Mitoxantrone and abacavir: An ALK protein-targeted in silico proposal for the treatment of non-small cell lung cancer
Juan Enrique Faya Castillo, Richard Junior Zapata Dongo, Paolo Alberto Wong Chero, Stefany Fiorella Infante Varillas
Abstract
Non-small cell lung cancer (NSCLC) is a type of lung cancer associated with translocation of the EML4 and ALK genes on the short arm of chromosome 2. This leads to the development of an aberrant protein kinase with a deregulated catalytic domain, the cdALK+. Currently, different ALK inhibitors (iALKs) have been proposed to treat ALK+ NSCLC patients. However, the recent resistance to iALKs stimulates the exploration of new iALKs for NSCLC. Here, we describe an in silico approach to finding FDA-approved drugs that can be used by pharmacological repositioning as iALK. We used homology modelling to obtain a structural model of cdALK+ protein and then performed molecular docking and molecular dynamics of the complex cdALK+-iALKs to generate the pharmacophore model. The pharmacophore was used to identify potential iALKs from FDA-approved drugs library by ligand-based virtual screening.
Introduction
Lung cancer (LC) is one of the major causes of cancer death worldwide and the most frequent cancer in men [1]. Although in the last decades there has been considerable research to understand its biological and clinical aspects, the overall survival remains poor [1]. Lung cancer is a very heterogeneous group and different parameters are used to classify them. From a histological point of view there are two types: small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC) [2, 3]. Molecular and clinical studies of NSCLC have identified functional mutations in tyrosine kinase (TK) receptors such as anaplastic lymphoma kinase (ALK), present in ~7% of adenocarcinoma tumors that can be used in targeted therapy [4]. Targeted therapy for ALK has shown better results in progression-free survival (PFS) and quality of life in patients with ALK+ NSCLC, compared to chemotherapy [5]. Thus, understanding the ALK genomic architecture, alterations and physicochemical activities could help us understand further candidates to be implemented in the clinical practice.
Materials and methods
2.1 Preparations for pharmacophoric model
Preparing the pharmacophoric model is a critical step in the search for drugs that can fulfill a drug repositioning role, for that reason, the following steps were performed prior to pharmacophore-based virtual screening.
2.1.1 Molecular modeling of cdALK+.
The cdALK+ sequence (UniProt code: J7MA22) was used for homology modelling with YASARA 21.6.2 (http://www.yasara.org/)., which presents the optimized functions so that the low-energy protein has a better chance of being modeled correctly in order to achieve local minima that is closer to native structure. YASARA also generates a hybrid using the best parts of the generated models to increase the accuracy of the model, in case the models based on the template are not optimal [24].
Results
3.1 Pharmacophore model generation
3.1.1 Modeling and molecular docking of cdALK+ with iALK exhibit better binding energy than ATP.
The structure of cdALK+ was modelled with YASARA™. Different models were generated using the three-dimensional structures as templates (PDB code: 4CLJ, 4FOD, 4ANL, 5FTO) stored in RCSB-PDB (https://www.rcsb.org/) obtaining a hybrid model that combines the best parts of the models previously obtained with each template, thus increasing the precision of the final model; these PDB templates were chosen since they present the structure of cdALK+ in complex with the specific inhibitors, but the structure is not complete. The Z-score of the hybrid model was 0.115 (Overall = 0.145*Dihedrals + 0.390*Packing1D + 0.465*Packing3D). Since the structure of cdALK+ in complex with ATP has not been resolved experimentally, we used cdALK in complex with ADP (PDB code: 3LCT) to couple the different ligands into our model. To model cdALK+-ATP complex structure, ADP molecules from cdALK were removed and then ATP from Human cyclin-dependent kinase 2 (PDB code: 1B39) was docked to obtain a new complex, which was later was minimized with YASARA™. The binding energy between ATP and cdALK+ in this complex was of 128.33 KJoul/mol.
Discussion
Despite the existence of iALKs for ALK+ NSCLC patients, resistance to iALKs has been seen across disease progression. Resistance to crizotinib, ceritinib, brigatinib, alectinib, and lorlatinib is produced by specific mutations in the ATP-binding site [35]. Therefore, understanding the cdALK+-iALK interaction allows us to propose molecules and/or drugs with potential pharmacological repositioning capacity. In our study, we use computational techniques (molecular modelling, molecular docking, molecular dynamics, and virtual screening) to identify new characteristics in existing drugs to propose them as candidates for pharmacological repositioning for ALK+ NSCLC treatment.
Conclusions
The results obtained by virtual screening of defined pharmacophores reveal six drugs with atomistic positions that complies the proposed characteristics given by the iALKS analysis in complex with cdALK+. Three of them (ribloflavin, abacavir and mitoxantrone), exhibit high affinity with the interaction pocket of ATP-binding site like iALKs in the same pocket. This lets us to consider these drugs as important candidates for pharmacological reposition. The interaction mechanisms of these drugs are based on hydrogen bonds with Glu82 and Met84 amino acids, which belong to hinge residues of interaction for iALKs. Our results reveal that the three drugs under study present similar coupling to the iALKs clinically used (crizotinib, ceritinib, brigatinib, alectinib and lorlatinib) showing encouraging results that can be tested in vitro. Although riboflavin exhibits superior binding energy to ATP, previous studies demonstrated its adverse activity by increasing cell proliferation and migration in A549 and H3255 non-small cell lung cancer cell models. Hence, riboflavin does not appear to be a promising candidate for the suggested pharmacological repositioning.
Acknowledgments
To PhD. Luis Córdoba Bahena for his advice and recommendations.
To PhD. Diego Leonardo Cabrejos for his recommendations in writing and reviewing of this paper. To PhD. Pedro Chimoy Effio, MD. Ms.C Julio Poterico, MD. Ms.C Franco Romani and MD. Diego Gutiérrez for their recommendations in the writing of this paper.
Citation: Faya Castillo JE, Zapata Dongo RJ, Wong Chero PA, Infante Varillas SF (2024) Mitoxantrone and abacavir: An ALK protein-targeted in silico proposal for the treatment of non-small cell lung cancer. PLoS ONE 19(2): e0295966. https://doi.org/10.1371/journal.pone.0295966
Editor: Chandrabose Selvaraj, Saveetha University - Poonamallee Campus: SIMATS Deemed University, INDIA
Received: July 5, 2023; Accepted: December 4, 2023; Published: February 6, 2024
Copyright: © 2024 Faya Castillo et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: The analyzed data are presented in the main text of the article, while the raw data can be accessed through the Dryad repository. doi:10.5061/dryad.ttdz08m4m.
Funding: This research was financially supported by CONCYTEC-PROCIENCIA under the call for Basic Research Projects 2019-01 [Contract No. 375-2019-FONDECYT] and Universidad de Piura (grant number PI2105). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0295966#ack
