Abstract 2345: Docking and molecular dynamic simulations of mithramycin against Sp1, Sp3, and survivin

Abstract

Abstract Purpose: Therapeutic targeting of transcription factors, Specificity protein (Sp)1 and Sp3 and their downstream effectors, such as survivin, are studied in various cancers. Due to role in in poorer cancer prognoses in several cancers their downregulation has been investigated as an effective treatment approach. Mithramycin (Mit) showed innate anti-cancer properties by targeting Sp proteins through GC/GT DNA binding interference. Recent studies have given new insights into further mechanisms of action of Mit, however in-depth binding and mechanistic studies are lacking. Our objective is to investigate Mit’s specific binding interactions with Sp1, Sp3, and survivin. Methods: Protein structures and sequences for Sp1, Sp3, and survivin (ID: P08047, Q02447, and O153392, respectively) were retrieved from UniProtKB database. Experimental predicted structures for Sp1 and Sp3 were obtained from AlphaFold. Sequence lengths of Sp1 and Sp3 were 785 and 781 amino acids (aa), domain regions of Sp1 (619-785) and Sp3 (461-781) were note. Survivin structure was obtained from PDB and was comprised of 142 aa. Co-crystallized compounds were removed during analyses using BIOVIA Discovery Studio 4.5 Visualizer. Prediction of binding sites and docking were performed using CASTp, GHECOM, DEPTH tools, glide, and AutoDock 4.2 software. Energy minimization and Molecular dynamics simulations were performed in the Schrödinger suite. Results: Binding sites were identified for Sp1, Sp3, and survivin. Simulated docking demonstrated multiple binding complexes and varying binding energies. The most efficient binding was seen with Sp1 and Sp3. RMSF and RMSD simulations revealed stabilization of Sp1-, Sp3-, and survivin-Mit complexes. This shows Mithramycin can potentially inhibit all three proteins, with slightly more stability with Sp1 and Sp3. Radius of gyration (rGyr), H-bond analysis, and solvent accessible surface area (SASA) support docking findings with Mit-protein complexes remaining stable in the binding pocket, forming new H-bonds, and altering hydrophilic and hydrophobic interaction areas. Conclusion: Our findings warrant further in vitro testing of the ability of Mit to interact with a wider range of oncogenic targets. While we only tested the ability of Mit to interact with Sp1, Sp3 and survivin, similar model can be used to evaluate the interaction with other critical proteins associated with cancer and to further elucidate mechanisms of action. These finding are crucial to understanding base mechanistic abilities and can be useful to test additional agents for their ability to interact with Sp1 or survivin. Citation Format: Christoffer Briggs Lambring, Santosh K. Behera, Riyaz Basha. Docking and molecular dynamic simulations of mithramycin against Sp1, Sp3, and survivin [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2345.