References
- Anandakrishnan, R., Aguilar, B., & Onufriev, A. V. (2012). H++ 3.0: Automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. Nucleic Acids Research, 40, W537–W541. https://doi.org/https://doi.org/10.1093/nar/gks375
- Angeletti, S., Benvenuto, D., Bianchi, M., Giovanetti, M., Pascarella, S., & Ciccozzi, M. (2020). COVID-2019: The role of the nsp2 and nsp3 in its pathogenesis. Journal of Medical Virology, 92(6), 584–588. https://doi.org/https://doi.org/10.1002/jmv.25719
- Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., Onufriev, A., Simmerling, C., Wang, B., & Woods, R. J. (2005). The Amber biomolecular simulation programs. Journal of Computational Chemistry, 26(16), 1668–1688. https://doi.org/https://doi.org/10.1002/jcc.20290
- Chan, J. F.-W., Kok, K.-H., Zhu, Z., Chu, H., To, K. K.-W., Yuan, S., & Yuen, K.-Y. (2020). Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. Emerging Microbes & Infections, 9(1), 221–236. https://doi.org/https://doi.org/10.1080/22221751.2020.1719902
- Chatterjee, A., Johnson, M. A., Serrano, P., Pedrini, B., Joseph, J. S., Neuman, B. W., Saikatendu, K., Buchmeier, M. J., Kuhn, P., & Wüthrich, K. (2009). Nuclear magnetic resonance structure shows that the severe acute respiratory syndrome coronavirus-unique domain contains a macrodomain fold. Journal of Virology, 83(4), 1823–1836. https://doi.org/https://doi.org/10.1128/JVI.01781-08
- Chen, C. Y.-C. (2011). TCM Database@Taiwan: The world's largest traditional Chinese medicine database for drug screening in silico. PLoS One, 6(1), e15939. https://doi.org/https://doi.org/10.1371/journal.pone.0015939
- Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S., & Richardson, D. C. (2010). MolProbity: All-atom structure validation for macromolecular crystallography. Acta Crystallographica Section D Biological Crystallography, 66(Pt 1), 12–21. https://doi.org/https://doi.org/10.1107/S0907444909042073
- Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7, 42717. https://doi.org/https://doi.org/10.1038/srep42717
- Davidchack, R. L., Handel, R., & Tretyakov, M. (2009). Langevin thermostat for rigid body dynamics. The Journal of Chemical Physics, 130(23), 234101. https://doi.org/https://doi.org/10.1063/1.3149788
- DeLano, W. L. (2002). Pymol: An open-source molecular graphics tool. CCP4 Newsletter on Protein Crystallography, 40(1), 82–92.
- Egloff, M.-P., Malet, H., Putics, A., Heinonen, M., Dutartre, H., Frangeul, A., Gruez, A., Campanacci, V., Cambillau, C., Ziebuhr, J., Ahola, T., & Canard, B. (2006). Structural and functional basis for ADP-ribose and poly(ADP-ribose) binding by viral macro domains. Journal of Virology, 80(17), 8493–8502. https://doi.org/https://doi.org/10.1128/JVI.00713-06
- Eriksson, K. K., Cervantes-Barragán, L., Ludewig, B., & Thiel, V. (2008). Mouse hepatitis virus liver pathology is dependent on ADP-ribose-1''-phosphatase, a viral function conserved in the alpha-like supergroup. Journal of Virology, 82(24), 12325–12334. https://doi.org/https://doi.org/10.1128/JVI.02082-08
- Fehr, A. R., Channappanavar, R., Jankevicius, G., Fett, C., Zhao, J., Athmer, J., Meyerholz, D. K., Ahel, I., & Perlman, S. (2016). The conserved coronavirus macrodomain promotes virulence and suppresses the innate immune response during severe acute respiratory syndrome coronavirus infection. mBio, 7(6), 598-610.
- Fehr, A. R., Jankevicius, G., Ahel, I., & Perlman, S. (2018). Viral macrodomains: Unique mediators of viral replication and pathogenesis. Trends in Microbiology, 26(7), 598–610. https://doi.org/https://doi.org/10.1016/j.tim.2017.11.011
- Fehr, A. R., & Perlman, S. (2015). Coronaviruses: An overview of their replication and pathogenesis Coronaviruses (pp. 1–23). Springer.
- Junaid, M., Shah, M., Khan, A., Li, C.-D., Khan, M. T., Kaushik, A. C., Ali, A., Mehmood, A., Nangraj, A. S., Choi, S., & Wei, D.-Q. (2019). Structural-dynamic insights into the H. pylori cytotoxin-associated gene A (CagA) and its abrogation to interact with the tumor suppressor protein ASPP2 using decoy peptides. Journal of Biomolecular Structure & Dynamics, 37(15), 4035–4050. https://doi.org/https://doi.org/10.1080/07391102.2018.1537895
- Khan, A., Ali, S. S., Khan, M. T., Saleem, S., Ali, A., Suleman, M., Babar, Z., Shafiq, A., Khan, M., & Wei, D.Q. (2020). Combined drug repurposing and virtual screening strategies with molecular dynamics simulation identified potent inhibitors for SARS-CoV-2 main protease (3CLpro). Journal of Biomolecular Structure and Dynamics, 1–12.
- Khan, A., Junaid, M., Kaushik, A. C., Ali, A., Ali, S. S., Mehmood, A., & Wei, D.-Q. (2018). Computational identification, characterization and validation of potential antigenic peptide vaccines from hrHPVs E6 proteins using immunoinformatics and computational systems biology approaches. PLoS One, 13(5), e0196484. https://doi.org/https://doi.org/10.1371/journal.pone.0196484
- Khan, A., Rehman, A-U., Junaid, M., Li, C.-D., Saleem, S., Humayun, F., Shamas, S., Ali, S. S., Babar, Z., & Wei, D.-Q. (2020). Dynamics insights into the gain of flexibility by Helix-12 in ESR1 as a mechanism of resistance to drugs in breast cancer cell lines. Frontiers in Molecular Biosciences, 6, 159. https://doi.org/https://doi.org/10.3389/fmolb.2019.00159
- Khan, A., Kaushik, A. C., Ali, S. S., Ahmad, N., & Wei, D.-Q. (2019). Deep-learning-based target screening and similarity search for the predicted inhibitors of the pathways in Parkinson's disease. RSC Advances, 9(18), 10326–10339. https://doi.org/https://doi.org/10.1039/C9RA01007F
- Khan, A., Saleem, S., Idrees, M., Ali, S. S., Junaid, M., Kaushik, A. C., & Wei, D.-Q. (2018). Allosteric ligands for the pharmacologically important Flavivirus target (NS5) from ZINC database based on pharmacophoric points, free energy calculations and dynamics correlation. Journal of Molecular Graphics & Modelling, 82, 37–47. https://doi.org/https://doi.org/10.1016/j.jmgm.2018.03.004
- Khan, A., Khan, M. T., Saleem, S., Junaid, M., Ali, A., Shujait Ali, S., Khan, M., & Wei, D.Q. (2020). Structural Insights into the mechanism of RNA recognition by the N-terminal RNA-binding domain of the SARS-CoV-2 nucleocapsid phosphoprotein. Computational and Structural Biotechnology Journal.
- Khan, M. T., Ali, A., Wang, Q., Irfan, M., Khan, A., Zeb, M. T., Zhang, Y.J., Chinnasamy, S., & Wei, D.Q. (2020). Marine natural compounds as potents inhibitors against the main protease of SARS-CoV-2. A molecular dynamic study. Journal of Biomolecular Structure and Dynamics, 1–14.
- Kräutler, V., van Gunsteren, W. F., & Hünenberger, P. H. (2001). A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations. Journal of Computational Chemistry, 22(5), 501–508. https://doi.org/https://doi.org/10.1002/1096-987X(20010415)22:5<501::AID-JCC1021>3.0.CO;2-V
- Kusov, Y., Tan, J., Alvarez, E., Enjuanes, L., & Hilgenfeld, R. (2015). A G-quadruplex-binding macrodomain within the “SARS-unique domain” is essential for the activity of the SARS-coronavirus replication-transcription complex. Virology, 484, 313–322. https://doi.org/https://doi.org/10.1016/j.virol.2015.06.016
- Land, H., & Humble, M. S. (2018). YASARA: A tool to obtain structural guidance in biocatalytic investigations protein engineering (pp. 43–67). Springer.
- Lei, J., Kusov, Y., & Hilgenfeld, R. (2018). Nsp3 of coronaviruses: Structures and functions of a large multi-domain protein. Antiviral Research, 149, 58–74. https://doi.org/https://doi.org/10.1016/j.antiviral.2017.11.001
- Lin, Y., Pan, D., Li, J., Zhang, L., & Shao, X. (2017). Application of Berendsen barostat in dissipative particle dynamics for nonequilibrium dynamic simulation. The Journal of Chemical Physics, 146(12), 124108. https://doi.org/https://doi.org/10.1063/1.4978807
- Lu, R., Zhao, X., Li, J., Niu, P., Yang, B., Wu, H., Wang, W., Song, H., Huang, B., Zhu, N., Bi, Y., Ma, X., Zhan, F., Wang, L., Hu, T., Zhou, H., Hu, Z., Zhou, W., Zhao, L., … Tan, W. (2020). Genomic characterisation and epidemiology of 2019 novel coronavirus: Implications for virus origins and receptor binding. The Lancet, 395(10224), 565–574. https://doi.org/https://doi.org/10.1016/S0140-6736(20)30251-8
- Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/https://doi.org/10.1002/jcc.21256
- Ntie-Kang, F., Telukunta, K. K., Döring, K., Simoben, C. V., A Moumbock, A. F., Malange, Y. I., Njume, L. E., Yong, J. N., Sippl, W., & Günther, S. (2017). NANPDB: A resource for natural products from Northern African sources. Journal of Natural Products, 80(7), 2067–2076. https://doi.org/https://doi.org/10.1021/acs.jnatprod.7b00283
- Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E., DeBolt, S., Ferguson, D., Seibel, G., & Kollman, P. (1995). AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Computer Physics Communications, 91(1–3), 1–41. https://doi.org/https://doi.org/10.1016/0010-4655(95)00041-D
- Piotrowski, Y., Hansen, G., Boomaars, van der Zanden, A. L., Snijder, E. J., Gorbalenya, A. E., & Hilgenfeld, R. (2009). Crystal structures of the X-domains of a Group-1 and a Group-3 coronavirus reveal that ADP-ribose-binding may not be a conserved property. Protein Science, 18(1), 6–16. https://doi.org/https://doi.org/10.1002/pro.15
- Putics, A., Filipowicz, W., Hall, J., Gorbalenya, A. E., & Ziebuhr, J. (2005). ADP-ribose-1"-monophosphatase: A conserved coronavirus enzyme that is dispensable for viral replication in tissue culture. Journal of Virology, 79(20), 12721–12731. https://doi.org/https://doi.org/10.1128/JVI.79.20.12721-12731.2005
- Quimque, M. T. J., Notarte, K. I. R., Fernandez, R. A. T., Mendoza, M. A. O., Liman, R. A. D., Lim, J. A. K., Pilapil, L. A. E., Ong, J. K. H., Pastrana, A. M., Khan, A., Wei, D.Q., & Macabeo, A. P. G. (2020). Virtual screening-driven drug discovery of SARS-CoV2 enzyme inhibitors targeting viral attachment, replication, post-translational modification and host immunity evasion infection mechanisms. Journal of Biomolecular Structure and Dynamics, 1–23.
- Raoult, D., Zumla, A., Locatelli, F., Ippolito, G., & Kroemer, G. (2020). Coronavirus infections: Epidemiological, clinical and immunological features and hypotheses. Cell Stress, 4(4), 66–75. https://doi.org/https://doi.org/10.15698/cst2020.04.216
- Roe, D. R., & Cheatham, I. I. I., T. E. (2013). PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data. Journal of Chemical Theory and Computation, 9(7), 3084–3095. https://doi.org/https://doi.org/10.1021/ct400341p
- Shimizu, J. F., Martins, D. O. S., McPhillie, M. J., Roberts, G. C., Zothner, C., Merits, A., Harris, M., & Jardim, A. C. G. (2020). Is the ADP ribose site of the Chikungunya virus NSP3 Macro domain a target for antiviral approaches? Acta Tropica, 207, 105490. https://doi.org/https://doi.org/10.1016/j.actatropica.2020.105490
- Sumoza-Toledo, A., & Penner, R. (2011). TRPM2: A multifunctional ion channel for calcium signalling. The Journal of Physiology, 589(Pt 7), 1515–1525. https://doi.org/https://doi.org/10.1113/jphysiol.2010.201855
- Sun, H., Li, Y., Tian, S., Xu, L., & Hou, T. (2014). Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set. Physical Chemistry Chemical Physics, 16(31), 16719–16729. https://doi.org/https://doi.org/10.1039/c4cp01388c
- Toukmaji, A., Sagui, C., Board, J., & Darden, T. (2000). Efficient particle-mesh Ewald based approach to fixed and induced dipolar interactions. The Journal of Chemical Physics, 113(24), 10913–10927. https://doi.org/https://doi.org/10.1063/1.1324708
- Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/https://doi.org/10.1002/jcc.21334
- Vassetti, D., Pagliai, M., & Procacci, P. (2019). Assessment of GAFF2 and OPLS-AA general force fields in combination with the water models TIP3P, SPCE, and OPC3 for the solvation free energy of druglike organic molecules. Journal of Chemical Theory and Computation, 15(3), 1983–1995. https://doi.org/https://doi.org/10.1021/acs.jctc.8b01039
- Vijayasri, S., & Hopper, W. (2017). Towards the identification of novel phytochemical leads as macrodomain inhibitors of chikungunya virus using molecular docking approach. Journal of Applied Pharmaceutical Science, 7, 74–82.
- Vilar, S., Cozza, G., & Moro, S. (2008). Medicinal chemistry and the molecular operating environment (MOE): Application of QSAR and molecular docking to drug discovery. Current Topics in Medicinal Chemistry, 8(18), 1555–1572. https://doi.org/https://doi.org/10.2174/156802608786786624
- Wang, J., Wang, W., Kollman, P. A., & Case, D. A. (2001). Antechamber: An accessory software package for molecular mechanical calculations. Journal of the American Chemical Society, 222U, 403.
- Wang, Y., Khan, A., Chandra Kaushik, A., Junaid, M., Zhang, X., & Wei, D.-Q. (2019). The systematic modeling studies and free energy calculations of the phenazine compounds as anti-tuberculosis agents. Journal of Biomolecular Structure & Dynamics, 37(15), 4051–4069. https://doi.org/https://doi.org/10.1080/07391102.2018.1537896
- Wu, Y., Ho, W., Huang, Y., Jin, D.-Y., Li, S., Liu, S.-L., Liu, X., Qiu, J., Sang, Y., Wang, Q., Yuen, K.-Y., & Zheng, Z.-M. (2020). SARS-CoV-2 is an appropriate name for the new coronavirus. The Lancet, 395(10228), 949–950. https://doi.org/https://doi.org/10.1016/S0140-6736(20)30557-2
- Zheng, M., Gao, Y., Wang, G., Song, G., Liu, S., Sun, D., Xu, Y., & Tian, Z. (2020). Functional exhaustion of antiviral lymphocytes in COVID-19 patients. Cellular & Molecular Immunology, 17(5), 533–535. https://doi.org/https://doi.org/10.1038/s41423-020-0402-2
- Zoete, V., Daina, A., Bovigny, C., & Michielin, O. (2016). SwissSimilarity: A web tool for low to ultra high throughput ligand-based virtual screening. ACS Publications.