version date: 1 December 2006 human thrombin 8.91 bCU human thrombin I D91 human thrombin 12.38 4010 ITOM human thrombi -11.2 5271 human thrombin 8.88 2.04 human thrombin 3.16 2YAS hydroxynitrile lyase YAS hydroxynitrile lya 3YAS ILID lipocyte lipid-binding protein 348 lipocyte lipid-binding protein retinol binding prote 32 retinol binding prote 00000 ITNK bovine trypsin ITN ITNL 1.90 ITNG 1.80 ITNH 1.80 3PTB IPPH 1.90 2663 lcX tryptophan syntethase 259 I C29 yptophan syntethase 2793 tryptophan synthethase tryptophan synthase 004 3094 8.92 ptophan synthethase IQOP tryptophan synthethase 1.40 2721 1A50 tryptophan synthase 2.30 2914 2TSY IBXO 1.40 BXO 4435 -11.62 IPPM 1.70 IPPK penicillopepsin 1.80 10.40 3859 12.23 4629 l.80 1FO4 saccharopepsin -10.70 ILGR glutamine synthetase 2268 triosephosphate isomerase IULB 7.23 IDIH ILYB cathepsin 4HMG 34 -14.71 IHVJ Hiv-l protease 14.25 IHXB Hiv-l protease 13.49 3135 Hiv-l protease 13.20 13.11 4PHV Hiv-l protease 2.10 A AA Hiv-l protease 3734 HVI Hiv-I 1.80 12.2 3415 Hiv. I DMP IG2K Hiv-l protease LAJV Hiv-l protease The protein-ligand HINWscArp felotbp @BlieennlesesrRernMides dherfellywing equation
11 1AE8 human thrombin 2.00 –8.91 3616 1AFE human thrombin 2.00 –6.25 3487 1BCU human thrombin 2.00 –6.85 1755 1D9I human thrombin 2.30 –12.38 4010 1TOM human thrombin 1.80 –11.28 5271 1D3T human thrombin 3.00 –8.73 1660 1D3Q human thrombin 2.90 –8.88 1734 1D3P human thrombin 2.10 –10.87 2094 1D3D human thrombin 2.04 –12.35 2339 1DWB human thrombin 3.16 –3.95 909 2YAS hydroxynitrile lyase 1.72 –7.14 1988 5YAS hydroxynitrile lyase 2.20 –4.43 1012 3YAS hydroxynitrile lyase 1.85 –2.07 1206 1ADL adipocyte lipid-binding protein 1.60 –9.16 3107 1LIE adipocyte lipid-binding protein 1.60 –9.62 3001 1LID adipocyte lipid-binding protein 1.60 –9.83 3486 1LIF adipocyte lipid-binding protein 1.60 –9.64 3445 1HBP retinol binding protein 1.90 –9.72 932 1ERB retinol binding protein 1.90 –9.57 816 1FEL retinol binding protein 1.80 –9.19 488 1TNJ bovine trypsin 1.80 –2.66 677 1TNK bovine trypsin 1.80 –2.02 720 1TNI bovine trypsin 1.90 –2.30 834 1TNL bovine trypsin 1.90 –2.54 1360 1TNG bovine trypsin 1.80 –3.98 923 1TNH bovine trypsin 1.80 –4.57 972 3PTB bovine trypsin 1.70 –6.43 1634 1PPH bovine trypsin 1.90 –8.04 2663 1CX9 tryptophan syntethase 2.30 –9.58 2595 1C29 tryptophan syntethase 2.30 –9.00 2793 1C9D tryptophan syntethase 2.30 –8.97 3094 1CW2 tryptophan syntethase 2.00 –8.76 3094 1C8V tryptophan syntethase 2.20 –8.92 2571 2TRS tryptophan syntethase 2.04 –7.20 2646 1QOP tryptophan syntethase 1.40 –7.20 2721 1A50 tryptophan syntethase 2.30 –8.56 2914 2TSY tryptophan syntethase 2.50 –4.65 905 1BXQ penicillopepsin 1.40 –10.02 4294 1BXO penicillopepsin 0.95 –13.59 4435 1PPL penicillopepsin 1.70 –11.62 3995 1PPM penicillopepsin 1.70 –9.13 3908 1PPK penicillopepsin 1.80 –10.40 3859 1APV penicillopepsin 1.80 –12.23 4629 1APW penicillopepsin 1.80 –10.87 4206 1FQ4 saccharopepsin 2.70 –8.70 4214 1FQ6 saccharopepsin 2.70 –10.70 3323 1FQ7 saccharopepsin 2.80 –7.37 3556 1LGR glutamine synthetase 2.80 –4.17 2268 1ADF alcohol dehydrogenase 2.90 –6.24 3467 2YPI triosephosphate isomerase 2.50 –6.55 1978 1ULB purine nucleoside phosphorylase 2.75 –7.23 2391 1DIH dihydrodipicolinate reductase 2.20 –7.83 5517 1LYB cathepsin 2.50 –15.5 5498 4HMG hemagglutinin 3.00 –3.48 3459 1HXW Hiv-1 protease 1.80 –14.71 3607 1HVJ Hiv-1 protease 2.00 –14.25 3460 1HXB Hiv-1 protease 2.30 –13.49 3135 1HTG Hiv-1 protease 2.00 –13.20 4226 7HVP Hiv-1 protease 2.40 –13.11 4311 1HPV Hiv-1 protease 1.90 –12.57 3080 1HPS Hiv-1 protease 2.30 –12.57 3124 4PHV Hiv-1 protease 2.10 –12.51 3932 1AAQ Hiv-1 protease 2.50 –11.45 3416 1HTF Hiv-1 protease 2.20 –11.04 2641 1HIH Hiv-1 protease 2.20 –10.97 3210 1SBG Hiv-1 protease 2.30 –10.56 3037 1HVK Hiv-1 protease 1.80 –13.80 3935 1HVI Hiv-1 protease 1.80 –13.74 3734 1HVL Hiv-1 protease 1.80 –12.27 3415 1HIV Hiv-1 protease 2.00 –12.27 3660 1HBV Hiv-1 protease 2.30 –8.68 2042 1QBT Hiv-1 protease 2.10 –14.44 5170 1DMP Hiv-1 protease 2.00 –12.99 4988 1AJX Hiv-1 protease 2.00 –10.79 3357 1G35 Hiv-1 protease 1.80 –11.06 4198 1G2K Hiv-1 protease 1.95 –10.82 3525 1AJV Hiv-1 protease 2.00 –10.52 3916 The protein-ligand HINT score for the 93 <www.iupac.org/publications/cd/medicinal_chemistry/> complexes provides the following equation: version date: 1 December 2006
version date: 1 December 2006 △G°=-00018HSpL-39041 withr=0.68 and Se=2. 33 kcal/mol This general relationship could be used to predict the behavior of any potential ligand, not belonging to a specific class of inhibitors △△ ● penicillopepsin HIV-1 protease 口 others E° 么 10 ▲ bovine thrombin 18◆ adipocyte Lb-p bovine trypsin 2000 3000 4000 5000 6000 Hint score units ig. 4 Plot of experimental AG vS. HINT score units, for a set of 93 different crystallographic protein-ligand complexes 2. CONSERVED WATER MOLECULES IN PROTEIN-LIGAND INTERACTIONS It is well known that water molecules play a very significant role in biological recognition and interactions, exploiting its bridging properties, between proteins and ligands, proteins and proteins and proteins and nucleic acids [37]. Water can act directly, in water-mediated hydrogen bonds and indirectly, in ligand, protein desolvation and hydrophobic interactions [37] The hint force field has been used to evaluate the role of conserved water molecules, through he same rapid protocol used to estimate protein-ligand interactions. Since water is integral in log Po/w, salvation/desolvation and hydrophobic effects, the solvent bulk effects are implicitly encoded in the HINT parameters, but the constrained individual solvent molecules, bridging protein an ligand associations, must be explicitly considered and evaluated Thus, the global hint score for a complex interaction mediated by water molecules is given by two different contributions HSTOTAL=HSprotein-ligand+ HSligand-water [ HSprotein-waterI If we assume that all the bridging interface-placed water molecules are pre-existing, and contribute to define the geometry and the chemical nature of the binding pocket, the latter protein <www.iupac.org/publications/cd/medicinalchemistry/>
12 ∆G° = –0.0018 HSP-L –3.9041 with R = 0.68 and SE = 2.33 kcal/mol. This general relationship could be used to predict the behavior of any potential ligand, not belonging to a specific class of inhibitors. Fig. 4 Plot of experimental ∆G° vs. HINT score units, for a set of 93 different crystallographic protein–ligand complexes 2. CONSERVED WATER MOLECULES IN PROTEIN–LIGAND INTERACTIONS It is well known that water molecules play a very significant role in biological recognition and interactions, exploiting its bridging properties, between proteins and ligands, proteins and proteins and proteins and nucleic acids [37]. Water can act directly, in water-mediated hydrogen bonds and, indirectly, in ligand, protein desolvation and hydrophobic interactions [37]. The HINT force field has been used to evaluate the role of conserved water molecules, through the same rapid protocol used to estimate protein–ligand interactions. Since water is integral in log Po/w, salvation/desolvation and hydrophobic effects, the solvent bulk effects are implicitly encoded in the HINT parameters, but the constrained individual solvent molecules, bridging protein and ligand associations, must be explicitly considered and evaluated. Thus, the global HINT score for a complex interaction mediated by water molecules is given by two different contributions: HSTOTAL = HSprotein-ligand + HSligand-water [+ HSprotein-water] If we assume that all the bridging interface-placed water molecules are pre-existing, and contribute to define the geometry and the chemical nature of the binding pocket, the latter proteinHint Score units 0 1000 2000 3000 4000 5000 6000 ∆G° (Kcal/mol) -18 -14 -10 -6 -2 bovine thrombin human thrombin hydroxynitrile lyase adipocyte l.b.p. retinol b.p. bovine trypsin tryptophan synthase penicillopepsin saccharopepsin HIV-1 protease others <www.iupac.org/publications/cd/medicinal_chemistry/> version date: 1 December 2006