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ADMET-Guided Docking and GROMACS Molecular Dynamics of Ziziphus lotus Phytochemicals Uncover Mutation-Agnostic Allosteric Stabilisers of the KRAS Switch-I/II Groove
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ADMET-Guided Docking and GROMACS Molecular Dynamics of Ziziphus lotus Phytochemicals Uncover Mutation-Agnostic Allosteric Stabilisers of the KRAS Switch-I/II Groove
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ADMET-Guided Docking and GROMACS Molecular Dynamics of Ziziphus lotus Phytochemicals Uncover Mutation-Agnostic Allosteric Stabilisers of the KRAS Switch-I/II Groove
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Journal Article
ADMET-Guided Docking and GROMACS Molecular Dynamics of Ziziphus lotus Phytochemicals Uncover Mutation-Agnostic Allosteric Stabilisers of the KRAS Switch-I/II Groove
2025
Overview
Background/Objectives: Oncogenic KRAS drives ~30% of solid tumours, yet the only approved G12C-specific drugs benefit ≈ 13% of KRAS-mutant patients, leaving a major clinical gap. We sought mutation-agnostic natural ligands from Ziziphus lotus, whose stereochemically rich phenolics may overcome this limitation by occupying the SI/II (Switch I/Switch II) groove and locking KRAS in its inactive state. Methods: Phytochemical mining yielded five recurrent phenolics, such as (+)-catechin, hyperin, astragalin, eriodictyol, and the prenylated benzoate amorfrutin A, benchmarked against the covalent inhibitor sotorasib. An in silico cascade combined SI/II docking, multi-parameter ADME/T (Absorption, Distribution, Metabolism, Excretion, and Toxicity) filtering, and 100 ns explicit solvent molecular dynamics simulations. Pharmacokinetic modelling predicted oral absorption, Lipinski compliance, mutagenicity, and acute-toxicity class. Results: Hyperin and astragalin showed the strongest non-covalent affinities (−8.6 kcal mol−1) by forging quadridentate hydrogen-bond networks that bridge the P-loop (Asp30/Glu31) to the α3-loop cleft (Asp119/Ala146). Catechin (−8.5 kcal mol−1) balanced polar anchoring with entropic economy. ADME ranked amorfrutin A the highest for predicted oral absorption (93%) but highlighted lipophilic solubility limits; glycosylated flavonols breached Lipinski rules yet remained non-mutagenic with class-5 acute-toxicity liability. Molecular dynamics trajectories confirmed that hyperin clamps the SI/II groove, suppressing loop RMSF below 0.20 nm and maintaining backbone RMSD stability, whereas astragalin retains pocket residence with transient re-orientation. Conclusions: Hyperin emerges as a low-toxicity, mutation-agnostic scaffold that rigidifies inactive KRAS. Deglycosylation, nano-encapsulation, or soft fluorination could reconcile permeability with durable target engagement, advancing Z. lotus phenolics toward broad-spectrum KRAS therapeutics.
