKs, and PIM kinases. <b><i>Future directions</i></b>Integrating QSAR with machine learning and experimental approaches, alongside collaborative efforts between computational and medicinal chemists, holds great promise for advancing precision medicine and developing next-generation kinase inhibitors. Integrating QSAR with machine learning and experimental approaches, alongside collaborative efforts between computational and medicinal chemists, holds great promise for advancing precision medicine and developing next-generation kinase inhibitors.