SAR ewso8 (Mar 2005) <31 March 2005> SAR ewso8 /// Perspective/Retrospective /// /// Cutting Edge /// General Model for Estimation of the Inhibition of Protein Kinases Using Monte Carlo Simulations ERG /// Activities /// 32 EuroQSAR 2004 2005 33
SAR ewso8 (Mar 2005) ///// Perspective/Retrospective ///// chemical genetics 1990 10 (1)
SAR ewso8 (Mar 2005) 1 K506 T (2-4) UCS (5-11)
SAR ewso8 (Mar 2005) MIT 20 10 I I I Iational Institute of ealth) 2002 4 I I I I 2003
SAR ewso8 (Mar 2005) ew Pathways to Discovery I I ew Pathways to Discovery I (1) (2) (3) (4) (5) I Chemical Genomics etwork Targets Targets Targets 2003 2004 Targets Investigator-Initiated I Chemical Genomics Center Assay Development I Small Molecule Repository Projects Assay Access Committee Selection Assignment Steering Committee 2003 2004 6 I ational uman Genome Research Institute Chemical Genomics Center I Screening Centers Assay Implementation TS its -validation Limited leads optimization ew Leads for Research and Therapeutics 2005 I Chemical Genomics etwork I Chemical Genomics etwork I Chemical Genomics I Chemical Genomics Center 100 I Center 100
SAR ewso8 (Mar 2005) I LM PubChem ew Pathways to Discovery I Chemical Genomics etwork I Chemical Genomics etwork * 1 S L Schreiber, C&E March 3, 51-61 (2003) 2 J Liu et al, Cell 66, 807-15 (Aug 23, 1991) 3 M W arding, A Galat, D E Uehling, S L Schreiber, ature 341, 758-60 (ct 26, 1989) 4 R Standaert, A Galat, G L Verdine, S L Schreiber, ature 346, 671-4 (Aug 16, 1990) 5 K Shokat, M Velleca, Drug Discov Today 7, 872-9 (Aug 15, 2002) 6 R Papa, C Zhang, K Shokat, P Walter, Science 302, 1533-7 (ov 28, 2003) 7 K Shah, K M Shokat, Methods Mol Biol 233, 253-71 (2003) 8 J R olt et al, Cell 108, 371-81 (eb 8, 2002) 9 A S Carroll, A C Bishop, J L DeRisi, K M Shokat, E K 'Shea, Proc atl Acad Sci U S A 98, 12578-83 (ct 23, 2001) 10 A C Bishop et al, ature 407, 395-401 (Sep 21, 2000) 11 K Shah, Y Liu, C Deirmengian, K M Shokat, Proc atl Acad Sci U S A 94, 3565-70 (Apr 15, 1997)
SAR ewso8 (Mar 2005) ///// Cutting Edge ///// General Model for Estimation of the Inhibition of Protein Kinases Using Monte Carlo Simulations () 1, Structure-based drug design,,,,, ree energy perturbation Thermodynamics integration +05kcal/mol,,, MM-PBSA Linear response,, +10kcal/mol, 2000 2 Yale W L Jorgensen Extended linear response, Linear Response Åqvist Linear responselr, 1, G C b LR G c b = 1/2 < E c > 1 E c,, < >, 05 LR, G LJ b, G LJ b = α < E vdw > 2
SAR ewso8 (Mar 2005) 1, 2 3, G b G b = α < E vdw > + 1/2 < E c > 3, α,, 4 Endothiapepsin α = 0161 Ligand G b ree Energy of Binding G b = RT ln K d Ligand Protein Åqvist, IV proteinase, Glucose binding protein, Trypsin 2 3Extended Linear Response Jorgensen LR, 3 3 3 Cavity, SASA 3 4 4,, 05, G b = α < E vdw > + β < E c > + γ < SASA> 4, 4 Thrombin, IV-1 Reverse Transcriptase, KBP12, SASA, 3 4-6, 4, 5 Extended Linear Response ELR G = ξ constant 5 b c n n + n, c n, ξ n DescriptorEXX-LJ, B total, SA, E int, #RB EXX-LJ B total : Lennard-Jones :
SAR ewso8 (Mar 2005) SA : E int : #RT : IV-1 Reverse Transcriptase, Thrombin, Cycloxygenase-2, Descriptor 7-10, Descriptor, General Model for Estimation of the Inhibition of Protein Kinases 11, ELR, Preotein kinase, Preotein kinase ATP Kinase, Kinase, Cyclin-dependent kinase 2 CDK2, P38 mitogen-activated protein kinasep38, Lymphocyte-specific kinaselck 3 Kinase 41 Individual ELR models Kinase ELR, 6-8 CDK2 : G calc = 0100 <EXX-C> + 0110 <EXX-LJ> - 0216 < B total > - 1350 6 = 61, RMS = 0729 kcal/mol, R 2 = 0759, Q 2 = 0722 Lck : G calc = 00989 <EXX-C> + 0257 <EXX-LJ> - 0320 < B total > + 0623 7 = 51, RMS = 0676 kcal/mol, R 2 = 0734, Q 2 = 0683 P38 : G calc = 00644 <EXX> + 000619 < SA> - 0760 (QPlogPo/w) - 0636 8 = 36, RMS = 0767 kcal/mol, R 2 = 0678, Q 2 = 0603, Descriptor EXX-C EXX : Coulomb : Coulomb+Lennard-Jones QPlogPo/w: QikProp / CDK2, Lck, Descriptor, P38 ATP Allosteric, Descriptor 42 Combination of two datasets to predict the third 2 Kinase ELR P38 2 utlier, CDK2 and Lck : G calc = 00995 <EXX> - 0269 < B total > + 00103 < SASA> - 375 (L corr ) + 3459 = 112, RMS = 0722 kcal/mol, R 2 = 0737, Q 2 = 0712
SAR ewso8 (Mar 2005) CDK2 and P38 : G calc = 00814 <EXX> - 0289 < B total > + 00110 < SASA> + 206 10 = 95, RMS = 0795 kcal/mol, R 2 = 0692, Q 2 = 0661 P38 and Lck : G calc = 00723 <EXX> - 0312 < B total > + 00147 < SASA> - 303 (L corr ) + 355 11 = 85, RMS = 0784 kcal/mol, R 2 = 0649, Q 2 = 0602 SASA : L corr : Lck 1, 0, Descriptor,,,,,, R 2 = 0538P38, 0704Lck, 0706CDK2 43 inal ELR model using all three datasets 3 Kinase, G calc = 00848 <EXX> - 0293 < B total > + 00123 < SASA> - 311 (L corr ) + 308 15 = 146, RMS = 0775 kcal/mol, R 2 = 0691, Q 2 = 0666 5 ELR, Jorgensen 6 [1] Åqvist, J; Medina, C; Samuelsson, J -E Protein Eng 1994, 7, 385-391 [2] ansson, T; Marelius, J; Åqvist, J J Comput Aided Mol Des 1998, 12, 27-35 [3] Carlson, A; Jorgensen, W L J Phys Chem 1995, 99, 10667-10673 [4] Jones-ertzong, D K; Jorgensen, W L J Med Chem 1997, 40, 1539-1549 [5] Smith, R J; Jorgensen, W L; Tirado-Rives, J; Lamb, M L; Janssen, P A J; Michejda, C J; Smith, M B K J Med Chem 1998, 41, 5272-5286 [6] Lamb, M L; Tirado-Rives, J; Jorgensen, W L Bioorg Med Chem 1999, 7, 851-860 [7] Rizzo, R C; Tirado-Rives, J; Jorgensen, W L J Med Chem 2001, 44, 145-154 [8] Rizzo, R C; Udier-Blagović, M; Wang, D; Watkins, E K; Smith, M B K; Smith, R J; Tirado-Rives, J; Jorgensen, W L J Med Chem 2002, 45, 2970-2987 [9] Pierce, A C; Jorgensen, W L J Med Chem 2001, 44, 1043-1050 [10] Wesolowski, S S; Jorgensen, W L Bioorg Med Chem Lett 2002, 12, 267-270 [11] Tominaga, Y; Jorgensen, W L J Med Chem 2004, 10, 2534
SAR ewso8 (Mar 2005) ///// Cutting Edge ///// 1 1 (1) 1 (1) MR X (2) (1) 2 n m 0 1 ( mn) (2) 1 1 0 0-1 2 -
SAR ewso8 (Mar 2005) n ( )2 n -x n! (1) x!( n x)! n Andrews 2 Andrews QSAR ( ) σ = S i a i (2) 2 1 i 2 S i i - a i i σ 2 S i 1 i 1 Z = 2 2 ( ) = σ S i a i Active Active i, Active S i 0 ( au + b) cu i i + d (3) (4) σ 0 (3) Z Z Active Z u i i Andrews au i + b cu i + d a,b,c,d { ( + )} = DB 2 1 Si aui b P exp (5) i, DB 2π ( cu + ) ( cui + d ) i d 2
SAR ewso8 (Mar 2005) P P P P = = = = 0 (6) a b c d P (6)P a,b,c,d (3)(5) S i (3) (6) (4) Z Z i S = i ( au + b) cu + d i i Andrews Z - (3) IV 40 Z 1B ErmC (MMP-3) drug-like 1000 MR X- GB/SA π 3 3 3 A,B 40 097 (3A) (3B) alse-positive C,D - Z- 4 Abbott MR KBP12 4
SAR ewso8 (Mar 2005) 3 +: - :Z :Z A,B: C,D: Z 1000 KBP12 DCK4 4 KBP12 Lead-like 4 alse-positive 250 4 [1]DAErlanson,et al JMedChem47:3463-3482(2004),DCRess,et al atrevdrugdiscov3:660-672(2004) [2]PRAndrews,et al JMedChem 27:1648-1657(1984) [3]GCPimentel,ALMcClellan The ydrogen Bond (1960), GRDesiraju,TSteiner The Weak ydrogen Bond (1999) [4]SBShuker, et al,science 274:1531-1534(1996)
SAR ewso8 (Mar 2005) ///// Cutting Edge ///// ERG MIZLASTIE GREPALXACI SPIRLACTE TAMSULSI S S BMCL131829-11 Cl BMCL131829-16 LEADMYCI S DESMETYL LAZAPIE TEREADIE PIMZIDE S QUIIDIE RISPERIDE Cl CLRPRMAZIE EXEADIE DRPERIDL DESMETYLASTEMIZLE
SAR ewso8 (Mar 2005) ernandez [1] S 2
SAR ewso8 (Mar 2005) S S S Cl S S S Cl + - Cl S CLARITRMYCI DETILIDE E-4031 PRAZSI BMCL131829-2 LIGCAIE CAREIC ACID SPARLXACI VERAPAMIL LUXETIE PRPAEE BMCL131829-2 TIRIDAZIE ZIPRASIDE CLZAPIE -XIDE DILTIAZEM DASETR DLASETR BEPRIDIL CITALPRAM 3 R=0824, RMSE=0865
SAR ewso8 (Mar 2005) 4 [1] ernandez, D, Ghanta, A, Kauffman, G W, Sanguinetti, M C Physicochemical eatures of the ERG Channel Drug Binding Site J Biol Chem 2004, 279, 10120-7 [2] Gasteiger, J; Marsili, M Iterative Partial Equalization of rbital Electronegativity - A Rapid Access to Atomic Charges Tetrahedron 36, 1980, 3219-3228 [3] Recanatini, M; Poluzzi, E; Masetti, M; Cavalli, A; De Ponti, QT Prolongation through erg K(+) Channel Blockade: Current Knowledge and Strategies for the Early Prediction During Drug Development Med Res Rev 2005, 25, 133-66
SAR ewso8 (Mar 2005) ///// Activities ///// () () sira mira sira mira ansch Journal of the American Chemical Society C ansch, T ujita, JAmChemSoc, 86, 1616(1964) KP15 KP20 ERG SAR ews 300
SAR ewso8 (Mar 2005) ///// Activities ///// 9 5 10 Esin AKI ŞEER EuroQSAR 2004The 15 th European Symposium on Quantitative Structure-Activity Relationships & Molecular Modeling 43 457 8 30 267 QSAR 9 2 QSAR J Am Chem Soc 1964 40 QSAR Corwin ansch ansch 40 QSAR QSAR
SAR ewso8 (Mar 2005) EuroQSAR Validation and productivity of QSAR models (ugo Kubinyi, University of eidelberg) QSAR q 2 r 2 q 2 r 2 pred r 2 q 2 r 2 pred r 2 q 2 r 2 pred MLECULAR IELD TPLGY AALYSIS (MTA) AD MLECULAR MDELIG: CMPARIS AD CMPLIMETARILY (Eugene V Radchenko et al, Moscow State University) MTA MTA 3D QSAR QSAR AIDS QSAR r 2 q 2 TMA TMA 3D QSAR EVALUATI DIERET CMPUTER PRGRAMS R PREDICTI MLECULAR LIPPILICITY (Ana Mornar et al, University of Zagreb) logp LogP 300 KowWin CLGP KowWinCLGPALGPs CLGPALGPs
SAR ewso8 (Mar 2005) ///// Activities ///// 2005 Combinatorial Chemistry 10:30 17:45 2-1-D TEL: 06-6832-2211 13 http://www senri-htlcojp 10:30-12:35 MRI 13:50-17:45 18:00-6,000 3,000 AX AX 0984866 00940-5-259936 565-0871 1-7 TEL/AX: 06-6879-2573 sar-pharm@sahsmedosaka-uacjp http://bukaipharmorjp/bukai_kozo/indexhtml
SAR ewso8 (Mar 2005) ///// Activities ///// 33 17 11 16 17 1-1 http://wwwosaka-uacjp/jp/about/map/suitahtml 20 30 JR 20 QSAR QSAR QSAR 25 A 15 B 5 7 15 E-mail 200 AB 9 22 URL 10 28 AX AX 0984854 00940-2-278412 8000 9000 3000 4000 1000 11 16 18:30-6000 8000 3000 4000 565-0871 1-7 TEL/AX 06-6879-2573 2577 E-mail sar@sahsmedosaka-uacjp URL http://bukaipharmorjp/bukai_kozo/indexhtml
SAR ewso8 (Mar 2005) ///// Activities ///// angzhou 565-0871 1-7 TEL/AX: 06-6879-2573 e-mail: fujiwara@sahsmedosaka-uacjp URL http://bukaipharmorjp/bukai_kozo/indexhtml SAR ews 8 Perspective/Retrospective Cutting Edge Activities 2 Perspective/Retrospective 4 Cutting Edge 32 2 6 28 2005 SAR ews o8 SAR ews