Structure-based Drug Design

1. Structure-based Drug Design 陸志豪 chlu@mail.cmu.edu.tw 生物醫學研究所 教材來源: 國立交通大學 楊進木博士 http://gemdock.life.nctu.edu.tw

2. 陸志豪副教授/生物醫學所 chlu@mail.cmu.edu.tw http://lulab.cmu.edu.tw/ 學歷 國立交通大學生物資訊所 博士 專長 結構生物資訊、計算生物學、演化式計算與機器學習、電腦輔助藥物設計 研究領域 蛋白質區域結構模組與功能預測 蛋白質結構與動力學的相關研究 蛋白質與分子的交互作用相關研究 蛋白質新藥篩選與開發

3. Outline • Current state of drug discovery • Structure-based drug discovery • Molecular docking • Method of iGEMDOCK • Practice of virtual screening • Prepare protein binding site • Prepare compounds library • Molecular docking • Post-screening analysis http://gemdock.life.nctu.edu.tw/dock/

5. Patents: Advair 氣喘 Manufacturer: GlaxoSmithKlineFDA approval: 2000Patent expiry: Feb. 12, 2008 US $6 billion/year: 15% income for GlaxoSmithKline http://images.businessweek.com/ss/08/02/0206_generic_drugs/index_01.htm

6. Drug Development Life Cycle Discovery (Lead discovery, Lead optimization, Toxicity prediction) Preclinical Testing (Lab and Animal Testing) $600-800 US Million! Phase I (20-80 Healthy Volunteers used to check for safety and dosage) Identify lead compounds Structure-based screening ligand-based screening High-throughput screening Phase II (36-300 Patient Volunteers used to check for efficacy and side effects) Phase III (300-3000 Patient Volunteers used to monitor reactions to long-term drug use) Lead optimization: QSAR FDA Review & Approval 2 to 10 Years Post-Marketing Testing Years 0 2 4 6 8 10 12 14 16 7 – 15 Years!

7. Classification of Drug Development Protein (receptor) Structure High-Throughput Screening (HTS) Compound similarity search Unknown query Similar compounds SBDD or de novo design Structure-based Drug Design (SBDD) Known DDT 2002 Known Unknown Compound structure

8. Comparison of SBDD and HTS SBDD: high hit rate HTS SBDD Yellow: virtual screening (SBDD) Blue: high-throughput screening (HTS) • Lipinski's Rule of Five • There are more than 5 H-bond donors. • The molecular weight is over 500. • The LogP is over 5. • There are more than 10 H-bond acceptors. Curr. opin. Chem. Biol. 2002, 439

9. Drugs derived from SBDD 瑞樂沙 克流感 Drug Discovery Today, 10, 895, 2005

10. Mechanism of drug actions • To identify drugs that inhibit target proteins involved in diseases and have therapeutic effect against diseases • Drugs often have stronger binding affinities than natural compounds Natural compound A pathway of disease x x x x Protein Protein Drug Target protein

11. Structure-based Drug Design Compound database Protein Virtual screening using molecular docking • iGEMDOCK Lead optimization SiMMap, QSAR Post-screening analysis iGEMDOCK, SiMMap Bioassay

12. What is the Molecular Docking ? Algorithm Search Evaluate Scoring function Energy -2 -30 Conformation • Problem: Given two biological molecules determines: 1. Whether the two molecules “interact” 2. Formulated as a force field minimization process • Goal: Retrieve molecules that can interact with query protein structure

13. Three Components of Docking PDB Representation of receptor binding site (blue) and ligand (red) ZINC, NCI, FDA... GA SA Sampling of configuration space of the ligand-receptor complex (Search methods) Protein-ligand complex -scores Evaluation of ligand-receptor Interactions (Scoring methods) ? configurations of the complex

14. Types of Scoring Functions Physics-based • Physics-based • nonbonded interaction terms as the score, sometimes in combination with solvation terms • Empirical • multivariate regression methods to fit coefficients of physically motivated structural functions by using a training set of ligand-receptor complexes with measured binding affinity • Knowledge-based • statistical atom pair potentials derived from structural databases as the score • Consensus scoring functions approach Empirical

15. Docking Software SDOCKER (Wu et al. 2004) QXP (McMartin & Bohacek 1997) Validate (Head et al. 1996) • de novo design tools LUDI (Boehm 1992), BUILDER (Roe & Kuntz 1995) SMOG (DeWitte et al. 1997) CONCEPTS (Pearlman & Murcko 1996) DLD/MCSS (Stultz & Karplus 2000) Genstar (Rotstein & Murcko 1993) Group-Build (Rotstein & Murcko 1993) Grow (Moon & Howe 1991) HOOK (Eisen et al. 1994) Legend (Nishibata & Itai 1993) MCDNLG (Gehlhaar et al. 1995) SPROUT (Gillet et al. 1993) GEMDOCK (Yang & Chen 2004) iGEMDOCK (Yang & HSU 2011) DOCK: (Kuntz et al. 1982) DOCK 4.0 (Ewing & Kuntz 1997) AutoDOCK (Goodsell & Olson 1990) AutoDOCK 3.0 (Morris et al. 1998) GOLD (Jones et al. 1997) FlexX: (Rarey et al. 1996) GLIDE: (Friesner et al. 2004) ADAM (Mizutani et al. 1994) CDOCKER (Wu et al. 2003) CombiDOCK (Sun et al. 1998) DIVALI (Clark & Ajay 1995) DockVision (Hart & Read 1992) FLOG (Miller et al. 1994) Hammerhead (Welch et al. 1996) LIBDOCK (Diller & Merz 2001) MCDOCK (Liu & Wang 1999) PRO_LEADS (Baxter et al. 1998)

16. 研究成果: iGEMDOCK 電腦輔助藥物設計 Easy use, high accuracy, and automatic GEMDOCK相關論文被引用次數超過 150次 GEMDOCK在實際應用上，與國內外超過十實驗室合作，發現20個潛力藥物

17. iGEMDOCK: Fitness Function • van der Waals Energy • Electrostatic Energy • H-Bond • Dihedral Parameter An example of van der Waals force: Gecko climbs on the glass • Ebind = Einter + Eintra + Epenal http://en.wikipedia.org/wiki/Van_der_Waals_force

18. Definition of Atom Types in iGEMDOCK both HIS ASP THR -0.5 -0.5

19. center Rotatable bonds Docking Problem Optimization steps • Fix the location of the receptor, Initialize the orientation and conformation • Adapt the orientation and conformation of ligand • Evaluate the interaction energy and select the configuration • Repeatedly execute step 2 and 3 (x1, x2, x3):3-dimensional location relating to the center of receptor (x4, x5, x6): rotational angles of ligand relating to axes (x7, …, xn): twisting angles of rotatable bonds in the ligand

20. The Evolution Approach of iGEMDOCK Population: 2 Generation: 3 Energy -2 -30 Conformation

21. Power of evolution Energy -30 Mutation Conformation Crossover Mutation

22. GEMDCOK – Docking Evaluation (100 complexes) On 100 complexes Proteins 2004 66% 69% 79% GEMDOCK Dataset http://gemdock.life.nctu.edu.tw/dock/download.php J.-M. Yang* and C.-C. Chen, “GEMDOCK: A generic evolutionary method for molecular docking,” Proteins, 55, 288-304, 2004

23. Old drugs  New Use (舊藥新用) • Reasons • It takes too long and costs too much to bring new drugs to market. • Nobel laureate James Black (1988) • the most fruitful basis for the discovery of a new drug is to start with an old drug. for their discoveries of important principles for drug treatment

24. Old drugs  New Use (舊藥新用) • Examples:舊藥新用的成功案例 • 治療癌症常用藥「顆粒球生長激素」 • 可刺激骨髓細胞游移到大腦、分化成神經細胞，取代受損或死亡的腦神經細胞，達到治療老年痴呆症的效果 (院士沈哲鯤) • 就利用該藥治療老年痴呆症，向美國、台灣、中國大陸和歐盟等地提出應用專利申請 • 葛蘭素史克公司（GSK） Seroxat: • 原本是丹麥人於1970年發現的一種用來抗抑鬱的藥 • 2001年(32億美元)，2004年又名列收入最高的50種處方藥 • 加拿大Apotex公司經過研究，發現其可以治療強迫症、後外傷性壓迫症 • 輝瑞的minoxidil • 治療高血壓的口服藥 • 發現能刺激毛髮生長，成為治療人類禿頭症的局部用藥

25. Steps of virtual screening Compound databases Target protein: 1kim Preparation of docking databases Molecular recognition >100,000 compounds Prepared binding site of the target protein Docking program iGEMDOCK Post-screening analysis Ranking

26. Thymidine kinase (TK) • TK is a drug target for the therapy of herpes simplex virus type-1 The role of TK Thymidine kinase 1kim DNA synthesis The reaction of TK Thymidine kinase ATP ADP Thymidine Thymidine 5’-phosphate

27. Thymidine: Drug design by modifying from substrate Blue is different Inhibitor

28. Preparation of protein binding site from Protein Data Bank (PDB)

29. Protein data bank (PDB) http://www.pdb.org/ • Techniques for determining protein structures • X-ray crystallography, NMR spectroscopy and electron microscopy • PDB contains information about experimentally-determined structures of biological marcomoleculeas (proteins, and DNA/RNA) Proteins (1kim) X-ray NMR DNAs/RNAs (2k7e) EM Biological complexes (1zrc)

30. Search protein structures in PDB • PDB provides search by protein name, ligand, or structrue related keywords Search example: thymidine kinase (TK) • Function: DNA synthesis • Therapeutic: Anticancer and antivirus drug target

31. Example: X-ray structures of virus’ thymidine kinase with substrates/inhibitors Protein name Thymidine kinase Source spices Viruses Experimental method 0.1 2.5 has ligands Yes

32. Search result of “X-ray structures of virus’ thymidine kinase with substrates/inhibitors” 23 structures for these keywords PDB ID of this structure TK of virus TK with ligand (substrate) X-ray structure

33. Structure and related data (1kim) Related data of this structure The title of this structure Visualization of biological assembly The citation of this structure

34. Structure and ligand data (1kim) Ligand in this structure

35. Domain Annotations Structure classification ID of 1kim

36. Advanced inspection for protein structure: download structure from PDB • Save the data on your PC • Open the file on a structure viewer program (swiss PDBviewer, pymol, and etc.)

39. Download iGEMDOCK iGEMDOCK is available at http://gemdock.life.nctu.edu.tw/dock/igemdock.php

40. Install of iGEMDOCK • Click the zip file, iGEMDOCKv2.0.zip, and then right click • Decompress to the user defined path Step 1. Step 2.

41. Docking/Screening: 1. Prepare binding site by iGEMDOCK (Define by the ligand in the protein structure) • Press the button binding site • Browse and select protein file (in \examples\protein\1KIM.pdb) 1 2

42. Binding site of TK

43. Preparation of compounds

44. ZINC, a free compound database http://zinc.docking.org/

45. Subset in ZINC1

46. Subset in ZINC1

47. Subset in ZINC2

48. Subset in ZINC2

49. Subset in ZINC2

50. Search compounds