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68. Kawasaki Y, Xu Z-Z, Wang X, Park JY, Zhuang Z-Y, Tan P-H, Gao Y-J, Roy K, Corfas G,
Lo EH, Ji R-R (2008) Distinct roles of matrix metalloproteases in the early- and late-phase
development of neuropathic pain. Nat Med 14(3):331–336. doi:10.1038/nm1723
69. Egeblad M, Werb Z (2002) New functions for the matrix metalloproteinases in cancer progression. Nat Rev Cancer 2(3):161–174. doi:10.1038/nrc745
70. Noël A, Jost M, Maquoi E (2008) Matrix metalloproteinases at cancer tumor–host interface.
Semin Cell Dev Biol 19(1):52–60. doi:10.1016/j.semcdb.2007.05.011
71. Tao P, Fisher JF, Shi Q, Mobashery S, Schlegel HB (2010) Matrix metalloproteinase 2
(MMP2) inhibition: DFT and QM/MM studies of the deprotonation-initialized ring-opening reaction of the sulfoxide analogue of SB-3CT. J Phys Chem B 114(2):1030–1037.
doi:10.1021/jp909327y
72. Tao P, Fisher JF, Shi Q, Vreven T, Mobashery S, Schlegel HB (2009) Matrix metalloproteinase 2 inhibition: combined quantum mechanics and molecular mechanics studies of the
inhibition mechanism of (4-phenoxyphenylsulfonyl)methylthiirane and its oxirane analogue.
Biochemistry 48(41):9839–9847. doi:10.1021/bi901118r
73. Augé F, Hornebeck W, Decarme M, Laronze J-Y (2003) Improved gelatinase a selectivity by novel zinc binding groups containing galardin derivatives. Bioorg Med Chem Lett
13(10):1783–1786. doi:10.1016/S0960-894X(03)00214-2
74. Rouffet M, Denhez C, Bourguet E, Bohr F, Guillaume D (2009) In silico study of MMP inhibition. Org Biomol Chem 7(18):3817–3825. doi:10.1039/b910543c
75. Li D, Zheng Q, Fang X, Ji H, Yang J, Zhang H (2008) Theoretical study on potency and
selectivity of novel non-peptide inhibitors of matrix metalloproteinases MMP-1 and MMP-3.
Polymer 49(15):3346–3351. doi:10.1016/j.polymer.2008.05.026
76. da Silva SL, Calgarotto AK, Maso V, Damico DC, Baldasso P, Veber CL, Villar JAFP, Oliveira ARM, Comar M, Oliveira KMT, Marangoni S (2009) Molecular modeling and inhibition
of phospholipase A2 by polyhydroxy phenolic compounds. Eur J Med Chem 44(1):312–321.
doi:10.1016/j.ejmech.2008.02.043
77. Šramko M, Garaj V, Remko M (2008) Thermodynamics of binding of angiotensin-converting
enzyme inhibitors to enzyme active site model, J Mol Struct—Theochem 869(1–3):19–28.
10.1016/j.theochem.2008.08.018
78. Opie LH, Gersh BJ (2009) Drugs for the Heart. WB Saunders, Philadelphia
79. Lorthiois E, Bernardelli P, Vergne F, Oliveira C, Mafroud A-K, Proust E, Heuze L, Moreau
F, Idrissi M, Tertre A, Bertin B, Coupe M, Wrigglesworth R, Descours A, Soulard P, Berna
P (2004) Spiroquinazolinones as novel, potent, and selective PDE7 inhibitors. Part 1. Bioorg
Med Chem Lett 14(18):4623–4626. doi:10.1016/j.bmcl.2004.07.011
80. Bernardelli P, Lorthiois E, Vergne F, Oliveira C, Mafroud A-K, Proust E, Pham N, Ducrot P,
Moreau F, Idrissi M, Tertre A, Bertin B, Coupe M, Chevalier E, Descours A, Berlioz-Seux F,
Berna P, Li M (2004) Spiroquinazolinones as novel, potent, and selective PDE7 inhibitors.
Part 2: Optimization of 5,8-disubstituted derivatives. Bioorg Med Chem Lett 14(18):4627–
4631. doi:10.1016/j.bmcl.2004.07.010
81. Daga PR, Doerksen RJ (2008) Stereoelectronic properties of spiroquinazolinones in differential PDE7 inhibitory activity. J Comput Chem 29(12):1945–1954. doi:10.1002/jcc.20960
82. Horenstein BA, Schramm VL (1993) Correlation of the molecular electrostatic potential
surface of an enzymatic transition state with novel transition-state inhibitors. Biochemistry
32(38):9917–9925. doi:10.1021/bi00089a007
83. Braunheim BB, Miles RW, Schramm VL, Schwartz SD (1999) Prediction of inhibitor binding free energies by quantum neural networks. Nucleoside analogues binding to trypanosomal nucleoside hydrolase. Biochemistry 38(49):16076–16083. doi:10.1021/bi990830t
84. Ehrlich JI, Schramm VL (1994) Electrostatic potential surface analysis of the transition state
for AMP nucleosidase and for formycin 5’-phosphate, a transition-state inhibitor. Biochemistry 33(30):8890–8896. doi:10.1021/bi00196a005
85. Debnath AK (2013) Rational design of HIV-1 entry inhibitors. In: Kortagere S (ed) Methods
in molecular biology. Springer, Clifton, p 185–204. doi:10.1007/978-1-62703-342-8_13
A. B. Rozhenko
68. Kawasaki Y, Xu Z-Z, Wang X, Park JY, Zhuang Z-Y, Tan P-H, Gao Y-J, Roy K, Corfas G,
Lo EH, Ji R-R (2008) Distinct roles of matrix metalloproteases in the early- and late-phase
development of neuropathic pain. Nat Med 14(3):331–336. doi:10.1038/nm1723
69. Egeblad M, Werb Z (2002) New functions for the matrix metalloproteinases in cancer progression. Nat Rev Cancer 2(3):161–174. doi:10.1038/nrc745
70. Noël A, Jost M, Maquoi E (2008) Matrix metalloproteinases at cancer tumor–host interface.
Semin Cell Dev Biol 19(1):52–60. doi:10.1016/j.semcdb.2007.05.011
71. Tao P, Fisher JF, Shi Q, Mobashery S, Schlegel HB (2010) Matrix metalloproteinase 2
(MMP2) inhibition: DFT and QM/MM studies of the deprotonation-initialized ring-opening reaction of the sulfoxide analogue of SB-3CT. J Phys Chem B 114(2):1030–1037.
doi:10.1021/jp909327y
72. Tao P, Fisher JF, Shi Q, Vreven T, Mobashery S, Schlegel HB (2009) Matrix metalloproteinase 2 inhibition: combined quantum mechanics and molecular mechanics studies of the
inhibition mechanism of (4-phenoxyphenylsulfonyl)methylthiirane and its oxirane analogue.
Biochemistry 48(41):9839–9847. doi:10.1021/bi901118r
73. Augé F, Hornebeck W, Decarme M, Laronze J-Y (2003) Improved gelatinase a selectivity by novel zinc binding groups containing galardin derivatives. Bioorg Med Chem Lett
13(10):1783–1786. doi:10.1016/S0960-894X(03)00214-2
74. Rouffet M, Denhez C, Bourguet E, Bohr F, Guillaume D (2009) In silico study of MMP inhibition. Org Biomol Chem 7(18):3817–3825. doi:10.1039/b910543c
75. Li D, Zheng Q, Fang X, Ji H, Yang J, Zhang H (2008) Theoretical study on potency and
selectivity of novel non-peptide inhibitors of matrix metalloproteinases MMP-1 and MMP-3.
Polymer 49(15):3346–3351. doi:10.1016/j.polymer.2008.05.026
76. da Silva SL, Calgarotto AK, Maso V, Damico DC, Baldasso P, Veber CL, Villar JAFP, Oliveira ARM, Comar M, Oliveira KMT, Marangoni S (2009) Molecular modeling and inhibition
of phospholipase A2 by polyhydroxy phenolic compounds. Eur J Med Chem 44(1):312–321.
doi:10.1016/j.ejmech.2008.02.043
77. Šramko M, Garaj V, Remko M (2008) Thermodynamics of binding of angiotensin-converting
enzyme inhibitors to enzyme active site model, J Mol Struct—Theochem 869(1–3):19–28.
10.1016/j.theochem.2008.08.018
78. Opie LH, Gersh BJ (2009) Drugs for the Heart. WB Saunders, Philadelphia
79. Lorthiois E, Bernardelli P, Vergne F, Oliveira C, Mafroud A-K, Proust E, Heuze L, Moreau
F, Idrissi M, Tertre A, Bertin B, Coupe M, Wrigglesworth R, Descours A, Soulard P, Berna
P (2004) Spiroquinazolinones as novel, potent, and selective PDE7 inhibitors. Part 1. Bioorg
Med Chem Lett 14(18):4623–4626. doi:10.1016/j.bmcl.2004.07.011
80. Bernardelli P, Lorthiois E, Vergne F, Oliveira C, Mafroud A-K, Proust E, Pham N, Ducrot P,
Moreau F, Idrissi M, Tertre A, Bertin B, Coupe M, Chevalier E, Descours A, Berlioz-Seux F,
Berna P, Li M (2004) Spiroquinazolinones as novel, potent, and selective PDE7 inhibitors.
Part 2: Optimization of 5,8-disubstituted derivatives. Bioorg Med Chem Lett 14(18):4627–
4631. doi:10.1016/j.bmcl.2004.07.010
81. Daga PR, Doerksen RJ (2008) Stereoelectronic properties of spiroquinazolinones in differential PDE7 inhibitory activity. J Comput Chem 29(12):1945–1954. doi:10.1002/jcc.20960
82. Horenstein BA, Schramm VL (1993) Correlation of the molecular electrostatic potential
surface of an enzymatic transition state with novel transition-state inhibitors. Biochemistry
32(38):9917–9925. doi:10.1021/bi00089a007
83. Braunheim BB, Miles RW, Schramm VL, Schwartz SD (1999) Prediction of inhibitor binding free energies by quantum neural networks. Nucleoside analogues binding to trypanosomal nucleoside hydrolase. Biochemistry 38(49):16076–16083. doi:10.1021/bi990830t
84. Ehrlich JI, Schramm VL (1994) Electrostatic potential surface analysis of the transition state
for AMP nucleosidase and for formycin 5’-phosphate, a transition-state inhibitor. Biochemistry 33(30):8890–8896. doi:10.1021/bi00196a005
85. Debnath AK (2013) Rational design of HIV-1 entry inhibitors. In: Kortagere S (ed) Methods
in molecular biology. Springer, Clifton, p 185–204. doi:10.1007/978-1-62703-342-8_13