Asian Pacific journal of cancer prevention : APJCP · 2026
α-Chaconine as a Potential Inhibitor of Mutant Phosphatidylinositol 3-Kinase Alpha in Breast Cancer Stem Cells: Insights from Structure Prediction and Molecular Dynamics.
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Saputra Bakti Wahyu, Ujiantari Navista Sri Octa, Rattyananda Badra Sanditya, Alwi Ratna Surya, Setiawati Agustina, Hermawan Adam
Аннотация
INTRODUCTION: Breast cancer stem cells (BCSCs) promote chemoresistance and metastasis by activating aberrant signaling pathways such as phosphatidylinositol 3-kinase/protein kinase B (PI3K/Akt). α-Chaconine (CHA) is a steroidal glycoalkaloid that has demonstrated cytotoxic and antiproliferative activity in various cancer models, possibly through modulation of the PI3K/Akt pathway. However, its direct interaction with PI3Kα and related alterations has not yet been elucidated. This study aimed to assess CHA as a potential BCSC-targeting agent, particularly as a PI3K inhibitor targeting both wild-type and mutant PI3Kα, using an in silico approach.
METHODS: Mutation data were retrieved from cBioPortal and analyzed using MutPred2. SWISS-MODEL was used to generate homology models of the wild-type and mutant PI3Kα structures. Structural validation was performed using PROCHECK and ERRAT. Molecular docking was employed to evaluate the binding affinity of the PI3Kα-CHA complex. Molecular dynamics simulations were conducted to assess the stability of the interaction between CHA and PI3Kα.
RESULTS: Three PIK3CA mutations were identified as pathogenic: E542K, E545K, and H1047R. Molecular docking revealed a strong binding affinity of alpelisib to both wild-type and mutant (E542K, E545K, and H1047R) forms of p110 α. CHA exhibited the lowest binding energy with the H1047R mutant, with a docking score of -9.93 kcal/mol. Molecular dynamics simulations demonstrated stable interactions of alpelisib with wild-type, E542K, and E545K mutants, whereas CHA showed stable interaction only with the H1047R mutant. MM-PBSA calculations confirmed the lowest binding free energies for alpelisib-wild-type p110α and CHA-H1047R complexes, with values of -29.21 kcal/mol and -25.88 kcal/mol, respectively.
CONCLUSION: These findings provide a basis for further in vitro and in vivo studies to evaluate CHA as a selective PI3K inhibitor targeting the H1047R PIK3CA mutation in breast cancer stem cells.
METHODS: Mutation data were retrieved from cBioPortal and analyzed using MutPred2. SWISS-MODEL was used to generate homology models of the wild-type and mutant PI3Kα structures. Structural validation was performed using PROCHECK and ERRAT. Molecular docking was employed to evaluate the binding affinity of the PI3Kα-CHA complex. Molecular dynamics simulations were conducted to assess the stability of the interaction between CHA and PI3Kα.
RESULTS: Three PIK3CA mutations were identified as pathogenic: E542K, E545K, and H1047R. Molecular docking revealed a strong binding affinity of alpelisib to both wild-type and mutant (E542K, E545K, and H1047R) forms of p110 α. CHA exhibited the lowest binding energy with the H1047R mutant, with a docking score of -9.93 kcal/mol. Molecular dynamics simulations demonstrated stable interactions of alpelisib with wild-type, E542K, and E545K mutants, whereas CHA showed stable interaction only with the H1047R mutant. MM-PBSA calculations confirmed the lowest binding free energies for alpelisib-wild-type p110α and CHA-H1047R complexes, with values of -29.21 kcal/mol and -25.88 kcal/mol, respectively.
CONCLUSION: These findings provide a basis for further in vitro and in vivo studies to evaluate CHA as a selective PI3K inhibitor targeting the H1047R PIK3CA mutation in breast cancer stem cells.