A fragment-based drug discovery developed on ciclopirox for inhibition of Hepatitis B virus core protein: An in silico study
Alireza Mohebbi ,Touba Ghorbanzadeh ,Shabnam Naderifar ,Fattaneh Khalaj ,Fatemeh Sana Askari ,Ali Salehnia Sammak
Abstract
The Hepatitis B virus (HBV) core protein is an attractive target for preventing capsid assembly and viral replication. Drug repurposing strategies have introduced several drugs targeting HBV core protein. This study used a fragment-based drug discovery (FBDD) approach to reconstruct a repurposed core protein inhibitor to some novel antiviral derivatives. Auto Core Fragment in silico Screening (ACFIS) server was used for deconstruction-reconstruction of Ciclopirox in complex with HBV core protein. The Ciclopirox derivatives were ranked based on their free energy of binding (ΔGB). A quantitative structure affinity relationship (QSAR) was established on the Ciclopirox derivatives. The model was validated by a Ciclopirox-property-matched decoy set. A principal component analysis (PCA) was also assessed to define the relationship of the predictive variable of the QSAR model. 24-derivatives with a ΔGB (-16.56±1.46 Kcal.mol-1) more than Ciclopirox was highlighted. A QSAR model with a predictive power of 88.99% (F-statistics = 9025.78, corrected df(25), Pr > F = 0.0001) was developed by four predictive descriptors (ATS1p, nCs, Hy, F08[C-C]). The model validation showed no predictive power for the decoy set (Q2 = 0). No significant correlation was observed between predictors. By directly attaching to the core protein carboxyl-terminal domain, Ciclopirox derivatives may be able to suppress HBV virus assembly and subsequent viral replication inhibition. Hydrophobic residue Phe23 is a critical amino acid in the ligand binding domain. These ligands share the same physicochemical properties that lead to the development of a robust QSAR mode. The same strategy may also be used for future drug discovery of viral inhibitors.
Introduction
The Hepatitis B virus (HBV) is the cause of chronic hepatitis B (CHB), liver cirrhosis, and hepatocellular carcinoma (HCC). Despite the recombinant vaccine, more than 300 million people worldwide have CHB, and more than 300,000 people die annually from complications of HBV infection, such as HCC [1, 2].
Approved treatments for HBV infection include nucleos(t)ide analogs (NUCs) that inhibit the reverse transcription activity of P protein, but in most cases, discontinuing therapy leads to viral replication relapse and the emergence of drug-resistant strains. Another approved treatment stimulates innate immunity by interferon-alpha (IFN-α). Long-term use of IFN-α has a low success rate and is associated with severe side effects in more than 30% of cases. In addition, viral particles empty of the genome are produced by S proteins, which can be active in modulating immune responses during replication. Also, the presence of cccDNA in liver cells is a factor in persistent virus replication activity [3]. Various research results show that it is impossible to get complete treatment except by reversing the positive serological responses to S antigen and abolishing reservoir cccDNA. Recent studies show that core proteins play an essential role in cccDNA formation and virus replication [4].
Material and methods
Data gathering of HBcAg and Ciclopirox
The crystallographic structure of HBcAg of HBV genotype D subtype adw was obtained from a protein data bank (PDB) with the PDB ID of 6j10 and 2.30 Å resolution [25]. The structure of HBcAg was cleaned from water molecules and other non-standard fragments, as previously shown [26, 27]. Furthermore, the chemical structure of Ciclopirox in complex with the HBcAg was also extracted from the same.pdb file. The complex.pdb file of HBcAg and Ciclopirox was used for fragment-based drug development.
Results
HBcAg and Ciclopirox
The cleaned complex structure of HBcAg and Ciclopirox was used for fragment-based drug discovery (FBDD). As shown in Fig 1, Ciclopirox was deconstructed into its core fragments. The core fragments were extended to the novel, efficient ligands. The novelty of the ligands was checked in the PubChem database [39]. Forty-one ligands were generated based on the Ciclopirox core fragments (data are not shown). ΔGB of the Ciclopirox (-14.79 Kcal/mol) was used as the binding affinity cut-off and the positive control to investigate the efficiency of the ligands. Accordingly, the ligands with lower affinities than that of Ciclopirox were discarded. Accordingly, 24 ligands (Table 1) were selected for ADMET prediction and for establishing a robust SAR model.
Discussion
Chronic HBV infection is a critical public health issue due to irresponsiveness to viral NUCs and immunotherapies. There are currently approved recombinant vaccine and NUCs, including lamivudine (3TC), adefovir disoproxil (ADF), entecavir (ETV), telbivudine (LdT), tenofovir disoproxil fumarate (TDF), and tenofovir alafenamide (TAF). Furthermore, pegylated interferon alpha (PEG-IFN -α) in complementation with NUCs is approved for HBV therapy. However, such interventions’ efficiency is inadequate owing to the residual hepatocytes carrying cccDNA, HBsAg production, drug-resistance mutation, and vaccine-scape mutants. Promising strategies targeting host receptor and viral HBV core protein are now undergoing clinical trials. However, the drug repurposing approach has gained much attention partly because of the COVID-19 pandemic [40].
Conclusion
The combination of computer-aided drug discovery and drug repurposing can pave the way to uncover the potential of FDA-approved drugs as antiviral agents. The present study’s findings demonstrated that Ciclopirox derivatives might inhibit HBV virus assembly and subsequent viral replication inhibition by directly binding to the viral core protein carboxyl-terminal domain. Phe23 at the CTD and Tyr118 potentially play the most important role in viral capsid assembly, partially due to the highest interactions with the Ciclopirox derivatives. These ligands also have the same physicochemical properties that led to establishing a unique structure-activity relationship model.
Acknowledgments
We thank the Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran for their spiritual support for this study.
Citation: Mohebbi A, Ghorbanzadeh T, Naderifar S, Khalaj F, Askari FS, Sammak AS (2023) A fragment-based drug discovery developed on ciclopirox for inhibition of Hepatitis B virus core protein: An in silico study. PLoS ONE 18(5): e0285941. https://doi.org/10.1371/journal.pone.0285941
Editor: Pramodkumar Pyarelal Gupta, D Y Patil Deemed To Be University, INDIA
Received: November 17, 2022; Accepted: May 5, 2023; Published: May 17, 2023
Copyright: © 2023 Mohebbi 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: All relevant data are within the paper and its Supporting Information files.
Funding: The author(s) received no specific funding for this work.
Competing interests: The authors have declared that no competing interests exist.
