Structure-Based Virtual Screening and Functional Validation of Potential Hit Molecules Targeting the SARS-CoV-2 Main Protease
Abstract
:1. Introduction
2. Materials and Methods
2.1. Retrieval and Preparation of Mpro for Virtual Screening
2.2. Library Selection
2.3. Ligand Extraction and Preparation
2.4. Docking Parameters
2.5. Virtual Drug Screening through Molecular Docking Studies
2.6. Analysis and Visualization of Mpro-Drug Complex
2.7. Drug Purchase Information
2.8. Prediction of Mpro-Hit Molecule Interactions Using Deep Learning
2.9. Cell Lysate Preparation for In Vitro BRET Assay
2.10. Expression and Purification of Recombinant SARS-CoV-2 Mpro
2.11. In Vitro BRET-Based Mpro Proteolytic Cleavage Inhibitor Assay
3. Results
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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e-Drug3D-lib | Ligand | Ciclesonide | Losartan | Telmisartan | |
Site-Specific Docking | Calculated Binding Affinity Score (kcal/mol) | 1 | −11.41 | −9.14 | −8.94 |
2 | −11.06 | −9.14 | −8.29 | ||
3 | −11.03 | −9.14 | −8.02 | ||
Blind Docking | Calculated Binding Affinity Score (kcal/mol) | 1 | −11.35 | −9.14 | −8.62 |
2 | −11.09 | −9.13 | −8.72 | ||
3 | −10.88 | −9.14 | −8.08 | ||
Drugs-lib | Ligand | Flezelastine | Hesperidin | Niceverine | |
Site-Specific Docking | Calculated Binding Affinity Score (kcal/mol) | 1 | −10.58 | −9.87 | −9.60 |
2 | −10.38 | −10.61 | −8.90 | ||
3 | −10.43 | −10.72 | −10.63 | ||
Blind Docking | Calculated Binding Affinity Score (kcal/mol) | 1 | −10.29 | −10.98 | −9.62 |
2 | −10.10 | −9.78 | −9.05 | ||
3 | −10.00 | −9.16 | −9.42 | ||
NP-lib | Ligand | NP1 | NP2 | NP3 | |
Site-Specific Docking | Calculated Binding Affinity Score (kcal/mol) | 1 | −11.73 | −10.55 | −10.28 |
2 | −10.66 | −10.37 | −10.28 | ||
3 | −10.12 | −10.47 | −10.28 | ||
Blind Docking | Calculated Binding Affinity Score (kcal/mol) | 1 | −10.43 | −10.70 | −10.28 |
2 | −10.14 | −10.84 | −10.28 | ||
3 | −10.34 | −10.65 | −10.28 |
Drug Library | Drug/Ligand Name | Drug ID | Clinical Application/Use |
---|---|---|---|
e-Drug3D-lib | Ciclesonide | CAS 126544-47-6 | Anti-Asthma |
Losartan | CAS 114798-26-4 | Anti-Hypertensive | |
Telmisartan | CAS 144701-48-4 | Anti-Hypertensive | |
Drugs-lib | Flezelastine | CAS 135381-77-0 | Anti-Asthma/Anti-Allergic |
Hesperidin | CAS 520-26-3 | Antioxidant/Anti-Inflammatory | |
Niceverine | CAS 2545-24-6 | Anti-Hypertensive | |
NP-lib | NP1 (2,3,2″,3″-Tetrahydroochnaflavone) | CAS 678138-59-5 MolPort-039-052-621 | - |
NP2 (Furowanin A) | CAS 911004-72-3 MolPort-039-141-993 | - | |
NP3 (3S,6bS,8aR,12aR,12bS,14bS)4,4,6b,8a,11,11,12b,14b-octamethyl 1,2,3,4,4a,5,6,6b,7,8,8a,9,10,11,12,12a,12b,13,14,14b-icosahydropicen-3-ol | MolPort-002-527-314 | - |
Library | Drugs | Determined EC50 (μM) | Predicted IC50 (μM) | Blind Docking Score (kcal/mol) | Calculated Affinity (Kd) from Blind Docking Score (μM) | |
---|---|---|---|---|---|---|
e-Drug3D-lib | 1 | Ciclesonide (CS) | Not determined | 6.4 | −11.35 | 0.00469 |
2 | Losartan (LT) | 260.05 ± 88.60 | 9.11 | −9.14 | 0.196 | |
3 | Telmisartan (TM) | Not determined | 3.67 | −8.72 | 0.399 | |
Drugs-lib | 1 | Flezelastine | Not tested | 2.04 | −10.29 | 0.0281 |
2 | Hesperidin (HP) | Not determined | 8.37 | −10.98 | 0.00876 | |
3 | Niceverine | Not tested | 3.4 | −9.62 | 0.0872 | |
NP-lib | 1 | NP1 | 901.1 ± 10.60 | 23.19 | −10.43 | 0.0222 |
2 | NP2 | 124.8 ± 207.5 | 3.45 | −10.84 | 0.0111 | |
3 | NP3 | Not tested | 7.73 | −10.28 | 0.0286 |
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Moovarkumudalvan, B.; Geethakumari, A.M.; Ramadoss, R.; Biswas, K.H.; Mifsud, B. Structure-Based Virtual Screening and Functional Validation of Potential Hit Molecules Targeting the SARS-CoV-2 Main Protease. Biomolecules 2022, 12, 1754. https://doi.org/10.3390/biom12121754
Moovarkumudalvan B, Geethakumari AM, Ramadoss R, Biswas KH, Mifsud B. Structure-Based Virtual Screening and Functional Validation of Potential Hit Molecules Targeting the SARS-CoV-2 Main Protease. Biomolecules. 2022; 12(12):1754. https://doi.org/10.3390/biom12121754
Chicago/Turabian StyleMoovarkumudalvan, Balasubramanian, Anupriya Madhukumar Geethakumari, Ramya Ramadoss, Kabir H. Biswas, and Borbala Mifsud. 2022. "Structure-Based Virtual Screening and Functional Validation of Potential Hit Molecules Targeting the SARS-CoV-2 Main Protease" Biomolecules 12, no. 12: 1754. https://doi.org/10.3390/biom12121754