Targeted covalent inhibitors

Last updated

Targeted covalent inhibitors (TCIs) or Targeted covalent drugs are rationally designed inhibitors that bind and then bond to their target proteins. These inhibitors possess a bond-forming functional group of low chemical reactivity that, following binding to the target protein, is positioned to react rapidly with a proximate nucleophilic residue at the target site to form a bond. [1]

Contents

This illustration describes the mechanism by which covalent drugs irreversibly bind and modify the protein, e.g. silencing its activity Covalent-drugs-silence-proteins.png
This illustration describes the mechanism by which covalent drugs irreversibly bind and modify the protein, e.g. silencing its activity

Historical impact of covalent drugs

Over the last 100 years covalent drugs have made a major impact on human health and have been highly successful drugs for the pharmaceutical industry. [2] These inhibitors react with their target proteins to form a covalent complex in which the protein has lost its function. The majority of these successful drugs, which include penicillin, omeprazole, clopidogrel, and aspirin were discovered through serendipity in phenotypic screens. [3]

A brief timeline representation of the history of covalent drugs that have been approved to be marketed Covalent Drugs Timeline.png
A brief timeline representation of the history of covalent drugs that have been approved to be marketed

However, key changes in screening approaches, along with safety concerns, have made pharma reluctant to pursue covalent inhibitors in a systematic way (Liebler & Guengerich, 2005). [4] [5] Recently, there has been considerable attention to using rational drug design to create highly selective covalent inhibitors called targeted covalent inhibitors. [6] The first published example of a targeted covalent drug was for the EGFR kinase. [7] [8] But this has now broadened to other kinases [9] [6] and other protein families. [10] [11] Aside from small molecules, covalent probes are also being derived from peptides or proteins. By incorporation of a reactive group into a binding peptide or protein via posttranslational chemical modification [12] or as an unnatural amino acid, [13] a target protein can be conjugated specifically via proximity-induced reaction.

Advantages of covalent drugs

Potency

Covalent bonding can lead to potencies and ligand efficiencies that are either exceptionally high or, for irreversible covalent interactions, even essentially infinite. Covalent bonding thus allows high potency to be routinely achieved in compounds of low molecular mass, along with all the beneficial pharmaceutical properties that are associated with small size. [14] [15]

Selectivity

Covalent inhibitors can be designed to target a nucleophile that is unique or rare across a protein family. [7] [6] [9] [16] Thereby ensuring that covalent bond formation cannot occur with most other family members. This approach can lead to high selectivity against closely related proteins because although the inhibitor might bind transiently to the active sites of such proteins, it will not covalently label them if they lack the targeted nucleophilic residue in the appropriate position.

Pharmacodynamics

The restoration of pharmacological activity after covalent irreversible inhibition requires re-synthesis of the protein target. This has important and potentially advantageous consequences for drug pharmacodynamics in which the level and frequency of dosing relates to the extent and duration of the resulting pharmacological effect. [17]

Built-in-biomarker

Covalent inhibitors can be used to assess target engagement which can sometimes be used pre-clinically and clinically to assess the relationship between dose of drug and efficacy or toxicity. [17] This approach was used for covalent Btk inhibitors pre-clinically and clinically to understand the relationship between dose administered and efficacy in animal models of arthritis and target occupancy in a clinical study of healthy volunteers. [18]

Design of covalent drugs

The design of covalent drugs requires careful optimization of both the non-covalent binding affinity (which is reflected in Ki) and the reactivity of the electrophilic warhead (which is reflected in k2).

Mechanism of Action of Covalent Drugs Mechanism of Action of Covalent Drugs.png
Mechanism of Action of Covalent Drugs

The initial design of TCIs involves three key steps. First, bioinformatics analysis is used to identify a nucleophilic amino acid (for example, cysteine) that is either inside or near to a functionally relevant binding site on a drug target, but is rare in that protein family. Next, a reversible inhibitor is identified for which the binding mode is known. Finally, structure-based computational methods are used to guide the design of modified ligands that have electrophilic functionality, and are positioned to react specifically with the nucleophilic amino acid in the target protein. [1]

EGFR kinase T790M mutant covalently inhibited by HKI-272 (neratinib) at Cys-797 (PDB ID: 2JIV) EGFR kinase covalently bound to HKI-272.png
EGFR kinase T790M mutant covalently inhibited by HKI-272 (neratinib) at Cys-797 (PDB ID: 2JIV)

Targeted covalent photoisomerizable ligands (photoswitches) have been developed to remotely and reversibly control the activity of receptor proteins with light. They have been used as molecular prostheses to restore visual input in the retina [19] and auditory input in the cochlea via glutamate receptors. [20] Ligand conjugation is targeted to specific lysine residues via an affinity labeling mechanism.

Toxicity risks associated with covalent modification of proteins

There has been a reluctance for modern drug discovery programs to consider covalent inhibitors due to toxicity concerns. [5] An important contributor has been the drug toxicities of several high-profile drugs believed to be caused by metabolic activation of reversible drugs. [5] For example, high dose acetaminophen can lead to the formation of the reactive metabolite N-acetyl-p-benzoquinone imine. Also, covalent inhibitors such as beta lactam antibiotics which contain weak electrophiles can lead to idiosyncratic toxicities (IDT) in some patients. It has been noted that many approved covalent inhibitors have been used safely for decades with no observed idiosyncratic toxicity. Also, that IDTs are not limited to proteins with a covalent mechanism of action. [21] A recent analysis has noted that the risk of idiosyncratic toxicities may be mitigated through lower doses of administered drug. Doses of less than 10 mg per day rarely lead to IDT irrespective of the drug mechanism. [22]

TCIs in clinical development

Despite the apparent lack of attention towards covalent inhibitor drug discovery by most pharmaceutical companies, there are several examples of covalent drugs that have been approved or are progressing to late-stage clinical development.

KRAS and lung, colorectal cancer

AMG 510 by Amgen is a KRAS p.G12C covalent inhibitor that has recently finished Phase I clinical trial. [23] The drug elicited partial responses in half of evaluable patients with KRAS G12C-mutant non–small cell lung cancer, and led to stable disease in most evaluable patients with colorectal (or appendix) cancer.

EGFR and lung cancer

The second generation EGFR inhibitors Afatinib and Mobocertinib have been approved for the treatment of EGFR driven lung cancer and Dacomitinib is in late stage clinical testing. The third generation EGFR inhibitors which target mutant EGFR which is specific to the tumor but are selective against wild-type EGFR that are expected to lead to a wider therapeutic index. [24]

ErbB family and breast cancer

The pan-ErbB inhibitor Neratinib was approved in the US in 2017 and in the EU in 2018 for the extended adjuvant treatment of adult patients with early-stage HER2-overexpressed/amplified breast cancer after trastuzumab-based therapy. [25] [26]

Btk and leukemia

Ibrutinib, a covalent inhibitor of Bruton's tyrosine kinase, has been approved for the treatment of chronic lymphocytic leukemia, waldenstrom’s macroglobulinemia and mantle cell lymphoma.

SARS-CoV-2 protease and COVID-19

Paxlovid is a covalent inhibitor of the 3CLpro (Mpro) enzyme. It is in Phase III trials for the early treatment of SARS-CoV-2 infected patients who have not progressed to severe COVID-19 disease, and who do not immediately require hospitalisation.

Related Research Articles

<span class="mw-page-title-main">Protein kinase</span> Enzyme that adds phosphate groups to other proteins

A protein kinase is a kinase which selectively modifies other proteins by covalently adding phosphates to them (phosphorylation) as opposed to kinases which modify lipids, carbohydrates, or other molecules. Phosphorylation usually results in a functional change of the target protein (substrate) by changing enzyme activity, cellular location, or association with other proteins. The human genome contains about 500 protein kinase genes and they constitute about 2% of all human genes. There are two main types of protein kinase. The great majority are serine/threonine kinases, which phosphorylate the hydroxyl groups of serines and threonines in their targets and most of the others are tyrosine kinases, although additional types exist. Protein kinases are also found in bacteria and plants. Up to 30% of all human proteins may be modified by kinase activity, and kinases are known to regulate the majority of cellular pathways, especially those involved in signal transduction.

<span class="mw-page-title-main">Agonist</span> Chemical which binds to and activates a biochemical receptor

An agonist is a chemical that activates a receptor to produce a biological response. Receptors are cellular proteins whose activation causes the cell to modify what it is currently doing. In contrast, an antagonist blocks the action of the agonist, while an inverse agonist causes an action opposite to that of the agonist.

<span class="mw-page-title-main">Receptor antagonist</span> Type of receptor ligand or drug that blocks a biological response

A receptor antagonist is a type of receptor ligand or drug that blocks or dampens a biological response by binding to and blocking a receptor rather than activating it like an agonist. Antagonist drugs interfere in the natural operation of receptor proteins. They are sometimes called blockers; examples include alpha blockers, beta blockers, and calcium channel blockers. In pharmacology, antagonists have affinity but no efficacy for their cognate receptors, and binding will disrupt the interaction and inhibit the function of an agonist or inverse agonist at receptors. Antagonists mediate their effects by binding to the active site or to the allosteric site on a receptor, or they may interact at unique binding sites not normally involved in the biological regulation of the receptor's activity. Antagonist activity may be reversible or irreversible depending on the longevity of the antagonist–receptor complex, which, in turn, depends on the nature of antagonist–receptor binding. The majority of drug antagonists achieve their potency by competing with endogenous ligands or substrates at structurally defined binding sites on receptors.

<span class="mw-page-title-main">Gefitinib</span> Drug used in fighting breast, lung, and other cancers

Gefitinib, sold under the brand name Iressa, is a medication used for certain breast, lung and other cancers. Gefitinib is an EGFR inhibitor, like erlotinib, which interrupts signaling through the epidermal growth factor receptor (EGFR) in target cells. Therefore, it is only effective in cancers with mutated and overactive EGFR, but resistances to gefitinib can arise through other mutations. It is marketed by AstraZeneca and Teva.

<span class="mw-page-title-main">Epidermal growth factor receptor</span> Transmembrane protein

The epidermal growth factor receptor is a transmembrane protein that is a receptor for members of the epidermal growth factor family of extracellular protein ligands.

Quinazoline is an organic compound with the formula C8H6N2. It is an aromatic heterocycle with a bicyclic structure consisting of two fused six-membered aromatic rings, a benzene ring and a pyrimidine ring. It is a light yellow crystalline solid that is soluble in water. Also known as 1,3-diazanaphthalene, quinazoline received its name from being an aza derivative of quinoline. Though the parent quinazoline molecule is rarely mentioned by itself in technical literature, substituted derivatives have been synthesized for medicinal purposes such as antimalarial and anticancer agents. Quinazoline is a planar molecule. It is isomeric with the other diazanaphthalenes of the benzodiazine subgroup: cinnoline, quinoxaline, and phthalazine. Over 200 biologically active quinazoline and quinoline alkaloids are identified.

<span class="mw-page-title-main">Erlotinib</span> EGFR inhibitor for treatment of non-small-cell lung cancer

Erlotinib, sold under the brand name Tarceva among others, is a medication used to treat non-small cell lung cancer (NSCLC) and pancreatic cancer. Specifically it is used for NSCLC with mutations in the epidermal growth factor receptor (EGFR) — either an exon 19 deletion (del19) or exon 21 (L858R) substitution mutation — which has spread to other parts of the body. It is taken by mouth.

Affinity labels are a class of enzyme inhibitors that covalently bind to their target causing its inactivation. The hallmark of an affinity label is the use of a targeting moiety to specifically and reversibly deliver a weakly reactive group to the enzyme that irreversibly binds to an amino acid residue. The targeting portion of the label often resembles the enzyme's natural substrate so that a similar mode of noncovalent binding is used prior to the covalent linkage. Their usefulness in medicine can be limited by the specificity of the first noncovalent binding step whereas indiscriminate action can be utilized for purposes such as affinity labeling - a technique for the validation of substrate-specific binding of compounds.

<span class="mw-page-title-main">Enzyme inhibitor</span> Molecule that blocks enzyme activity

An enzyme inhibitor is a molecule that binds to an enzyme and blocks its activity. Enzymes are proteins that speed up chemical reactions necessary for life, in which substrate molecules are converted into products. An enzyme facilitates a specific chemical reaction by binding the substrate to its active site, a specialized area on the enzyme that accelerates the most difficult step of the reaction.

<span class="mw-page-title-main">KRAS</span> Protein-coding gene in the species Homo sapiens

KRAS is a gene that provides instructions for making a protein called K-Ras, a part of the RAS/MAPK pathway. The protein relays signals from outside the cell to the cell's nucleus. These signals instruct the cell to grow and divide (proliferate) or to mature and take on specialized functions (differentiate). It is called KRAS because it was first identified as a viral oncogene in the KirstenRAt Sarcoma virus. The oncogene identified was derived from a cellular genome, so KRAS, when found in a cellular genome, is called a proto-oncogene.

A protein kinase inhibitor is a type of enzyme inhibitor that blocks the action of one or more protein kinases. Protein kinases are enzymes that phosphorylate (add a phosphate, or PO4, group) to a protein and can modulate its function.

<span class="mw-page-title-main">Staurosporine</span> Chemical compound

Staurosporine is a natural product originally isolated in 1977 from the bacterium Streptomyces staurosporeus. It was the first of over 50 alkaloids to be isolated with this type of bis-indole chemical structure. The chemical structure of staurosporine was elucidated by X-ray analysis of a single crystal and the absolute stereochemical configuration by the same method in 1994.

Bioconjugation is a chemical strategy to form a stable covalent link between two molecules, at least one of which is a biomolecule.

Molecular binding is an attractive interaction between two molecules that results in a stable association in which the molecules are in close proximity to each other. It is formed when atoms or molecules bind together by sharing of electrons. It often, but not always, involves some chemical bonding.

<span class="mw-page-title-main">Tyrosine kinase inhibitor</span> Drug typically used in cancer treatment

A tyrosine kinase inhibitor (TKI) is a pharmaceutical drug that inhibits tyrosine kinases. Tyrosine kinases are enzymes responsible for the activation of many proteins by signal transduction cascades. The proteins are activated by adding a phosphate group to the protein (phosphorylation), a step that TKIs inhibit. TKIs are typically used as anticancer drugs. For example, they have substantially improved outcomes in chronic myelogenous leukemia. They have also been used to treat other diseases, such as idiopathic pulmonary fibrosis.

Bcr-Abl tyrosine-kinase inhibitors (TKI) are the first-line therapy for most patients with chronic myelogenous leukemia (CML). More than 90% of CML cases are caused by a chromosomal abnormality that results in the formation of a so-called Philadelphia chromosome. This abnormality was discovered by Peter Nowell in 1960 and is a consequence of fusion between the Abelson (Abl) tyrosine kinase gene at chromosome 9 and the break point cluster (Bcr) gene at chromosome 22, resulting in a chimeric oncogene (Bcr-Abl) and a constitutively active Bcr-Abl tyrosine kinase that has been implicated in the pathogenesis of CML. Compounds have been developed to selectively inhibit the tyrosine kinase.

c-Met inhibitors are a class of small molecules that inhibit the enzymatic activity of the c-Met tyrosine kinase, the receptor of hepatocyte growth factor/scatter factor (HGF/SF). These inhibitors may have therapeutic application in the treatment of various types of cancers.

<span class="mw-page-title-main">Osimertinib</span> Chemical compound, used as a medication to treat lung cancer

Osimertinib, sold under the brand name Tagrisso, is a medication used to treat non-small-cell lung carcinomas with specific mutations. It is a third-generation epidermal growth factor receptor tyrosine kinase inhibitor.

<span class="mw-page-title-main">Olmutinib</span>

Olmutinib (INN) is an investigational anti-cancer drug. It acts by covalently bonding to a cysteine residue near the kinase domain of epidermal growth factor receptor (EGFR).

<span class="mw-page-title-main">Mobocertinib</span> Small molecule tyrosine kinase inhibitor


Mobocertinib, sold under the brand name Exkivity, is used for the treatment of non-small cell lung cancer.

References

  1. 1 2 3 Singh J, Petter RC, Baillie TA, Whitty A (April 2011). "The resurgence of covalent drugs". Nature Reviews. Drug Discovery. 10 (4): 307–317. doi: 10.1038/nrd3410 . PMID   21455239. S2CID   5819338.
  2. ↑ Robertson JG (April 2005). "Mechanistic basis of enzyme-targeted drugs". Biochemistry. 44 (15): 5561–5571. doi:10.1021/bi050247e. PMID   15823014.
  3. ↑ Potashman MH, Duggan ME (March 2009). "Covalent modifiers: an orthogonal approach to drug design". Journal of Medicinal Chemistry. 52 (5): 1231–1246. doi:10.1021/jm8008597. PMID   19203292.
  4. ↑ Liebler DC, Guengerich FP (May 2005). "Elucidating mechanisms of drug-induced toxicity". Nature Reviews. Drug Discovery. 4 (5): 410–420. doi:10.1038/nrd1720. PMID   15864270. S2CID   6791573.
  5. 1 2 3 Park BK, Boobis A, Clarke S, Goldring CE, Jones D, Kenna JG, et al. (April 2011). "Managing the challenge of chemically reactive metabolites in drug development". Nature Reviews. Drug Discovery. 10 (4): 292–306. doi:10.1038/nrd3408. PMID   21455238. S2CID   29283248.
  6. 1 2 3 Singh J, Petter RC, Kluge AF (August 2010). "Targeted covalent drugs of the kinase family". Current Opinion in Chemical Biology. 14 (4): 475–480. doi:10.1016/j.cbpa.2010.06.168. PMID   20609616.
  7. 1 2 Singh J, Dobrusin EM, Fry DW, Haske T, Whitty A, McNamara DJ (March 1997). "Structure-based design of a potent, selective, and irreversible inhibitor of the catalytic domain of the erbB receptor subfamily of protein tyrosine kinases". Journal of Medicinal Chemistry. 40 (7): 1130–1135. doi:10.1021/jm960380s. PMID   9089334.
  8. ↑ Fry DW, Bridges AJ, Denny WA, Doherty A, Greis KD, Hicks JL, et al. (September 1998). "Specific, irreversible inactivation of the epidermal growth factor receptor and erbB2, by a new class of tyrosine kinase inhibitor". Proceedings of the National Academy of Sciences of the United States of America. 95 (20): 12022–12027. Bibcode:1998PNAS...9512022F. doi: 10.1073/pnas.95.20.12022 . PMC   21758 . PMID   9751783.
  9. 1 2 Cohen MS, Zhang C, Shokat KM, Taunton J (May 2005). "Structural bioinformatics-based design of selective, irreversible kinase inhibitors". Science. 308 (5726): 1318–1321. doi:10.1126/science1108367. PMC   3641834 . PMID   15919995.
  10. ↑ Hagel M, Niu D, St Martin T, Sheets MP, Qiao L, Bernard H, et al. (January 2011). "Selective irreversible inhibition of a protease by targeting a noncatalytic cysteine". Nature Chemical Biology. 7 (1): 22–24. doi:10.1038/nchembio.492. PMID   21113170.
  11. ↑ Ostrem JM, Peters U, Sos ML, Wells JA, Shokat KM (November 2013). "K-Ras(G12C) inhibitors allosterically control GTP affinity and effector interactions". Nature. 503 (7477): 548–551. Bibcode:2013Natur.503..548O. doi:10.1038/nature12796. PMC   4274051 . PMID   24256730.
  12. ↑ Holm L, Moody P, Howarth M (November 2009). "Electrophilic affibodies forming covalent bonds to protein targets". The Journal of Biological Chemistry. 284 (47): 32906–32913. doi: 10.1074/jbc.M109.034322 . PMC   2781706 . PMID   19759009.
  13. ↑ Xiang Z, Ren H, Hu YS, Coin I, Wei J, Cang H, Wang L (September 2013). "Adding an unnatural covalent bond to proteins through proximity-enhanced bioreactivity". Nature Methods. 10 (9): 885–888. doi:10.1038/nmeth.2595. PMC   3882359 . PMID   23913257.
  14. ↑ Smith AJ, Zhang X, Leach AG, Houk KN (January 2009). "Beyond picomolar affinities: quantitative aspects of noncovalent and covalent binding of drugs to proteins". Journal of Medicinal Chemistry. 52 (2): 225–233. doi:10.1021/jm800498e. PMC   2646787 . PMID   19053779.
  15. ↑ Srinivasan B (March 2021). "Explicit Treatment of Non-Michaelis-Menten and Atypical Kinetics in Early Drug Discovery*". ChemMedChem. 16 (6): 899–918. doi:10.1002/cmdc.202000791. PMID   33231926. S2CID   227157473.
  16. ↑ Liu Q, Sabnis Y, Zhao Z, Zhang T, Buhrlage SJ, Jones LH, Gray NS (February 2013). "Developing irreversible inhibitors of the protein kinase cysteinome". Chemistry & Biology. 20 (2): 146–159. doi:10.1016/j.chembiol.2012.12.006. PMC   3583020 . PMID   23438744.
  17. 1 2 Durham TB, Blanco MJ (March 2015). "Target engagement in lead generation". Bioorganic & Medicinal Chemistry Letters. 25 (5): 998–1008. doi: 10.1016/j.bmcl.2014.12.076 . PMID   25630223.
  18. ↑ Advani RH, Buggy JJ, Sharman JP, Smith SM, Boyd TE, Grant B, et al. (January 2013). "Bruton tyrosine kinase inhibitor ibrutinib (PCI-32765) has significant activity in patients with relapsed/refractory B-cell malignancies". Journal of Clinical Oncology. 31 (1): 88–94. doi:10.1200/JCO.2012.42.7906. PMC   5505166 . PMID   23045577.
  19. ↑ Izquierdo-Serra M, Bautista-Barrufet A, Trapero A, Garrido-Charles A, Díaz-Tahoces A, Camarero N, et al. (July 2016). "Optical control of endogenous receptors and cellular excitability using targeted covalent photoswitches". Nature Communications. 7 (1): 12221. Bibcode:2016NatCo...712221I. doi:10.1038/ncomms12221. PMC   4961765 . PMID   27436051.
  20. ↑ Garrido-Charles A, Huet A, Matera C, Thirumalai A, Hernando J, Llebaria A, et al. (June 2022). "Fast Photoswitchable Molecular Prosthetics Control Neuronal Activity in the Cochlea". Journal of the American Chemical Society. 144 (21): 9229–9239. bioRxiv   10.1101/2021.05.25.445123 . doi:10.1021/jacs.1c12314. PMC   9164239 . PMID   35584208.
  21. ↑ Bauer RA (September 2015). "Covalent inhibitors in drug discovery: from accidental discoveries to avoided liabilities and designed therapies". Drug Discovery Today. 20 (9): 1061–1073. doi:10.1016/j.drudis.2015.05.005. PMID   26002380.
  22. ↑ Nakayama S, Atsumi R, Takakusa H, Kobayashi Y, Kurihara A, Nagai Y, et al. (September 2009). "A zone classification system for risk assessment of idiosyncratic drug toxicity using daily dose and covalent binding". Drug Metabolism and Disposition. 37 (9): 1970–1977. doi:10.1124/dmd.109.027797. PMID   19487250. S2CID   16997956.
  23. ↑ Clinical trial number NCT03600883 for "A Phase 1/2, Study Evaluating the Safety, Tolerability, PK, and Efficacy of AMG 510 in Subjects With Solid Tumors With a Specific KRAS Mutation." at ClinicalTrials.gov
  24. ↑ Tan CS, Kumarakulasinghe NB, Huang YQ, Ang YL, Choo JR, Goh BC, Soo RA (February 2018). "Third generation EGFR TKIs: current data and future directions". Molecular Cancer. 17 (1): 29. doi:10.1186/s12943-018-0778-0. PMC   5817792 . PMID   29455654.
  25. ↑ "Nerlynx (neratinib maleate) Tablets". U.S. Food and Drug Administration (FDA). 21 August 2017. Retrieved 14 July 2021.
  26. ↑ "Nerlynx EPAR". European Medicines Agency (EMA). 17 September 2018. Retrieved 14 July 2021.
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.