DACH-Platinum-DNA Interactions: An Investigation into the Basis for. Binding and Recognition by parallel molecular modelling

Transcription

1 DACH-Platinum-DNA Interactions: An Investigation into the Basis for Binding and Recognition by parallel molecular modelling Yang lifeng 1,2, Ding Jeak Ling 1 1 Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore Computational and Systems Biology, Singapore-MIT Alliance, 4 Engineering Drive 3, Singapore Abstract To clarify the pattern of stereoisomers of the DACH group, new platinum parameters was introduced to the AMBER software successfully. Moreover, stereoisomers of the DACH group which formed 1,2-GG intrastrand cross-links with DNA were studied by molecular dynamics (MD) simulations using AMBER. The calculated binding energies between R,R-DACH-Pt, S,S-DACH-Pt and cis-dach-pt moieties and DNA revealed a strong correlation with antitumour activities. The result provided more clues to understand the biological interactions of chiral platinum drugs. DNA structure analysis indicated that DNA tolerated the distortion resulted in the different Pt-DNA adducts and various local and global structure distortions were found. Natural bond orbital (NBO) analysis of hydrogen bonding on Pt-DNA adducts at a AGGC site revealed that R,R-DACH-Pt moiety alleviated the repulsion by unwinding the DNA, whereas the S,S-DACH-Pt adduct avoided the interaction by distorting the H bonds of binding site basepairs. Hence, the structural differences of chiral platinum drug led to its distinct activity.

2 Introduction Cancer is a leading cause of death throughout the world. It was reported by World Health Organization (WHO) that out of 58 million deaths worldwide in 2005, 7.6 million people died of cancer. Based on estimation, cancer deaths will continue to rise with an approximated 9 million people in 2015, to 11.4 million in Chemotherapy is the primary treatment now. Thus drug research and discovery are of critical importance in human health care. In the past decades, rational drug design has complemented the conventional drug discovery technologies. With the development of computer science, computer-aided drug design (CADD) was introduced and proven successful in structurebased drug discovery, which meets the minds of the rational design. Platinum drugs are significant therapeutic agents for treating cancer. Over 3000 platinum analogues were tested and about 30 platinum compounds have been evaluated in clinical trials. Only a sub set continued to be investigated 1-3. The empirical determination of the structure-activity relationship of proteins can be very demanding. Where wet benchwork study is problematic, computational simulation work becomes necessary and can provide very useful clues. However, simulating macromolecules is extremely challenging even on very large supercomputers, due to the need to simulate the movement for long time scales. A generally accepted fact is that cytotoxic activity of cisplatin results from its interaction with DNA 4. Although cisplatin is also able to interact with many types of proteins that are vital to DNA replication and cell division, its primary target remains to be DNA 4-7. Of the four nucleic acid residues, platinum is apt to associate with guanine 5. These include the major 1,2-intrastrand cross-links. They specifically recognize two N7 atoms to form 1,2-interstrand d(g*pg*)(70%) and d(a*pg*) (15%) (in which * indicates a platinated base) crosslinks of DNA-cisplatin adducts and inhibit their repair The

3 formation of complexes between DNA and proteins in the presence of cisplatin and the changes in the cell architecture may account for the drug cytotoxicity. Failure to fully understand the mechanism of antitumor activity could be responsible for the low success rate in the development of new platinum drugs able to overcome cisplatin resistance. The molecular modeling methods were developed to investigate the interaction between platinum drugs and DNA. Previously, Hambley reviewed the potential role of molecular modeling in the study of Pt-DNA interactions and demonstrated it would be a powerful technology to combine with NMR 10, Force field based on molecular dynamics simulation has provided complementary information on the dynamics and flexibility of cisplatin and other Pt-based drug-dna complexes. For the various difficulties, force field parameters are available for very few Pt-based ligands 16,17. Therefore, it is important to develop new applicable platinum parameters. In an effort to contribute to understanding the effect of spectator ligands of platinum complexes on the structural perturbation of DNA due to the formation of the 1,2-GG intrastrand cross-links, we used molecular modeling techniques in this work to investigate the structures of adducts formed by R,R-Pt-DACH, S,S-Pt-DACH and cis- DACH-Pt moieties with a 12-bp DNA duplex. The newly force field parameters were generated and used in this work as described in Table 1. Table 1. Comparison of the different parameters structure without hydrogen Angle( ) (N4-PT-N5) Crystal Reported This work

4 Results and Discussion The charge of platinum moiety was calculated by NBO analysis (BP86/LANL2DZ) was performed using the Gaussian 03 program to determine the atomic charges of the Pt-GG residues. +2 charge was redistributed on the Pt-GG moiety. Given the similarities between DACH-Pt moieties with regards to their binding siteselectivity and fundamental chemical and steric features, the structure of DNA bound by DACH-Pt moieties provides a convenient and realistic initial structure in these investigations. H 2 N NH 2 Pt CCTCAGGCCTCC GGAGTCCGGAGG Figure 1. Sequence of 1PG9. As a starting point for the computational examination of R,R-DACH-Pt, S,S-DACH-Pt and cis-dach-pt binding to the 12mers DNA (PDB ID: 1PG9) investigations, a NMR structure of R,R-DACH-Pt bound d(cctcaggcctcc)2 was used. To create a binding site, R,R-DACH-Pt was replaced with above DACH-Pt moieties. Electroneutrality of each docked structure was achieved through the addition of 22 Na+ and 2Cl- counter ions using standard procedures to balance the 11 phosphate anions provided by each single-strand of DNA and the positively-charged platinum moiety. Subsequently, solvation of each DNA complex was achieved using a TIP3P

5 water box that provided a 10 Å solvent shell in all directions. Electrostatics was evaluated with the Particle Mesh Ewald (PME) method. The analysis of trajectories used the programs VWD. Helical parameters, backbone and the whole conformation of all DNA molecules were analyzed using the software CURVES 5.3. The initial models of the complexes were constructed and energy minimized using LEAP, PARM and MINMD modules of AMBER 9. The steepest descent method were implemented for an initial cycles followed by the use of the conjugated gradient method for energy minimization until the energy gradient norm difference between successive steps was < kal mol -1 Å -1 and the RMS value was < kal mol -1 Å -1. A 10 Å cutoff value was chosen to calculate all nonbonded interactions in the system. A typical simulation in a 10ns time scale for one complex with a typical configuration can run for 3 days using 16 CPUs. Figure 2 shows the simulation result which were carried out on the Atlas3 and Atlas4 cluster (queue: quad_parallel) in the Computer Centre, NUS. We observed that the linear speedup using this system. When running an algorithm with linear speedup, doubling the number of processors doubles the speed. It means the Amber 9 code is ideally parallelized. This parallelized code carries on smoothly and the powerful compute resources enabled us to complete our simulation in a very short time.

6 Figure 2. Speedup ratio against various numbers of processors employed Figure 3. Coordination geometry of R,R-DACH-Pt-GG moiety 1 is the initial structure from NMR structure; 2 is the MM/MD structure averaged and 3 is the superposition of platinated moiety of NMR structure and MM/MD structure averaged. To obtain a complex that has low free energy, which is thermodynamically stable is a common problem and goal in computational chemistry as well as in pharmaceutical chemistry. Accurate free energy estimation is challenging because the environment (usually aqueous) must be taken into account. However, reasonable progress has been

7 made in recent years. Many models with varying degrees of accuracy have been proposed for the estimation of solvent effects. The model based on molecular mechanics force fields, Poisson-Boltzmann equation, and MM/PBSA. This method can be used to evaluate free energies of binding or to calculate the absolute free energies of molecules in solution. In this work, we design a protocol for the estimation of the free energy of molecular conformations of DACH-Pt and DNA using the MM/PBSA approach. In this case, our goal was to compare the free energies of the corresponding R,R-DACH-Pt- DNA, S,S-DACH-Pt-DNA and cis-dach-pt-dna pairs. These results suggest that MM/PBSA free energy estimation is good for Pt/DNA moieties. -4 log GI 50 (µμ) -5-6 R,R S,S Cis Cis S,S R,R NCI y=0.1097x R 2 = NCI y= x R 2 = DMC y=0.0994x R 2 = DMC y= x R 2 = Cis-down Binding Energy (kcal/mol) Cis-up -94 Binding Energy (kcal/mol) -96 S,S R,R y = R = Bending Angle ( o ) Figure 4. Binding energy and Bending Angle against log GI Figure 4 shows the relationship between log GI 50 50, binding energy and overall bending angle of two series DACH-Pt-DNA compounds. One is obtained from NCI

8 database, the other DMC group is the novel compounds of our group. A similar trend was obtained from the regression results of two series of DACH-Pt compounds binding to DNA. According to the regression results, these three descriptors have strong relationship with each other, especially of NCI data. With the decrease of binding energy, the log GI 50 decreased and the bioactivity increased accordingly. R,R-DACH-Pt moiety has the lowest binding energy to DNA. R,R-DACH-Pt moiety binds more easily binding to DNA and this compound is envisaged to lead to the higher antitumour potency of this compound. Based on the above results, there is a large distortion when platinum moiety binds to the DNA. However, for a target DNA, the distortion in the DNA structure induced different ligands with different binding mode. In this case, R,R-DACH-Pt moiety distorts the palatinate G,G and slightly bend it towards the major groove compared to B-DNA (roll). But when compared to non-platinum binding DNA, it bends towards the minor groove, opposite to other stereoisomers. This makes the whole DNA double-helix unwound, resulting in a large overall bend angle. It is consistent with the MM/PBSA result where R,R-DACH-Pt moiety has the lowest binding energy in this case. The other stereoisomers distort the platinated adjacent base pairs structure and destroyed the Watson-Crick hydrogen bond. At the same time, adducts were stabilized by the hydrogen bond formed between DACH-Pt moiety and platinated adjacent base pairs. The less overall distortion of DNA meets higher binding energy result congruently. It can be concluded that the novel platinum force field parameters and MM/MD approach described here are useful in this platinum-dna model, especially for stereoisomers conformations. Based on the powerful and convenient computational

9 interface at the NUS, other platinum-based drug models are currently under investigation to design new drugs with improved potency. Reference 1. Judson, I.; Kelland, L. R., New Developments and Approaches in the Platinum Arena Drugs 2000, 59, (Supplement 4), Jakupec, M. A.; Galanski, M.; Keppler, B. K., Gumour-inhibiting platinum complexes-state of the art and future perspectives. Review Physiol Biochem Pharmacol 2003, 146, Pasetto, L. M.; D Andrea, M. R.; Brandes, A. A.; Rossi, E.; Monfardini, S., The development of platinum compounds and their possible combination. Critical Reviews in Oncology/Hematology 2006, 60, Wozniak, K.; Blasiake, J., Recognition and repair of DNA-cisplatin adducts. Acta Biochimica Polonica 2002, 49, (3), Pratt, W. B., Ruddon, Raymond W., The Anticancer Drugs. Oxford University Press: 1979; p Hartley, F. R., Palladium and platinum. Coordination Chemistry Reviews 1985, 67, Farrell, N., Transition Metal Complexes as Drugs and Chemotherapeutic Agents. Kluwer Academic Publishers: 1989; p Anne, M. J.; Fichtinger-Schepman; Veer, J. L. v. d.; Hartog, J. H. J. d.; Lohman, P. H. M.; Reedijks, J., Adducts of the Antitumor Drug cis-diamminedichloroplatinum(ii) with DNA:Formation, Identification, and Quantitation. Biochemistry 1985, 24, Hambley, T. W., The Influence of Structure on the Activity and Toxicity of Pt Anticancer Drugs. Coordination Chemistry Reviews 1997, 166, Jamieson, E. R.; Lippard, S. J., Structure, Recognition, and Processing of Cisplatin-DNA Adducts. Chemical Reviews 1999, 99, (9), Lippert, B., Cisplatin :chemistry and biochemistry of a leading anticancer drug. Verlag Helvetica Chimica Acta: Zürich 1999; p Reedijk, J., Why does Cisplatin reach Guanine-n7 with competing s-donor ligands available in the cell? Chemical Reviews 1999, 99, (9), Gelasco, A.; Lippard, S. J., NMR Solution Structure of a DNA Dodecamer Duplex Containing a cis-diammineplatinum(ii) d(gpg) Intrastrand Cross-Link, the Major Adduct of the Anticancer Drug Cisplatin Biochemistry 1998, 37, (26), Hambley, T. W.; Jones, A. R., Molecular mechanics modelling of Pt/nucleotide and Pt/DNA interactions. Coordination Chemistry Reviews 2001, 212, Chaney, S. G.; Campbell, S. L.; Temple, B.; Bassett, E.; Wu, Y.; Faldu, M., Protein interactions with platinum DNA adducts:from structure to function. Journal of Inorganic Biochemistry 2004, 98, Brabec, V.; Sip, M.; Leng, M., DNA conformational change produced by the site-specific interstrand cross-link of trans-diamminedichloroplatinum(ii). Biochemistry 1993, 32, Yao, S. J.; Plastaras, J. P.; Marzilli, L. G., A Molecular Mechanics Amber-Type Force-Field for Modeling Platinum Complexes of Guanine Derivatives. Inorganic Chemistry 1994, 33, (26),