Validation on the molecular docking efficiency of lipocalin family of proteins

Sriram Sokalingam; Ganapathiraman Munussami; Jung-Rae Kim; Sun-Gu Lee

Journal of Industrial and Engineering Chemistry, Vol.67, 293-300, November, 2018

DOI10.1016/j.jiec.2018.06.041 Export Citation

Validation on the molecular docking efficiency of lipocalin family of proteins

Sriram Sokalingam, Ganapathiraman Munussami, Jung-Rae Kim, and Sun-Gu Lee^†

Department of Chemical Engineering, Pusan National University, Busan, Republic of Korea

E-mail:

Lipocalins are diverse group of small extracellular proteins found in various organisms. In this study, members of 10 non-homologous lipocalin.ligand crystal complex structures were remodeled using rigid and flexible ligand modes to validate the prediction efficiency of molecular docking simulation. The modeled ligand conformations indicated a high prediction accuracy in rigid ligand mode using cluster based analysis for most cases whereas the flexible ligand mode required further considerations such as ligand binding energy and RMSD for some cases. This in silico study is expected to serve as a platform in the screening of novel ligands against lipocalin family of proteins.

Keywords:Lipocalins;Ligand-binding;Molecular docking simulation;Protein engineering

[References]

Flower DR, J. Mol. Recognit., 8, 185 (1995)
Akerstrom B, Flower DR, Salier JP, Biochim. Biophys. Acta, 1482, 1 (2000)
Pervaiz S, Brew K, FASEB J., 1, 209 (1987)
Flower DR, Febs Lett., 354, 7 (1994)
Flower DR, Biochem. J., 318(Pt. 1), 1 (1996)
Cowan SW, Newcomer ME, Jones TA, Proteins, 8, 44 (1990)
Flower DR, North AC, Sansom CE, Biochim. Biophys. Acta, 1482, 9 (2000)
Gebauer M, Skerra A, Curr. Opin. Chem. Biol., 13, 245 (2009)
Richter A, Eggenstein E, Skerra A, Febs Lett., 588, 213 (2014)
Mishra J, Dent C, Tarabishi R, Mitsnefes MM, Ma Q, Kelly C, Ruff SM, Zahedi K, Shao M, Bean J, Mori K, Barasch J, Devarajan P, Lancet, 365, 1231 (2005)
Hochepied T, Berger FG, Baumann H, Libert C, Cytokine Growth Factor Rev., 14, 25 (2003)
Xu S, Venge P, Biochim. Biophys. Acta Protein Struct. Mol. Enzymol., 1482, 298 (2000)
Bruno R, Olivares R, Berille J, Chaikin P, Vivier N, Hammershaimb L, Rhodes GR, Rigas JR, Clin. Cancer Res., 9, 1077 (2003)
Vincent C, Kew MC, Bouic P, Flacher M, Revillard JP, Br. J. Cancer, 59, 415 (1989)
Mantyjarvi R, Rautiainen J, Virtanen T, Biochim. Biophys. Acta, 1482, 308 (2000)
Teraoka Y, Kume S, Lin Y, Atsuji S, Inui T, Mol. Pharm., 14, 3558 (2017)
Jensen-Jarolim E, Pacios L, Bianchini R, Hofstetter G, Roth-Walter F, Allergy, 71, 286 (2016)
Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, et al., Acta Crystallogr. Sect. D-Biol. Crystallogr., 58, 899 (2002)
Acharya KR, Lloyd MD, Trends Pharmacol. Sci., 26, 10 (2005)
Pagadala NS, Syed K, Tuszynski J, Biophys. Rev., 9, 91 (2017)
Sousa SF, Fernandes PA, Ramos MJ, Proteins, 65, 15 (2006)
Morris GM, Huey R, Lindstrom W, Sanner WF, Belew RK, Goodsell DS, Olson AJ, J. Comput. Chem., 30, 2785 (2009)
Dassault Systemes BIOVIA, Discovery Studio Modeling Environment, Release 2017, San Diego: Dassault Systemes, 2017.
Bocskei Z, Groom CR, Flower DR, Wright CE, Phillips SEV, Cavaggioni A, Findlay JBC, North ACT, Nature, 360, 186 (1992)
Kuser PR, Franzoni L, Ferrari E, Spisni A, Polikarpov I, Acta Crystallogr. Sect. D-Biol. Crystallogr., 57, 1863 (2001)
Silvaroli JA, Arne JM, Chelstowska S, Kiser PD, Banerjee S, Golczak M, J. Biol. Chem., 291, 8528 (2016)
Kleywegt GJ, Bergfors T, Senn H, Le Motte P, Gsell B, Shudo K, Jones TA, Structure, 2, 1241 (1994)
Huber R, Schneider M, Mayr I, Muller R, Deutzmann R, Suter F, Zuber H, Falk H, Kayser H, J. Mol. Biol., 198, 499 (1987)
Cianci M, Rizkallah PJ, Olczak A, Raftery J, Chayen NE, Zagalsky PF, Helliwell JR, Proc. Natl. Acad. Sci. U. S. A., 99, 9795 (2002)
Eichinger A, Nasreen A, Kim HJ, Skerra A, J. Biol. Chem., 282, 31068 (2007)
Ramoni R, Vincent F, Grolli S, Conti V, Malosse C, Boyer FD, Nagnan-Le Meillour P, Spinelli S, Cambillau C, Tegoni M, J. Biol. Chem., 276, 7150 (2001)
Kontopidis G, Holt C, Sawyer L, J. Mol. Biol., 318, 1043 (2002)
Paesen GC, Adams PL, Harlos K, Nuttall PA, Stuart DI, Mol. Cell, 3, 661 (1999)
Weichsel A, Berry RE, Walker FA, Montfort WR, a nitric oxide transport protein from rhodnius prolixus.

[1] Flower DR, J. Mol. Recognit., 8, 185 (1995)

[2] Akerstrom B, Flower DR, Salier JP, Biochim. Biophys. Acta, 1482, 1 (2000)

[3] Pervaiz S, Brew K, FASEB J., 1, 209 (1987)

[4] Flower DR, Febs Lett., 354, 7 (1994)

[5] Flower DR, Biochem. J., 318(Pt. 1), 1 (1996)

[6] Cowan SW, Newcomer ME, Jones TA, Proteins, 8, 44 (1990)

[7] Flower DR, North AC, Sansom CE, Biochim. Biophys. Acta, 1482, 9 (2000)

[8] Gebauer M, Skerra A, Curr. Opin. Chem. Biol., 13, 245 (2009)

[9] Richter A, Eggenstein E, Skerra A, Febs Lett., 588, 213 (2014)

[10] Mishra J, Dent C, Tarabishi R, Mitsnefes MM, Ma Q, Kelly C, Ruff SM, Zahedi K, Shao M, Bean J, Mori K, Barasch J, Devarajan P, Lancet, 365, 1231 (2005)

[11] Hochepied T, Berger FG, Baumann H, Libert C, Cytokine Growth Factor Rev., 14, 25 (2003)

[12] Xu S, Venge P, Biochim. Biophys. Acta Protein Struct. Mol. Enzymol., 1482, 298 (2000)

[13] Bruno R, Olivares R, Berille J, Chaikin P, Vivier N, Hammershaimb L, Rhodes GR, Rigas JR, Clin. Cancer Res., 9, 1077 (2003)

[14] Vincent C, Kew MC, Bouic P, Flacher M, Revillard JP, Br. J. Cancer, 59, 415 (1989)

[15] Mantyjarvi R, Rautiainen J, Virtanen T, Biochim. Biophys. Acta, 1482, 308 (2000)

[16] Teraoka Y, Kume S, Lin Y, Atsuji S, Inui T, Mol. Pharm., 14, 3558 (2017)

[17] Jensen-Jarolim E, Pacios L, Bianchini R, Hofstetter G, Roth-Walter F, Allergy, 71, 286 (2016)

[18] Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, et al., Acta Crystallogr. Sect. D-Biol. Crystallogr., 58, 899 (2002)

[19] Acharya KR, Lloyd MD, Trends Pharmacol. Sci., 26, 10 (2005)

[20] Pagadala NS, Syed K, Tuszynski J, Biophys. Rev., 9, 91 (2017)

[21] Sousa SF, Fernandes PA, Ramos MJ, Proteins, 65, 15 (2006)

[22] Morris GM, Huey R, Lindstrom W, Sanner WF, Belew RK, Goodsell DS, Olson AJ, J. Comput. Chem., 30, 2785 (2009)

[23] Dassault Systemes BIOVIA, Discovery Studio Modeling Environment, Release 2017, San Diego: Dassault Systemes, 2017.

[24] Bocskei Z, Groom CR, Flower DR, Wright CE, Phillips SEV, Cavaggioni A, Findlay JBC, North ACT, Nature, 360, 186 (1992)

[25] Kuser PR, Franzoni L, Ferrari E, Spisni A, Polikarpov I, Acta Crystallogr. Sect. D-Biol. Crystallogr., 57, 1863 (2001)

[26] Silvaroli JA, Arne JM, Chelstowska S, Kiser PD, Banerjee S, Golczak M, J. Biol. Chem., 291, 8528 (2016)

[27] Kleywegt GJ, Bergfors T, Senn H, Le Motte P, Gsell B, Shudo K, Jones TA, Structure, 2, 1241 (1994)

[28] Huber R, Schneider M, Mayr I, Muller R, Deutzmann R, Suter F, Zuber H, Falk H, Kayser H, J. Mol. Biol., 198, 499 (1987)

[29] Cianci M, Rizkallah PJ, Olczak A, Raftery J, Chayen NE, Zagalsky PF, Helliwell JR, Proc. Natl. Acad. Sci. U. S. A., 99, 9795 (2002)

[30] Eichinger A, Nasreen A, Kim HJ, Skerra A, J. Biol. Chem., 282, 31068 (2007)

[31] Ramoni R, Vincent F, Grolli S, Conti V, Malosse C, Boyer FD, Nagnan-Le Meillour P, Spinelli S, Cambillau C, Tegoni M, J. Biol. Chem., 276, 7150 (2001)

[32] Kontopidis G, Holt C, Sawyer L, J. Mol. Biol., 318, 1043 (2002)

[33] Paesen GC, Adams PL, Harlos K, Nuttall PA, Stuart DI, Mol. Cell, 3, 661 (1999)

[34] Weichsel A, Berry RE, Walker FA, Montfort WR, a nitric oxide transport protein from rhodnius prolixus.