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95. Waelbroeck M (1982) The pH dependence of insulin binding. A quantitative study. J Biol
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inhibition. J Am Chem Soc 137:9543–9546. https://doi.org/10.1021/jacs.5b05891
97. Mongan J, Case DA, McCammon JA (2004) Constant pH molecular dynamics in
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jcc.20139
98. Kim MO, Blachly PG, McCammon JA (2015) Conformational dynamics and binding free
energies of inhibitors of BACE-1: from the perspective of protonation equilibria. PLoS
Comput Biol 11:1–28. https://doi.org/10.1371/journal.pcbi.1004341
99. Hodge CN, Aldrich PE, Bacheler LT et al (1996) Improved cyclic urea inhibitors of the
HIV-1 protease: synthesis, potency, resistance profile, human pharmacokinetics and X-ray
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(96)90110-6
100. Lam PY, Jadhav PK, Eyermann CJ et al (1994) Rational design of potent, bioavailable,
nonpeptide cyclic ureas as HIV protease inhibitors. Science 263(80):380–384. https://doi.
org/10.1126/science.8278812
101. Kumalo HM, Bhakat S, Soliman MES (2015) Theory and applications of covalent docking
in drug discovery: merits and pitfalls. Molecules 20:1984–2000. https://doi.org/10.3390/
molecules20021984
102. Lecomte M, Laneuville O, Ji C et al (1994) Acetylation of human prostaglandin
endoperoxide synthase-2 (cyclooxygenase-2) by aspirin. J Biol Chem 269:13207–13215
103. Hadváry P, Lengsfeld H, Wolfer H (1988) Inhibition of pancreatic lipase in vitro by the
covalent inhibitor tetrahydrolipstatin. Biochem J 256:357–361. https://doi.org/10.1042/
bj2560357
104. Scarpino A, Ferenczy GG, Keserű GM (2018) Comparative evaluation of covalent docking
tools. J Chem Inf Model acs.jcim.8b00228. https://doi.org/10.1021/acs.jcim.8b00228
105. Zhu K, Borrelli KW, Greenwood JR et al (2014) Docking covalent inhibitors: a parameter
free approach to pose prediction and scoring. J Chem Inf Model 54:1932–1940. https://doi.
org/10.1021/ci500118s
106. Bianco G, Forli S, Goodsell DS, Olson AJ (2016) Covalent docking using autodock:
two-point attractor and flexible side chain methods. Protein Sci 25:295–301. https://doi.org/
10.1002/pro.2733
107. Corbeil CR, Englebienne P, Moitessier N (2007) Docking ligands into flexible and solvated
macromolecules. 1. Development and validation of FITTED 1.0. J Chem Inf Model 47:435–
449. https://doi.org/10.1021/ci6002637
108. MOE: Molecular Operating Environment (2018) http://www.chemcomp.com/MOEMolecular_Operating_Environment.htm. Accessed 7 Feb 2018
109. Katritch V, Byrd CM, Tseitin V et al (2007) Discovery of small molecule inhibitors of
ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking
approaches. J Comput Aided Mol Des 21:549–558. https://doi.org/10.1007/s10822-0079138-7
110. Verdonk ML, Cole JC, Hartshorn MJ et al (2003) Improved protein–ligand docking using
GOLD. Proteins Struct Funct Bioinform 623:609–623. https://doi.org/10.1002/prot.10465
166
S. K. Panday and I. Ghosh
antimalarial activity of artemisinin: a computational approach. Sci Rep 3:2513
92. Li J, Zhou B (2010) Biological actions of artemisinin: insights from medicinal chemistry
studies. Molecules 15:1378–1397
93. Eckstein-Ludwig U, Webb RJ, Van Goethem IDA et al (2003) Artemisinins target the
SERCA of Plasmodium falciparum. Nature 424:957
94. Pawan K, Shandilya A, Jayaram B, Ghosh I (2016) Integrative method for finding
antimalarials using in silico approach. In: Kholmurodov KT (ed) Computer design for new
drugs and materials. Nova Science Publishers, New York, NY, pp 13–38
95. Waelbroeck M (1982) The pH dependence of insulin binding. A quantitative study. J Biol
Chem 257:8284–8291
96. Ellis CR, Shen J (2015) pH-dependent population shift regulates BACE1 activity and
inhibition. J Am Chem Soc 137:9543–9546. https://doi.org/10.1021/jacs.5b05891
97. Mongan J, Case DA, McCammon JA (2004) Constant pH molecular dynamics in
generalized Born implicit solvent. J Comput Chem 25:2038–2048. https://doi.org/10.1002/
jcc.20139
98. Kim MO, Blachly PG, McCammon JA (2015) Conformational dynamics and binding free
energies of inhibitors of BACE-1: from the perspective of protonation equilibria. PLoS
Comput Biol 11:1–28. https://doi.org/10.1371/journal.pcbi.1004341
99. Hodge CN, Aldrich PE, Bacheler LT et al (1996) Improved cyclic urea inhibitors of the
HIV-1 protease: synthesis, potency, resistance profile, human pharmacokinetics and X-ray
crystal structure of DMP 450. Chem Biol 3:301–314. https://doi.org/10.1016/s1074-5521
(96)90110-6
100. Lam PY, Jadhav PK, Eyermann CJ et al (1994) Rational design of potent, bioavailable,
nonpeptide cyclic ureas as HIV protease inhibitors. Science 263(80):380–384. https://doi.
org/10.1126/science.8278812
101. Kumalo HM, Bhakat S, Soliman MES (2015) Theory and applications of covalent docking
in drug discovery: merits and pitfalls. Molecules 20:1984–2000. https://doi.org/10.3390/
molecules20021984
102. Lecomte M, Laneuville O, Ji C et al (1994) Acetylation of human prostaglandin
endoperoxide synthase-2 (cyclooxygenase-2) by aspirin. J Biol Chem 269:13207–13215
103. Hadváry P, Lengsfeld H, Wolfer H (1988) Inhibition of pancreatic lipase in vitro by the
covalent inhibitor tetrahydrolipstatin. Biochem J 256:357–361. https://doi.org/10.1042/
bj2560357
104. Scarpino A, Ferenczy GG, Keserű GM (2018) Comparative evaluation of covalent docking
tools. J Chem Inf Model acs.jcim.8b00228. https://doi.org/10.1021/acs.jcim.8b00228
105. Zhu K, Borrelli KW, Greenwood JR et al (2014) Docking covalent inhibitors: a parameter
free approach to pose prediction and scoring. J Chem Inf Model 54:1932–1940. https://doi.
org/10.1021/ci500118s
106. Bianco G, Forli S, Goodsell DS, Olson AJ (2016) Covalent docking using autodock:
two-point attractor and flexible side chain methods. Protein Sci 25:295–301. https://doi.org/
10.1002/pro.2733
107. Corbeil CR, Englebienne P, Moitessier N (2007) Docking ligands into flexible and solvated
macromolecules. 1. Development and validation of FITTED 1.0. J Chem Inf Model 47:435–
449. https://doi.org/10.1021/ci6002637
108. MOE: Molecular Operating Environment (2018) http://www.chemcomp.com/MOEMolecular_Operating_Environment.htm. Accessed 7 Feb 2018
109. Katritch V, Byrd CM, Tseitin V et al (2007) Discovery of small molecule inhibitors of
ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking
approaches. J Comput Aided Mol Des 21:549–558. https://doi.org/10.1007/s10822-0079138-7
110. Verdonk ML, Cole JC, Hartshorn MJ et al (2003) Improved protein–ligand docking using
GOLD. Proteins Struct Funct Bioinform 623:609–623. https://doi.org/10.1002/prot.10465
166
S. K. Panday and I. Ghosh