///// Perspective/Retrospective ///// NMR Fragment-based Lead Discovery Cambridge Isotope Laboratories, Inc. 1. NMR NMR Ligand-detected NMR Protein-de
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1 <1 October 2005> AR NewsNo.9 /// Perspective/Retrospective /// NMR Fragment-based Drug Discovery /// Cutting Edge /// QAR Classical QAR, Quantum Chemical QAR CoMFA /// Activities /// AR Promotion Award 33 Bio-Chemo-Informatics
2 ///// Perspective/Retrospective ///// NMR Fragment-based Lead Discovery Cambridge Isotope Laboratories, Inc. 1. NMR NMR Ligand-detected NMR Protein-detected NMR Vertex Pharmaceuticals Lepre The HAPE strategy [1] Ligand-detected NMR Abbott Laboratories Fesik AR by NMR [2] Protein-detected NMR Fragment-based Lead Discovery [3] 2. Fragment-based Lead Discovery High-Throughput creening (HT) IC 50 (Fragments) HT AR a) (diversity) (complexity) [4]b) c) Fragments caffolds Needles Fragment-based Lead
![Abbott Laboratories Fesik AR by NMR [2] Protein-detected NMR Fragment-based Lead Discovery [3] 2.](/docs-images/41/22552978/images/page_2.jpg "Fragment-based Lead Discovery High-Throughput creening (HT) IC 50 (Fragments) HT AR a) (diversity) (complexity) [4]b) c)")
3 Discovery K d ~10-3 a) MW=100~250 1 b) Receptor K d ~10-4 Receptor K d <10-8 c) Hansch-Fujita Receptor Receptor QARPharmacophore EMIL [5] Fragment-based Lead Discovery (10µM-mM range) 3. NMR Fragment-based Lead Fragment-based Lead HT High-concentration screening = HC (urface Plasmon Resonance = PR) NMR (LC/M/M) X 3-1) HT (HC) HC Plexxikon Fragments 200µM X [6]X Pharmacophore Plexxikon X 3-2) (PR) PR (Biacore) [7]
4 HC 3-3) NMR Ligand- detected NMR Protein-detected NMR Ligand-detected NMR 1 H 19 F- NMR [8] 2- [9] a) b) 50~500 Protein-detected NMR 1 H/ 15 N 1 H/ 13 C NMR [10] (Ile219) [11] a) b) Ligand-detected NMR Ligand-detected NMR 35kDa NMR ( MHz) TROY 100kDa Protein-detected NMR (AR by NMR) Combinature Biopharm Abbott Laboratories
![(Ile219) [11] a) b) Ligand-detected NMR Ligand-detected NMR 35kDa NMR (800-900](/docs-images/41/22552978/images/page_4.jpg "MHz) TROY 100kDa Protein-detected NMR (AR by NMR) Combinature Biopharm Abbott")
5 NMR 3-4) (LC/M/M) unesis Tethering (Fragments)- - LC/M/M Tethering 20-50µM NeoGenesis chering-plough ALI Chiron H R R R R O OH O O - Target + Target + Target + HPLC LC/M/M Fragment-based Lead 550 HT II Pharmaceuticals wayze Fragment-based Lead AR by M [12] 3-5) X High Throughput X-ray Crystallography X Astex Therapeutics Jhoti 300 MW= MAP [13] tructure-based drug design 4. NMR 2000 AC Vertex Pharmaceuticals Lepre
![Pharmaceuticals wayze Fragment-based Lead AR by M [12] 3-5) X High Throughput X-ray Crystallography X Astex](/docs-images/41/22552978/images/page_5.jpg "Therapeutics Jhoti 300 MW=100-250 MAP [13] tructure-based drug design 4.")
6 NMR Lepre NMR CIL NMR NMR Tecan NMR AstraZeneca 15 N, 13 C, D- Bioexpress Pharmacogenetics (PGx) decision-making 10 proof-of-concept Fragment-based Lead Discovery HT NMR LC/M/MPRX in silico 5. [1] Fejzo J, et al., The HAPE strategy: an NMR-based approach for lead generation in drug discovery. Chem. Biol. 1999, 6, 755. [2] huker, B et al., Discovering high-affinity ligands for proteins: AR by NMR. cience, 1996, 274, [3] Ferna ndez C, et al., New approaches for NMR screening in drug discovery. Drug Discov. Today: Technology 2004, 1, 277. [4] Hann MM, et al., Molecular complexity and its impact on the probability of finding leads for drug discovery. J. Chem. Inf. Comput. ci., 2001, 41, 856. [5] Fujita T., imilarities in bioanalogous structural transformation patterns among various bioactive compound series. Biosci. Biotechnol. Biochem. 1996, 60, 557. [6] Card GL, et al., A family of phosphodiesterase inhibitors discovered by cocrystallography and scaffold-based drug design. Nat. Biotechnol. 2005, 23, 201. [7] Yoshitani N, et al., A structure-based strategy for discovery of small ligands binding to functionally unknown proteins: combination of in silico screening and surface plasmon resonance measurements. Proteomics 2005, 5, [8] Lepre CA, et al., Chem. Rev. 2004, 104, [9] Peng JW, et al., Methods Enzymol. 2001, 338, 202. [10] Pellecchia M, et al., NMR in drug discovery. Nat. Rev. Drug Discov. 2002, 1, 211. [11] zczepankiewicz BG, et al., Discovery of a potent, selective protein tyrosine phosphatase 1B inhibitor using a linked-fragment strategy. J. Am. Chem. oc. 2003, 125, [12] wayze EE et al, AR by M: a ligand based technique for drug lead discovery against structured RNA targets. J. Med. Chem. 2002, 45, [13] Hartshorn MJ, et al. Fragment-based lead discovery using X-ray crystallography. J. Med. Chem. 2005, 48, 403.
![, Discovering high-affinity ligands for proteins: AR by NMR. cience, 1996, 274, 1531. [3] Ferna ndez C, et al., New approaches for NMR screening in drug discovery. Drug Discov.](/docs-images/41/22552978/images/page_6.jpg "Today: Technology 2004, 1, 277. [4] Hann MM, et al., Molecular complexity and its impact on the probability of finding leads for drug discovery. J. Chem. Inf. Comput. ci., 2001, 41, 856. [5] Fujita T.")
7 ///// Cutting Edge ///// QAR Classical QAR, Quantum Chemical QAR CoMFA 1. Curcumin( ) Curcumin QAR Dehydrozingerone(half curcumin, 4-Hydroxy-3-methoxy-benzalacetone) 2- or 4-Hydroxybenzalacetone QAR chain reaction LOO. + ArOH LOOH + ArO. 1) QAR Hydroxybenzalacetones MO CoMFA computer assisted chemistry approach classical QAR Y trans 4 CH=CHCOCH 3 HO X,Y 7OH X 2OH-BZ 4OH-BZ trans CH=CHCOCH (RBC)OH-BZ t-butyl hydroperoxide(buooh) γ (γ-irradiation) RBC 50% OH-BZ (IC 50 ) DPPH(1,1-diphenyl-2-picryl hydrazil radical) OH-BZ DPPH OH-BZ 15 DPPH 50% OH-BZ (25, 513nm) Table OH σ + σ + (ortho) = σ + (para) σ + (E s )OH ortho ortho (σ +, E s Table 1 )2OH-BZ 4OH-BZ I p =1 indicator variable OH 2- or 4-OH ( )MO semi-empirical MO AM1, PM5 CoMFA ybyl 6.8, Advanced CoMFA module
8 Table 1. Activities and physicochemical parameters for hydroxybenzalacetones log(1/ic 50 ) a σ + b No. ubstituent(s) BuOOH γ-irradiation DPPH (Σσ + )* Es c (ΣEs)* HB I p 2OH-BZ 1 H Me t-Bu F OMe OEt OH OMe Me t-Bu Cl OMe OH ,5-di-Cl - d - d * ,5-di-t-Bu - d - d * OH-BZ 16 H OMe OH ,5-di-Me * -2.48* ,5-di-OMe * -1.10* 1 1 a IC 50 : M. b Σσ + = σ + (X) + σ + (Y). c ΣEs = Es(X) +Es(Y). d Not tested because of low solubility of the compounds. 3. QAR σ + Hansch. 2) σ + E s 2OH-BZ BuOOH, γ Eq. 1, Eq. 2. 3) BuOOH log(1/ic 50 ) = (±0.255) σ (±0.124)E s (±0.151) (1) n = 13, r = 0.933, s = 0.153, F = 33.8, q 2 = γ-irradiation log(1/ic 50 ) = 1.279(±0.357) σ (±0.174) E s (±0.212) (2) n = 13, r = 0.942, s = 0.214, F = 39.1, q 2 = (2OH-BZ + 4OH-BZ) I p Eqs.3-4
9 BuOOH log(1/ic 50 ) = (±0.189)Σσ (±0.099)ΣE s (3) 0.338(±0.191) I p (±0.125) n = 18, r = 0.948, s = 0.153, F = 41.2, q 2 = γ-irradiation log(1/ic 50 ) = 1.091(±0.322) Σσ (±0.169)ΣE s (4) (±0.325)I p (±0.213) n = 18, r = 0.909, s = 0.261, F = 22.1, q 2 = , 20 Σσ + = σ +, ΣE s = E s Σσ + (CH=CHCOMe)σ + 2OH-BZ 4OH-BZ OH ortho para 2OH-BZ ΣE s E s (CH=CHCOMe) 2OH-BZ I p Eq. 1 Eq. 3 Eq. 2 Eq. 4 OH-BZ log P log P Eqs. 3-4 RBC QAR σ + E s (1) (2) DPPH test RBC DPPH-test ( r = 0.7 ~ 0.8) DPPH. + ArOH DPPH:H + ArO. DPPH (5, 6, 20) HB = 1 indicator variable Eq. 5 DPPH log(1/ic 50 ) = 2.979(±0.432) Σσ (±0.166)ΣE s 2.220(±0.501) HB (5) 0.297(±0.378) I p (±0.238) n = 20, r = 0.975, s = 0.311, F = 71.4, q 2 = HB Fig. 1 OH ortho OR (R = Me, Et) HB HB RBC QAR DPPH assay X (or CH=CHCOMe) DPPH MeOH RBC assay DMO O RO H HB RBC (Eqs, 3-4) Fig. 1 Hydrogen-bonding DPPH (Eq. 5) (HB = 1) DPPH
10 ortho Fig. 2 bulky ( ) hielding OH O H δ δ OOL effect X OH bulky ortho Fig. 2 tructural requirements Σσ + (ρ) Eqs. 3-5 ΣE s ρ DPPH, DPPH OH-BZ RBC DPPH QAR hydroxyphenylurea (σ + ) (E s (AMD)). 1) assay QAR Classical QAR ( ) empirical MO HOMO-energy (E HOMO ), HOMO (F H,O ), O-H R(O phenol ) = -100 x F H,O /E HOMO (superdelocalizability),r(o phenol ),. 1) E HOMO F H,O (AM1 PM5 PM5 ). 4) BuOOH log(1/ic 50 ) = 1.466(±0.591) E HOMO (±1.899) ΣF H,O 0.315(±0.109)ΣE s (6) (±0.213)I p (±5.28) n = 18, r = 0.942, s = 0.168, F = 25.4, q 2 = γ-irradiation log(1/ic 50 ) =2.312(±0.566) E HOMO (±1.816) ΣF H,O 0.283(±0.104)ΣE s (7) 0.495(±0.204) I p (±5.05) n = 18, r = 0.969, s = 0.160, F = 49.8, q 2 = ΣF H,O OH (7, 13, 18) F H,O Eq. 6 Eq. 7 ΣE s I p Eq. 3 Eq. 4 E HOMO ΣF H,O HOMO HOMO- classical QAR CoMFA 2OH-BZ 1, 2, 4, 7 4OH-BZ 3, 4, 6, 7 CoMFA field terms electrostatic, steric
11 BuOOH γ CoMFA CoMFA atomic charge(q) quantum chemical QAR Q Eqs. 6-7 CoMFA Q E HOMO ΣF H,O. 4) PM5 BuOOH log(1/ic 50 ) =1.200 E HOMO ΣF H,O + [CoMFA steric field term] (8) n = 18, CN = 4, r 2 = 0.842, s = 0.198, q 2 = 0.756, s CV =0.168, RC(%): E HOMO = 0.238, ΣF H,O = 0.246, steric = γ-irradiation log(1/ic 50 ) =2.163 E HOMO ΣF H,O + [CoMFA steric field trm] (9) n = 18, CN = 4, r 2 = 0.902, s = 0.203, q 2 = 0.768, s CV =0.312, RC(%): E HOMO = 0.306, ΣF H,O = 0.295, steric = (CN:number of component, s CV :standard error of the leave-one-out cross validation, RC:relative contribution) teric field ( )OH ortho classical QAR OH para 4OH-BZ 4OH-BZ 2OH-BZ CoMFA classical QAR rational Hydroxybenzalacetone classical QAR RBC DPPH MO classical QAR CoMFA 4. CoMFA 5. 1) Nakao K., himizu R., Kubota H., Yasuhara M., Hashimura Y., uzuki T., Fujita T., Ohmizu H., Bioorg. Med. Chem., 1998, 6, ) Hansch C., Gao H., Chem. Rev., 1997, 97, ) Yamagami C., Motohashi N., Emoto T., Hamasaki A., Tanahashi T., Nagakura N., Takeuchi Y., Biorg. Med. Chem. Lett., 2004, 14, ) Yamagami C., Akamatsu M., Motohashi N., Hamada., Tanahashi T., Biorg. Med. Chem. Lett,. 2005, 15,
![311 ΣF H,O + [CoMFA steric field trm] + 19.98 (9) n = 18, CN = 4, r 2 = 0.902, s = 0.203, q 2 = 0.768, s CV =0.312, RC(%): E HOMO = 0.306, ΣF H,O = 0.295, steric = 0.](/docs-images/41/22552978/images/page_11.jpg "399 (CN:number of component, s CV :standard error of the leave-one-out cross validation, RC:relative contribution) teric field ( )OH ortho classical QAR OH para 4OH-BZ 4OH-BZ 2OH-BZ CoMFA classical")
12 ///// Activities ///// MRI
13 ///// Activities ///// AR Promotion Award Award Molecular mechanism of selective toxicity of neonicotinoids 1 COMBINE analysis predicts binding affinities of ligands with a new scaffold 2 AR News
14 ///// Activities ///// :45 9:50 MO 9:50 10:30 KI MO 10:30 10:45 K01 3DMET 10:45 11:00 K02 11:00 11:25 K03* Jose Martin Ciloy 11:25 11:40 K04 D2 11:40 12:05 K05* 12:05 12:35 [ ] MO 12:45 13:45 [ ] [ I] MO 14:00 15:00 J PL 15:00 17:00 KP01-KP25 KP01 HIV-1 protease KP02 COMBINE HIV-1 protease
![11:00 11:25 K03* Jose Martin Ciloy 11:25 11:40 K04 D2 11:40 12:05 K05* 12:05 12:35 [ ] MO](/docs-images/41/22552978/images/page_14.jpg "12:45 13:45 [ ] [ I] MO 14:00 15:00 J PL 15:00 17:00 KP01-KP25 KP01 HIV-1 protease KP02")
15 KP03 3D-QAR KP04 KP05 NMR lariatin A KP06 KP07 ite KP08 hcrm1/exportin1 KP09 Rho Kinase KP10 HERG KP11 MMP-1 KP12 CYP2B3A 51 KP13 Clinical QAR (3) KP14 Determination of lipophilicity by reversed-phase high-performance liquid chromatography (RP-HPLC) Xiangli Liu, Hideji Tanaka, Aiko Yamauchi, Bernard Testa and Hiroshi Chuman KP15 KP16 KP17 Organic Cation Transporter 1 (OCT1) KP18
16 KP19 upport Vector Machine KP20 ( Jose Martin Ciloy KP21NTG KP22 GF KP23 KP24 PPAR David B. attelle [ ] 18:00 20:00 MO 9:15 9:40 K06* 9:40 9:55 K07 Eldanolide 9:55 10:10 K15 creening for Novel Leads of Various Therapeutic Areas by upport Vector Machines Zsolt Lepp 10:10 10:35 K08* 10:35 10:50 [ II] MO 10:50 11:50 K 12:00 13:00 [ ] MO 13:10 13:35 K09* CYP2C9dH MD 3 13:35 14:00 K10* tructure-based design of highly-selective factor VIIa inhibitor
![Various Therapeutic Areas by upport Vector Machines Zsolt Lepp 10:10 10:35 K08* 10:35 10:50 [ II] MO 10:50](/docs-images/41/22552978/images/page_16.jpg "11:50 K 12:00 13:00 [ ] MO 13:10 13:35 K09* CYP2C9dH MD 3 13:35 14:00 K10* tructure-based design of")
17 MO 14:00 14:40 KIMolecular hape and Electrostatics for creening, QAR and Lead Optimization OpenEye cientific oftware, Inc.A. Nicholls 14:40 14:55 MO 14:55 15:20 K11* tructure-based Drug Design 15:20 15:45 K12* AmpC β-lactamase 15:45 16:10 K13* 3-D QAR analysis of non-steroidal ecdysone agonists and homology modeling of the ligand-receptor binding Craig E. Wheelock, Toshiyuki Harada, Guy magghe, Luc wevers, Kostas Iatrou, Miki Akamatsu, Yoshiaki Nakagawa 16:10 16:35 K14* GPCR MO 16:40 17: 00 8,000 3,000 9,000 4, ,000 3,000 8,000 4, Tel&Fax
18 ///// Activities ///// 5 Bio-Chemo-Informatics JBi Bio-Chemo-Informatics Bioinformatics Chemoinformatics( tructure-based Drug Design) JBi JBi JBi Chemoinformatics, BDD 2 Bioinformatics Atomic reconstruction of metabolism (ARM) Enzyme catalytic mechanism database (EzCatDB) URL: jimu@jsbi.org
19 ( ) AR News AR News 9 Perspective/Retrospective NMR Cutting Edge QAR Activities AR Promotion Award AR News No. 9 AR News
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