Jurnal Pijar MIPA
Vol. 21 No. 2 (2026): in Progress

Computational Evaluation of Vitamin D3 Binding to KRAS and TGF-β1 in Colorectal Cancer–Associated Signalling Pathways

Jauharotus Shobahah (Department of Biotechnology, Faculty of Food Security, Universitas Negeri Surabaya, Surabaya, Indonesia)
Wahyuningsih Sri Puji Astuti (Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia)
Mochammad Aqilah Herdiansyah (Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia)
M. Ainun Najib Aly (Faculty of Pharmacy, Universitas Airlangga, Surabaya, Indonesia)



Article Info

Publish Date
09 Apr 2026

Abstract

Vitamin D3 has been widely investigated for its anticancer properties, yet the structural basis of its interaction with key oncogenic signaling proteins remains incompletely understood. This study aimed to evaluate the molecular interactions between vitamin D3 and KRAS and TGF-β1 using molecular docking and molecular dynamics simulations. Molecular docking analysis was performed using AutoDock Vina, followed by molecular dynamics simulation using CABS-flex to evaluate structural stability using root mean square deviation (RMSD), root mean square fluctuation (RMSF), and radius of gyration (Rg). Comparative benchmarking was performed against the reference inhibitors Sotorasib (KRAS) and Galunisertib (TGF-β pathway). Docking analysis revealed that vitamin D3 binds to KRAS (PDB ID: 4OBE) with a binding affinity of –7.8 kcal/mol, compared to –8.6 kcal/mol for Sotorasib. The interaction was localized within the nucleotide-binding pocket adjacent to the Switch I and Switch II regions, which are critical for conformational regulation. For TGF-β1 (PDB ID: 3KFD), vitamin D3 demonstrated a binding affinity of –8.2 kcal/mol, slightly exceeding that of Galunisertib (–8.1 kcal/mol), with interaction occurring at the receptor-binding interface. Molecular dynamics simulation showed stable complex formation, with RMSD values of 2.79 Å for the KRAS complex and 1.535 Å for the TGF-β1 complex, indicating acceptable structural stability. Residue fluctuation analysis further supported moderate flexibility without global destabilization. These findings suggest that vitamin D3 may function as a multi-target signaling modulator interacting with both intracellular and extracellular regulators of colorectal cancer pathways, providing a structural basis for further experimental investigation.

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Journal Info

Abbrev

JPM

Publisher

Subject

Biochemistry, Genetics & Molecular Biology Chemistry Mathematics Physics

Description

Jurnal Pijar MIPA (e-ISSN: 2460-1500 & p-ISSN: 1907-1744) is an open-access scientific periodical journal published by the Department of Mathematics and Science Education, Faculty of Teacher Training and Education, University of Mataram. Jurnal Pijar MIPA publishes original articles on current ...