IN SILICO STUDY OF THE INTERACTION OF CATIONIC PORPHYRIN-ANTHRAQUINONE HYBRIDS TO DNA DUPLEXES, DNA G-QUADRUPLEXES, AND HSP90

• Main Author: Arba, Muhammad
• Format: Dissertations
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/45825
• Institution: Institut Teknologi Bandung

Cancer is one of the most threatening disease of human being. One treatment of cancer is by using chemotherapy, which act on certain target. At least, three targets of anticancer drugs have been evidenced in vivo, namely DNA duplex, DNA G-quadruplex, and Hsp90. Tenths of anticancer drugs targeting DNA duplex, DNA G-quadruplex, and Hsp90 have been developed, however there are increasingly need to new anticancer drug, which has better efficacy and selectivity due to the nonselective of existing anticancer drugs, heterogenity of cancer, as well as resistance of cancer strain to certain drug. In the present study, cationic porphyrin-anthraquinone hybrids bearing meso substituents, either pyridine, imidazole, or pyrazole rings have been investigated for their interaction with DNA duplexes, DNA G- quadruplexes, and Hsp90, to determine their potency and selectivity on certain target. Molecular docking simulation was utilized to determine binding mode of cationic porphyrin- anthraquinone hybrids on each target, while molecular dynamics simulation was used to monitor the stability of each complex of ligand/target. Four kinds of DNA duplexes, which represent intercalation and groove binding modes, and three types of DNA G-quadruplexes, which comprise parallel, antiparallel, and mixed-hybrid topologies, were used. AutoDock 4.2 was used to dock nine hybrid compounds to four DNA duplexes, three DNA G-quadruplexes, and Hsp90, while monitoring of conformational changes of ligand:DNA duplexes, ligand:DNA quadruplexes, and ligand:Hsp90 during 6 ns was performed by Amber12 molecular dynamics package. The binding energy calculation of each complex was then carried out using Molecular Mechanics-Poisson Boltzmann Surface Area method (MM- PBSA). The hybrid compounds interacted with DNA duplexes by non-covalent binding through intercalation site, minor groove, and major groove of DNA duplexes. The major groove binding interaction was energetically unfavourable. Molecular dynamics simulation of complex of minor groove and intercalation binding interaction indicated the stability of each complex. Analysis of binding free energy showed that the electrostatic contribution of minor groove binding were much more favourable than those of intercalation binding. The van der Waals contribution between the two binding modes was not greatly different, except for mono-H2PzP-AQ/1Z3F, which appear to be due to its binding conformation. The binding through minor groove between GC-rich and AT-rich sequence was not significantly different, while those of intercalation favor of AT-rich sequence. It was noted that bis-H2PyP-AQ has stronger affinity as compared to that of natural ligands (distamycin to 2DND and nogalamycin to 182D). The porphyrin hybrids have a preference to be bound to parallel and mixed hybrid structures compared to antiparallel G-quadruplex. The preference arise concomitantly from end stacking of porphyrin moiety following G-stem and loop binding of anthraquinone tail, which were not found in antiparallel due to the presence of diagonal and lateral loops crowding G- quartet. Binding to antiparallel, instead, occurred with poorer affinity through both loop and wide groove. All sites of porphyrin binding were confirmed by 6 ns molecular dynamics simulation, as well as by the negative value of total binding free energies calculated by using MM-PBSA method. Free energy analysis show that the favorable contribution came from electrostatic term, which is supposedly originated from either cationic pyridinium, pyrazolium, or imidazolium groups and anionic phosphate backbone, and also from van der Waals energy, which was primarily supported by end stacking interaction. Ligand interaction with Hsp90 occurred through the binding site of Hsp90, in which each ligand except for bis-H2ImP-AQ was able to form hydrogen bond with Phe138 residue. The hydrogen bond was also established between porphyrin and Asp54 as observed in all porphyrin hybrids except for bis-H2ImP-AQ and tris-H2ImP-AQ. The additional pi-cationic interactions between porphyrin and Lys58 and between benzene ring and Lys112 were observed, which was absent in the interaction of geldanamycin (GD) with Hsp90. The six-ns molecular dynamics simulation confirmed the stability of the ligand-Hsp90 complexes, while residue fluctuation analysis indicated that each complex has similar RMSF distribution. Prediction of binding free energy showed that favorable energy contribution was originated from electrostatic, van der Waals, and nonpolar desolvation energies. The binding energy of each ligand was more negative compared to that of GD, indicating the potencial of designed ligands to be developed as new Hsp inhibitor.