BMVC-8C3O is a G-quadruplex ligand with anticancer properties (1). G-quadruplex secondary structures are formed in nucleic acids by sequences that are rich in guanine (2). Lu et al. (3) demonstrated that BMVC-8C3O suppresses c-FOS expression by stabilizing G-rich sequences located at the c-FOS promoter. The suppression of c-FOS expression by BMVC-8C3O increased the sensitivity of acquired resistant cancer cells to osimertinib, an epidermal growth factor receptor inhibitor. Combining BMVC-8C3O and osimertinib had a synergistic effect in inhibiting the growth of acquired resistant cancers both in vitro and in animal models. To further investigate this effect, we have performed a molecular docking study.
Molecular docking was done with AutoDock Vina Extended on the SAMSON platform (OneAngstrom, Grenoble, France). SAMSON is an interface for molecular design that has an open architecture and applicability for drug design. AutoDock Vina Extended achieves approximately 2 orders of magnitude acceleration compared with the molecular docking software AutoDock 4 while also significantly improving the accuracy of the binding mode predictions. Further speed is achieved from parallelism by using multithreading on multicore machines. AutoDock Vina Extended automatically calculates the grid maps and clusters the results in a way transparent to the user (4). UCSF Chimera, version 1.14 (Resource for Biocomputing, Visualization, and Informatics, San Francisco, CA), was used for molecular visualization (5).
The BMVC-8C3O molecule is from PubChem (compound CID: 52934752). The molecular sequence of c-FOS (Homo sapiens), a 380-amino acid protein, is from the National Center for Biotechnology Information (accession: AAC98315.1 GI: 4063509). We determined the c-FOS 3-dimensional structure from its molecular sequence using AlphaFold, version 2.3.2 (DeepMind, Hinxton, UK) (6). AlphaFold structure predictions are often indistinguishable from those using gold-standard experimental methods such as x-ray crystallography and, in recent years, cryoelectron microscopy.
Results of our analysis are presented in Figure 1. The c-FOS molecule is in Figure 1, A. The promoter region is within the ɑ helix. Figure 1, B shows the BMVC-8C3O molecule. Figure 1, C shows the c-FOS promoter region docked to BMVC-8C3O. Figure 1, D is a close-up view of the c-FOS promoter docked to BMVC-8C3O.
Figure 1.
Molecular docking of the c-FOS promoter to BMVC-8C3O. A) The c-FOS molecule. The promoter region is within the ɑ helix. B) The BMVC-8C3O molecule. C) The c-FOS promoter region docked to BMVC-8C3O (arrow). D) Close-up of BMVC-8C3O docked to c-FOS at arg143 and arg146 in the hydrophilic section of the promoter region.
G-quadruplex binding proteins are rich in glycine and arginine residues (7). BMVC-8C3O, though not a protein, docked to a hydrophilic arginine-rich portion of the c-FOS promoter in the regions of arg143 and arg146, quite close to arg155, arg157, arg158, and arg159 (Figure 1, D). Only 1 docking position with root mean square deviation of atomic positions = 0 was highly valid, and this position is shown in Figure 1, C and D. The next 6 root mean square deviation docking calculations were greater than 0, indicating that docking was less likely. The binding energy of BMVC-8C3O docked to c-FOS was −6.5 kcal/mol, and the binding constant (Ki) was 16.7 µmol.
Lu et al. (3) found that the combined inhibitory effect on cancer cell growth was not limited to BMVC-8C3O and osimertinib; several G-quadruplex ligands showed varying levels of inhibition activity. Our elucidation of the BMVC-8C3O–to–c-FOS promoter docking position, presented here, may allow synthesis of even more potent suppressors of the c-FOS promoter.
Acknowledgements
The funder did not play a role in the design of the study; the collection, analysis, and interpretation of the data; the writing of the manuscript; and the decision to submit the manuscript for publication.
Contributor Information
Steven Lehrer, Department of Radiation Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Peter H Rheinstein, Severn Health Solutions, Severna Park, MD, USA.
Data availability
Data sources are publicly available.
Author contributions
Steven Lehrer, MD (Conceptualization; Data curation; Formal analysis), Peter Rheinstein, MD, JD, MS (Conceptualization; Data curation; Formal analysis).
Funding
This work was supported in part through the computational resources and staff expertise provided by Scientific Computing at the Icahn School of Medicine at Mount Sinai. Research reported in this paper was also supported by the Office of Research Infrastructure of the National Institutes of Health under award No. S10OD018522 and S10OD026880. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
Conflicts of interest
None declared.
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Data Availability Statement
Data sources are publicly available.