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Liang JJ, Pitsillou E, Lau HLY, Mccubbery CP, Gan H, Hung A, Karagiannis TC. Utilization of the EpiMed Coronabank Chemical Collection to identify potential SARS-CoV-2 antivirals: in silico studies targeting the nsp14 ExoN domain and PL pro naphthalene binding site. J Mol Graph Model 2024; 131:108803. [PMID: 38815531 DOI: 10.1016/j.jmgm.2024.108803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/01/2024]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome encodes 29 proteins including four structural, 16 nonstructural (nsps), and nine accessory proteins (https://epimedlab.org/sars-cov-2-proteome/). Many of these proteins contain potential targetable sites for the development of antivirals. Despite the widespread use of vaccinations, the emergence of variants necessitates the investigation of new therapeutics and antivirals. Here, the EpiMed Coronabank Chemical Collection (https://epimedlab.org/crl/) was utilized to investigate potential antivirals against the nsp14 exoribonuclease (ExoN) domain. Molecular docking was performed to evaluate the binding characteristics of our chemical library against the nsp14 ExoN site. Based on the initial screen, trisjuglone, ararobinol, corilagin, and naphthofluorescein were identified as potential lead compounds. Molecular dynamics (MD) simulations were subsequently performed, with the results highlighting the stability of the lead compounds in the nsp14 ExoN site. Protein-RNA docking revealed the potential for the lead compounds to disrupt the interaction with RNA when bound to the ExoN site. Moreover, hypericin, cyanidin-3-O-glucoside, and rutin were previously identified as lead compounds targeting the papain-like protease (PLpro) naphthalene binding site. Through performing MD simulations, the stability and interactions of lead compounds with PLpro were further examined. Overall, given the critical role of the exonuclease activity of nsp14 in ensuring viral fidelity and the multifunctional role of PLpro in viral pathobiology and replication, these nsps represent important targets for antiviral drug development. Our databases can be utilized for in silico studies, such as the ones performed here, and this approach can be applied to other potentially druggable SARS-CoV-2 protein targets.
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Affiliation(s)
- Julia J Liang
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC, 3053, Australia; School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia; Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC, 3004, Australia
| | - Eleni Pitsillou
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC, 3053, Australia; School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia
| | - Hannah L Y Lau
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC, 3053, Australia; Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Cian P Mccubbery
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC, 3053, Australia; Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Hockxuen Gan
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC, 3053, Australia; Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Andrew Hung
- School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC, 3053, Australia; Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC, 3004, Australia; Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia.
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Liang JJ, Pitsillou E, Hung A, Karagiannis TC. A repository of COVID-19 related molecular dynamics simulations and utilisation in the context of nsp10-nsp16 antivirals. J Mol Graph Model 2024; 126:108666. [PMID: 37976980 DOI: 10.1016/j.jmgm.2023.108666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic highlighted the importance of establishing systems and infrastructure to develop vaccines, antiviral drugs, and therapeutic antibodies against emerging pathogens. Typical drug discovery processes involve targeting suitable proteins to effect pathogen replication or to attenuate host responses, by examining either large chemical databases or protein-protein interactions. Following initial screens, molecular dynamics (MD) simulations are critical for gaining further insight into molecular interactions. During the COVID-19 pandemic, many research groups made their simulations widely available, as highlighted by the comprehensive D.E. Shaw Research trajectory database. To investigate protein target sites and evaluate potential lead compounds, we performed over 300 MD simulations relating to COVID-19. We organised our simulations into a repository, which is publicly available at https://epimedlab.org/trajectories/. The trajectories cover a large part of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteome, and the majority of our MD simulations focused on the identification of potential antivirals. For example, we focused on the S-adenosyl-l-methionine binding site of the nsp10-nsp16 complex, a critical component of viral replication, revealing verbascoside as a potential lead. Moreover, we utilised MD trajectories to explore the interface between the spike protein receptor binding domain and human angiotensin-converting enzyme 2 receptor, with the ultimate aim being investigation of new variants in real-time. Overall, MD simulations are a critical component of the in silico drug discovery process and as highlighted throughout the pandemic, data sharing enables accelerated progress. We have organised our extensive collection of COVID-19 related MD trajectories into an easily accessible repository.
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Affiliation(s)
- Julia J Liang
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC, 3004, Australia; Epigenomic Medicine Laboratory at prospED Training, Carlton, VIC, 3053, Australia; School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Eleni Pitsillou
- Epigenomic Medicine Laboratory at prospED Training, Carlton, VIC, 3053, Australia; School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Andrew Hung
- School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Tom C Karagiannis
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC, 3004, Australia; Epigenomic Medicine Laboratory at prospED Training, Carlton, VIC, 3053, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia; Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia.
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Pitsillou E, Logothetis ANO, Liang JJ, El-Osta A, Hung A, AbuMaziad AS, Karagiannis TC. Identification of Potential Modulators of a Pathogenic G Protein-Gated Inwardly Rectifying K + Channel 4 Mutant: In Silico Investigation in the Context of Drug Discovery for Hypertension. Molecules 2023; 28:7946. [PMID: 38138436 PMCID: PMC10745636 DOI: 10.3390/molecules28247946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 11/24/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Genetic abnormalities have been associated with primary aldosteronism, a major cause of secondary hypertension. This includes mutations in the KCNJ5 gene, which encodes G protein-gated inwardly rectifying K+ channel 4 (GIRK4). For example, the substitution of glycine with glutamic acid gives rise to the pathogenic GIRK4G151E mutation, which alters channel selectivity, making it more permeable to Na+ and Ca2+. While tertiapin and tertiapin-Q are well-known peptide inhibitors of the GIRK4WT channel, clinically, there is a need for the development of selective modulators of mutated channels, including GIRK4G151E. Using in silico methods, including homology modeling, protein-peptide docking, ligand-binding site prediction, and molecular docking, we aimed to explore potential modulators of GIRK4WT and GIRK4G151E. Firstly, protein-peptide docking was performed to characterize the binding site of tertiapin and its derivative to the GIRK4 channels. In accordance with previous studies, the peptide inhibitors preferentially bind to the GIRK4WT channel selectivity filter compared to GIRK4G151E. A ligand-binding site analysis was subsequently performed, resulting in the identification of two potential regions of interest: the central cavity and G-loop gate. Utilizing curated chemical libraries, we screened over 700 small molecules against the central cavity of the GIRK4 channels. Flavonoids, including luteolin-7-O-rutinoside and rutin, and the macrolides rapamycin and troleandomycin bound strongly to the GIRK4 channels. Similarly, xanthophylls, particularly luteoxanthin, bound to the central cavity with a strong preference towards the mutated GIRK4G151E channel compared to GIRK4WT. Overall, our findings suggest potential lead compounds for further investigation, particularly luteoxanthin, that may selectively modulate GIRK4 channels.
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Affiliation(s)
- Eleni Pitsillou
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC 3053, Australia
- School of Science, STEM College, RMIT University, Melbourne, VIC 3001, Australia
| | - Alexander N. O. Logothetis
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC 3053, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Julia J. Liang
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC 3053, Australia
- School of Science, STEM College, RMIT University, Melbourne, VIC 3001, Australia
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC 3004, Australia
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC 3004, Australia
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
- Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong, 3/F Lui Che Woo Clinical Sciences Building, 30-32 Ngan Shing Street, Sha Tin, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
- Biomedical Laboratory Science, Department of Technology, Faculty of Health, University College Copenhagen, 1799 Copenhagen, Denmark
| | - Andrew Hung
- School of Science, STEM College, RMIT University, Melbourne, VIC 3001, Australia
| | - Asmaa S. AbuMaziad
- Department of Pediatrics, College of Medicine Tucson, The University of Arizona, Tucson, AZ 85724, USA
| | - Tom C. Karagiannis
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC 3053, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC 3010, Australia
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC 3004, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3010, Australia
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