Interindividual variability in drug response constitutes a major concern in pharmacotherapy. While polymorphisms in genes involved in drug disposition have been extensively studied, drug target variability remains underappreciated. By mapping the genomic variability of all human drug target genes onto high-resolution crystal structures of drug target complexes, we identified 1094 variants localized within 6 Å of drug-binding pockets and directly affecting their geometry, topology, or physicochemical properties. We experimentally show that binding site variants affect pharmacodynamics with marked drug- and variant-specific differences. In addition, we demonstrate that a common BCHE variant confers resistance to tacrine and rivastigmine, which can be overcome by the use of derivatives based on squaric acid scaffolds or tryptophan conjugation. These findings underscore the importance of genetic drug target variability and demonstrate that integration of genomic data and structural information can inform personalized drug selection and genetically guided drug development to overcome resistance.

Biomedical Research Centre University Hospital Hradec Králové Sokolská 581 500 05 Hradec Králové Czech Republic

Department of Physiology and Pharmacology Karolinska Institutet 171 77 Stockholm Sweden

Dr Margarete Fischer Bosch Institute of Clinical Pharmacology Stuttgart Germany

Estonian Genome Center Institute of Genomics University of Tartu Tartu Estonia

Institute of Molecular and Cell Biology University of Tartu Tartu Estonia

Orion Pharma R and D P O Box 65 FI 02101 Espoo Finland

Pharmaceutical Informatics Institute College of Pharmaceutical Sciences Zhejiang University 310058 Hangzhou China

Zobrazit více v PubMed

Harrison R. K., Phase II and phase III failures: 2013–2015. Nat. Rev. Drug Discov. 15, 817–818 (2016). PubMed

Smietana K., Siatkowski M., Møller M., Trends in clinical success rates. Nat. Rev. Drug Discov. 15, 379–380 (2016). PubMed

Johnson J. A., Ethnic differences in cardiovascular drug response: Potential contribution of pharmacogenetics. Circulation 118, 1383–1393 (2008). PubMed PMC

Porcelli S., Drago A., Fabbri C., Gibiino S., Calati R., Serretti A., Pharmacogenetics of antidepressant response. J. Psychiatry Neurosci. 36, 87–113 (2011). PubMed PMC

Lacombe P. S., Vicente L., Pagès J. C., Morselli P. L., Causes and problems of nonresponse or poor response to drugs. Drugs 51, 552–570 (1996). PubMed

Trivedi M. H., Rush A. J., Wisniewski S. R., Nierenberg A. A., Warden D., Ritz L., Norquist G., Howland R. H., Lebowitz B., McGrath P. J., Shores-Wilson K., Biggs M. M., Balasubramani G. K., Fava M.; STAR*D Study Team , Evaluation of outcomes with citalopram for depression using measurement-based care in STAR*D: Implications for clinical practice. Am. J. Psychiatry 163, 28–40 (2006). PubMed

Zanger U. M., Schwab M., Cytochrome P450 enzymes in drug metabolism: Regulation of gene expression, enzyme activities, and impact of genetic variation. Pharmacol. Ther. 138, 103–141 (2013). PubMed

Lauschke V. M., Zhou Y., Ingelman-Sundberg M., Novel genetic and epigenetic factors of importance for inter-individual differences in drug disposition, response and toxicity. Pharmacol. Ther. 197, 122–152 (2019). PubMed PMC

Henricks L. M., Lunenburg C. A. T. C., de Man F. M., Meulendijks D., Frederix G. W. J., Kienhuis E., Creemers G.-J., Baars A., Dezentjé V. O., Imholz A. L. T., Jeurissen F. J. F., Portielje J. E. A., Jansen R. L. H., Hamberg P., ten Tije A. J., Droogendijk H. J., Koopman M., Nieboer P., van de Poel M. H. W., Mandigers C. M. P. W., Rosing H., Beijnen J. H., Werkhoven E., van Kuilenburg A. B. P., van Schaik R. H. N., Mathijssen R. H. J., Swen J. J., Gelderblom H., Cats A., Guchelaar H. J., Schellens J. H. M., DPYD genotype-guided dose individualisation of fluoropyrimidine therapy in patients with cancer: A prospective safety analysis. Lancet Oncol. 19, 1459–1467 (2018). PubMed

Klein M. D., Williams A. K., Lee C. R., Stouffer G. A., Clinical utility of CYP2C19 genotyping to guide antiplatelet therapy in patients with an acute coronary syndrome or undergoing percutaneous coronary intervention. Arterioscler. Thromb. Vasc. Biol. 39, 647–652 (2019). PubMed

He W., Grassmann F., Eriksson M., Eliasson E., Margolin S., Thorén L., Hall P., Czene K., CYP2D6 genotype predicts tamoxifen discontinuation and prognosis in patients with breast cancer. J. Clin. Oncol. 38, 548–557 (2020). PubMed PMC

Overington J. P., Al-Lazikani B., Hopkins A. L., How many drug targets are there? Nat. Rev. Drug Discov. 5, 993–996 (2006). PubMed

Imming P., Sinning C., Meyer A., Drugs, their targets and the nature and number of drug targets. Nat. Rev. Drug Discov. 5, 821–834 (2007). PubMed

Minikel E. V., Karczewski K. J., Martin H. C., Cummings B. B., Whiffin N., Rhodes D., Alföldi J., Trembath R. C., van Heel D. A., Daly M. J.; Genome Aggregation Database Production Team; Genome Aggregation Database Consortium, Schreiber S. L., MacArthur D. G., Evaluating drug targets through human loss-of-function genetic variation. Nature 581, 459–464 (2020). PubMed PMC

Hauser A. S., Chavali S., Masuho I., Jahn L. J., Martemyanov K. A., Gloriam D. E., Babu M. M., Pharmacogenomics of GPCR drug targets. Cell 172, 41–54.e19 (2018). PubMed PMC

Santos R., Ursu O., Gaulton A., Bento A. P., Donadi R. S., Bologa C. G., Karlsson A., al-Lazikani B., Hersey A., Oprea T. I., Overington J. P., A comprehensive map of molecular drug targets. Nat. Rev. Drug Discov. 16, 19–34 (2017). PubMed PMC

Wang Y., Zhang S., Li F., Zhou Y., Zhang Y., Wang Z., Zhang R., Zhu J., Ren Y., Tan Y., Qin C., Li Y., Li X., Chen Y., Zhu F., Therapeutic target database 2020: Enriched resource for facilitating research and early development of targeted therapeutics. Nucleic Acids Res. 48, D1031–D1041 (2020). PubMed PMC

Reisberg S., Krebs K., Lepamets M., Kals M., Mägi R., Metsalu K., Lauschke V. M., Vilo J., Milani L., Translating genotype data of 44,000 biobank participants into clinical pharmacogenetic recommendations: Challenges and solutions. Genet. Med. 21, 1345–1354 (2019). PubMed PMC

Zhou Y., Fujikura K., Mkrtchian S., Lauschke V. M., Computational methods for the pharmacogenetic interpretation of next generation sequencing data. Front. Pharmacol. 9, 1437 (2018). PubMed PMC

Lauschke V. M., Ingelman-Sundberg M., Emerging strategies to bridge the gap between pharmacogenomic research and its clinical implementation. NPJ Genom. Med. 5, 9 (2020). PubMed PMC

Wang H., Huang Y., Zhao X., Gong W., Wang Y., Cheng Y., A novel aggregation-induced emission based fluorescent probe for an angiotensin converting enzyme (ACE) assay and inhibitor screening. Chem. Commun. 50, 15075–15078 (2014). PubMed

Mukhtar E., Adhami V. M., Mukhtar H., Targeting microtubules by natural agents for cancer therapy. Mol. Cancer Ther. 13, 275–284 (2014). PubMed PMC

Svobodova B., Mezeiova E., Hepnarova V., Hrabinova M., Muckova L., Kobrlova T., Jun D., Soukup O., Jimeno M. L., Marco-Contelles J., Korabecny J., Exploring structure-activity relationship in tacrine-squaramide derivatives as potent cholinesterase inhibitors. Biomolecules 9, 379 (2019). PubMed PMC

Chalupova K., Korabecny J., Bartolini M., Monti B., Lamba D., Caliandro R., Pesaresi A., Brazzolotto X., Gastellier A. J., Nachon F., Pejchal J., Jarosova M., Hepnarova V., Jun D., Hrabinova M., Dolezal R., Zdarova Karasova J., Mzik M., Kristofikova Z., Misik J., Muckova L., Jost P., Soukup O., Benkova M., Setnicka V., Habartova L., Chvojkova M., Kleteckova L., Vales K., Mezeiova E., Uliassi E., Valis M., Nepovimova E., Bolognesi M. L., Kuca K., Novel tacrine-tryptophan hybrids: Multi-target directed ligands as potential treatment for Alzheimer’s disease. Eur. J. Med. Chem. 168, 491–514 (2019). PubMed

Di L., Kerns E. H., Fan K., McConnell O. J., Carter G. T., High throughput artificial membrane permeability assay for blood-brain barrier. Eur. J. Med. Chem. 38, 223–232 (2003). PubMed

Nelson M. R., Wegmann D., Ehm M. G., Kessner D., St. Jean P., Verzilli C., Shen J., Tang Z., Bacanu S. A., Fraser D., Warren L., Aponte J., Zawistowski M., Liu X., Zhang H., Zhang Y., Li J., Li Y., Li L., Woollard P., Topp S., Hall M. D., Nangle K., Wang J., Abecasis G., Cardon L. R., Zöllner S., Whittaker J. C., Chissoe S. L., Novembre J., Mooser V., An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science 337, 100–104 (2012). PubMed PMC

Dewey F. E., Murray M. F., Overton J. D., Habegger L., Leader J. B., Fetterolf S. N., O’Dushlaine C., Van Hout C. V., Staples J., Gonzaga-Jauregui C., Metpally R., Pendergrass S. A., Giovanni M. A., Kirchner H. L., Balasubramanian S., Abul-Husn N. S., Hartzel D. N., Lavage D. R., Kost K. A., Packer J. S., Lopez A. E., Penn J., Mukherjee S., Gosalia N., Kanagaraj M., Li A. H., Mitnaul L. J., Adams L. J., Person T. N., Praveen K., Marcketta A., Lebo M. S., Austin-Tse C. A., Mason-Suares H. M., Bruse S., Mellis S., Phillips R., Stahl N., Murphy A., Economides A., Skelding K. A., Still C. D., Elmore J. R., Borecki I. B., Yancopoulos G. D., Davis F. D., Faucett W. A., Gottesman O., Ritchie M. D., Shuldiner A. R., Reid J. G., Ledbetter D. H., Baras A., Carey D. J., Distribution and clinical impact of functional variants in 50,726 whole-exome sequences from the DiscovEHR study. Science 354, aaf6814 (2016). PubMed

Schärfe C. P. I., Tremmel R., Schwab M., Kohlbacher O., Marks D. S., Genetic variation in human drug-related genes. Genome Med. 9, 117–115 (2017). PubMed PMC

Yan C., Pattabiraman N., Goecks J., Lam P., Nayak A., Pan Y., Torcivia-Rodriguez J., Voskanian A., Wan Q., Mazumder R., Impact of germline and somatic missense variations on drug binding sites. Pharmacogenomics J. 17, 128–136 (2017). PubMed PMC

Peterson T. A., Doughty E., Kann M. G., Towards precision medicine: Advances in computational approaches for the analysis of human variants. J. Mol. Biol. 425, 4047–4063 (2013). PubMed PMC

Zhou Y., Lauschke V. M., Computational tools to assess the functional consequences of rare and noncoding pharmacogenetic variability. Clin. Pharmacol. Ther. 10.1002/cpt.2289 , (2021). PubMed

Bose T. O., Colpitts S. L., Pham Q.-M., Puddington L., Lefrancois L., CD11a is essential for normal development of hematopoietic intermediates. J. Immunol. 193, 2863–2872 (2014). PubMed PMC

Mutsaers S. E., Prele C. M., Brody A. R., Idell S., Pathogenesis of pleural fibrosis. Respirology 9, 428–440 (2004). PubMed

McGuire M. C., Nogueira C. P., Bartels C. F., Lightstone H., Hajra A., van der Spek A. F., Lockridge O., la du B. N., Identification of the structural mutation responsible for the dibucaine-tesistant (atypical) variant form of human serum cholinesterase. Proc. Natl. Acad. Sci. 86, 953–957 (1989). PubMed PMC

Kandiah N., Pai M. C., Senanarong V., Looi I., Ampil E., Park K. W., Karanam A. K., Christopher S., Rivastigmine: The advantages of dual inhibition of acetylcholinesterase and butyrylcholinesterase and its role in subcortical vascular dementia and Parkinson’s disease dementia. Clin. Interv. Aging 12, 697–707 (2017). PubMed PMC

Perry E. K., Perry R. H., Blessed G., Tomlinson B. E., Changes in brain cholinesterases in senile dementia of Alzheimer type. Neuropathol. Appl. Neurobiol. 4, 273–277 (1978). PubMed

Ciro A., Park J., Burkhard G., Yan N., Geula C., Biochemical differentiation of cholinesterases from normal and Alzheimer’s disease cortex. Curr. Alzheimer Res. 9, 138–143 (2012). PubMed PMC

Nishimura J.-i., Yamamoto M., Hayashi S., Ohyashiki K., Ando K., Brodsky A. L., Noji H., Kitamura K., Eto T., Takahashi T., Masuko M., Matsumoto T., Wano Y., Shichishima T., Shibayama H., Hase M., Li L., Johnson K., Lazarowski A., Tamburini P., Inazawa J., Kinoshita T., Kanakura Y., Genetic variants in C5 and poor response to eculizumab. N. Eng. J. Med. 370, 632–639 (2014). PubMed

Dishy V., Landau R., Sofowora G. G., Xie H. G., Smiley R. M., Kim R. B., Byrne D. W., Wood A. J. J., Stein C. M., Beta2-adrenoceptor Thr164Ile polymorphism is associated with markedly decreased vasodilator and increased vasoconstrictor sensitivity in vivo. Pharmacogenetics 14, 517–522 (2004). PubMed

Wolking S., Moreau C., Nies A. T., Schaeffeler E., McCormack M., Auce P., Avbersek A., Becker F., Krenn M., Møller R. S., Nikanorova M., Weber Y. G., Weckhuysen S., Cavalleri G. L., Delanty N., Depondt C., Johnson M. R., Koeleman B. P. C., Kunz W. S., Marson A. G., Sander J. W., Sills G. J., Striano P., Zara F., Zimprich F., Schwab M., Krause R., Sisodiya S. M., Cossette P., Girard S. L., Lerche H.; EpiPGX Consortium , Testing association of rare genetic variants with resistance to three common antiseizure medications. Epilepsia 61, 657–666 (2020). PubMed

Myers K. A., Bennett M. F., Grinton B. E., Dabscheck G., Chan E. K., Bello-Espinosa L. E., Sadleir L. G., D’Alfonso S., Schneider A. L., Damiano J. A., Hildebrand M. S., Bahlo M., Berkovic S. F., Buchhalter J., Scheffer I. E., Contribution of rare genetic variants to drug response in absence epilepsy. Epilepsy Res. 170, 106537 (2021). PubMed

Xiao Q., Zhou Y., Winter S., Büttner F., Schaeffeler E., Schwab M., Lauschke V. M., Germline variant burden in multidrug resistance transporters is a therapy-specific predictor of survival in breast cancer patients. Int. J. Cancer 146, 2475–2487 (2020). PubMed

Lek M., Karczewski K. J., Minikel E. V., Samocha K. E., Banks E., Fennell T., O’Donnell-Luria A. H., Ware J. S., Hill A. J., Cummings B. B., Tukiainen T., Birnbaum D. P., Kosmicki J. A., Duncan L. E., Estrada K., Zhao F., Zou J., Pierce-Hoffman E., Berghout J., Cooper D. N., Deflaux N., De Pristo M., Do R., Flannick J., Fromer M., Gauthier L., Goldstein J., Gupta N., Howrigan D., Kiezun A., Kurki M. I., Moonshine A. L., Natarajan P., Orozco L., Peloso G. M., Poplin R., Rivas M. A., Ruano-Rubio V., Rose S. A., Ruderfer D. M., Shakir K., Stenson P. D., Stevens C., Thomas B. P., Tiao G., Tusie-Luna M. T., Weisburd B., Won H.-H., Yu D., Altshuler D. M., Ardissino D., Boehnke M., Danesh J., Donnelly S., Elosua R., Florez J. C., Gabriel S. B., Getz G., Glatt S. J., Hultman C. M., Kathiresan S., Laakso M., Carroll S. M., McCarthy M. I., Govern D. M., Pherson R. M., Neale B. M., Palotie A., Purcell S. M., Saleheen D., Scharf J. M., Sklar P., Sullivan P. F., Tuomilehto J., Tsuang M. T., Watkins H. C., Wilson J. G., Daly M. J., MacArthur D. G.; Exome Aggregation Consortium , Analysis of protein-coding genetic variation in 60,706 humans. Nature 536, 285–291 (2016). PubMed PMC

Berman H. M., Westbrook J., Feng Z., Gilliland G., Bhat T. N., Weissig H., Shindyalov I. N., Bourne P. E., The Protein Data Bank. Nucleic Acids Res. 28, 235–242 (2000). PubMed PMC

Kelley L. A., Mezulis S., Yates C. M., Wass M. N., Sternberg M. J. E., The Phyre2 web portal for protein modeling, prediction and analysis. Nat. Protoc. 10, 845–858 (2015). PubMed PMC

Denny J. C., Ritchie M. D., Basford M. A., Pulley J. M., Bastarache L., Brown-Gentry K., Wang D., Masys D. R., Roden D. M., Crawford D. C., PheWAS: Demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations. Bioinformatics 26, 1205–1210 (2010). PubMed PMC

Natesh R., Schwager S. L. U., Evans H. R., Sturrock E. D., Acharya K. R., Structural details on the binding of antihypertensive drugs captopril and enalaprilat to human testicular angiotensin I-converting enzyme. Biochemistry 43, 8718–8724 (2004). PubMed

Nachon F., Carletti E., Ronco C., Trovaslet M., Nicolet Y., Jean L., Renard P.-Y., Crystal structures of human cholinesterases in complex with huprine W and tacrine: Elements of specificity for anti-Alzheimer’s drugs targeting acetyl- and butyryl-cholinesterase. Biochem. J. 453, 393–399 (2013). PubMed

Vainio M. J., Puranen J. S., Johnson M. S., ShaEP: Molecular overlay based on shape and electrostatic potential. J. Chem. Inf. Model. 49, 492–502 (2009). PubMed