Quantitative Structure-Activity Relationship (
QSAR) modeling is a foundational computational methodology in early-stage drug discovery, heavily relied upon for predicting compound toxicity, bioavailability, and therapeutic potential. However, classical methods often struggle to effectively map the highly complex, non-linear, and high-dimensional interactions inherent in molecular data, leading to reduced predictive accuracy and costly late-stage clinical failures. In this paper, we present a Quantum Multiple Kernel Learning (
QMKL) framework, dubbed Next-Gen
Q2SAR, that leverages Quantum Support Vector Machines (
QSVMs) to overcome these classical limitations. By encoding molecular descriptors into exponentially large quantum Hilbert spaces, our approach substantially enhances the expressiveness of non-linear modeling. Benchmarking our quantum-enhanced framework on a dataset targeting the
DYRK1A kinase (a critical target for Alzheimer's disease), the
QMKL-
SVM achieves an impressive Area Under the Curve (
AUC) score of
0.8750, significantly outperforming classical state-of-the-art Gradient Boosting models (
AUC=0.8037). Furthermore, we establish a theoretical and empirical pathway toward resolving classical data bottlenecks through projected quantum kernels (
PQK) and measurement accelerators. As quantum computing architecture matures, this framework paves the way for autonomous cognitive architectures and self-improving drug discovery pipelines, promising to unlock deeper insights across vast chemical spaces and to accelerate the development of life-saving therapeutics.