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Homology modeling of Forkhead box protein C2: identification of potential inhibitors using ligand and structure-based virtual screening

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Abstract

Overexpression of Forkhead box protein C2 (FOXC2) has been associated with different types of carcinomas. FOXC2 plays an important role in the initiation and maintenance of the epithelial–mesenchymal transition (EMT) process, which is essential for the development of higher-grade tumors with an enhanced ability for metastasis. Thus, FOXC2 has become a therapeutic target for the development of anticancer drugs. MC-1-F2, the only identified experimental inhibitor of FOXC2, interacts with the full length of FOXC2. However, only the DNA-binding domain (DBD) of FOXC2 has resolved crystal structure. In this work, a three-dimensional (3D) structure of the full-length FOXC2 using homology modeling was developed and used for structure-based drug design (SBDD). The quality of this 3D model of the full-length FOXC2 was evaluated using MolProbity, ERRAT, and ProSA modules. Molecular dynamics (MD) simulation was also carried out to verify its stability. Ligand-based drug design (LBDD) was carried out to identify similar analogues for MC-1-F2 against 15 million compounds from ChEMBL and ZINC databases. 792 molecules were retrieved from this similarity search. De novo SBDD was performed against the full-length 3D structure of FOXC2 through homology modeling to identify novel inhibitors. The combination of LBDD and SBDD helped in gaining a better insight into the binding of MC-1-F2 and its analogues against the full length of the FOXC2. The binding free energy of the top hits was further investigated using MD simulations and MM/GBSA calculations to result in eight promising hits as lead compounds targeting FOXC2.

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Acknowledgements

Research reported in this paper was supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award no. R15GM122013. Computational time was generously provided by Southern Methodist University’s Center for Research Computing. The authors would like to thank OpenEye Scientific Software Inc. for providing an academic license for their computer-aided drug design programs.

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Authors and Affiliations

  1. Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, TX, USA

    Mayar Tarek Ibrahim & Peng Tao

  2. Department of Chemistry and Biochemistry, The University of Texas at Tyler, Tyler, TX, USA

    Jiyong Lee

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Contributions

MTI contributed to conceptualization, methodology, formal analysis and investigation, and writing and preparation of the original draft. JL contributed to writing, reviewing, and editing of the manuscript and supervision. PT contributed to conceptualization and writing, reviewing, and editing of the manuscript, funding acquisition, and supervision.

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Correspondence to Peng Tao.

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The authors declare no competing financial or non-financial interests that are directly or indirectly related to the work submitted for publication.

Data availability

Experimental data: The crystal structure of DBD of Forkhead Box Protein C2 (PDB ID: 6O3T)) can be obtained free of charge from the Protein Data Bank (https://www.rcsb.org/). The sequence of Forkhead Box Protein C2 (UniprotKB Q99958) can be obtained free of charge from Uniprot (https://www.uniprot.org). Packages: The multi-fingerprint browser can be used free of charge from http://dcb-reymond23.unibe.ch:8080/MCSS/. KNIME package can be downloaded free of charge from (https://www.knime.com/). OpenMM. The package can be downloaded free of charge from (https://openmm.org). I-TASSER server can be used free of charge from (https://zhanggroup.org/I-TASSER/). BindScope server can be used free of charge from (https://playmolecule.com/BindScope/). LIGANN server can be used free of charge from (https://playmolecule.com/LiGANN/). MakeReceptor module, Omega, and FRED can be obtained from OpenEye Scientific using (https://www.eyesopen.com). PyMOL 2.4.0 (can be obtained free of charge from (https://pymol.org/2/). Molprobity can be used free of charge from (http://molprobity.biochem.duke.edu). ProSA module can be used free of charge from https://prosa.services.came.sbg.ac.at/prosa.php.

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Ibrahim, M.T., Lee, J. & Tao, P. Homology modeling of Forkhead box protein C2: identification of potential inhibitors using ligand and structure-based virtual screening. Mol Divers 27, 1661–1674 (2023). https://doi.org/10.1007/s11030-022-10519-0

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