Druggability#Undruggable targets

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){{cite journal | doi = 10.1038/nrd2275 | title = Determining druggability | year = 2007 | vauthors = Owens J | journal = Nature Reviews Drug Discovery | volume = 6 | issue = 3 | pages = 187 | doi-access = free }} 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.{{cite journal | vauthors = Dixon SJ, Stockwell BR | title = Identifying druggable disease-modifying gene products | journal = Current Opinion in Chemical Biology | volume = 13 | issue = 5–6 | pages = 549–555 | date = December 2009 | pmid = 19740696 | pmc = 2787993 | doi = 10.1016/j.cbpa.2009.08.003 }} Disease relevance alone however is insufficient for a protein to become a drug target. In addition, the target must be druggable.

Prediction of druggability

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.{{cite book |vauthors=Al-Lazikani B, Gaulton A, Paolini G, Lanfear J, Overington J, Hopkins A | chapter = The Molecular Basis of Predicting Druggability |veditors=Wess G, Schreiber SL, Kapoor TM | title = Chemical Biology: From Small Molecules to Systems Biology and Drug Design | publisher = Wiley-VCH | location = Weinheim | year = 2007 | volume = 1–3 | pages = 804–823 | isbn = 978-3-527-31150-7 }}

= Precedence-based =

A protein is predicted to be "druggable" if it is a member of a protein family{{cite journal | vauthors = Hopkins AL, Groom CR | title = The druggable genome | journal = Nature Reviews. Drug Discovery | volume = 1 | issue = 9 | pages = 727–730 | date = September 2002 | pmid = 12209152 | doi = 10.1038/nrd892 | s2cid = 13166282 }} 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|date=July 2011}}

= Structure-based =

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:{{cite journal | vauthors = Halgren TA | title = Identifying and characterizing binding sites and assessing druggability | journal = Journal of Chemical Information and Modeling | volume = 49 | issue = 2 | pages = 377–389 | date = February 2009 | pmid = 19434839 | doi = 10.1021/ci800324m }}{{cite journal | vauthors = Nayal M, Honig B | title = On the nature of cavities on protein surfaces: application to the identification of drug-binding sites | journal = Proteins | volume = 63 | issue = 4 | pages = 892–906 | date = June 2006 | pmid = 16477622 | doi = 10.1002/prot.20897 | s2cid = 23887061 }}{{cite journal | vauthors = Seco J, Luque FJ, Barril X | title = Binding site detection and druggability index from first principles | journal = Journal of Medicinal Chemistry | volume = 52 | issue = 8 | pages = 2363–2371 | date = April 2009 | pmid = 19296650 | doi = 10.1021/jm801385d }}{{cite journal | vauthors = Bakan A, Nevins N, Lakdawala AS, Bahar I | title = Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules | journal = Journal of Chemical Theory and Computation | volume = 8 | issue = 7 | pages = 2435–2447 | date = July 2012 | pmid = 22798729 | pmc = 3392909 | doi = 10.1021/ct300117j }}

Identifying cavities or pockets on the structure
Calculating physicochemical and geometric properties of the pocket
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{{cite journal | vauthors = An J, Totrov M, Abagyan R | title = Comprehensive identification of "druggable" protein ligand binding sites | journal = Genome Informatics. International Conference on Genome Informatics | volume = 15 | issue = 2 | pages = 31–41 | year = 2004 | pmid = 15706489 }} and then Fesik and coworkers,{{cite journal | vauthors = Hajduk PJ, Huth JR, Fesik SW | title = Druggability indices for protein targets derived from NMR-based screening data | journal = Journal of Medicinal Chemistry | volume = 48 | issue = 7 | pages = 2518–2525 | date = April 2005 | pmid = 15801841 | doi = 10.1021/jm049131r }} 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.{{cite journal | vauthors = Schmidtke P, Barril X | title = Understanding and predicting druggability. A high-throughput method for detection of drug binding sites | journal = Journal of Medicinal Chemistry | volume = 53 | issue = 15 | pages = 5858–5867 | date = August 2010 | pmid = 20684613 | doi = 10.1021/jm100574m }}{{cite journal | vauthors = Gupta A, Gupta AK, Seshadri K | title = Structural models in the assessment of protein druggability based on HTS data | journal = Journal of Computer-Aided Molecular Design | volume = 23 | issue = 8 | pages = 583–592 | date = August 2009 | pmid = 19479324 | doi = 10.1007/s10822-009-9279-y | bibcode = 2009JCAMD..23..583G | s2cid = 10718301 }}

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.{{cite web | url = https://www.ebi.ac.uk/chembl/drugebility/ | title = DrugEBIlity Portal | work = ChEMBL | publisher = European Bioinformatics Institute }}

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.{{cite journal | vauthors = Jochim AL, Arora PS | title = Systematic analysis of helical protein interfaces reveals targets for synthetic inhibitors | journal = ACS Chemical Biology | volume = 5 | issue = 10 | pages = 919–923 | date = October 2010 | pmid = 20712375 | pmc = 2955827 | doi = 10.1021/cb1001747 }} This is an increasingly popular approach in addressing the druggability of protein-protein interactions.{{cite journal | vauthors = Kozakov D, Hall DR, Chuang GY, Cencic R, Brenke R, Grove LE, Beglov D, Pelletier J, Whitty A, Vajda S | display-authors = 6 | title = Structural conservation of druggable hot spots in protein-protein interfaces | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 108 | issue = 33 | pages = 13528–13533 | date = August 2011 | pmid = 21808046 | pmc = 3158149 | doi = 10.1073/pnas.1101835108 | doi-access = free | bibcode = 2011PNAS..10813528K }}

= Predictions based on other properties =

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) 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).{{cite journal | vauthors = Agüero F, Al-Lazikani B, Aslett M, Berriman M, Buckner FS, Campbell RK, Carmona S, Carruthers IM, Chan AW, Chen F, Crowther GJ, Doyle MA, Hertz-Fowler C, Hopkins AL, McAllister G, Nwaka S, Overington JP, Pain A, Paolini GV, Pieper U, Ralph SA, Riechers A, Roos DS, Sali A, Shanmugam D, Suzuki T, Van Voorhis WC, Verlinde CL | display-authors = 6 | title = Genomic-scale prioritization of drug targets: the TDR Targets database | journal = Nature Reviews. Drug Discovery | volume = 7 | issue = 11 | pages = 900–907 | date = November 2008 | pmid = 18927591 | pmc = 3184002 | doi = 10.1038/nrd2684 }}{{cite journal | vauthors = Barelier S, Krimm I | title = Ligand specificity, privileged substructures and protein druggability from fragment-based screening | journal = Current Opinion in Chemical Biology | volume = 15 | issue = 4 | pages = 469–474 | date = August 2011 | pmid = 21411360 | doi = 10.1016/j.cbpa.2011.02.020 }}

= The importance of training sets =

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;{{cite journal | vauthors = Overington JP, Al-Lazikani B, Hopkins AL | title = How many drug targets are there? | journal = Nature Reviews. Drug Discovery | volume = 5 | issue = 12 | pages = 993–996 | date = December 2006 | pmid = 17139284 | doi = 10.1038/nrd2199 | s2cid = 11979420 }}{{cite journal | vauthors = Knox C, Law V, Jewison T, Liu P, Ly S, Frolkis A, Pon A, Banco K, Mak C, Neveu V, Djoumbou Y, Eisner R, Guo AC, Wishart DS | display-authors = 6 | title = DrugBank 3.0: a comprehensive resource for 'omics' research on drugs | journal = Nucleic Acids Research | volume = 39 | issue = Database issue | pages = D1035–D1041 | date = January 2011 | pmid = 21059682 | pmc = 3013709 | doi = 10.1093/nar/gkq1126 | author14-link = David S. Wishart }} 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

About 3% of human proteins are known to be "mode of action" drug targets, i.e., proteins through which approved drugs act.{{cite journal | vauthors = Oprea TI, Bologa CG, Brunak S, Campbell A, Gan GN, Gaulton A, Gomez SM, Guha R, Hersey A, Holmes J, Jadhav A, Jensen LJ, Johnson GL, Karlson A, Leach AR, Ma'ayan A, Malovannaya A, Mani S, Mathias SL, McManus MT, Meehan TF, von Mering C, Muthas D, Nguyen DT, Overington JP, Papadatos G, Qin J, Reich C, Roth BL, Schürer SC, Simeonov A, Sklar LA, Southall N, Tomita S, Tudose I, Ursu O, Vidovic D, Waller A, Westergaard D, Yang JJ, Zahoránszky-Köhalmi G | display-authors = 6 | title = Unexplored therapeutic opportunities in the human genome | journal = Nature Reviews. Drug Discovery | volume = 17 | issue = 5 | pages = 317–332 | date = May 2018 | pmid = 29472638 | doi = 10.1038/nrd.2018.14 | pmc = 6339563 }} Another 7% of the human proteins interact with small molecule chemicals. Based on DrugCentral, 1795 human proteins annotated to interact with 2455 approved drugs.{{cite journal | vauthors = Halip L, Avram S, Curpan R, Borota A, Bora A, Bologa C, Oprea TI | title = Exploring DrugCentral: from molecular structures to clinical effects | journal = Journal of Computer-Aided Molecular Design | volume = 37 | issue = 12 | pages = 681–694 | date = December 2023 | pmid = 37707619 | pmc = 10692006 | doi = 10.1007/s10822-023-00529-x | bibcode = 2023JCAMD..37..681H }}

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.{{cite web | url = http://medicalxpress.com/news/2011-05-chemical-biologist-undruggable-proteins-linked.html | title = Chemical biologist targets 'undruggable' proteins linked to cancer in quest for new cures | vauthors = Kwon B | date = 2011-05-16 | work = Brent Stockwell interview | publisher = Medical Xpress | access-date = 2012-05-17 }}{{cite book | vauthors = Stockwell BR | title = The Quest for the Cure: The Science and Stories Behind the Next Generation of Medicines | publisher = Columbia University Press | location = New York | year = 2011 | isbn = 978-0-231-15212-9 | url = https://archive.org/details/questforcurescie00stoc }}{{cite journal | vauthors = Stockwell B | title = Outsmarting Cancer. A biologist talks about what makes disease-causing proteins so difficult to target with drugs | journal = Scientific American | volume = 305 | issue = 4 | pages = 20 | date = October 2011 | pmid = 22106796 | url = http://www.scientificamerican.com/article.cfm?id=outsmarting-cancer }}

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.{{cite journal | vauthors = Buchwald P | title = Small-molecule protein-protein interaction inhibitors: therapeutic potential in light of molecular size, chemical space, and ligand binding efficiency considerations | journal = IUBMB Life | volume = 62 | issue = 10 | pages = 724–731 | date = October 2010 | pmid = 20979208 | doi = 10.1002/iub.383 | s2cid = 205970009 }}{{cite journal | vauthors = Morelli X, Bourgeas R, Roche P | title = Chemical and structural lessons from recent successes in protein-protein interaction inhibition (2P2I) | journal = Current Opinion in Chemical Biology | volume = 15 | issue = 4 | pages = 475–481 | date = August 2011 | pmid = 21684802 | doi = 10.1016/j.cbpa.2011.05.024 }} 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.{{cite journal | vauthors = Verdine GL, Walensky LD | title = The challenge of drugging undruggable targets in cancer: lessons learned from targeting BCL-2 family members | journal = Clinical Cancer Research | volume = 13 | issue = 24 | pages = 7264–7270 | date = December 2007 | pmid = 18094406 | doi = 10.1158/1078-0432.CCR-07-2184 | doi-access = | s2cid = 7918779 }}{{cite journal | vauthors = Arkin MR, Whitty A | title = The road less traveled: modulating signal transduction enzymes by inhibiting their protein-protein interactions | journal = Current Opinion in Chemical Biology | volume = 13 | issue = 3 | pages = 284–290 | date = June 2009 | pmid = 19553156 | doi = 10.1016/j.cbpa.2009.05.125 }}

Chemoproteomics techniques have recently expanded the scope of what is deemed a druggable target through the identification of covalently modifiable sites across the proteome.{{cite journal | vauthors = Spradlin JN, Zhang E, Nomura DK | title = Reimagining Druggability Using Chemoproteomic Platforms | journal = Accounts of Chemical Research | volume = 54 | issue = 7 | pages = 1801–1813 | date = April 2021 | pmid = 33733731 | doi = 10.1021/acs.accounts.1c00065 | s2cid = 232303398 }}

References

External links

{{cite web | url = https://www.ebi.ac.uk/chembl/drugebility/structure |title=DrugEBIlity | publisher = ChEMBL }}
{{cite web | url = http://dgidb.org/ | title = The Drug Gene Interaction Database (DGIdb) | publisher = Washington University School of Medicine }}
{{cite web | url = http://tdrtargets.org/ | title = TDR Targets Database | publisher = The TDR Drug Targets Network }}

Category:Drug discovery