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Druggability

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Druggability is a term used in drug discovery to describe a biological target (such as a protein) that is known to or is predicted to bind with high affinity to a drug. Furthermore, by definition, the binding of the drug to a druggable target must alter the function of the target with a therapeutic benefit to the patient. The concept of druggability is most often restricted to small molecules (low molecular weight organic substances)[1] but also has been extended to include biologic medical products such as therapeutic monoclonal antibodies.

Drug discovery comprises a number of stages that lead from a biological hypothesis to an approved drug. Target identification is typically the starting point of the modern drug discovery process. Candidate targets may be selected based on a variety of experimental criteria. These criteria may include disease linkage (mutations in the protein are known to cause a disease), mechanistic rationale (for example, the protein is part of a regulatory pathway that is involved in the disease process), or genetic screens in model organisms.[2] Disease relevance alone however is insufficient for a protein to become a drug target. In addition, the target must be druggable.

Prediction of druggability

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If a drug has already been identified for a target, that target is by definition druggable. If no known drugs bind to a target, then druggability is implied or predicted using different methods that rely on evolutionary relationships, 3D-structural properties or other descriptors.[3]

Precedence-based

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A protein is predicted to be "druggable" if it is a member of a protein family[4] for which other members of the family are known to be targeted by drugs (i.e., "guilt" by association). While this is a useful approximation of druggability, this definition has limitations for two main reasons: (1) it highlights only historically successful proteins, ignoring the possibility of a perfectly druggable, but yet undrugged protein family; and (2) assumes that all protein family members are equally druggable.[citation needed]

Structure-based

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This relies on the availability of experimentally determined 3D structures or high quality homology models. A number of methods exist for this assessment of druggability but all of them consist of three main components:[5][6][7][8]

  1. Identifying cavities or pockets on the structure
  2. Calculating physicochemical and geometric properties of the pocket
  3. Assessing how these properties fit a training set of known druggable targets, typically using machine learning algorithms

Early work on introducing some of the parameters of structure-based druggability came from Abagyan and coworkers[9] and then Fesik and coworkers,[10] the latter by assessing the correlation of certain physicochemical parameters with hits from an NMR-based fragment screen. There has since been a number of publications reporting related methodologies.[5][11][12]

There are several commercial tools and databases for structure-based druggability assessment. A publicly available database of pre-calculated druggability assessments for all structural domains within the Protein Data Bank (PDB) is provided through the ChEMBL's DrugEBIlity portal.[13]

Structure-based druggability is usually used to identify suitable binding pocket for a small molecule; however, some studies have assessed 3D structures for the availability of grooves suitable for binding helical mimetics.[14] This is an increasingly popular approach in addressing the druggability of protein-protein interactions.[15]

Predictions based on other properties

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As well as using 3D structure and family precedence, it is possible to estimate druggability using other properties of a protein such as features derived from the amino-acid sequence (feature-based druggability)[3] which is applicable to assessing small-molecule based druggability or biotherapeutic-based druggability or the properties of ligands or compounds known to bind the protein (Ligand-based druggability).[16][17]

The importance of training sets

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All methods for assessing druggability are highly dependent on the training sets used to develop them. This highlights an important caveat in all the methods discussed above: which is that they have learned from the successes so far. The training sets are typically either databases of curated drug targets;[18][19] screened targets databases (ChEMBL, BindingDB, PubChem etc.); or on manually compiled sets of 3D structure known by the developers to be druggable. As training sets improve and expand, the boundaries of druggability may also be expanded.

Undruggable targets

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About 3% of human proteins are known to be "mode of action" drug targets, i.e., proteins through which approved drugs act.[20] Another 7% of the human proteins interact with small molecule chemicals.[20] Based on DrugCentral, 1795 human proteins annotated to interact with 2455 approved drugs.[21]

Furthermore, it is estimated that only 10-15% of human proteins are disease modifying while only 10-15% are druggable (there is no correlation between the two), meaning that only between 1 and 2.25% of disease modifying proteins are likely to be druggable. Hence it appears that the number of new undiscovered drug targets is very limited.[22][23][24]

A potentially much larger percentage of proteins could be made druggable if protein–protein interactions could be disrupted by small molecules. However the majority of these interactions occur between relatively flat surfaces of the interacting protein partners and it is very difficult for small molecules to bind with high affinity to these surfaces.[25][26] Hence these types of binding sites on proteins are generally thought to be undruggable but there has been some progress (by 2009) targeting these sites.[27][28]

Chemoproteomics techniques have recently expanded the scope of what is deemed a druggable target through the identification of covalently modifiable sites across the proteome.[29]

References

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  1. ^ Owens J (2007). "Determining druggability". Nature Reviews Drug Discovery. 6 (3): 187. doi:10.1038/nrd2275.
  2. ^ Dixon SJ, Stockwell BR (December 2009). "Identifying druggable disease-modifying gene products". Current Opinion in Chemical Biology. 13 (5–6): 549–555. doi:10.1016/j.cbpa.2009.08.003. PMC 2787993. PMID 19740696.
  3. ^ a b Al-Lazikani B, Gaulton A, Paolini G, Lanfear J, Overington J, Hopkins A (2007). "The Molecular Basis of Predicting Druggability". In Wess G, Schreiber SL, Kapoor TM (eds.). Chemical Biology: From Small Molecules to Systems Biology and Drug Design. Vol. 1–3. Weinheim: Wiley-VCH. pp. 804–823. ISBN 978-3-527-31150-7.
  4. ^ Hopkins AL, Groom CR (September 2002). "The druggable genome". Nature Reviews. Drug Discovery. 1 (9): 727–730. doi:10.1038/nrd892. PMID 12209152. S2CID 13166282.
  5. ^ a b Halgren TA (February 2009). "Identifying and characterizing binding sites and assessing druggability". Journal of Chemical Information and Modeling. 49 (2): 377–389. doi:10.1021/ci800324m. PMID 19434839.
  6. ^ Nayal M, Honig B (June 2006). "On the nature of cavities on protein surfaces: application to the identification of drug-binding sites". Proteins. 63 (4): 892–906. doi:10.1002/prot.20897. PMID 16477622. S2CID 23887061.
  7. ^ Seco J, Luque FJ, Barril X (April 2009). "Binding site detection and druggability index from first principles". Journal of Medicinal Chemistry. 52 (8): 2363–2371. doi:10.1021/jm801385d. PMID 19296650.
  8. ^ Bakan A, Nevins N, Lakdawala AS, Bahar I (July 2012). "Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules". Journal of Chemical Theory and Computation. 8 (7): 2435–2447. doi:10.1021/ct300117j. PMC 3392909. PMID 22798729.
  9. ^ An J, Totrov M, Abagyan R (2004). "Comprehensive identification of "druggable" protein ligand binding sites". Genome Informatics. International Conference on Genome Informatics. 15 (2): 31–41. PMID 15706489.
  10. ^ Hajduk PJ, Huth JR, Fesik SW (April 2005). "Druggability indices for protein targets derived from NMR-based screening data". Journal of Medicinal Chemistry. 48 (7): 2518–2525. doi:10.1021/jm049131r. PMID 15801841.
  11. ^ Schmidtke P, Barril X (August 2010). "Understanding and predicting druggability. A high-throughput method for detection of drug binding sites". Journal of Medicinal Chemistry. 53 (15): 5858–5867. doi:10.1021/jm100574m. PMID 20684613.
  12. ^ Gupta A, Gupta AK, Seshadri K (August 2009). "Structural models in the assessment of protein druggability based on HTS data". Journal of Computer-Aided Molecular Design. 23 (8): 583–592. Bibcode:2009JCAMD..23..583G. doi:10.1007/s10822-009-9279-y. PMID 19479324. S2CID 10718301.
  13. ^ "DrugEBIlity Portal". ChEMBL. European Bioinformatics Institute.
  14. ^ Jochim AL, Arora PS (October 2010). "Systematic analysis of helical protein interfaces reveals targets for synthetic inhibitors". ACS Chemical Biology. 5 (10): 919–923. doi:10.1021/cb1001747. PMC 2955827. PMID 20712375.
  15. ^ Kozakov D, Hall DR, Chuang GY, Cencic R, Brenke R, Grove LE, et al. (August 2011). "Structural conservation of druggable hot spots in protein-protein interfaces". Proceedings of the National Academy of Sciences of the United States of America. 108 (33): 13528–13533. Bibcode:2011PNAS..10813528K. doi:10.1073/pnas.1101835108. PMC 3158149. PMID 21808046.
  16. ^ Agüero F, Al-Lazikani B, Aslett M, Berriman M, Buckner FS, Campbell RK, et al. (November 2008). "Genomic-scale prioritization of drug targets: the TDR Targets database". Nature Reviews. Drug Discovery. 7 (11): 900–907. doi:10.1038/nrd2684. PMC 3184002. PMID 18927591.
  17. ^ Barelier S, Krimm I (August 2011). "Ligand specificity, privileged substructures and protein druggability from fragment-based screening". Current Opinion in Chemical Biology. 15 (4): 469–474. doi:10.1016/j.cbpa.2011.02.020. PMID 21411360.
  18. ^ Overington JP, Al-Lazikani B, Hopkins AL (December 2006). "How many drug targets are there?". Nature Reviews. Drug Discovery. 5 (12): 993–996. doi:10.1038/nrd2199. PMID 17139284. S2CID 11979420.
  19. ^ Knox C, Law V, Jewison T, Liu P, Ly S, Frolkis A, et al. (January 2011). "DrugBank 3.0: a comprehensive resource for 'omics' research on drugs". Nucleic Acids Research. 39 (Database issue): D1035–D1041. doi:10.1093/nar/gkq1126. PMC 3013709. PMID 21059682.
  20. ^ a b Oprea TI, Bologa CG, Brunak S, Campbell A, Gan GN, Gaulton A, et al. (May 2018). "Unexplored therapeutic opportunities in the human genome". Nature Reviews. Drug Discovery. 17 (5): 317–332. doi:10.1038/nrd.2018.14. PMC 6339563. PMID 29472638.
  21. ^ Halip L, Avram S, Curpan R, Borota A, Bora A, Bologa C, Oprea TI (December 2023). "Exploring DrugCentral: from molecular structures to clinical effects". Journal of Computer-Aided Molecular Design. 37 (12): 681–694. Bibcode:2023JCAMD..37..681H. doi:10.1007/s10822-023-00529-x. PMC 10692006. PMID 37707619.
  22. ^ Kwon B (2011-05-16). "Chemical biologist targets 'undruggable' proteins linked to cancer in quest for new cures". Brent Stockwell interview. Medical Xpress. Retrieved 2012-05-17.
  23. ^ Stockwell BR (2011). The Quest for the Cure: The Science and Stories Behind the Next Generation of Medicines. New York: Columbia University Press. ISBN 978-0-231-15212-9.
  24. ^ Stockwell B (October 2011). "Outsmarting Cancer. A biologist talks about what makes disease-causing proteins so difficult to target with drugs". Scientific American. 305 (4): 20. PMID 22106796.
  25. ^ Buchwald P (October 2010). "Small-molecule protein-protein interaction inhibitors: therapeutic potential in light of molecular size, chemical space, and ligand binding efficiency considerations". IUBMB Life. 62 (10): 724–731. doi:10.1002/iub.383. PMID 20979208. S2CID 205970009.
  26. ^ Morelli X, Bourgeas R, Roche P (August 2011). "Chemical and structural lessons from recent successes in protein-protein interaction inhibition (2P2I)". Current Opinion in Chemical Biology. 15 (4): 475–481. doi:10.1016/j.cbpa.2011.05.024. PMID 21684802.
  27. ^ Verdine GL, Walensky LD (December 2007). "The challenge of drugging undruggable targets in cancer: lessons learned from targeting BCL-2 family members". Clinical Cancer Research. 13 (24): 7264–7270. doi:10.1158/1078-0432.CCR-07-2184. PMID 18094406. S2CID 7918779.
  28. ^ Arkin MR, Whitty A (June 2009). "The road less traveled: modulating signal transduction enzymes by inhibiting their protein-protein interactions". Current Opinion in Chemical Biology. 13 (3): 284–290. doi:10.1016/j.cbpa.2009.05.125. PMID 19553156.
  29. ^ Spradlin JN, Zhang E, Nomura DK (April 2021). "Reimagining Druggability Using Chemoproteomic Platforms". Accounts of Chemical Research. 54 (7): 1801–1813. doi:10.1021/acs.accounts.1c00065. PMID 33733731. S2CID 232303398.

Further reading

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