What Really Happens When I Take a Drug? Philip E. Bourne University of California San Diego pbourne@ucsd.edu http://www.sdsc.edu/pb Vancouver April 12, 2012 Big Questions in the Lab {In the spirit of Hamming} 1. 2. 3. 4. 5. Erren et al 2007 PLoS Comp. Biol., 3(10): e213 Motivators Can we improve how science is disseminated and comprehended? What is the ancestry and organization of the protein structure universe and what can we learn from it? Are there alternative ways to represent proteins from which we can learn something new? What really happens when we take a drug? Can we contribute to the treatment of neglected {tropical} diseases? Our Motivation • Tykerb – Breast cancer • Gleevac – Leukemia, GI cancers • Nexavar – Kidney and liver cancer • Staurosporine – natural product – alkaloid – uses many e.g., antifungal antihypertensive Motivators Collins and Workman 2006 Nature Chemical Biology 2 689-700 Our Broad Approach • Involves the fields of: – Structural bioinformatics – Cheminformatics – Biophysics – Systems biology – Pharmaceutical chemistry • • L. Xie, L. Xie, S.L. Kinnings and P.E. Bourne 2012 Novel Computational Approaches to Polypharmacology as a Means to Define Responses to Individual Drugs, Annual Review of Pharmacology and Toxicology 52: 361-379 L. Xie, S.L. Kinnings, L. Xie and P.E. Bourne 2012 Predicting the Polypharmacology of Drugs: Identifying New Uses Through Bioinformatics and Cheminformatics Approaches in Drug Repurposing M. Barrett and D. Frail (Eds.) Wiley and Sons. (available upon request) Disciplines Touched & 2012 Reviews A Quick Aside – RCSB PDB Pharmacology/Drug View 2012 Asp Drug Name Aspirin % Similarity to Drug Molecule Has Bound Drug 100 Mockups of drug view features RCSB PDB’s Drug Work • Establish linkages to drug resources (FDA, PubChem, DrugBank, ChEBI, BindingDB etc.) • Create query capabilities for drug information • Provide superposed views of ligand binding sites • Analyze and display protein-ligand interactions Led by Peter Rose RCSB PDB Team A Quick Aside PDB Scope/Deliverables • Part I: small molecule drugs, nutraceuticals, and their targets ( DrugBank) - 2012 • Part II: peptide derived compounds (PRD)- tbd • Part III: toxins and toxin targets (T3DB), human metabolites (HMDB) • Part IV: biotherapeutics, i.e., monoclonal antibodies • Part V: veterinary drugs (FDA Green Book) RCSB PDB’s Drug Work Our Approach • We characterize a known protein-ligand binding site from a 3D structure (primary site) and search for similar sites (secondary sites) on a proteome wide scale independent of global structure similarity • We try a static and dynamic networkbased approach to understand the implications of drug binding to multiple sites Methodology Applications Thus Far • Repositioning existing pharmaceuticals and NCEs (e.g., tolcapone, entacapone, nelfinavir) • Early detection of side-effects (J&J) • Late detection of side-effects (torcetrapib) • Lead optimization (e.g., SERMs, Optima, Limerick) • Drugomes (TB, P. falciparum, T. cruzi) Applications Approach - Need to Start with a 3D DrugReceptor Complex – Either Experimental or Modeled Generic Name Other Name Treatment PDBid Lipitor Atorvastatin High cholesterol 1HWK, 1HW8… Testosterone Testosterone Osteoporosis 1AFS, 1I9J .. Taxol Paclitaxel Cancer 1JFF, 2HXF, 2HXH Viagra Sildenafil citrate ED, pulmonary arterial hypertension 1TBF, 1UDT, 1XOS.. Digoxin Lanoxin Congestive heart failure 1IGJ Computational Methodology Some Numbers to Show Limitations TB-drugome Drugome Target gene 3996 Target protein in PDB 284 Solved structure in PDB 749 Reliable homology models 1446 Structure coverage 43.29% Drugs 274 Drug binding sites 962 Pf5491 136 333 1236 25.02% 321 1569 A Reverse Engineering Approach to Drug Discovery Across Gene Families Characterize ligand binding site of primary target (Geometric Potential) Identify off-targets by ligand binding site similarity (Sequence order independent profile-profile alignment) Extract known drugs or inhibitors of the primary and/or off-targets Search for similar small molecules … Dock molecules to both primary and off-targets Statistics analysis of docking score correlations Computational Methodology Xie and Bourne 2009 Bioinformatics 25(12) 305-312 Characterization of the Ligand Binding Site - The Geometric Potential Conceptually similar to hydrophobicity or electrostatic potential that is dependant on both global and local environments • Initially assign Ca atom with a value that is the distance to the environmental boundary • Update the value with those of surrounding Ca atoms dependent on distances and orientation – atoms within a 10A radius define i GP P neighbors Pi cos(ai) 1.0 Di 1.0 2.0 Computational Methodology Xie and Bourne 2007 BMC Bioinformatics, 8(Suppl 4):S9 Discrimination Power of the Geometric Potential 4 binding site non-binding site 3.5 • Geometric potential can distinguish binding and non-binding sites 3 2.5 2 1.5 1 0.5 100 99 88 77 66 55 44 33 22 11 0 0 Geometric Potential 0 Geometric Potential Scale For Residue Clusters Computational Methodology Xie and Bourne 2007 BMC Bioinformatics, 8(Suppl 4):S9 Local Sequence-order Independent Alignment with Maximum-Weight Sub-Graph Algorithm Structure A Structure B LER VKDL LER VKDL • Build an associated graph from the graph representations of two structures being compared. Each of the nodes is assigned with a weight from the similarity matrix • The maximum-weight clique corresponds to the optimum alignment of the two structures Computational Methodology Xie and Bourne 2008 PNAS, 105(14) 5441 Similarity Matrix of Alignment Chemical Similarity • Amino acid grouping: (LVIMC), (AGSTP), (FYW), and (EDNQKRH) • Amino acid chemical similarity matrix Evolutionary Correlation • Amino acid substitution matrix such as BLOSUM45 • Similarity score between two sequence profiles d f a Sb f b S a i i i i i i fa, fb are the 20 amino acid target frequencies of profile a and b, respectively Sa, Sb are the PSSM of profile a and b, respectively Computational Methodology Xie and Bourne 2008 PNAS, 105(14) 5441 Scoring The Point is this Approach Can Now be Applied on a Proteome-wide Scale a) b) Blosum45 and b) McLachlan substitution matrices. • Scores for binding site matching by SOIPPA follow an extreme value distribution (EVD). Benchmark studies show that the EVD model performs at least two-orders faster and is more accurate than the non-parametric statistical method in the previous SOIPPA version Xie, Xie and Bourne 2009 Bioinformatics 25(12) 305-312 Applications Thus Far • Repositioning existing pharmaceuticals and NCEs (e.g., tolcapone, entacapone, nelfinavir) • Early detection of side-effects (J&J) • Late detection of side-effects (torcetrapib) • Lead optimization (e.g., SERMs, Optima, Limerick) • Drugomes (TB, P. falciparum, T. cruzi) Applications Nelfinavir • Nelfinavir may have the most potent antitumor activity of the HIV protease inhibitors Joell J. Gills et al, Clin Cancer Res, 2007; 13(17) Warren A. Chow et al, The Lancet Oncology, 2009, 10(1) • Nelfinavir can inhibit receptor tyrosine kinase(s) • Nelfinavir can reduce Akt activation • Our goal: • to identify off-targets of Nelfinavir in the human proteome • to construct an off-target binding network • to explain the mechanism of anti-cancer activity Possible Nelfinavir Repositioning PLoS Comp. Biol., 2011 7(4) e1002037 Possible Nelfinavir Repositioning drug target off-target? structural proteome binding site comparison 1OHR protein ligand docking MD simulation & MM/GBSA Binding free energy calculation network construction & mapping Possible Nelfinavir Repositioning Clinical Outcomes Binding Site Comparison • 5,985 structures or models that cover approximately 30% of the human proteome are searched against the HIV protease dimer (PDB id: 1OHR) • Structures with SMAP p-value less than 1.0e-3 were retained for further investigation • A total 126 structures have significant p-values < 1.0e-3 Possible Nelfinavir Repositioning PLoS Comp. Biol., 2011 2011 7(4) e1002037 Enrichment of Protein Kinases in Top Hits • The top 7 ranked off-targets belong to the same EC family - aspartyl proteases - with HIV protease • Other off-targets are dominated by protein kinases (51 off-targets) and other ATP or nucleotide binding proteins (17 off-targets) • 14 out of 18 proteins with SMAP p-values < 1.0e-4 are protein kinases Possible Nelfinavir Repositioning PLoS Comp. Biol., 2011 2011 7(4) e1002037 Distribution of Top Hits on the Human Kinome p-value < 1.0e-4 p-value < 1.0e-3 Manning et al., Science, 2002, V298, 1912 Possible Nelfinavir Repositioning Interactions between Inhibitors and Epidermal Growth Factor Receptor (EGFR) – 74% of binding site resides are comparable 1. Hydrogen bond with main chain amide of Met793 (without it 3700 fold loss of inhibition) 2. Hydrophobic interactions of aniline/phenyl with gatekeeper Thr790 and other residues EGFR-DJK Co-crys ligand H-bond: Met793 with quinazoline N1 DJK = N-[4-(3-BROMO-PHENYLAMINO)-QUINAZOLIN-6-YL]-ACRYLAMIDE EGFR-Nelfinavir H-bond: Met793 with benzamide hydroxy O38 Off-target Interaction Network Identified off-target Intermediate protein Possible Nelfinavir Repositioning Pathway Cellular effect Activation Inhibition PLoS Comp. Biol., 2011 7(4) e1002037 Other Experimental Evidence to Show Nelfinavir inhibition on EGFR, IGF1R, CDK2 and Abl is Supportive The inhibitions of Nelfinavir on IGF1R, EGFR, Akt activity were detected by immunoblotting. The inhibition of Nelfinavir on Akt activity is less than a known PI3K inhibitor Joell J. Gills et al. Clinic Cancer Research September 2007 13; 5183 Nelfinavir inhibits growth of human melanoma cells by induction of cell cycle arrest Nelfinavir induces G1 arrest through inhibition of CDK2 activity. Such inhibition is not caused by inhibition of Akt signaling. Jiang W el al. Cancer Res. 2007 67(3) BCR-ABL is a constitutively activated tyrosine kinase that causes chronic myeloid leukemia (CML) Druker, B.J., et al New England Journal of Medicine, 2001. 344(14): p. 1031-1037 Nelfinavir can induce apoptosis in leukemia cells as a single agent Bruning, A., et al. , Molecular Cancer, 2010. 9:19 Nelfinavir may inhibit BCR-ABL Possible Nelfinavir Repositioning Summary • The HIV-1 drug Nelfinavir appears to be a broad spectrum low affinity kinase inhibitor • Most targets are upstream of the PI3K/Akt pathway • Findings are consistent with the experimental literature • More direct experiment is needed Possible Nelfinavir Repositioning PLoS Comp. Biol., 2011 2011 7(4) e1002037 Applications Thus Far • Repositioning existing pharmaceuticals and NCEs (e.g., tolcapone, entacapone, nelfinavir) • Early detection of side-effects (J&J) • Late detection of side-effects (torcetrapib) • Lead optimization (e.g., SERMs, Optima, Limerick) • Drugomes (TB, P. falciparum, T. cruzi) Applications Case Study: Torcetrapib Side Effect • Cholesteryl ester transfer protein (CETP) inhibitors treat cardiovascular disease by raising HDL and lowering LDL cholesterol (Torcetrapib, Anacetrapib, JTT-705). • Torcetrapib withdrawn due to occasional lethal side effect, severe hypertension. • Cause of suggested. hypertension undetermined; off-target effects • Predicted off-targets include metabolic enzymes. Renal function is strong determinant of blood pressure. Causal off-targets may be found through modeling kidney metabolism. Constraint-based Metabolic Modeling Flux space Metabolic network reactions Steady-state assumption S·v=0 Perturbation constraint Flux HEX1 ? PGI ? PFK ? FBA ? TPI ? GAPD ? PGK ? PGM ? ENO ? Matrix representation of network PYK ? Change in system capacity Recon1: A Human Metabolic Network Global Metabolic Map Comprehensively represents known reactions in human cells Pathways (98) Reactions (3,311) Compounds (2,712) Genes (1,496) Transcripts (1,905) Proteins (2,004) http://bigg.ucsd.edu Compartments (7) (Duarte et al Proc Natl Acad Sci USA 2007) Context-specific Modeling Pipeline metabolomic biofluid & tissue localization data metabolic network gene expression data constrain exchange fluxes preliminary model refine based on capabilities model set flux constraints objective function literature normalize & set threshold GIMME metabolic influx set minimum objective flux metabolic efflux Predicted Hypertension Causal Drug Off-Targets Official Symbol PTGIS Protein Prostacyclin synthase Impacts Functional Reactions Renal Off-Target Site Limited by Function in Prediction Overlap Expression Simulation Stronger Drug Binding Affinity Cryptic Genetic Risk Factors x x x x x ACOX1 Acyl CoA oxidase x x x x x AK3L1 Adenylate kinase 4 x x x x HAO2 Hydroxyacid oxidase 2 x x x x SLC3A1; SLC7A9; SLC7A10; ABCC1 x x x CYP27B1; ABCC1 x x x CYP27B1; ABCC1 Mitochondrial cytochrome c oxidase I Ubiquinol-cytochrome c UQCRC1 reductase core protein I MT-COI *Clinically linked to hypertension. Applications Thus Far • Repositioning existing pharmaceuticals and NCEs (e.g., tolcapone, entacapone, nelfinavir) • Early detection of side-effects (J&J) • Late detection of side-effects (torcetrapib) • Lead optimization (e.g., SERMs, Optima, Limerick) • Drugomes (TB, P. falciparum, T. cruzi) Applications The Future as a High Throughput Approach….. The Problem with Tuberculosis • • • • One third of global population infected 1.7 million deaths per year 95% of deaths in developing countries Anti-TB drugs hardly changed in 40 years • MDR-TB and XDR-TB pose a threat to human health worldwide • Development of novel, effective and inexpensive drugs is an urgent priority Repositioning - The TB Story The TB-Drugome 1. Determine the TB structural proteome 2. Determine all known drug binding sites from the PDB 3. Determine which of the sites found in 2 exist in 1 4. Call the result the TB-drugome A Multi-target/drug Strategy Kinnings et al 2010 PLoS Comp Biol 6(11): e1000976 1. Determine the TB Structural Proteome 3, 996 2, 266 284 1, 446 • High quality homology models from ModBase (http://modbase.compbio.ucsf.edu) increase structural coverage from 7.1% to 43.3% A Multi-target/drug Strategy Kinnings et al 2010 PLoS Comp Biol 6(11): e1000976 2. Determine all Known Drug Binding Sites in the PDB No. of drugs • Searched the PDB for protein crystal structures bound with FDA-approved drugs • 268 drugs bound in a total of 931 binding sites 140 120 Acarbose Darunavir Alitretinoin Conjugated estrogens Chenodiol 100 80 60 40 Methotrexate 20 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 No. of drug binding sites A Multi-target/drug Strategy Kinnings et al 2010 PLoS Comp Biol 6(11): e1000976 Map 2 onto 1 – The TB-Drugome http://funsite.sdsc.edu/drugome/TB/ Similarities between the binding sites of M.tb proteins (blue), and binding sites containing approved drugs (red). From a Drug Repositioning Perspective • Similarities between drug binding sites and TB proteins are found for 61/268 drugs • 41 of these drugs could potentially inhibit more than one TB protein 20 18 16 chenodiol No. of drugs 14 12 testosterone 10 conjugated estrogens & methotrexate raloxifene ritonavir 8 levothyroxine alitretinoin 6 4 2 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 No. of potential TB targets A Multi-target/drug Strategy Kinnings et al 2010 PLoS Comp Biol 6(11): e1000976 Top 5 Most Highly Connected Drugs Drug Intended targets Indications levothyroxine transthyretin, thyroid hormone receptor α & β-1, thyroxine-binding globulin, mu-crystallin homolog, serum albumin hypothyroidism, goiter, chronic lymphocytic thyroiditis, myxedema coma, stupor alitretinoin conjugated estrogens retinoic acid receptor RXR-α, β & γ, retinoic acid receptor cutaneous lesions in patients α, β & γ-1&2, cellular retinoic with Kaposi's sarcoma acid-binding protein 1&2 estrogen receptor menopausal vasomotor symptoms, osteoporosis, hypoestrogenism, primary ovarian failure dihydrofolate reductase, serum albumin gestational choriocarcinoma, chorioadenoma destruens, hydatidiform mole, severe psoriasis, rheumatoid arthritis methotrexate No. of TB proteins connections 14 adenylyl cyclase, argR, bioD, CRP/FNR trans. reg., ethR, glbN, glbO, kasB, lrpA, nusA, prrA, secA1, thyX, trans. reg. protein 13 adenylyl cyclase, aroG, bioD, bpoC, CRP/FNR trans. reg., cyp125, embR, glbN, inhA, lppX, nusA, pknE, purN 10 acetylglutamate kinase, adenylyl cyclase, bphD, CRP/FNR trans. reg., cyp121, cysM, inhA, mscL, pknB, sigC 10 acetylglutamate kinase, aroF, cmaA2, CRP/FNR trans. reg., cyp121, cyp51, lpd, mmaA4, panC, usp raloxifene estrogen receptor, estrogen receptor β osteoporosis in postmenopausal women 9 adenylyl cyclase, CRP/FNR trans. reg., deoD, inhA, pknB, pknE, Rv1347c, secA1, sigC Vignette within Vignette • Entacapone and tolcapone shown to have potential for repositioning • Direct mechanism of action avoids M. tuberculosis resistance mechanisms • Possess excellent safety profiles with few side effects – already on the market • In vivo support • Assay of direct binding of entacapone and tolcapone to InhA reveals a possible lead with no chemical relationship to existing drugs Kinnings et al. 2009 PLoS Comp Biol 5(7) e1000423 Summary from the TB Alliance – Medicinal Chemistry • The minimal inhibitory concentration (MIC) of 260 uM is higher than usually considered • MIC is 65x the estimated plasma concentration • Have other InhA inhibitors in the pipeline Repositioning - The TB Story Kinnings et al. 2009 PLoS Comp Biol 5(7) e1000423 Acknowledgements Lei Xie Li Xie Roger Chang Bernhard Palsson Jian Wang Sarah Kinnings http://funsite.sdsc.edu