COVID-19 Coronavirus spike protein analysis for synthetic vaccines, a peptidomimetic antagonist, and therapeutic drugs, and analysis of a proposed achilles’ heel conserved region to minimize probability of escape mutations and drug resistance
Tóm tắt
Từ khóa
Tài liệu tham khảo
Masters, 2006, The molecular biology of coronaviruses, Adv. Virus Res., 66, 193, 10.1016/S0065-3527(06)66005-3
Lu
Robson, 2020, Computers and viral diseases. Preliminary bioinformatics studies on the design of a synthetic vaccine and a preventative peptidomimetic antagonist against the SARS-CoV-2 (2019-nCoV, COVID-19) coronavirus, Comput. Biol. Med., 103670, 10.1016/j.compbiomed.2020.103670
Robson, 2020
Li, 2016, Structure, function, and evolution of coronavirus spike proteins, Annual Reviews in Virology, 3, 237, 10.1146/annurev-virology-110615-042301
Kam, 2009, Cleavage of the SARS coronavirus spike glycoprotein by airway proteases enhances virus entry into human bronchial epithelial cells in vitro published, PloS One, 4, 1, 10.1371/journal.pone.0007870
Belouzard, S., Chu, V. C. and Whittaker, G. R., Activation of the SARS coronavirus spike protein via sequential proteolytic cleavage at two distinct sites, Proc. Natl. Acad. Sci., 106(14, 5871-5876; https://doi.org/10.1073/pnas.0809524106 (last accessed 1/26/2020).
Gui, 2017, Entity 1 containing Chain A, B, C SARS-CoV spike glycoprotein, Cell Res., 27, 119, 10.1038/cr.2016.152
Liu, 2013, Peptides corresponding to the predicted heptad repeat 2 domain of the feline coronavirus spike protein are potent inhibitors of viral infection, PloS One, 8
Forni, 2015, The heptad repeat region is a major selection target in MERS-CoV and related coronaviruses, Sci. Rep., 5, 4480, 10.1038/srep14480
Berend, 2008, Coronavirus escape from heptad repeat 2 (HR2)-Derived peptide entry inhibition as a result of mutations in the HR1 domain of the spike fusion protein, Journal of Virology, March, 2580
Robson, 1998
Sachdeva, 2017, Peptides as ‘drugs’: the journey so far, Int. J. Pept. Res. Therapeut., 23, 49, 10.1007/s10989-016-9534-8
Fishleigh, 1990
Fishleigh, 1995
Fishleigh, 1995
Fishleigh, 1998
Citywire
Robson
Robson, 1986, Computer aided peptide and protein engineering, vol. 1, B9
Robson, 1986, The EPSITRON concept of peptide and protein engineering. Applications of computer-aided molecular design”, Chem. Des. Autom. News, 1, 9
Robson, 1987, An expert system for protein engineering. Its application in the study of chloramphenicol acetyltransferase and avian pancreatic polypeptide, J. Mol. Graph., 5, 8, 10.1016/0263-7855(87)80038-3
Fishleigh, 1987, Studies on rationales for an expert system approach to the analysis of protein sequence data - preliminary analysis of the human epidermal growth factor receptor, FEBS Lett., 2, 219, 10.1016/0014-5793(87)80060-1
Garnier, 1988
Ball, 1990, A polymorphic programming environment for the chemical pharmaceutical and biotechnology industries, 107
Robson, 1992, Computer aided design of biomolecules: the big hammer approach, 207
Clark, 1995, PRO_LIGAND: an approach to de novo molecular design. 1. Application to the design of organic molecules, J. Comp.Aided.Mol.Des., 9, 13, 10.1007/BF00117275
Waszkowycz, 1994, PRO_LIGAND: an approach to de novo design. 2. Design of novel molecules from molecular field analysis (MFA) models and pharmacophores, J. Med. Chem., 37, 3994, 10.1021/jm00049a019
Westehad, 1995, PRO_LIGAND: an approach to de novo molecular design. 3. A genetic algorithm for structure refinement, B. J. Comp.A ided. Mol. Des., 9, 139, 10.1007/BF00124404
Frenkel, 1995, PRO_LIGAND: an approach to de novo molecular design. 4. Application to the design of peptides, D. Frenkel, D. E. Clark, J. Li, C. W. Murray, B. Robson, B. Waszkowycz and D. R. Westhead. (1995), J. Comput. Aided Mol. Des., 9, 213, 10.1007/BF00124453
Kumar, 2018, Receptor pharmacophore ensemble (REPHARMBLE): a probabilistic pharmacophore modeling approach using multiple protein-ligand complexes, J. Mol. Model., 24, 282, 10.1007/s00894-018-3820-7
Robson, 2013, Suggestions for a web based universal exchange and inference language for medicine”, Comput. Biol. Med., 43, 2297, 10.1016/j.compbiomed.2013.09.010
Robson, 2015, Implementation of a web based universal exchange and inference language for medicine. Sparse data, probabilities and inference in data mining of clinical data repositories, Comput. Biol. Med., 66, 82, 10.1016/j.compbiomed.2015.07.015
Robson, 2016, Studies in using a universal exchange and inference language for evidence based medicine, Semi-Automated Learning and Reasoning for PICO Methodology, Systematic Review, and Environmental Epidemiology”, Computers in Biology and Medicine, 79, 299
Robson, 2018, Studies in the extensively automatic construction of large odds-based inference networks from structured data. Examples from medical, bioinformatics, and Health insurance Claims data, Comput. Biol. Med., 95, 147, 10.1016/j.compbiomed.2018.02.013
Robson, 2020, Extension of the Quantum Universal Exchange Language to precision medicine and drug lead discovery. Preliminary example studies using the mitochondrial genome, Comput. Biol. Med., 117, 10.1016/j.compbiomed.2020.103621
The Biology Workbench
U.S. National Library of Medicine, National center for biotechnology information, national institutes of Health, BLASTP SUITEhttps://blast.ncbi.nlm.nih.gov/Blast.cgi (last accessed 1/28/2020).
Garnier, 1989, 417
De Lima, 1999, Synthesis of angiotensin-converting enzyme (ACE) inhibitors: an important class of antihypertensive drugs, Quim. Nova, 22
Figliozzi, 1996, Chemical synthesis and activity of D, superoxide dismutase, Protein Sci., 5
Robson, 1998
Rai, 2019, Peptide and protein mimetics by retro and retroinverso analogs, Chem. Biol. Drug Des., 93, 724, 10.1111/cbdd.13472
Hagler, 1980, Monte Carlo simulation of water behaviour around the dipeptide N-acetylalanyl-N'methylamide, Science, 208, 599, 10.1126/science.7367882
Robson, 1982, Some views of solvation effects in the light of a Monte Carlo simulation, 66
Robson, 2011, Drug discovery using very large numbers of patents: general strategy with extensive use of match and edit operations, J. Computer Aided Molecular Design, 25, 427, 10.1007/s10822-011-9429-x
Soria-Guerr, 2015, An overview of bioinformatics tools for epitope prediction: implications on vaccine development, J. Biomed. Inf., 53, 405, 10.1016/j.jbi.2014.11.003
Kao, 2009, Advantages of a synthetic peptide immunogen over a protein immunogen in the development of an anti-pilus vaccine for Pseudomonas aeruginosa, Chem. Biol. Drug Des., 74, 33, 10.1111/j.1747-0285.2009.00825.x
Palatnik-de-Sousa1, 2018, Epitope discovery and synthetic vaccine design, Front. Immunol., 9
Grifoni
Wan, 2020, An analysis based on decade-long structural studies of SARS 3, J. Virol., 10.1128/JVI.00127-20
Katz, 2004, Dissecting and designing inhibitor selectivity determinants at the S1 site using an artificial Ala190 protease (Ala190 uPA), J. Mol. Biol., 344, 527, 10.1016/j.jmb.2004.09.032
Lennart, 2017, Different residues in the SARS-CoV spike protein determine cleavage and activation by the host cell protease TMPRSS2, PloS One, 12
Barr’e, 2014, Cleavage specificity analysis of six type II transmembrane serine proteases (TTSPs) using PICS with proteome-derived peptide libraries, PloS One, 9
Ho, 2007, Emodin blocks the SARS coronavirus spike protein and angiotensin-converting enzyme 2 interaction, Antivir. Res., 74, 92, 10.1016/j.antiviral.2006.04.014
Schwarz, 2011, Emodin inhibits current through SARS-associated coronavirus 3a protein, Antivir. Res., 90, 64, 10.1016/j.antiviral.2011.02.008
Adedeji, 2013, Novel inhibitors of severe acute respiratory syndrome coronavirus entry that act by three distinct mechanisms, J. virology, 87, 8017, 10.1128/JVI.00998-13
Feng, 2010, Emodin, a natural product, selectively inhibits 11β-hydroxysteroid dehydrogenase type 1 and ameliorates metabolic disorder in diet-induced obese mice, British Journal of J Pharmacology, 161, 113, 10.1111/j.1476-5381.2010.00826.x
Westphal, 1986, Hydrophobicity and hydrophilicity of steroid binding sites, vol. 27
Kaliamurthi, 2019, Exploring the papillomaviral proteome to identify potential candidates for a chimeric vaccine against cervix papilloma using immunomics and computational structural vaccinology, Viruses, 11, 63, 10.3390/v11010063
Mehmood, 2019, Prediction and validation of potent peptides against herpes simplex virus type 1 via immunoinformatic and systems biology approach, Chem. Biol. Drug Des., 94, 1868, 10.1111/cbdd.13602
Chu, 2019, DTI-CDF: a cascade deep forest model towards the prediction of drug-target interactions based on hybrid features, Briefings Bioinf., 152
Kaushik, 2019
Kaushik, 2020, A-CaMP: a tool for anti-cancer and antimicrobial peptide generation, J. Biomol. Struct. Dyn.
Khan, 2019, Mechanism & inhibition kinetics of bioassay-guided fractions of Indian medicinal plants and foods as ACE inhibitors, J. Tradit., Complementary . Med., 9, 73, 10.1016/j.jtcme.2018.02.001
Niespodziana, 2011, Misdirected antibody responses against an N-terminal epitope on human rhinovirus VP1 as explanation for recurrent RV infections, Faseb. J., 26, 1001, 10.1096/fj.11-193557
Morris, 2006, Cooperative molecular and cellular networks regulate Toll-like receptor-dependent inflammatory responses, Faseb. J., 20, 2153, 10.1096/fj.06-5910fje
Ma-Lauer, 2016, p53 down-regulates SARS coronavirus replication and is targeted by the SARS-unique domain and PLpro via E3 ubiquitin ligase RCHY1, 113, E5192
M. Hoffmann, H. Kleine-Weber, S. Schroeder, N. Krüger, T. Herrler, N-H. Nai-Huei Wu, M.A. Müller, C. Drosten, S. Stefan Pöhlmann, SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor, Cell Press, Available online 5 March 2020. https://doi.org/10.1016/j.cell.2020.02.052.
Di Guardo
Loeffler, 2020, STACKED – Solvation theory of aromatic complexes as key for estimating drug binding, J. Chem. Inf. Model., 10.1021/acs.jcim.9b01165
Fulford, 2000, The jenneration of disease: vaccination, romanticism, and revolution, 39, 139
Hamming, 2004, Tissue distribution of ACE2 protein, the functional receptor for SARS coronavirus. A first step in understanding SARS pathogenesis, J. Pathol., 2203, 631, 10.1002/path.1570
Yang, 2018, 11β-Hydroxysteroid dehydrogenase 1 human tissue distribution, selective inhibitor, and role in doxorubicin, Drug Metabol. Dispos., 46, 1023, 10.1124/dmd.118.081083
Bruley, 2006, A novel promoter for the 11β-hydroxysteroid dehydrogenase type 1 gene is active in lung and is C/EBPα Independent,Charlotte Bruley, val lyons, alan G. F. Worsley, margaret D. Wilde, gretchen D. Darlington, nik M. Morton, jonathan R. Seckl, karen E. Chapman, Endocrinology, 147, 2879, 10.1210/en.2005-1621
Gurwitz, 2020