[1]
|
Hilgenfeld, R. (2014) From SARS to MERS: Crystallographic Studies on Coronaviral Proteases Enable Antiviral Drug Design. FEBS Journal, 281, 4085-4096.
https://doi.org/10.1111/febs.12936
|
[2]
|
Pillaiyar, T., Manickam, M., Namasivayam, V., Hayashi, Y. and Jung, S.-H. (2016) An Overview of Severe Acute Respiratory Syndrome-Coronavirus (SARS-CoV) 3CL Protease Inhibitors: Peptidomimetics and Small Molecule Chemotherapy. Journal of Medicinal Chemistry, 59, 6595-6628.
https://doi.org/10.1021/acs.jmedchem.5b01461
|
[3]
|
Anand, K. (2003) Coronavirus Main Proteinase (3CLpro) Structure: Basis for Design of Anti-SARS Drugs. Science, 300, 1763-1767.
https://doi.org/10.1126/science.1085658
|
[4]
|
Zhang, L., Lin, D., Sun, X., Curth, U., Drosten, C., Sauerhering, L., Becker, S., Rox, K. and Hilgenfeld, R. (2020) Crystal Structure of SARS-CoV-2 Main Protease Provides a Basis for Design of Improved α-Ketoamide Inhibitors. Science, 368, eabb3405.
https://doi.org/10.1126/science.abb3405
|
[5]
|
Borah, P., Deb, P.K., Deka, S., Venugopala, K.N., Singh, V., Mailavaram, R.P., Kalia, K. and Tekade, R.K. (2020) Current Scenario and Future Prospect in the Management of COVID-19. Current Medicinal Chemistry. (In Press)
https://doi.org/10.2174/0929867327666200908113642
|
[6]
|
Poater, A. (2020) Michael Acceptors Tuned by the Pivotal Aromaticity of Histidine to Block COVID-19 Activity. The Journal of Physical Chemistry Letters, 11, 6262-6265.
https://doi.org/10.1021/acs.jpclett.0c01828
|
[7]
|
Cavallo, L. and Oliva, R. (2020) D936Y and Other Mutations in the Fusion Core of the SARS-Cov-2 Spike Protein Heptad Repeat 1 Undermine the Post-Fusion Assembly. https://doi.org/10.1101/2020.06.08.140152
|
[8]
|
da Silva Hage-Melim, L.I., Federico, L.B., de Oliveira, N.K.S., Francisco, V.C.C., Correia, L.C., de Lima, H.B., Gomes, S.Q., Barcelos, M.P., Francischini, I.A.G. and de Paula da Silva, C.H.T. (2020) Virtual Screening, ADME/Tox Predictions and the Drug Repurposing Concept for Future Use of Old Drugs against the COVID-19. Life Sciences, 256, Article ID: 117963. https://doi.org/10.1016/j.lfs.2020.117963
|
[9]
|
Sternberg, A., McKee, D.L. and Naujokat, C. (2020) Novel Drugs Targeting the SARS-CoV-2/COVID-19 Machinery. Current Topics in Medicinal Chemistry, 20, 1423-1433. https://doi.org/10.2174/1568026620999200517043137
|
[10]
|
Fernández-García, M. (2015) Fármacos Inhibidores de Proteasas Virales. Universidad Complutense de Madrid, Madrid.
|
[11]
|
Dong, E., Du, H. and Gardner, L. (2020) An Interactive WEB-Based Dashboard to Track COVID-19 in Real Time. The Lancet Infectious Diseases, 20, 533-534.
https://doi.org/10.1016/S1473-3099(20)30120-1
|
[12]
|
Karthick, T. and Tandon, P. (2016) Computational Approaches to Find the Active Binding Sites of Biological Targets against Busulfan. Journal of Molecular Modeling, 22, 142. https://doi.org/10.1007/s00894-016-3015-z
|
[13]
|
Cumming, J.G., Davis, A.M., Muresan, S., Haeberlein, M. and Chen, H. (2013) Chemical Predictive Modelling to Improve Compound Quality. Nature Reviews Drug Discovery, 12, 948-962. https://doi.org/10.1038/nrd4128
|
[14]
|
van Tamelen, E.E. (1956) Progress in the Chemistry of Organic Natural Products. Journal of the American Chemical Society, 78, 1266-1266.
https://doi.org/10.1021/ja01587a062
|
[15]
|
Yu, R., Chen, L., Lan, R., Shen, R. and Li, P. (2020) Computational Screening of Antagonists against the SARS-CoV-2 (COVID-19) Coronavirus by Molecular Docking. International Journal of Antimicrobial Agents, 56, Article ID: 106012.
https://doi.org/10.1016/j.ijantimicag.2020.106012
|
[16]
|
Sencanski, M., Perovic, V., Pajovic, S.B., Adzic, M., Paessler, S. and Glisic, S. (2020) Drug Repurposing for Candidate SARS-CoV-2 Main Protease Inhibitors by a Novel in Silico Method. Molecules, 25, 3830. https://doi.org/10.3390/molecules25173830
|
[17]
|
Yamamoto, N., Matsuyama, S., Hoshino, T. and Yamamoto, N. (2020) Nelfinavir Inhibits Replication of Severe Acute Respiratory Syndrome Coronavirus 2 in Vitro.
https://doi.org/10.1101/2020.04.06.026476
|
[18]
|
Sterling, T. and Irwin, J.J. (2015) ZINC 15—Ligand Discovery for Everyone. Journal of Chemical Information and Modeling, 55, 2324-2337.
https://doi.org/10.1021/acs.jcim.5b00559
|
[19]
|
Shen, C.-H., Wang, Y.-F., Kovalevsky, A.Y., Harrison, R.W. and Weber, I.T. (2010) Amprenavir Complexes with HIV-1 Protease and Its Drug-Resistant Mutants Altering Hydrophobic Clusters. FEBS Journal, 277, 3699-3714.
https://doi.org/10.1111/j.1742-4658.2010.07771.x
|
[20]
|
Reviriego, C. (2012) Asunaprevir. Drugs of the Future, 37, 247-254.
https://doi.org/10.1358/dof.2012.037.04.1789350
|
[21]
|
Piliero, P.J. (2002) Atazanavir: A Novel HIV-1 Protease Inhibitor. Expert Opinion on Investigational Drugs, 11, 1295-1301.
https://doi.org/10.1517/13543784.11.9.1295
|
[22]
|
Prashantha, C., Gouthami, K., Lavanya, L., Bhavanam, S., Jakhar, A., Shakthiraju, R., Suraj, V., Sahana, K., Sujana, H., Guruprasad, N. and Ramachandra, R. (2021) Molecular Screening of Antimalarial, Antiviral, Anti-Inflammatory and HIV Protease Inhibitors against Spike Glycoprotein of Coronavirus. Journal of Molecular Graphics and Modelling, 102, Article ID: 107769.
https://doi.org/10.1016/j.jmgm.2020.107769
|
[23]
|
Eron, J., Yeni, P., Gathe, J., Estrada, V., DeJesus, E., Staszewski, S., Lackey, P., Katlama, C., Young, B., Yau, L., Sutherland-Phillips, D., Wannamaker, P., Vavro, C., Patel, L., Yeo, J. and Shaefer, M. (2006) The KLEAN Study of Fosamprenavir-Ritonavir versus Lopinavir-Ritonavir, Each in Combination with Abacavir-Lamivudine, for Initial Treatment of HIV Infection over 48 Weeks: A Randomised Non-Inferiority Trial. The Lancet, 368, 476-482. https://doi.org/10.1016/S0140-6736(06)69155-1
|
[24]
|
Fischer, J. (2006) Analogue-Based Drug Discovery. Wiley-VCH, Weinheim.
https://doi.org/10.1002/3527608001
|
[25]
|
Zhang, K.E., Wu, E., Patick, A.K., Kerr, B., Zorbas, M., Lankford, A., Kobayashi, T., Maeda, Y., Shetty, B. and Webber, S. (2001) Circulating Metabolites of the Human Immunodeficiency Virus Protease Inhibitor Nelfinavir in Humans: Structural Identification, Levels in Plasma, and Antiviral Activities. Antimicrobial Agents and Chemotherapy, 45, 1086-1093. https://doi.org/10.1128/AAC.45.4.1086-1093.2001
|
[26]
|
Revill, P., Serradell, N., Bolós, J. and Rosa, E. (2007) Telaprevir. Drugs of the Future, 32, 788. https://doi.org/10.1358/dof.2007.032.09.1138229
|
[27]
|
Doyon, L., Tremblay, S., Bourgon, L., Wardrop, E. and Cordingley, M.G. (2005) Selection and Characterization of HIV-1 Showing Reduced Susceptibility to the Non-Peptidic Protease Inhibitor Tipranavir. Antiviral Research, 68, 27-35.
https://doi.org/10.1016/j.antiviral.2005.07.003
|
[28]
|
Zhang, B., Zhao, Y., Jin, Z., Liu, X., Yang, H. and Rao, Z. (2020) The Crystal Structure of COVID-19 Main Protease in Apo Form.
https://doi.org/10.2210/pdb6m03/pdb
|
[29]
|
Parr, R. and Yang, W. (1989) Density-Functional Theory of Atoms and Molecules. Oxford University Press, New York.
|
[30]
|
Chermette, H. (1999) Chemical Reactivity Indexes in Density Functional Theory. Journal of Computational Chemistry, 20, 129-154.
https://doi.org/10.1002/(SICI)1096-987X(19990115)20:1<129::AID-JCC13>3.0.CO;2-A
|
[31]
|
Geerlings, P., De Proft, F. and Langenaeker, W. (2003) Conceptual Density Functional Theory. Chemical Reviews, 103, 1793-1873.
https://doi.org/10.1021/cr990029p
|
[32]
|
Geerlings, P., Chamorro, E., Chattaraj, P.K., Proft, F.D., Gázquez, J.L., Liu, S., Morell, C., Toro-Labbé, A., Vela, A. and Ayers, P. (2020) Conceptual Density Functional Theory: Status, Prospects, Issues. Theoretical Chemistry Accounts, 139, Article No. 36. https://doi.org/10.1007/s00214-020-2546-7
|
[33]
|
Gázquez, J.L. (2009) Chemical Reactivity Concepts in Density Functional Theory. In: Chattaraj, P.K. Ed., Chemical Reactivity Theory: A Density Functional View, CRC Press, Taylor & Francis Group, Boca Raton, Ch. 2, 7-22.
https://doi.org/10.1201/9781420065442.ch2
|
[34]
|
Basak, S.C., Mills, D., Natarajan, R. and Gute, B.D. (2009) Predicting Chemical Reactivity and Bioactivity of Molecules from Structure. In: Chattaraj, P.K. Ed., Chemical Reactivity Theory: A Density Functional View, CRC Press, Taylor & Francis Group, Boca Raton, Ch. 31, 479-502.
https://doi.org/10.1201/9781420065442.ch31
|
[35]
|
Toro-Labbé, A., Gutiérrez-Oliva, S., Politzer, P. and Murray, J.S. (2009) Reaction Force: A Rigorously Defined Approach to Analyzing Chemical and Physical Processes. In: Chattaraj, P.K. Ed., Chemical Reactivity Theory: A Density Functional View, CRC Press, Taylor & Francis Group, Boca Raton, Ch. 21, 293-302.
https://doi.org/10.1201/9781420065442.ch21
|
[36]
|
Matito, E., Poater, J., Solá, M. and von Ragué Schleyer, P. (2009) Aromaticity and Chemical Reactivity. In: Chattaraj, P.K. Ed., Chemical Reactivity Theory: A Density Functional View, CRC Press, Taylor & Francis Group, Boca Raton, Ch. 28, 419-438.
https://doi.org/10.1201/9781420065442.ch28
|
[37]
|
Chakraborty, A., Pan, S. and Chattaraj, P.K. (2012) Biological Activity and Toxicity: A Conceptual DFT Approach. In: Structure and Bonding, Springer, Berlin, 143-179.
https://doi.org/10.1007/978-3-642-32750-6_5
|
[38]
|
Chattaraj, P., Sarkar, U. and Roy, D. (2006) Electrophilicity Index. Chemical Reviews, 106, 2065-2091. https://doi.org/10.1021/cr040109f
|
[39]
|
Gázquez, J., Cedillo, A. and Vela, A. (2007) Electrodonating and Electroaccepting Powers. Journal of Physical Chemistry A, 111, 1966-1970.
https://doi.org/10.1021/jp065459f
|
[40]
|
Rosales-Hernández, M.C. and Correa-Basurto, J. (2015) The Importance of Employing Computational Resources for the Automation of Drug Discovery. Expert Opinion on Drug Discovery, 10, 213-219.
https://doi.org/10.1517/17460441.2015.1005071
|
[41]
|
Flores-Holgun, N., Frau, J. and Glossman-Mitnik, D. (2020) A Fast and Simple Evaluation of the Chemical Reactivity Properties of the Pristinamycin Family of Antimicrobial Peptides. Chemical Physics Letters, 739, Article ID: 137021.
https://doi.org/10.1016/j.cplett.2019.137021
|
[42]
|
Flores-Holgun, N., Frau, J. and Glossman-Mitnik, D. (2020) Conceptual DFT-Based Computational Peptidology of Marine Natural Compounds: Discodermins A-H. Molecules, 25, 4158. https://doi.org/10.3390/molecules25184158
|
[43]
|
Flores-Holgun, N., Frau, J. and Glossman-Mitnik, D. (2020) Virtual Screening of Marine Natural Compounds by Means of Chemoinformatics and CDFT-Based Computational Peptidology. Marine Drugs, 18, 478.
https://doi.org/10.3390/md18090478
|
[44]
|
Komatsu, T.S., Okimoto, N., Koyama, Y.M., Hirano, Y., Morimoto, G., Ohno, Y. and Taiji, M. (2020) Drug Binding Dynamics of the Dimeric SARS-CoV-2 Main Protease, Determined by Molecular Dynamics Simulation. Scientific Reports, 10, Article No. 16986. https://doi.org/10.1038/s41598-020-74099-5
|
[45]
|
Sang, P., Tian, S.-H., Meng, Z.-H. and Yang, L.-Q. (2020) Anti-HIV Drug Repurposing against SARS-CoV-2. RSC Advances, 10, 15775-15783.
https://doi.org/10.1039/D0RA01899F
|
[46]
|
Ngo, S.T., Pham, N.Q.A., Le, L.T., Pham, D.-H. and Vu, V.V. (2020) Computational Determination of Potential Inhibitors of SARS-CoV-2 Main Protease. Journal of Chemical Information and Modeling. https://doi.org/10.1021/acs.jcim.0c00491
|
[47]
|
Kumar, S., Sharma, P.P., Shankar, U., Kumar, D., Joshi, S.K., Pena, L., Durvasula, R., Kumar, A., Kempaiah, P., Poonam and Rathi, B. (2020) Discovery of New Hydroxyethylamine Analogs against 3CLpro Protein Target of SARS-CoV-2: Molecular Docking, Molecular Dynamics Simulation, and Structure-Activity Relationship Studies. Journal of Chemical Information and Modeling.
https://doi.org/10.1021/acs.jcim.0c00326
|
[48]
|
Irwin, J.J., Sterling, T., Mysinger, M.M., Bolstad, E.S., Coleman, R.G. (2012) ZINC: A Free Tool to Discover Chemistry for Biology. Journal of Chemical Information and Modeling, 52, 1757-1768. https://doi.org/10.1021/ci3001277
|
[49]
|
Halgren, T.A. (1996) Merck Molecular Force Field. I. Basis, Form, Scope, Parameterization, and Performance of MMFF94. Journal of Computational Chemistry, 17, 490-519.
https://doi.org/10.1002/(SICI)1096-987X(199604)17:5/6<490::AID-JCC1>3.0.CO;2-P
|
[50]
|
Halgren, T.A. (1996) Merck Molecular Force Field. II. MMFF94 van der Waals and Electrostatic Parameters for Intermolecular Interactions. Journal of Computational Chemistry, 17, 520-552.
https://doi.org/10.1002/(SICI)1096-987X(199604)17:5/6<520::AID-JCC2>3.0.CO;2-W
|
[51]
|
Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G.A., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H.P., Izmaylov, A.F., Bloino, J., Zheng, G., Sonnenberg, J.L., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Vreven, T., Montgomery Jr., J.A., Peralta, J.E., Ogliaro, F., Bearpark, M., Heyd, J.J., Brothers, E., Kudin, K.N., Staroverov, V.N., Kobayashi, R., Normand, J., Raghavachari, K., Rendell, A., Burant, J.C., Iyengar, S.S., Tomasi, J., Cossi, M., Rega, N., Millam, J.M., Klene, M., Knox, J.E., Cross, J.B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R.E., Yazyev, O., Austin, A.J., Cammi, R., Pomelli, C., Ochterski, J.W., Martin, R.L., Morokuma, K., Zakrzewski, V.G., Voth, G.A., Salvador, P., Dannenberg, J.J., Dapprich, S., Daniels, A.D., Farkas, O., Foresman, J.B., Ortiz, J.V., Cioslowski, J. and Fox, D.J. (2016) Gaussian 09 Revision E.01. Gaussian Inc., Wallingford.
|
[52]
|
Peverati, R. and Truhlar, D.G. (2012) Screened-Exchange Density Functionals with Broad Accuracy for Chemistry and Solid-State Physics. Physical Chemistry Chemical Physics, 14, 16187-16191. https://doi.org/10.1039/c2cp42576a
|
[53]
|
Weigend, F. and Ahlrichs, R. (2005) Balanced Basis Sets of Split Valence, Triple Zeta Valence and Quadruple Zeta Valence Quality for H to Rn: Design and Assessment of Accuracy. Physical Chemistry Chemical Physics, 7, 3297-3305.
https://doi.org/10.1039/b508541a
|
[54]
|
Weigend, F. (2006) Accurate Coulomb-Fitting Basis Sets for H to R. Physical Chemistry Chemical Physics, 8, 1057-1065. https://doi.org/10.1039/b515623h
|
[55]
|
Marenich, A., Cramer, C. and Truhlar, D. (2009) Universal Solvation Model Based on Solute Electron Density and a Continuum Model of the Solvent Defined by the Bulk Dielectric Constant and Atomic Surface Tensions. Journal of Physical Chemistry B, 113, 6378-6396. https://doi.org/10.1021/jp810292n
|
[56]
|
Chattaraj, P., Chakraborty, A. and Giri, S. (2009) Net Electrophilicity. Journal of Physical Chemistry A, 113, 10068-10074. https://doi.org/10.1021/jp904674x
|
[57]
|
Morris, G.M., Huey, R., Lindstrom, W., Sanner, M.F., Belew, R.K., Goodsell, D.S. and Olson, A.J. (2009) AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility. Journal of Computational Chemistry, 30, 2785-2791.
https://doi.org/10.1002/jcc.21256
|
[58]
|
Morris, G.M., Goodsell, D.S., Halliday, R.S., Huey, R., Hart, W.E., Belew, R.K. and Olson, A.J. (1998) Automated Docking Using a Lamarckian Genetic Algorithm and an Empirical Binding Free Energy Function. Journal of Computational Chemistry, 19, 1639-1662.
https://doi.org/10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B
|
[59]
|
Domingo, L.R., Chamorro, E. and Perez, P. (2008) Understanding the Reactivity of Captodative Ethylenes in Polar Cycloaddition Reactions. A Theoretical Study. The Journal of Organic Chemistry, 73, 4615-4624. https://doi.org/10.1021/jo800572a
|
[60]
|
Jaramillo, P., Domingo, L.R., Chamorro, E. and Pérez, P. (2008) A Further Exploration of a Nucleophilicity Index Based on the Gas-Phase Ionization Potentials. Journal of Molecular Structure: THEOCHEM, 865, 68-72.
https://doi.org/10.1016/j.theochem.2008.06.022
|
[61]
|
Domingo, L.R. and Sáez, J.A. (2009) Understanding the Mechanism of Polar Diels-Alder Reactions. Organic and Biomolecular Chemistry, 7, 3576-3583.
https://doi.org/10.1039/b909611f
|
[62]
|
Domingo, L.R. and Perez, P. (2011) The Nucleophilicity N Index in Organic Chemistry. Organic and Biomolecular Chemistry, 9, 7168-7175.
https://doi.org/10.1039/c1ob05856h
|
[63]
|
Domingo, L.R., Ríos-Gutiérrez, M. and Pérez, P. (2016) Applications of the Conceptual Density Functional Theory Indices to Organic Chemistry Reactivity. Molecules, 21, 748. https://doi.org/10.3390/molecules21060748
|
[64]
|
Thomas, G. (2003) Fundamentals of Medicinal Chemistry. J. Wiley & Sons, New York.
|
[65]
|
Patrick, G.L. (2013) An Introduction to Medicinal Chemistry. Oxford University Press, Oxford.
|
[66]
|
Jeffrey, G. (1997) An Introduction to Hydrogen Bonding. Oxford University Press, New York.
|