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Volumn 31, Issue 7, 2013, Pages 765-778

Molecular modeling, dynamics, and an insight into the structural inhibition of cofactor independent phosphoglycerate mutase isoform 1 from Wuchereria bancrofti using cheminformatics and mutational studies

Author keywords

MM GBSA; Molecular docking; Molecular dynamics simulation; Molecular modeling; Phosphoglycerate mutase; Virtual screening

Indexed keywords

ANTHELMINTIC AGENT; AZANIUM PYRROLIDINE 1 CARBODITHIOIC ACID; BISPHOSPHOGLYCERATE MUTASE; BISPHOSPHOGLYCERATE MUTASE 1; CYCLOLEUCYLGLYCINE; ENOLASE; ENZYME INHIBITOR; HISTAMINE; INDEPENDENT PHOSPHOGLYCERATE MUTASE; LACTACYSTIN BETA LACTONE; MECYSTEINE; METHYL(PHENYL THIO)ACETIC ACID; N ACETYLTRYPTOPHAN; PHOSPHOGLYCERATE KINASE; UNCLASSIFIED DRUG;

EID: 84880227818     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2012.709460     Document Type: Article
Times cited : (11)

References (45)
  • 2
    • 34548206866 scopus 로고    scopus 로고
    • Molecular dynamics studies of AChBP with nicotine and carbamylcholine: The role of water in the binding pocket
    • Amiri, S., Sansom, M.S., & Biggin, P.C. (2007). Molecular dynamics studies of AChBP with nicotine and carbamylcholine: The role of water in the binding pocket. Protein Engineering, Design & Selection, 20, 353-359.
    • (2007) Protein Engineering, Design & Selection , vol.20 , pp. 353-359
    • Amiri, S.1    Sansom, M.S.2    Biggin, P.C.3
  • 6
    • 15044362303 scopus 로고    scopus 로고
    • Energy generation in insect stages of Trypanosoma brucei: Metabolism in flux
    • Besteiro, S., Barrett, M.P., Riviere, L., & Bringaud, F. (2005). Energy generation in insect stages of Trypanosoma brucei: Metabolism in flux. Trends in Parasitology, 21, 185-191.
    • (2005) Trends in Parasitology , vol.21 , pp. 185-191
    • Besteiro, S.1    Barrett, M.P.2    Riviere, L.3    Bringaud, F.4
  • 7
    • 0033563772 scopus 로고    scopus 로고
    • Structural studies on a 2,3-diphosphoglycerate independent phosphoglycerate mutase from Bacillus stearothermophilus
    • Chander, M., Setlow, P., Lamani, E., & Jedrzejas, M.J. (1999). Structural studies on a 2,3-diphosphoglycerate independent phosphoglycerate mutase from Bacillus stearothermophilus. Journal of Structural Biology, 126, 156-165.
    • (1999) Journal of Structural Biology , vol.126 , pp. 156-165
    • Chander, M.1    Setlow, P.2    Lamani, E.3    Jedrzejas, M.J.4
  • 9
    • 0030767485 scopus 로고    scopus 로고
    • VERIFY3D: Assessment of protein models with three-dimensional profiles
    • Eisenberg, D., Luthy, R., & Bowie, J.U. (1997). VERIFY3D: Assessment of protein models with three-dimensional profiles. Methods in Enzymology, 277, 396-404.
    • (1997) Methods in Enzymology , vol.277 , pp. 396-404
    • Eisenberg, D.1    Luthy, R.2    Bowie, J.U.3
  • 12
    • 0035082495 scopus 로고    scopus 로고
    • Identification of related proteins with weak sequence identity using secondary structure information
    • Geourjon, C., Combet, C., Blanchet, C., & Deleage, G. (2001). Identification of related proteins with weak sequence identity using secondary structure information. Protein Science, 10, 788-797.
    • (2001) Protein Science , vol.10 , pp. 788-797
    • Geourjon, C.1    Combet, C.2    Blanchet, C.3    Deleage, G.4
  • 15
    • 0033824470 scopus 로고    scopus 로고
    • DaliLite workbench for protein structure comparison
    • Holm, L., & Park, J. (2000). DaliLite workbench for protein structure comparison. Bioinformatics, 16, 566-567.
    • (2000) Bioinformatics , vol.16 , pp. 566-567
    • Holm, L.1    Park, J.2
  • 16
    • 70349553668 scopus 로고    scopus 로고
    • An allele specific PCR assay for screening for drug resistance among Wuchereria bancrofti populations in India
    • Hoti, S.L., Dhamodharan, R., Subramaniyan, K., & Das, P.K. (2009). An allele specific PCR assay for screening for drug resistance among Wuchereria bancrofti populations in India. Indian Journal of Medical Research, 130, 193-199.
    • (2009) Indian Journal of Medical Research , vol.130 , pp. 193-199
    • Hoti, S.L.1    Dhamodharan, R.2    Subramaniyan, K.3    Das, P.K.4
  • 17
    • 0030039296 scopus 로고    scopus 로고
    • PROMOTIF - A program to identify and analyze structural motifs in proteins
    • Hutchinson, E.G., & Thornton, J.M. (1996). PROMOTIF-a program to identify and analyze structural motifs in proteins. Protein Science, 5, 212-220.
    • (1996) Protein Science , vol.5 , pp. 212-220
    • Hutchinson, E.G.1    Thornton, J.M.2
  • 19
    • 0036428851 scopus 로고    scopus 로고
    • The structure and function of novel proteins of Bacillus anthracis and other spore-forming bacteria: Development of novel prophylactic and therapeutic agents
    • Jedrzejas, M.J. (2002). The structure and function of novel proteins of Bacillus anthracis and other spore-forming bacteria: Development of novel prophylactic and therapeutic agents. Critical Reviews in Biochemistry and Molecular Biology, 37, 339-373.
    • (2002) Critical Reviews in Biochemistry and Molecular Biology , vol.37 , pp. 339-373
    • Jedrzejas, M.J.1
  • 20
    • 0034725637 scopus 로고    scopus 로고
    • Mechanism of catalysis of the cofactor-independent phosphoglycerate mutase from Bacillus stearothermophilus. Crystal structure of the complex with 2-phosphoglycerate
    • Jedrzejas, M.J., Chander, M., Setlow, P., & Krishnasamy, G. (2000). Mechanism of catalysis of the cofactor-independent phosphoglycerate mutase from Bacillus stearothermophilus. Crystal structure of the complex with 2-phosphoglycerate. Journal of Biological Chemistry, 275, 23146-23153.
    • (2000) Journal of Biological Chemistry , vol.275 , pp. 23146-23153
    • Jedrzejas, M.J.1    Chander, M.2    Setlow, P.3    Krishnasamy, G.4
  • 21
    • 0033990053 scopus 로고    scopus 로고
    • The NCBI. Publicly available tools and resources on the Web
    • Jenuth, J.P. (2000). The NCBI. Publicly available tools and resources on the Web. Methods in Molecular Biology, 132, 301-312.
    • (2000) Methods in Molecular Biology , vol.132 , pp. 301-312
    • Jenuth, J.P.1
  • 22
    • 77957935995 scopus 로고    scopus 로고
    • Cheminformatics-based drug design approach for identification of inhibitors targeting the characteristic residues of MMP-13 hemopexin domain
    • doi:10.1371/journal.pone.0012494
    • Kothapalli, R., Khan, A.M., Basappa, Gopalsamy, A., & Chong, Y.S. (2010). Cheminformatics-based drug design approach for identification of inhibitors targeting the characteristic residues of MMP-13 hemopexin domain. PLoS One 5. doi:10.1371/journal.pone.0012494
    • (2010) PLoS One , pp. 5
    • Kothapalli, R.1    Khan, A.M.2    Basappa Gopalsamy, A.3    Chong, Y.S.4
  • 23
    • 0035175679 scopus 로고    scopus 로고
    • PDBsum: Summaries and analyses of PDB structures
    • Laskowski, R.A. (2001). PDBsum: Summaries and analyses of PDB structures. Nucleic Acids Research, 29, 221-222.
    • (2001) Nucleic Acids Research , vol.29 , pp. 221-222
    • Laskowski, R.A.1
  • 25
    • 18744394070 scopus 로고    scopus 로고
    • Q-SiteFinder: An energy-based method for the prediction of protein-ligand binding sites
    • Laurie, A.T., & Jackson, R.M. (2005). Q-SiteFinder: An energy-based method for the prediction of protein-ligand binding sites. Bioinformatics, 21, 1908-1916.
    • (2005) Bioinformatics , vol.21 , pp. 1908-1916
    • Laurie, A.T.1    Jackson, R.M.2
  • 26
    • 0023203461 scopus 로고
    • Cyclo (Leu-Gly) attenuates the striatal dopaminergic supersensitivity induced by chronic morphine
    • Lee, J.M., DeLeon-Jones, F., Fields, J.Z., & Ritzmann, R.F. (1987). Cyclo (Leu-Gly) attenuates the striatal dopaminergic supersensitivity induced by chronic morphine. Alcohol and Drug Research, 7, 1-10.
    • (1987) Alcohol and Drug Research , vol.7 , pp. 1-10
    • Lee, J.M.1    Deleon-Jones, F.2    Fields, J.Z.3    Ritzmann, R.F.4
  • 27
    • 0028336824 scopus 로고
    • Cloning and nucleotide sequences of the genes encoding triose phosphate isomerase, phosphoglycerate mutase, and enolase from Bacillus subtilis
    • Leyva-Vazquez, M.A., & Setlow, P. (1994). Cloning and nucleotide sequences of the genes encoding triose phosphate isomerase, phosphoglycerate mutase, and enolase from Bacillus subtilis. Journal of Bacteriology, 176, 3903-3910.
    • (1994) Journal of Bacteriology , vol.176 , pp. 3903-3910
    • Leyva-Vazquez, M.A.1    Setlow, P.2
  • 28
    • 79952900210 scopus 로고    scopus 로고
    • Identification and characterization of the cofactor-independent phosphoglycerate mutases of Dirofilaria immitis and its Wolbachia endosymbiont
    • Li, Z., Galvin, B.D., Raverdy, S., & Carlow, C.K. (2011). Identification and characterization of the cofactor-independent phosphoglycerate mutases of Dirofilaria immitis and its Wolbachia endosymbiont. Veterinary Parasitology, 176, 350-356.
    • (2011) Veterinary Parasitology , vol.176 , pp. 350-356
    • Li, Z.1    Galvin, B.D.2    Raverdy, S.3    Carlow, C.K.4
  • 30
    • 43149095780 scopus 로고    scopus 로고
    • Identification of human-to-human transmissibility factors in PB2 proteins of influenza A by large-scale mutual information analysis
    • Miotto, O., Heiny, A., Tan, T.W., August, J.T., & Brusic, V. (2008). Identification of human-to-human transmissibility factors in PB2 proteins of influenza A by large-scale mutual information analysis. BMC Bioinformatics, 9(Suppl 1), S18.
    • (2008) BMC Bioinformatics , vol.9 , Issue.SUPPL. 1
    • Miotto, O.1    Heiny, A.2    Tan, T.W.3    August, J.T.4    Brusic, V.5
  • 31
    • 79551583902 scopus 로고    scopus 로고
    • The binding modes and binding affinities of artemisinin derivatives with Plasmodium falciparum Ca2+-ATPase (PfATP6)
    • Naik, P.K., Srivastava, M., Bajaj, P., Jain, S., Dubey, A., Ranjan, P., ... Singh, H. (2011). The binding modes and binding affinities of artemisinin derivatives with Plasmodium falciparum Ca2+-ATPase (PfATP6). Journal of Molecular Modeling, 17, 333-357.
    • (2011) Journal of Molecular Modeling , vol.17 , pp. 333-357
    • Naik, P.K.1    Srivastava, M.2    Bajaj, P.3    Jain, S.4    Dubey, A.5    Ranjan, P.6    Singh, H.7
  • 32
    • 0033198038 scopus 로고    scopus 로고
    • The role of albendazole in programmes to eliminate lymphatic filariasis
    • Ottesen, E.A., Ismail, M.M., & Horton, J. (1999). The role of albendazole in programmes to eliminate lymphatic filariasis. Parasitology Today, 15, 382-386.
    • (1999) Parasitology Today , vol.15 , pp. 382-386
    • Ottesen, E.A.1    Ismail, M.M.2    Horton, J.3
  • 33
    • 0019707626 scopus 로고
    • Polymorphic transitions in single crystals: A new molecular dynamics method
    • Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52, 7182-7191.
    • (1981) Journal of Applied Physics , vol.52 , pp. 7182-7191
    • Parrinello, M.1    Rahman, A.2
  • 34
    • 35348938128 scopus 로고    scopus 로고
    • Molecular and biochemical characterization of nematode cofactor independent phosphoglycerate mutases
    • Raverdy, S., Zhang, Y., Foster, J., & Carlow, C.K. (2007). Molecular and biochemical characterization of nematode cofactor independent phosphoglycerate mutases. Molecular and Biochemical Parasitology, 156, 210-216.
    • (2007) Molecular and Biochemical Parasitology , vol.156 , pp. 210-216
    • Raverdy, S.1    Zhang, Y.2    Foster, J.3    Carlow, C.K.4
  • 35
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali, A., & Blundell, T.L. (1993). Comparative protein modelling by satisfaction of spatial restraints. Journal of Molecular Biology, 234, 779-815.
    • (1993) Journal of Molecular Biology , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 36
    • 7544226311 scopus 로고    scopus 로고
    • PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica. Section D
    • Schuttelkopf, A.W., & van Aalten, D.M. (2004). PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica. Section D, Biological Crystallography, 60, 1355-1363.
    • (2004) Biological Crystallography , vol.60 , pp. 1355-1363
    • Schuttelkopf, A.W.1    Van Aalten, D.M.2
  • 38
    • 84866417258 scopus 로고    scopus 로고
    • Modeling, docking, simulation, and inhibitory activity of the benzimidazole analogue against β- Tubulin protein from Brugia malayi for treating lymphatic filariasis
    • doi:10.1007/ s00044-011-9763-9765
    • Sharma, O.P., Pan, A., Hoti, S.L., Jadhav, A., Kannan, M., & Mathur, P.P. (2011). Modeling, docking, simulation, and inhibitory activity of the benzimidazole analogue against β- tubulin protein from Brugia malayi for treating lymphatic filariasis. Medicinal Chemistry Research. doi:10.1007/ s00044-011-9763-5.
    • (2011) Medicinal Chemistry Research
    • Sharma, O.P.1    Pan, A.2    Hoti, S.L.3    Jadhav, A.4    Kannan, M.5    Mathur, P.P.6
  • 39
    • 77954762177 scopus 로고    scopus 로고
    • Benzimidazole resistance allele haplotype diversity in United Kingdom isolates of Teladorsagia circumcincta supports a hypothesis of multiple origins of resistance by recurrent mutation
    • Skuce, P., Stenhouse, L., Jackson, F., Hypsa, V., & Gilleard, J. (2010). Benzimidazole resistance allele haplotype diversity in United Kingdom isolates of Teladorsagia circumcincta supports a hypothesis of multiple origins of resistance by recurrent mutation. International Journal for Parasitology, 40, 1247-1255.
    • (2010) International Journal for Parasitology , vol.40 , pp. 1247-1255
    • Skuce, P.1    Stenhouse, L.2    Jackson, F.3    Hypsa, V.4    Gilleard, J.5
  • 40
    • 0035132705 scopus 로고    scopus 로고
    • Selecting the right compounds for screening: Does Lipinski's Rule of 5 for pharmaceuticals apply to agrochemicals?
    • Tice, C.M. (2001). Selecting the right compounds for screening: Does Lipinski's Rule of 5 for pharmaceuticals apply to agrochemicals? Pest Management Science, 57, 3-16.
    • (2001) Pest Management Science , vol.57 , pp. 3-16
    • Tice, C.M.1
  • 41
    • 6044236552 scopus 로고    scopus 로고
    • Analysis for free: Comparing programs for sequence analysis
    • Tippmann, H.F. (2004). Analysis for free: Comparing programs for sequence analysis. Briefings in Bioinformatics, 5, 82- 87.
    • (2004) Briefings in Bioinformatics , vol.5 , pp. 82-87
    • Tippmann, H.F.1
  • 43
    • 77956235807 scopus 로고    scopus 로고
    • Optimizing working parameters of the smooth particle mesh Ewald algorithm in terms of accuracy and efficiency
    • Wang, H., Dommert, F., & Holm, C. (2010). Optimizing working parameters of the smooth particle mesh Ewald algorithm in terms of accuracy and efficiency. Journal of Chemical Physics, 133, 034117.
    • (2010) Journal of Chemical Physics , vol.133 , pp. 034117
    • Wang, H.1    Dommert, F.2    Holm, C.3
  • 44
    • 33847607391 scopus 로고    scopus 로고
    • Modifying the OPLS-AA force field to improve hydration free energies for several amino acid side chains using new atomic charges and an off-plane charge model for aromatic residues
    • Xu, Z., Luo, H.H., & Tieleman, D.P. (2007). Modifying the OPLS-AA force field to improve hydration free energies for several amino acid side chains using new atomic charges and an off-plane charge model for aromatic residues. Journal of Computational Chemistry, 28, 689-697.
    • (2007) Journal of Computational Chemistry , vol.28 , pp. 689-697
    • Xu, Z.1    Luo, H.H.2    Tieleman, D.P.3
  • 45
    • 4344566444 scopus 로고    scopus 로고
    • Cofactor-independent phosphoglycerate mutase has an essential role in Caenorhabditis elegans and is conserved in parasitic nematodes
    • Zhang, Y., Foster, J.M., Kumar, S., Fougere, M., & Carlow, C. K. (2004). Cofactor-independent phosphoglycerate mutase has an essential role in Caenorhabditis elegans and is conserved in parasitic nematodes. Journal of Biological Chemistry, 279, 37185-37190.
    • (2004) Journal of Biological Chemistry , vol.279 , pp. 37185-37190
    • Zhang, Y.1    Foster, J.M.2    Kumar, S.3    Fougere, M.4    Carlow, C.K.5


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