In silico design and assessment of novel polyelectrophylic chemotherapy agents

Project Information

SN2DNA

Grant agreement ID: 101026616

DOI

10.3030/101026616

Project closed

EC signature date 23 February 2021

Start date 1 June 2021

End date 31 May 2024

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 259 398,72

EU contribution

€ 259 398,72

Coordinated by

UNIVERSIDAD DEL PAIS VASCO/ EUSKAL HERRIKO UNIBERTSITATEA
Spain

Periodic Reporting for period 1 - SN2DNA (In silico design and assessment of novel polyelectrophylic chemotherapy agents)

Reporting period: 2021-06-01 to 2024-05-31

Summary of the context and overall objectives of the project

DNA-damaging agents remain one of the most important chemotherapeutic strategies for the treatment of cancer(1). The drugs designed for this purpose generally contain two leaving groups that, by means SN2 reactions, form cross-linking DNA complexes of type (1,2)-intrastrand, (1,3)-intrastrand or (1,2’)-interstrand. In this kind of chemical transformations, the nucleophile (Nu:)—a DNA base, in most cases guanine (G) and, into a lesser extent, adenine (A)—attacks the chemotherapeutic reagent, which acts as an electrophile, to release a leaving group (Lg). Thus, assuming Nu:= G and Lg = Cl, the general reaction is DNA-G + E-Cl → DNA-G(+)-E+ Cl(-) (Figure 1).
Although this reaction implicates in serious harm to the double-helix structure those damages can be reversed by repair pathways in cancer cells, thus limiting the therapeutic success of these reagents, especially in further rounds of chemotherapy(2). To address this issue, platinum-based compounds, named Aurkine, were synthetized, based on increasing the number of electrophilic positions (En), that must generate interstrand crosslink adducts that should result in irreversible lesions in the DNA of cancer cells. Within this context, we have applied computational chemistry methods based on Quantum Mechanics (QM) and Molecular Dynamics (MD), for a better understanding how those compounds compromise the structure of a DNA sequence. These studies have given us insights on the structural distortions induced by these drug candidates as well as to predict the kinetics of these processes via successive SN2 reactions on guanine residues.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Similar to cisplatin (cis-PtII) and its analogs, Aurkine is a platinum compound. The main differences between Aurkine and its famous relatives are the presence of intercalating (pi-stacking) moieties and a third electrophilic position (En) aimed at generating interstrand crosslink adducts that should result in irreversible lesions in the DNA of cancer cells. To understand how SN2-type chemotherapeutic reagents such as Aurkine interact with DNA bases, it seems appropriate to subject the drug to a series of SN2 reactions according to the generally accepted mechanism. The details on how platinum drugs such as cis-PtII and its analogs react with DNA bases are not fully understood; however, there is agreement that such a system interacts according to the following steps:
1. Once in the cytoplasm, cis-PtII is transformed into a mono- or diaqua cationic species through an SN2 reaction in which chloride acts as the leaving group.
2. When the mono- or diaqua cation reaches the DNA, it reacts with the purine bases G and A through additional SN2 reactions.
3. The process continues until the total replacement of the leaving groups by purine bases.3
Based on the points made above, we first studied the reaction pathway of Aurkine aquation and the reaction between the formed cationic mono- or diaqua species and G molecules. The DFT analysis of the less energetic route of the reaction between Aurkine and G is shown in Figure 2. The SN2 reaction starts with the activation process whereby a water molecule, the nucleophile, reacts with Aurkine by displacing, preferentially, the chloride from the west side. A second SN2 reaction occurs, and a guanine displaces the water molecule (structure 2 in Figure 2), resulting in the adduct [Aurkine-G]+1. Note that the Pt-N covalent bond involves the N7 of the guanine. The reaction continues until the entrance of the second guanine to form the dicationic complex [Aurkine-GG]+2. Finally, a guanine molecule displaces the chloride on the third electrophilic position to form [Aurkine-GGG]+3 cation. The monoaqua cation (structure 1 in Figure 2) was used as a ligand in the unbiased MD simulation.
The MD of three Aurkine monoaqua cations and an 18-mer B-DNA sequence were performed (Figure 3a). A set of 10 independent production simulations was run at 300 K for 5 µs of production. These simulations revealed several different binding modes, notably the intercalation in the DNA’s major groove. Ligand intercalation takes place between the GpC base steps at approximately 0.7 µs, causing damage to the DNA’s structure (Figure 3c and 3d). As shown in Figure 3, binding is concomitant with distortions in the B-DNA structure. The damages resulting from the ligand intercalation observed in the DNA sequence were preserved until the end of the simulation. The results indicate that after approximately one microsecond, both RMSD and Pt-N7 distances are stabilized until the end of the simulation (Figure 3e).
To exploit and disseminate the activities of the SN2-DNA project I’ve attended scientific meetings and conferences around Europe such as the Reunión BienaL de la Sociedad Española de Química and The Inaugural Lennard-Jones Centre Meeting. Furthermore, as I am keen on developing projects focused on theoretical chemistry to contribute to the advancement of scientific research in Brazil, I launched a project named Escola in Silico (In silico School), aimed at teaching general chemistry through computational chemistry tools to secondary school students. The lessons were focused on DNA and the process of the discovery of its structure.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Although the structures of distorted DNA through (1,2)-intrastrand and (1,3)-intrastrand crosslinks with cisplatin have been determined by X-ray diffraction analyses, the structures of distorted interstrand crosslinks remain unclear, most likely due to the poor diffracting capability of these adducts. In this context, our findings are crucial to understanding the structural distortions induced by these agents and predicting the kinetics of these processes via successive SN2 reactions on G residues. QM calculations helped us identify the least energetic route through which Aurkine forms intra- and interstrand crosslinks with DNA purines. MD calculations revealed the extent of damage that the ligand provokes in the DNA double helix sequence.
As mentioned earlier, a major challenge in chemotherapy is the efficient repair pathways in cancer cells, which can reverse DNA damage and thus limit therapeutic success. For example, cholangiocarcinoma, a group of malignant tumors in the biliary tree, is considered a major clinical challenge in oncology due to limited therapeutic options, potent resistance mechanisms, and potential side effects. Moreover, the median overall survival achieved with current therapies remains modest, with a one-year estimate.
The ability of Aurkine to provoke serious and irreversible damage to DNA was validated experimentally. These results revealed that Aurkine induces DNA double-strand breaks, higher cytotoxicity, and apoptosis in cholangiocarcinoma cells compared to cisplatin, along with malignancy selectivity, positioning Aurkine as a promising candidate for cholangiocarcinoma treatment. (No website has been developed for the project).

Frames from MD simulations showing the DNA distortion after ligand intercalation.

DNA-ligand SN2 reaction.

QM analysis of the reaction between the Aurkine and guanine molecules.