Predictive Molecular Simulation for Drug Discovery
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- Meredith Lloyd
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1 Predictive Molecular Simulation for Drug Discovery 생명과학 의약연구소의약설계팀이승주
2 Outline Challenging problems in drug discovery Binding affinity calculation New paradigm for scientific computing
3 Challenging problems in Drug Discovery Prediction of Binding Affinity
4 Challenges for molecular simulation in Drug Discovery: Prediction Prediction ( 미래형 ) Use faster and cheaper methods to predict outcomes of more expensive methods 기상청 : 내일의날씨 내일폭등할주식 Retrodiction ( 과거형 ) Explain what happened Unavailable until after the fact El Nino 현상분석 어제폭등한주식
5 Cycle of Drug Discovery Lead(hit) Identification -> Lead Optimization -> Preclinical Development 10 4 ~ 10 5 개 ~10 mm ~10 nm
6 Lead identification is feasible Find starting material IC 50 < 10 mm virtual HTS docking or QSAR Linux cluster 6 x 10 5 cpd in days CPU: ~minute per compound comparable to HTS ~mm activity 까지는찾을수있다. ~mm 이하는변별력이없다 Docking score vs Experiment Need predictive strength in the ~nm range for lead optimization Reducing hit to lead time is important: 6months ~ 9months Org. Biomol. Chem., 2004, 2, (22),
7 Lead optimization is difficult: what is necessary? Hardware Linux cluster CPU scavenging Software accurate force field fast molecular dynamics code Theory Free energy calculation methodology Linear Interaction Energy Free energy perturbation Bennett s acceptance ratio JCP,123, , cpu days
8 High Throughput Molecular Dynamics at LG Life Sciences Docking Glide Protein Modeling BACE inhibitor 치매치료제 Partial Charge Force Field GAFF AMBER99 TIP3P Molecular Dynamics Gromacs on PC United! Linux cluster Free Energy Calculation Linear Interaction Energy
9 Docking -> MD Docking mode might be wrong, but DG might be similar Multiple binding modes observed in xtal structures Multiple binding modes can be Boltzmann weighted Camacho and Vajda PNAS 2001,10636
10 Protein modeling: BACE Protonation state of important Asp residues not resolved 8 possible states Protonation state may depend on ligand
11 Free Energy Calculation Linear Interaction Energy(LIE) input Protein+drug+water의 MD 계산결과 drug+water 의 MD 계산결과 output Protein+ drug 의 free energy 계산 G binding ( V ( V elec ligand protein vdw ligand protein V V elec ligand solvent vdw ligand solvent ) ) J Aqvist et al Acc. Chem. Res, 2002,35,358 Van Lipzig, J Med Chem, 2004,47,1018
12 CPU LG Life Sciences 사내 Condor high throughput computing 시스템구축 PC United 프로젝트 (2006 년 10 월개시 ) client 설치자동화 유휴 CPU 활용 Configuration 1 central server ( Linux PC ) ~100 Microsoft Windows XP clients 30 CPU개 cluster와비슷 Condor queueing system Wisconsin 대학개발 ( 무료 ) Windows, Linux, Unix 지원 Windows에서 compile가능한 code 실행가능 (cygwin) 현재 Gromacs 실행
13
14 The Sixth Paradigm? 1997: $30,000/GFLOPS Linux cluster 2000: $640/GFLOPS, Linux cluster 2003: $82/GFLOPS Linux cluster 2005: $2.60/GFLOPS Xbox : $1/GFLOPS ATI graphics card
15 Supercomputing s Next Revolution GPU based computing Supercomputing s Next Revolution 11/9/2006, Wired News
16 Supercomputing s Next Revolution GPU based computing Game Console Computing Sony PS3 runs MD (Folding@Home) 2.18 TFlops total /PS3 ~100GFlops / PS3 for Gromacs Xbox 360 ~1TFlops Graphics Card Computing Gromacs runs on GPU (Folding@Home) 1 TFlop Graphics Card (ATI, Jan 2006) Radeon X1900, x , first Tflop computer ASCI Red 9,200 Pentium II chips Gromacs runs 20~40 times faster
17 GPU based Computing Environment C programming environment BrooksGPU (Stanford) Nvidia CUDA ATI (AMD) support from games to genes GPU version of MD Gromacs
18 Molecular Simulation Based drug toxicity prediction Drug cytochrome P450 binding affinity drug-drug interaction 예측가능 최근 X-ray 구조발표보다정확하게예측가능함 Nature 424, ,2003 J. Med. Chem., 47 (22), 5340, 2004 Homology model + docking
19 Molecular Simulation Based drug toxicity prediction Drug HERG K+ channel binding affinity 예측 HERG 를 inhibit 하면 cardiovascular toxicity 보임 Homology model+docking PNAS 2000 vol cited 257 times 독성예측은 hot topic user base 넓다 web based service 가능 commercialize 가능 ADMET in silico modelling: towards prediction paradise? Nature Review Drug Discovery, 2003, 2: 192
20 Summary Challenging problems in drug discovery Many challenging problems for molecular simulation Accurate prediction of binding affinity < mm Revolution in speed: stream computing Application for molecular simulation Cytochrome P450 inhibition HERG channel inhibition
21 Thanks to LG 생명과학 Dr. 임동철 Dr. 고종성 Kaist 이장환 ICU Computational Systems Biology 선충현, 김진기
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