메뉴 건너뛰기




Volumn 15, Issue 1, 2015, Pages

Human coronavirus OC43 3CL protease and the potential of ML188 as a broad-spectrum lead compound: Homology modelling and molecular dynamic studies

Author keywords

3CLpro; Homology modeling; Human coronavirus; Molecular dynamics; OC43

Indexed keywords

ACETAMIDE DERIVATIVE; CORONAVIRUS 3 CHYMOTRYPSIN LIKE PROTEASE; ENZYME INHIBITOR; LIGAND; N(TERT BUTYL) 2 (N ARYLAMIDO) 2 (PYRIDIN 3 YL)ACETAMIDE; UNCLASSIFIED DRUG; VIRUS ENZYME; 3C-LIKE PROTEASE, SARS CORONAVIRUS; CYSTEINE PROTEINASE; VIRAL PROTEIN;

EID: 84928533657     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/s12900-015-0035-3     Document Type: Article
Times cited : (13)

References (42)
  • 2
    • 27544516178 scopus 로고    scopus 로고
    • Clinical and molecular epidemiological features of coronavirus HKU1- associated community-acquired pneumonia
    • Woo PC, Lau SK, Tsoi H-w, Huang Y, Poon RW, Chu C-m, et al. Clinical and molecular epidemiological features of coronavirus HKU1- associated community-acquired pneumonia. J Infect Dis. 2005; 192 (11): 1898-907.
    • (2005) J Infect Dis. , vol.192 , Issue.11 , pp. 1898-1907
    • Woo, P.C.1    Lau, S.K.2    H-W, T.3    Huang, Y.4    Poon, R.W.5    C-M, C.6
  • 3
    • 0037445549 scopus 로고    scopus 로고
    • An outbreak of coronavirus OC43 respiratory infection in Normandy France
    • Vabret A, Mourez T, Gouarin S, Petitjean J, Freymuth F. An outbreak of coronavirus OC43 respiratory infection in Normandy, France. Clin Infect Dis. 2003; 36 (8): 985-9.
    • (2003) Clin Infect Dis. , vol.36 , Issue.8 , pp. 985-989
    • Vabret, A.1    Mourez, T.2    Gouarin, S.3    Petitjean, J.4    Freymuth, F.5
  • 4
    • 33745157184 scopus 로고    scopus 로고
    • Coronavirus HKU1 and Other Coronavirus Infections in Hong Kong
    • Lau SKP, Woo PCY, Yip CCY, Tse H, Tsoi H, Cheng VCC, et al. Coronavirus HKU1 and Other Coronavirus Infections in Hong Kong. J Clin Microbiol. 2006; 44 (6): 2063-71.
    • (2006) J Clin Microbiol. , vol.44 , Issue.6 , pp. 2063-2071
    • Skp, L.1    Pcy, W.2    Ccy, Y.3    Tse, H.4    Tsoi, H.5    Vcc, C.6
  • 5
    • 65649127759 scopus 로고    scopus 로고
    • Human coronavirus and acute respiratory illness in older adults with chronic obstructive pulmonary disease
    • Gorse GJ, O'Connor TZ, Hall SL, Vitale JN, Nichol KL. Human coronavirus and acute respiratory illness in older adults with chronic obstructive pulmonary disease. J Infect Dis. 2009; 199 (6): 847-57.
    • (2009) J Infect Dis. , vol.199 , Issue.6 , pp. 847-857
    • Gorse, G.J.1    O'Connor, T.Z.2    Hall, S.L.3    Vitale, J.N.4    Nichol, K.L.5
  • 6
    • 84876295728 scopus 로고    scopus 로고
    • Severity and outcome associated with human coronavirus OC43 infections among children
    • Jean A, Quach C, Yung A, Semret M. Severity and outcome associated with human coronavirus OC43 infections among children. Pediatr Infect Dis J. 2013; 32 (4): 325-9.
    • (2013) Pediatr Infect Dis J. , vol.32 , Issue.4 , pp. 325-329
    • Jean, A.1    Quach, C.2    Yung, A.3    Semret, M.4
  • 7
    • 77954217014 scopus 로고    scopus 로고
    • Synthesis docking studies, and evaluation of pyrimidines as inhibitors of SARS-CoV 3CL protease
    • Ramajayam R, Tan KP, Liu HG, Liang PH. Synthesis, docking studies, and evaluation of pyrimidines as inhibitors of SARS-CoV 3CL protease. Bioorg Med Chem Lett. 2010; 20 (12): 3569-72.
    • (2010) Bioorg Med Chem Lett. , vol.20 , Issue.12 , pp. 3569-3572
    • Ramajayam, R.1    Tan, K.P.2    Liu, H.G.3    Liang, P.H.4
  • 8
    • 33751551251 scopus 로고    scopus 로고
    • Drug Design targeting the main protease, the Achilles heel of Coronaviruses
    • Yang H, Bartlam M, Rao Z. Drug Design targeting the main protease, the Achilles heel of Coronaviruses. Curr Pharm Des. 2006; 12 (35): 4573-90.
    • (2006) Curr Pharm Des. , vol.12 , Issue.35 , pp. 4573-4590
    • Yang, H.1    Bartlam, M.2    Rao, Z.3
  • 9
    • 33947376439 scopus 로고    scopus 로고
    • The novel human coronaviruses NL63 and HKU1
    • Pyrc K, Berkhout B, van der Hoek L. The novel human coronaviruses NL63 and HKU1. J Virol. 2007; 81 (7): 3051-7.
    • (2007) J Virol. , vol.81 , Issue.7 , pp. 3051-3057
    • Pyrc, K.1    Berkhout, B.2    Van Der Hoek, L.3
  • 11
    • 0142200324 scopus 로고    scopus 로고
    • Prediction of proteinase cleavage sites in polyproteins of coronaviruses and its applications in analyzing SARS-CoV genomes
    • Gao F, Ou H-Y, Chen L-L, Zheng W-X, Zhang C-T. Prediction of proteinase cleavage sites in polyproteins of coronaviruses and its applications in analyzing SARS-CoV genomes. FEBS Lett. 2003; 553 (3): 451-6.
    • (2003) FEBS Lett. , vol.553 , Issue.3 , pp. 451-456
    • Gao, F.1    Ou, H.-Y.2    Chen, L.-L.3    Zheng, W.-X.4    Zhang, C.-T.5
  • 12
    • 84872775313 scopus 로고    scopus 로고
    • Discovery, synthesis, and structure-based optimization of a series of N- (tert-butyl)- 2- (N-arylamido)-2- (pyridin-3-yl) acetamides (ML188) as potent noncovalent small molecule inhibitors of the severe acute respiratory syndrome coronavirus (SARS-CoV) 3CL protease
    • Jacobs J, Grum-Tokars V, Zhou Y, Turlington M, Saldanha SA, Chase P, et al. Discovery, synthesis, and structure-based optimization of a series of N- (tert-butyl)- 2- (N-arylamido)-2- (pyridin-3-yl) acetamides (ML188) as potent noncovalent small molecule inhibitors of the severe acute respiratory syndrome coronavirus (SARS-CoV) 3CL protease. J Med Chem. 2013; 56 (2): 534-46.
    • (2013) J Med Chem. , vol.56 , Issue.2 , pp. 534-546
    • Jacobs, J.1    Grum-Tokars, V.2    Zhou, Y.3    Turlington, M.4    Saldanha, S.A.5    Chase, P.6
  • 13
    • 26444498493 scopus 로고    scopus 로고
    • Design of wide-spectrum inhibitors targeting coronavirus main proteases
    • Yang H, Xie W, Xue X, Yang K, Ma J, Liang W, et al. Design of wide-spectrum inhibitors targeting coronavirus main proteases. PLoS Biol. 2005; 3 (10), e324.
    • (2005) PLoS Biol. , vol.3 , Issue.10 , pp. e324
    • Yang, H.1    Xie, W.2    Xue, X.3    Yang, K.4    Ma, J.5    Liang, W.6
  • 14
    • 65549145945 scopus 로고    scopus 로고
    • Structural basis of inhibition specificities of 3C and 3C-like proteases by zinc-coordinating and peptidomimetic compounds
    • Lee CC, Kuo CJ, Ko TP, Hsu MF, Tsui YC, Chang SC, et al. Structural basis of inhibition specificities of 3C and 3C-like proteases by zinc-coordinating and peptidomimetic compounds. J Biol Chem. 2009; 284 (12): 7646-55.
    • (2009) J Biol Chem. , vol.284 , Issue.12 , pp. 7646-7655
    • Lee, C.C.1    Kuo, C.J.2    Ko, T.P.3    Hsu, M.F.4    Tsui, Y.C.5    Chang, S.C.6
  • 15
    • 50149107929 scopus 로고    scopus 로고
    • Structure of the main protease from a global infectious human coronavirus, HCoV-HKU1
    • Zhao Q, Li S, Xue F, Zou Y, Chen C, Bartlam M, et al. Structure of the main protease from a global infectious human coronavirus, HCoV-HKU1. J Virol. 2008; 82 (17): 8647-55.
    • (2008) J Virol. , vol.82 , Issue.17 , pp. 8647-8655
    • Zhao, Q.1    Li, S.2    Xue, F.3    Zou, Y.4    Chen, C.5    Bartlam, M.6
  • 16
    • 0036187709 scopus 로고    scopus 로고
    • Conservation of substrate specificities among coronavirus main proteases
    • Hegyi A, Ziebuhr J. Conservation of substrate specificities among coronavirus main proteases. J Gen Virol. 2002; 83 (3): 595-9.
    • (2002) J Gen Virol. , vol.83 , Issue.3 , pp. 595-599
    • Hegyi, A.1    Ziebuhr, J.2
  • 17
    • 80355146292 scopus 로고    scopus 로고
    • Profiling of substrate specificities of 3C-like proteases from group 1, 2a, 2b, and 3 coronaviruses
    • Chuck C-P, Chow H-F, Wan DC-C, Wong K-B. Profiling of substrate specificities of 3C-like proteases from group 1, 2a, 2b, and 3 coronaviruses. PLoS One. 2011; 6 (11), e27228.
    • (2011) PLoS One. , vol.6 , Issue.11 , pp. e27228
    • Chuck, C.-P.1    Chow, H.-F.2    Dc-C, W.3    Wong, K.-B.4
  • 18
    • 0038120984 scopus 로고    scopus 로고
    • Coronavirus main proteinase (3CLpro) structure: Basis for design of anti-SARS drugs
    • Anand K, Ziebuhr J, Wadhwani P, Mesters JR, Hilgenfeld R. Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs. Science. 2003; 300 (5626): 1763-7.
    • (2003) Science , vol.300 , Issue.5626 , pp. 1763-1767
    • Anand, K.1    Ziebuhr, J.2    Wadhwani, P.3    Mesters, J.R.4    Hilgenfeld, R.5
  • 19
    • 39749091131 scopus 로고    scopus 로고
    • Structures of two coronavirus main proteases: Implications for substrate binding and antiviral drug design
    • Xue X, Yu H, Yang H, Xue F, Wu Z, Shen W, et al. Structures of two coronavirus main proteases: implications for substrate binding and antiviral drug design. J Virol. 2008; 82 (5): 2515-27.
    • (2008) J Virol. , vol.82 , Issue.5 , pp. 2515-2527
    • Xue, X.1    Yu, H.2    Yang, H.3    Xue, F.4    Wu, Z.5    Shen, W.6
  • 20
    • 24744432305 scopus 로고    scopus 로고
    • Mechanism of the maturation process of SARS-CoV 3CL protease
    • Hsu MF, Kuo CJ, Chang KT, Chang HC, Chou CC, Ko TP, et al. Mechanism of the maturation process of SARS-CoV 3CL protease. J Biol Chem. 2005; 280 (35): 31257-66.
    • (2005) J Biol Chem. , vol.280 , Issue.35 , pp. 31257-31266
    • Hsu, M.F.1    Kuo, C.J.2    Chang, K.T.3    Chang, H.C.4    Chou, C.C.5    Ko, T.P.6
  • 21
    • 0034072633 scopus 로고    scopus 로고
    • Virus-encoded proteinases and proteolytic processing in the Nidovirales
    • Ziebuhr J, Snijder EJ, Gorbalenya AE. Virus-encoded proteinases and proteolytic processing in the Nidovirales. J Gen Virol. 2000; 81 (4): 853-79.
    • (2000) J Gen Virol. , vol.81 , Issue.4 , pp. 853-879
    • Ziebuhr, J.1    Snijder, E.J.2    Gorbalenya, A.E.3
  • 22
    • 0028051828 scopus 로고
    • Derivation of rules for comparative protein modeling from a database of protein structure alignments
    • Šali A, Overington JP. Derivation of rules for comparative protein modeling from a database of protein structure alignments. Protein Sci. 1994; 3 (9): 1582-96.
    • (1994) Protein Sci. , vol.3 , Issue.9 , pp. 1582-1596
    • Šali, A.1    Overington, J.P.2
  • 23
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Šali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol. 1993; 234 (3): 779-815.
    • (1993) J Mol Biol. , vol.234 , Issue.3 , pp. 779-815
    • Šali, A.1    Blundell, T.L.2
  • 24
    • 32144432437 scopus 로고    scopus 로고
    • The SWISS-MODEL workspace: A web-based environment for protein structure homology modelling
    • Arnold K, Bordoli L, Kopp J, Schwede T. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics. 2006; 22 (2): 195-201.
    • (2006) Bioinformatics. , vol.22 , Issue.2 , pp. 195-201
    • Arnold, K.1    Bordoli, L.2    Kopp, J.3    Schwede, T.4
  • 25
    • 43949095157 scopus 로고    scopus 로고
    • On the applicability of GPCR homology models to computer-aided drug discovery: A comparison between in silico and crystal structures of the β2-adrenergic receptor
    • Costanzi S. On the applicability of GPCR homology models to computer-aided drug discovery: a comparison between in silico and crystal structures of the β2-adrenergic receptor. J Med Chem. 2008; 51 (10): 2907-14.
    • (2008) J Med Chem. , vol.51 , Issue.10 , pp. 2907-2914
    • Costanzi, S.1
  • 27
    • 33846028793 scopus 로고    scopus 로고
    • Insight into the activity of SARS main protease: Molecular dynamics study of dimeric and monomeric form of enzyme
    • Zheng K, Ma G, Zhou J, Zen M, Zhao W, Jiang Y, et al. Insight into the activity of SARS main protease: Molecular dynamics study of dimeric and monomeric form of enzyme. Proteins. 2007; 66 (2): 467-79.
    • (2007) Proteins. , vol.66 , Issue.2 , pp. 467-479
    • Zheng, K.1    Ma, G.2    Zhou, J.3    Zen, M.4    Zhao, W.5    Jiang, Y.6
  • 28
    • 0035855917 scopus 로고    scopus 로고
    • Ordered water and ligand mobility in the HIV-1 integrase-5CITEP complex: A molecular dynamics study
    • Ni H, Sotriffer CA, McCammon JA. Ordered water and ligand mobility in the HIV-1 integrase-5CITEP complex: a molecular dynamics study. J Med Chem. 2001; 44 (19): 3043-7.
    • (2001) J Med Chem. , vol.44 , Issue.19 , pp. 3043-3047
    • Ni, H.1    Sotriffer, C.A.2    McCammon, J.A.3
  • 29
    • 84986483798 scopus 로고
    • The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies
    • Eisenhaber F, Lijnzaad P, Argos P, Sander C, Scharf M. The double cubic lattice method: efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies. J Comput Chem. 1995; 16 (3): 273-84.
    • (1995) J Comput Chem. , vol.16 , Issue.3 , pp. 273-284
    • Eisenhaber, F.1    Lijnzaad, P.2    Argos, P.3    Sander, C.4    Scharf, M.5
  • 30
    • 0041784950 scopus 로고    scopus 로고
    • All-atom empirical potential for molecular modeling and dynamics studies of proteins
    • MacKerell AD, Bashford D, Bellott M, Dunbrack R, Evanseck J, Field MJ, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B. 1998; 102 (18): 3586-616.
    • (1998) J Phys Chem B. , vol.102 , Issue.18 , pp. 3586-3616
    • Mackerell, A.D.1    Bashford, D.2    Bellott, M.3    Dunbrack, R.4    Evanseck, J.5    Field, M.J.6
  • 31
    • 33749578940 scopus 로고    scopus 로고
    • Statistical potential for assessment and prediction of protein structures
    • My S, Šali A. Statistical potential for assessment and prediction of protein structures. Protein Sci. 2006; 15 (11): 2507-24.
    • (2006) Protein Sci. , vol.15 , Issue.11 , pp. 2507-2524
    • My, S.1    Šali, A.2
  • 33
    • 34547566446 scopus 로고    scopus 로고
    • ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins
    • Wiederstein M, Sippl MJ. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res. 2007; 35 suppl 2: W407-10.
    • (2007) Nucleic Acids Res , vol.35 , pp. W407-W410
    • Wiederstein, M.1    Sippl, M.J.2
  • 34
    • 0027490731 scopus 로고
    • Recognition of errors in three-dimensional structures of proteins
    • Sippl MJ. Recognition of errors in three-dimensional structures of proteins. Proteins: Struct, Funct, Bioinf. 1993; 17 (4): 355-62.
    • (1993) Proteins: Struct, Funct, Bioinf. , vol.17 , Issue.4 , pp. 355-362
    • Sippl, M.J.1
  • 35
    • 0000243829 scopus 로고
    • PROCHECK: A program to check the stereochemical quality of protein structures
    • Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr. 1993; 26 (2): 283-91.
    • (1993) J Appl Crystallogr. , vol.26 , Issue.2 , pp. 283-291
    • Laskowski, R.A.1    Macarthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 36
    • 0001513484 scopus 로고
    • PROCHECK: A program to produce both detailed and schematic plots of proteins
    • Laskowski R, MacArthur M, Moss D, Thornton J. PROCHECK: A program to produce both detailed and schematic plots of proteins. J Appl Crystallogr. 1993; 24: 946-56.
    • (1993) J Appl Crystallogr. , vol.24 , pp. 946-956
    • Laskowski, R.1    Macarthur, M.2    Moss, D.3    Thornton, J.4
  • 37
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
    • Jorgensen WL, Maxwell DS, Tirado-Rives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc. 1996; 118 (45): 11225-36.
    • (1996) J Am Chem Soc. , vol.118 , Issue.45 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 38
    • 77952415408 scopus 로고    scopus 로고
    • Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field
    • Shivakumar D, Williams J, Wu Y, Damm W, Shelley J, Sherman W. Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field. J Chem Theory Computation. 2010; 6 (5): 1509-19.
    • (2010) J Chem Theory Computation. , vol.6 , Issue.5 , pp. 1509-1519
    • Shivakumar, D.1    Williams, J.2    Wu, Y.3    Damm, W.4    Shelley, J.5    Sherman, W.6
  • 39
    • 0036310711 scopus 로고    scopus 로고
    • On the role of the crystal environment in determining protein side-chain conformations
    • Jacobson MP, Friesner RA, Xiang Z, Honig B. On the role of the crystal environment in determining protein side-chain conformations. J Mol Biol. 2002; 320 (3): 597-608.
    • (2002) J Mol Biol. , vol.320 , Issue.3 , pp. 597-608
    • Jacobson, M.P.1    Friesner, R.A.2    Xiang, Z.3    Honig, B.4
  • 41
    • 79958841703 scopus 로고    scopus 로고
    • SwissParam: A fast force field generation tool for small organic molecules
    • Zoete V, Cuendet MA, Grosdidier A, Michielin O. SwissParam: a fast force field generation tool for small organic molecules. J Comput Chem. 2011; 32 (11): 2359-68.
    • (2011) J Comput Chem. , vol.32 , Issue.11 , pp. 2359-2368
    • Zoete, V.1    Cuendet, M.A.2    Grosdidier, A.3    Michielin, O.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.