In silico identification of inhibitors targeting N-Terminal domain of human Replication Protein A

Replication Protein A (RPA) mediates DNA Damage Response (DDR) pathways through protein-protein interactions (PPIs). Targeting the PPIs formed between RPA and other DNA Damage Response (DDR) mediators has become an intriguing area of research for cancer drug discovery. A number of studies applied di...

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Bibliographic Details
Published in:Journal of molecular graphics & modelling 2019-01, Vol.86, p.149-159
Main Authors: Çınaroğlu, Süleyman Selim, Timuçin, Emel
Format: Article
Language:English
Subjects:
Binding Sites
Drug Discovery - methods
Humans
Ligands
MM-PBSA
Molecular docking
Molecular Docking Simulation
Molecular dynamics
Molecular Dynamics Simulation
Protein Binding
Protein Interaction Domains and Motifs - drug effects
Quantitative Structure-Activity Relationship
Replication protein A
Replication Protein A - antagonists & inhibitors
Replication Protein A - chemistry
Small Molecule Libraries
Virtual screening
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Summary:Replication Protein A (RPA) mediates DNA Damage Response (DDR) pathways through protein-protein interactions (PPIs). Targeting the PPIs formed between RPA and other DNA Damage Response (DDR) mediators has become an intriguing area of research for cancer drug discovery. A number of studies applied different methods ranging from high throughput screening approaches to fragment-based drug design tools to discover RPA inhibitors. Although these methods are robust, virtual screening approaches may be allocated as an alternative to such experimental methods, especially for screening of large libraries. Here we report the comprehensive screening of the large database, ZINC15 composed of ∼750 M compounds and the comparison of the identified ligands with the previously known inhibitors by means of binding affinity and drug-likeness. Initially, a ligand library sharing similarity with a promising inhibitor of the N-terminal domain of the RPA70 subunit (RPA70N) was generated by screening of the ZINC15 library. 46,999 ligands were collected and screened by LeDock which produced a satisfactory correlation with the experimental values (R2 = 0.77). 10 of the top-scoring ligands in LeDock were directly progressed to molecular dynamics (MD) simulations, while 10 additional ligands were also selected based on their LeDock scores and the presence of a functional group that could interact with the key amino acids in the RPA70N cleft. MD simulations were used to predict the binding free energy of the ligands by the MM-PBSA method which produced a high level of agreement with the experiments (R2 = 0.85). Binding free energy predictions pointed out 2 ligands with higher binding affinity than any of the reference inhibitors. Particularly the ligand ZINC000753854163 exhibited superior drug-likeness features than any of the known inhibitors. Overall, this study reports ZINC000753854163 as a possible inhibitor of RPA70N, reflecting its possible use in RPA70N targeted cancer therapy. [Display omitted] •Targeting RPA is of high potential for cancer drug discovery, owing to its crucial roles played in during replication stress.•A multi-step virtual screening methodology was applied to identify new inhibitors of RPA70N from ZINC12 and ZINC15 databases.•Structure-based screening tools were validated by using two benchmark ligand sets that were experimentally characterized.•A promising ligand was identified to have higher affinity and better drug-likeness features than the benchmark ligan
ISSN:1093-3263
1873-4243
DOI:10.1016/j.jmgm.2018.10.011