Molecular interaction of quercetin and its derivatives against nucleolin in breast cancer: in-silico and in-vitro study

Abstract

Nucleolin, a multifaceted RNA binding domain protein is overexpressed in various cancers leading to dysfunction of several cellular signaling pathways. Quercetin, a distinctive bioactive molecule, along with its derivatives have shown exclusive physio-chemical properties which makes them appealing choices for drug development, yet their role in targeted cancer therapy is limited. Here, the RBD domain structure of Nucleolin was modeled and stabilized by MD simulations for a period of 1000 ns. Molecular docking was performed to determine the binding capability of ligands with the target. To determine the stability of the ligand inside the binding pocket of the protein, MD simulation was performed for a period of 250 ns each for Quercetin-4'-o'-Glucoside, Quercetin_9 and Quercetin complexes. Further, in-vitro studies including cytotoxicity and RT-PCR assays were performed to validate quercetin against Nucleolin. Molecular docking and MD Simulation studies suggested a potential mechanism of interaction of Quercetin-4'-o'-Glucoside, Querectin_9 and Quercetin with Nucleolin with the binding free energy of −63.653, −58.86 and −46.9 kcal/mol, respectively. Moreover, Lys 348 and Glu379 were identified as important amino acids in ligand interaction located at the RRM2 motif of Nucleolin. In-vitro studies showed significant downregulation in Nucleolin expression by 15.18 and 2.51-fold at 48h and 72h respectively in MCF-7 cells with Quercetin (IC₅₀ = 160 µM). Our findings suggested the potential role of specific RRM motifs in interaction with natural compounds targeting Nucleolin. This could be an effective strategy in the identification of potential molecules in targeting Nucleolin which can be further explored for developing targeted therapies for breast cancer.

Communicated by Ramaswamy H. Sarma

Keywords:

• Nucleolin
• cancer
• targeted therapy
• nutraceuticals
• molecular docking
• MM-GBSA
• MD simulation

Acknowledgments

S.S., M.C., R.N., M.P.G., S.S. and S.B. acknowledge the facilities provided by Amity University, Noida, UP, India. supported by Amity Institute of Biotechnology in the form of resources and space required for the research. S.S. and S.B. acknowledges Dr. B. C. Das, Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Noida, UP, India for providing necessary instrumentation facilities for experimentation. S.S. and S.S. acknowledge Schrödinger, Bengaluru, India for assisting with MD simulation and analysis performed in the paper. S.B. and R.N is thankful to Ministry of Science and Technology, Dept. of Science and Technology, New Delhi (DST/INT/AUS/P-80/2020(G)). M.C. is thankful to Council of Science and Technology, U.P (CST/Biotech/RS/-1986/D-1226) for funding. T.K. is thankful to the University of New South Wales for support and Scientia award.

Author contributions

SS: designing, writing-original-draft, writing-reviewing and editing manuscript, performing in-silico study and in-vitro experimentation. MC: computational analysis and editing manuscript. RN and TK: critically reviewing and editing the manuscript. MPG: resources. SB and SS: conceptualization, reviewing, formal analysis and providing resources.

Disclosure statement

No potential conflict of interest was reported by the authors.

Data and software availability

The input file used in this research can be found on Zenodo data repository: https://zenodo.org/record/7970207#.ZHBO-C0RppQ (doi:10.5281/zenodo.7970207). MD trajectories are available on request-you can contact me by email for the data which is required. Additionally, the software used for the study are mentioned in the manuscript along with the references.

SAVES server (Free Software) Structure Validation.

PubChem (Public Database) for obtaining ligand structure (quercetin, Quercetin-4′-o’-Glucoside and Quercetin pentaacetate).

Macromodel, Schrödinger, LLC, New York, NY, 2021 (Commercially Licenced Software).

Protein Preparation Wizard, Schrödinger, LLC, New York, NY, 2021 (Commercially Licenced Software).

SiteMap, Schrödinger, LLC, New York, NY, 2021 (Commercially Licenced Software).

Glide, Schrödinger, LLC, New York, NY, 2021 (Commercially Licenced Software).

Molecular Builder Maestro, Schrödinger, LLC, New York, NY, 2021 (Commercially Licenced Software).

Jaguar, Schrödinger, LLC, New York, NY, 2021 (Commercially Licenced Software).

Prime, Schrödinger, LLC, New York, NY, 2021 (Commercially Licenced Software).

DESMOND, Schrödinger, LLC, New York, NY, 2021 (Commercially Licenced Software).

Additional information

Funding

The author(s) reported there is no funding associated with the work featured in this article.