New design of nucleotide excision repair (NER) inhibitors for combination cancer therapy
Graphical abstract
Introduction
Cancer is a set of diseases whose main cellular result is the transformation of normal cells into anomalous cells, which grow, proliferate, undergo uncontrolled division, and often invade the organism by metastases. The disease is affecting millions of patients worldwide, raising immense economical and social burdens on the patients and their families. DNA damage is among the major factors that contribute to cancer initiation and progression [1]. Several exogenous and endogenous agents can interact with the DNA, leading to critical mutations in the human genome. This includes reactive oxygen and nitrogen species [2], UV radiations [3] and polycyclic aromatic hydrocarbons [4]. To protect the genome from such frequently occurring lesions, the cells have developed an intricate enzymatic network of DNA repair mechanisms to detect, isolate and repair the damaged part of the DNA chain, allowing for proper genome replication and correct cell division and differentiation [5].
The nucleotide excision repair (NER) pathway is responsible for removing bulky DNA adducts induced by UV radiation, external agents, lipid peroxidation or reactive oxygen species [5]. These adducts distort the helix structure, halting the replication cycle and inducing apoptosis [6]. While these adducts could cause severe damage to normal cells, inducing them is, in fact, a desirable and promising way to destroy cancer cells. In this context, platinum-based therapy (e.g., cisplatin) has been developed to deliberately crosslink the DNA molecule, causing bulky lesions in cancer cells resulting in apoptosis. However, in this case, an over-activated NER pathway can act in a reverse way to this therapy, reducing its efficacy and benefit [7]. A relatively new promising approach is to design selective NER inhibitors to potentiate the efficacy of platinum-based therapy in a synergistic fashion.
NER involves at least thirty proteins that interact with each other at different stages of the pathway. Among these proteins is the excision repair cross-complementation group 1 (ERCC1) protein. ERCC1 is over-expressed in many cancer cells and its high expression is also correlated with resistance to cisplatin treatment [8], [9], [10]. Targeting this protein has been demonstrated to enhance the sensitivity of cancer cells to cisplatin [11], [12]. ERCC1 forms a heterodimer endonuclease complex with the excision repair cross-complementation group 4 (XPF) protein. The ERCC1-XPF endonuclease cleaves the damaged DNA strand at the 5′ position [13], [14]. The endonuclease complex is recruited to the damage through a specific interaction between ERCC1 and another member of the NER proteins, namely xeroderma pigmentosum, complementation group A (XPA) protein [15]. Besides ERCC1, also the expression level of XPA has been shown to directly influence the response to cisplatin treatment [16], [17], [18]. Interestingly, the XPA–ERCC1 interaction is specific, essential to NER and no other functions have been known for XPA apart from the recruitment of the ERCC1-XPF complex [19]. The schematic representation of NER is reported in Fig. 1 (adopted from the KEGG database [20], [21]).
Two different strategies to regulate the NER pathway through the XPA–ERCC1 interaction have been proposed so far. The first employs a short peptide that mimics the XPA binding domain to ERCC1, which has the ability to compete with the full-length XPA protein for binding to ERCC1 [15]. The second approach, which we follow here, is to use small molecules binding to ERCC1, preventing its interaction with XPA. The first proof of concept for the latter strategy was provided through the cell cycle checkpoint abrogators, such as UCN-01, which was shown to inhibit the XPA–ERCC1 interaction [22]. Following that, our group rationally identified a set of novel XPA–ERCC1 inhibitors by modelling the interaction and employing a sophisticated relaxed complex scheme (RCS) docking approach. These efforts led to the discovery of NERI01, a selective inhibitor of the XPA–ERCC1 interaction. This inhibitor was successfully validated experimentally as a regulator of the NER pathway in cancer cell lines. Another similar compound (compound 10) showed a less potent but still interesting modulator activity [23].
Here, we build upon these discoveries aiming at identifying chemically similar but biologically more effective molecules as well as new scaffolds for the XPA–ERCC1 inhibition. In this work, we employed both ligand-based and structure-based virtual screening techniques to identify novel potential inhibitors for the XPA–ERCC1 interaction. On one hand, we concentrated our efforts on searching a large library of compounds similar to the two previously identified lead structures, in order to find more potent structures. On the other hand, we developed a hybrid structure/ligand-based pharmacophore model to screen a library containing diverse structures to identify novel scaffolds that can be further optimized to obtain additional structures inhibiting the interaction.
Section snippets
Similarity search-based virtual screening
The structures of the two lead compounds (hereafter referred as NERI01 and compound 10) are depicted in Fig. 2. Both the compounds were able to sensitize cancer cells (especially colon cancer) to UV radiation and NERI01, in particular, was demonstrated to act in synergy with cisplatin. Moreover, the direct binding of both structures to ERCC1 was also validated [23]. The traditional similarity search has been performed using each structure as input; for NERI01, there were 8,848 compounds from
Conclusion
The inhibition of the NER repair pathway has been demonstrated as a promising approach to overcome drug resistance to platinum-based therapies in cancer cells. One of the essential steps of this machinery is the interaction between the XPA and the ERCC1 proteins, which represents an attractive target for pharmacological intervention. This is mainly due to the specificity of this interaction to the NER pathway and its correlation with resistance to platinum-based treatment. Our group has
Similarity search
A similarity score is usually calculated between the chemical fingerprints of known active molecules and the compounds in a database. The objective is to identify new active structures [33]. Among the different similarity scores, here we used the Tanimoto index due to its rapidity and reliable performance [34]. The score can be computed between two binary chemical fingerprints of the same length aswhere A and B are the fingerprint representations of the two molecules A and B. The c
Conflict of interest
The authors declare no conflict of interest.
Acknowledgements
Computer simulations have been run on PharmaMatrix (University of Alberta) and WestGrid clusters. This research was supported through funding from The Natural Sciences and Engineering Research Council of Canada (NSERC), the Allard Foundation and the Alberta Cancer Foundation (ACF).
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