Enzymes

Enzymes

Enzymes are proteins which act as catalysts to facilitate the conversion of substrates into products.

Enzyme classification has been developed by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB), which arranges enzymes into six large familes:

EC 1.-.-.- Oxidoreductases
EC 2.-.-.- Transferases (includes the protein kinases EC 2.7.-.-)
EC 3.-.-.- Hydrolases
EC 4.-.-.- Lyases
EC 5.-.-.- Isomerases
EC 6.-.-.- Ligases

Enzymes may also be grouped according to the pyhsiological pathway or process in which they are involved. For example, L-arginine turnover, cyclic nucleotide turnover, eicosanoid turnover or chromatin modifying enzymes.

The majority of drugs which act on enzymes act as inhibitors and most of these are competitive, in that they compete for binding with the enzyme's substrate- for example the majority of the original (first generation) kinase inhibitors bind to the ATP pocket of the enzyme. Some inhibitors are non-competitive, binding away from the substrate binding domain, competing for co-factor/co-enzyme binding, or causing an allosteric conformational change in the 3-dimensional protein structure that prevents substrate interaction. Yet other inhibitors are irreversible and these covalently bind to the enzyme, permanently inactivating catalytic function (these are also known as suicide inhibitors).

The topics below highlight a cross-section of the clinical uses of enzyme inhibitors, from inflammation to cancer.

Cyclooxygenase (COX) inhibitors

Cyclooxygenase (COX) inhibitors are non-steroidal anti-inflammatory drugs (NSAIDs), used clinically to relieve fever and pain, such as those associated with headaches, colds, flu, and arthritis. NSAIDs are available by prescription and over-the-counter (OTC).

COX inhibitors can act at one or both of the isozymes, COX-1 and COX-2.

COX-1 is involved in the synthesis of prostaglandins which are responsible for maintenance and protection of the gastrointestinal tract, whilst COX-2 produces the pro-inflammatory prostaglandins responsible for causing inflammation and pain.

Inhibitors differ in their relative specificities for COX-1 and COX-2, with examples such as aspirin, ibuprofennaproxen and diclofenac being non-selective. Selective COX-2 inhibitors were developed to reduce the liability of gastrointestinal damage associated with COX-1 inhibition. Non-selective COX inhibitors are often prescribed with a proton pump inhibitor such as omeprazole to reduce the risk of causing gastrointestinal ulceration and bleeding. Meloxicam, valdecoxibparecoxib and rofecoxib are examples of selective COX-2 inhibitors. However, some COX-2 selective inhibitors have been shown to cause an increased risk of heart attacks and strokes. Because of this risk all non-aspirin NSAID medications (prescription or OTC) must carry boxed warnings to alert patients to the potential danger associated with their use. The US FDA issued an updated safety warning in late 2015: FDA Drug Safety Communication: FDA strengthens warning that non-aspirin nonsteroidal anti-inflammatory drugs (NSAIDs) can cause heart attacks or strokes.

A short article and video-cast explaining the proposed molecular mechanism(s) underlying the increased risk of heart attack and stroke associated with COX-2 inhibitor use. Produced by Garret FitzGerald MD FRS from University of Pennsylvania, Perelman School of Medicine.

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Cyclooxygenase (COX) inhibitors are non-steroidal anti-inflammatory drugs (NSAIDs), used clinically to relieve fever and pain, such as those associated with headaches, colds, flu, and arthritis. NSAIDs are available by prescription and over-the-counter (OTC).

COX inhibitors can act at one or both of the isozymes, COX-1 and COX-2.

COX-1 is involved in the synthesis of prostaglandins which are responsible for maintenance and protection of the gastrointestinal tract, whilst COX-2 produces the pro-inflammatory prostaglandins responsible for causing inflammation and pain.

Inhibitors differ in their relative specificities for COX-1 and COX-2, with examples such as aspirin, ibuprofennaproxen and diclofenac being non-selective. Selective COX-2 inhibitors were developed to reduce the liability of gastrointestinal damage associated with COX-1 inhibition. Non-selective COX inhibitors are often prescribed with a proton pump inhibitor such as omeprazole to reduce the risk of causing gastrointestinal ulceration and bleeding. Meloxicam, valdecoxibparecoxib and rofecoxib are examples of selective COX-2 inhibitors. However, some COX-2 selective inhibitors have been shown to cause an increased risk of heart attacks and strokes. Because of this risk all non-aspirin NSAID medications (prescription or OTC) must carry boxed warnings to alert patients to the potential danger associated with their use. The US FDA issued an updated safety warning in late 2015: FDA Drug Safety Communication: FDA strengthens warning that non-aspirin nonsteroidal anti-inflammatory drugs (NSAIDs) can cause heart attacks or strokes.

A very short YouTube video highlighting the pros and cons of NSAID use. Produced by Major Peter Strube for crnatoday.com, an online learning resource providing clinical anesthesia and pharmacology courses to nurse anesthetists.

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Phosphodiesterase inhibitors

Phosphodiesterases (PDEs) are enzymes responsible for the inactivation of the intracellular second messengers cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP). There are many subtypes of phosphodiesterases and many inhibitors which can be either non-specific, or selective in their inhibitory profile.

Methylated xanthine derivatives act as nonselective PDE inhibitors. Examples include the natural product theophylline (aminophylline) which is used for its bronchodilatory effects and pentoxifylline. Xanthine derivatives can also act as nonselective adenosine receptor antagonists. Their combined action on phosphodiesterases and adenosine receptors likely underlies the anti-inflammatory action of pan-phosphodiesterase inhibitors.

Selective phosphodiesterase inhibitors

PDE3 inhibitors: milrinone, enoximone, and inamrinone are cardiotonic agents used to treat congestive heart failure. Cilostazol (used to treat intermittent claudication) and anagrelide (used to treat essential thrombocythaemia) are also PDE3-selective inhibitors.

PDE4 inhibitors: roflumilast and apremilast are used for their anti-inflammatory action, to treat asthma and chronic obstructive pulmonary disease (COPD), and psoriatic arthritis respectively. PDE4 inhibitors suppress the release of cytokines and other inflammatory signals to achieve an anti-inflammatory action.

PDE5 inhibitors: sildenafil, tadalafil, vardenafil, and the newer drug avanafil selectively inhibit PDE5, a cGMP-selective phosphodiesterase expressed in the smooth muscle cells lining the blood vessels of the corpus cavernosum and other tissues. This set of drugs are used primarily to treat erectile dysfunction. Certain of these drugs also show efficacy in treating pulmonary arterial hypertension (PAH) and benign prostatic hyperplasia (BPH).

 

Dihydrofolate reductase inhibitors

Dihydrofolate reductase (DHFR) inhibitors reduce the production of folate (folic acid) required by rapidly dividing cells to make thymine for DNA synthesis.

This antifolate activity is used as cancer chemotherapy because it reduces neoplastic cell proliferation. Methotrexate, pemetrexed and pralatrexate are antifolate drugs used in chemotherapy.

Inhibitors selective for bacterial/microbial DHFR compared to host DHFR are used as as antimicobial agents. Examples are the antimalarial drugs pyrimethamine and proguanil, and the antibiotic trimethoprim which is used in the treatment of urinary tract infections (UTIs), acute otitis media (AOM) caused by Streptococcus pneumoniae and Haemophilus influenzae and Pneumocystis jirovecii (formerly Pneumocystis carinii) pneumonia (PCP).

Kinase inhibitors

Protein and (lipid kinases) represent an important target class for treating human disorders, as their aberrant activity underlies a variety of pathologies, ranging from cancer, inflammatory diseases, diabetes, infectious diseases, and cardiovascular disorders.

To date more than 35 small molecule protein kinase inhibitors have been approved for human use around the world. The majority of these are for oncology indications, but a growing number are targeting immune-related conditions such as rheumatoid arthritis (tofacitinib, a Janus kinase 3 inhibitor). Two earlier inhibitors, sirolimus and everolimus (mTOR inhibitors) are used as immunosuppressants to reduce rejection of transplanted organs. Subsequently everolimus has been approved for oncology use, for the treatment of progressive, well-differentiated non-functional, neuroendocrine tumors (NET) of gastrointestinal (GI) or lung origin, in patients with unresectable, locally advanced or metastatic disease.

Approved kinase inhibitors (worldwide)

INN Target/s Indication/s Year first approved
fasudil ROCK (ROCK1 & ROCK2) cerebral vasospasm 1995- China & Japan only
sirolimus mTOR kidney transplants 1999
imatinib  ABL, PDGFR (alpha & beta), KIT CML, Ph+ B-ALL, CMML, HES, GIST 2001
gefitinib EGFR NSCLC 2003
erlotinib EGFR NSCLC, pancreatic cancer 2004
sorafenib  VEGFR2, PDGFR (alpha & beta), KIT, FLT3, BRAF RCC, HCC 2005
sunitinib  VEGFR1, VEGFR2 & VEGFR3, KIT, PDGFR (alpha & beta) , RET, CSF1R, FLT3   RCC, imatinib resistant GIST 2006
dasatinib  ABL, PDGFR (alpha & beta), KIT, SRC  CML 2007
lapatinib EGFR, ERBB2 BC 2007
nilotinib  ABL, PDGFR (alpha & beta), KIT CML 2007
everolimus  mTOR RCC, SEGA, transplantation  2009
temsirolimus  mTOR RCC 2009
axitinib VEGFR1, VEGFR2 & VEGFR3, KIT, PDGFR (alpha & beta), RET, CSF1R, FLT3 RCC 2011
ruxolitinib JAK2 IMF with JAK2V617F 2011
  RET, VEGFR1 & VEGFR2, FGFRs, EGFR  MTC 2011
vemurafenib BRAF m-Melanoma with BRAFV600E 2011
crizotinib  MET, ALK  NSCLC with ALK translocations 2011
tofacitinib JAK3 RA 2012
pazopanib VEGFR1, VEGFR2 & VEGFR3, PDGFR (alpha & beta), KIT RCC 2012
bosutinib ABL  CML resistant/ intolerant to therapy 2012
cabozantinib VEGFR2, PDGFR (alpha & beta), KIT, FLT3 MTC 2012
ponatinib ABL T315 resistant CML 2012
regorafenib VEGFR2, Tie2 CRC, GIST 2012
afatinib EGFR NSCLC with EGFR activating mutations  2013
dabrafenib BRAF m-Melanoma with BRAFV600E 2013
trametinib  MEKs m-Melanoma with BRAFV600E 2013
ibrutinib BTK MCL  2013
nintedanib VEGFR1, VEGFR2 & VEGFR3, PDGFR (alpha & beta), FGFRs IPF 2014
idelalisib   PI3Kδ leukemia and lymphomas 2014
ceritinib ALK NSCLC with ALK translocations 2014
alectinib ALK ALK-rearranged NSCLC 2014- FDA 2015
cobimetinib MEK1 & MEK2 melanoma, BC, other solid tumours 2015
lenvatinib VEGFR1, VEGFR2 & VEGFR3 progressive, differentiated thyroid cancer, advanced renal cell carcinoma (in combination with everolimus) 2015
palbociclib CDK4 & 6 advanced (metastatic) BC 2015
radotinib BRC- ABL & PDGFR (alpha & beta) CML 2015-S Korea only
osimertinib mutant EGFR  T790M +ve NSCLC 2015
brigatinib ALK, EGFR  ALK-rearranged metastatic NSCLC, resistant to crizotinib 2017

Disease abbreviations: BC (breast cancer), CMML (chronic myelomonocytic leukaemia), CML (chronic myeloid leukaemia), CRC (colorectal cancer), GIST (gastrointestinal cancer), HES (hypereosinophilic syndrome), IPF (idiopathic pulmonary fibrosis), MCL (Mantle cell lymphoma), MTC (medullary thyroid cancer), NSCLC (non-small cell lung cancer), Ph+ B-ALL (Philadelphia chormosome positive acute lymphoblastic leukemia), RA (rheumatiod arthritis), RCC (renal cell carcinoma), SEGA (subependymal giant cell astrocytoma)

lipid kinases, protein kinases

A review of the progress and achievements made using kinase inhibitors to treat a wide variety of diseases, plus discussion of the future potential of these small molecules.

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Protein and (lipid kinases) represent an important target class for treating human disorders, as their aberrant activity underlies a variety of pathologies, ranging from cancer, inflammatory diseases, diabetes, infectious diseases, and cardiovascular disorders.

To date more than 35 small molecule protein kinase inhibitors have been approved for human use around the world. The majority of these are for oncology indications, but a growing number are targeting immune-related conditions such as rheumatoid arthritis (tofacitinib, a Janus kinase 3 inhibitor). Two earlier inhibitors, sirolimus and everolimus (mTOR inhibitors) are used as immunosuppressants to reduce rejection of transplanted organs. Subsequently everolimus has been approved for oncology use, for the treatment of progressive, well-differentiated non-functional, neuroendocrine tumors (NET) of gastrointestinal (GI) or lung origin, in patients with unresectable, locally advanced or metastatic disease.

Approved kinase inhibitors (worldwide)

INN Target/s Indication/s Year first approved
fasudil ROCK (ROCK1 & ROCK2) cerebral vasospasm 1995- China & Japan only
sirolimus mTOR kidney transplants 1999
imatinib  ABL, PDGFR (alpha & beta), KIT CML, Ph+ B-ALL, CMML, HES, GIST 2001
gefitinib EGFR NSCLC 2003
erlotinib EGFR NSCLC, pancreatic cancer 2004
sorafenib  VEGFR2, PDGFR (alpha & beta), KIT, FLT3, BRAF RCC, HCC 2005
sunitinib  VEGFR1, VEGFR2 & VEGFR3, KIT, PDGFR (alpha & beta) , RET, CSF1R, FLT3   RCC, imatinib resistant GIST 2006
dasatinib  ABL, PDGFR (alpha & beta), KIT, SRC  CML 2007
lapatinib EGFR, ERBB2 BC 2007
nilotinib  ABL, PDGFR (alpha & beta), KIT CML 2007
everolimus  mTOR RCC, SEGA, transplantation  2009
temsirolimus  mTOR RCC 2009
axitinib VEGFR1, VEGFR2 & VEGFR3, KIT, PDGFR (alpha & beta), RET, CSF1R, FLT3 RCC 2011
ruxolitinib JAK2 IMF with JAK2V617F 2011
  RET, VEGFR1 & VEGFR2, FGFRs, EGFR  MTC 2011
vemurafenib BRAF m-Melanoma with BRAFV600E 2011
crizotinib  MET, ALK  NSCLC with ALK translocations 2011
tofacitinib JAK3 RA 2012
pazopanib VEGFR1, VEGFR2 & VEGFR3, PDGFR (alpha & beta), KIT RCC 2012
bosutinib ABL  CML resistant/ intolerant to therapy 2012
cabozantinib VEGFR2, PDGFR (alpha & beta), KIT, FLT3 MTC 2012
ponatinib ABL T315 resistant CML 2012
regorafenib VEGFR2, Tie2 CRC, GIST 2012
afatinib EGFR NSCLC with EGFR activating mutations  2013
dabrafenib BRAF m-Melanoma with BRAFV600E 2013
trametinib  MEKs m-Melanoma with BRAFV600E 2013
ibrutinib BTK MCL  2013
nintedanib VEGFR1, VEGFR2 & VEGFR3, PDGFR (alpha & beta), FGFRs IPF 2014
idelalisib   PI3Kδ leukemia and lymphomas 2014
ceritinib ALK NSCLC with ALK translocations 2014
alectinib ALK ALK-rearranged NSCLC 2014- FDA 2015
cobimetinib MEK1 & MEK2 melanoma, BC, other solid tumours 2015
lenvatinib VEGFR1, VEGFR2 & VEGFR3 progressive, differentiated thyroid cancer, advanced renal cell carcinoma (in combination with everolimus) 2015
palbociclib CDK4 & 6 advanced (metastatic) BC 2015
radotinib BRC- ABL & PDGFR (alpha & beta) CML 2015-S Korea only
osimertinib mutant EGFR  T790M +ve NSCLC 2015
brigatinib ALK, EGFR  ALK-rearranged metastatic NSCLC, resistant to crizotinib 2017

Disease abbreviations: BC (breast cancer), CMML (chronic myelomonocytic leukaemia), CML (chronic myeloid leukaemia), CRC (colorectal cancer), GIST (gastrointestinal cancer), HES (hypereosinophilic syndrome), IPF (idiopathic pulmonary fibrosis), MCL (Mantle cell lymphoma), MTC (medullary thyroid cancer), NSCLC (non-small cell lung cancer), Ph+ B-ALL (Philadelphia chormosome positive acute lymphoblastic leukemia), RA (rheumatiod arthritis), RCC (renal cell carcinoma), SEGA (subependymal giant cell astrocytoma)

lipid kinases, protein kinases

This review article presents a brief history of kinase research and inhibitor development, highlighting landmarks in the drug discovery process and pointing to the limitations of their use.

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Drug metabolizing enzymes

Cytochrome P450 enzymes are the main drug metabolising enzymes (xenobiotic inactivators) in humans, and these are the primary contributors to Phase I oxidative metabolism of drugs and other chemicals.

The main families of CYP450 enzymes involved in drug metabolism are the monooxygenases of the CYP1, CYP2 and CYP3 families.

CYP3A4 is the most common and most versatile CYP450 enzyme involved in drug metabolism. Most drugs undergo deactivation by CYP3A4, whilst others are bioactivated to form their active compounds. CYP3A4 is inhibited by grapefriut, pomegranate and other friut jiuces so patients should be made aware of the consequences of ingesting these juices whilst taking susceptible drugs.

Prescribers need to be aware of drug interactions with any of these enzymes that may alter responses to any other prescribed medications.

Examples of specific CYP450 enzyme drug metabolism.

Enzyme isoform Drugs metabolised
CYP1A2

caffeine

theophylline

nicotine

pazopanib

CYP2A6

5-fluorouracil

coumarin

bupropion

CYP2B6

propofol

cyclophosphamide

CYP2C8

paclitaxel

phenytoin

warfarin

dabrafenib

pazopanib

ponatinib

CYP2C9

cabozantinib (minor contribution)

NSAIDs

sulfonylureas

CYP2C19

omeprazole

tricyclic antidepressants

codeine

tofacitinib (minor contribution)

CYP2D6

some antipsychotics

some antiarrythmics

some beta-blockers

CYP2E1

paracetamol

midazolam

triazolam

cyclosporin A

CYP3A4

 

erythromycin

HIV protease inhibitors

calcium channel blockers (e.g. diltiazem, nifedipine and verapamil)

many chemotherapeutics (e.g. docetaxel, paclitaxel and doxorubicin)

many protein kinase inhibitors (e.g. sorafenibimatinib, sunitinib and gefitinib)

PDE5 inhibitors (sildenafil and tadalafil)

 

This web page provides a brief overview of the drug metabolism process, rate of metabolism, the cytochrome P450 enzymes of Phase I reactions and the effects of Phase II conjugation reactions. The information was written by Jennifer Le, PharmD, MAS, BCPS-ID.

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Cytochrome P450 enzymes are the main drug metabolising enzymes (xenobiotic inactivators) in humans, and these are the primary contributors to Phase I oxidative metabolism of drugs and other chemicals.

The main families of CYP450 enzymes involved in drug metabolism are the monooxygenases of the CYP1, CYP2 and CYP3 families.

CYP3A4 is the most common and most versatile CYP450 enzyme involved in drug metabolism. Most drugs undergo deactivation by CYP3A4, whilst others are bioactivated to form their active compounds. CYP3A4 is inhibited by grapefriut, pomegranate and other friut jiuces so patients should be made aware of the consequences of ingesting these juices whilst taking susceptible drugs.

Prescribers need to be aware of drug interactions with any of these enzymes that may alter responses to any other prescribed medications.

Examples of specific CYP450 enzyme drug metabolism.

Enzyme isoform Drugs metabolised
CYP1A2

caffeine

theophylline

nicotine

pazopanib

CYP2A6

5-fluorouracil

coumarin

bupropion

CYP2B6

propofol

cyclophosphamide

CYP2C8

paclitaxel

phenytoin

warfarin

dabrafenib

pazopanib

ponatinib

CYP2C9

cabozantinib (minor contribution)

NSAIDs

sulfonylureas

CYP2C19

omeprazole

tricyclic antidepressants

codeine

tofacitinib (minor contribution)

CYP2D6

some antipsychotics

some antiarrythmics

some beta-blockers

CYP2E1

paracetamol

midazolam

triazolam

cyclosporin A

CYP3A4

 

erythromycin

HIV protease inhibitors

calcium channel blockers (e.g. diltiazem, nifedipine and verapamil)

many chemotherapeutics (e.g. docetaxel, paclitaxel and doxorubicin)

many protein kinase inhibitors (e.g. sorafenibimatinib, sunitinib and gefitinib)

PDE5 inhibitors (sildenafil and tadalafil)

 

This is a short interactive teaching resource provided by the University of Nottingham for their nursing and midwifery students. It guides the user easily through the drug metabolism process.

No votes yet

Cytochrome P450 enzymes are the main drug metabolising enzymes (xenobiotic inactivators) in humans, and these are the primary contributors to Phase I oxidative metabolism of drugs and other chemicals.

The main families of CYP450 enzymes involved in drug metabolism are the monooxygenases of the CYP1, CYP2 and CYP3 families.

CYP3A4 is the most common and most versatile CYP450 enzyme involved in drug metabolism. Most drugs undergo deactivation by CYP3A4, whilst others are bioactivated to form their active compounds. CYP3A4 is inhibited by grapefriut, pomegranate and other friut jiuces so patients should be made aware of the consequences of ingesting these juices whilst taking susceptible drugs.

Prescribers need to be aware of drug interactions with any of these enzymes that may alter responses to any other prescribed medications.

Examples of specific CYP450 enzyme drug metabolism.

Enzyme isoform Drugs metabolised
CYP1A2

caffeine

theophylline

nicotine

pazopanib

CYP2A6

5-fluorouracil

coumarin

bupropion

CYP2B6

propofol

cyclophosphamide

CYP2C8

paclitaxel

phenytoin

warfarin

dabrafenib

pazopanib

ponatinib

CYP2C9

cabozantinib (minor contribution)

NSAIDs

sulfonylureas

CYP2C19

omeprazole

tricyclic antidepressants

codeine

tofacitinib (minor contribution)

CYP2D6

some antipsychotics

some antiarrythmics

some beta-blockers

CYP2E1

paracetamol

midazolam

triazolam

cyclosporin A

CYP3A4

 

erythromycin

HIV protease inhibitors

calcium channel blockers (e.g. diltiazem, nifedipine and verapamil)

many chemotherapeutics (e.g. docetaxel, paclitaxel and doxorubicin)

many protein kinase inhibitors (e.g. sorafenibimatinib, sunitinib and gefitinib)

PDE5 inhibitors (sildenafil and tadalafil)

 

This webpage produced by Indiana University Department of Medicine lists clinically relevant CYP450 enzyme substrate drugs, and drugs which either inhibit or induce CYP450 activities, tabulated against the corresponding enzyme subtype.

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Enzymes of epigenetic regulation

Epigenetic control of genes can alter phenotype without altering genotype and the underlying DNA sequence. Epigenetic modifications such as acetylation, methylation, phosphorylation, and ubiquitination, alter the accessibility of DNA to transcription machinery and therefore influence gene expression. Specific epigenetic processes include imprinting, gene silencing, X chromosome inactivation and maternal effects. Epigenetic processes are responsible for many effects of teratogens, and are often associated with the development of cancer. Experimental studies are providing evidence of the influence of epigenetics in disease states, and are establishing a range of novel therapeutic targets

Important epigenetic mechanisms include DNA methylation, histone modification, chromatin remodelling and non-coding RNA-associated gene silencing.

The proteins that carry out these modifications are often described as being either "writers", "readers" or "erasers". Writer enzymes catalyze the addition of chemical groups onto either histone tails or the DNA itself, creating epigenetic marks. Eraser enzymes remove epigenetic marks providing plasticity in epigenetic regulation by facilitating epigenetic reprogramming of genes. DNA demethylation (methylation mark removal) is involved in many important disease mechanisms such as tumor progression. Readers can be enzymes or other proteins which contain structural domains which recognise specific epigenetic marks. See the table below.

In this section we will provide information about DNA methylation and histone modification, including details of some of the enzymes which carry out DNA and histone modifications, implications for disease and pharmacological (drug) interventions at the level of epigenetic control.

Epigenetic regulation: mechanisms and effectors

Epigenetic mechanism Writer enzymes Reader domains Eraser enzymes
DNA methylation Histone methyltransferases methyl-cpg binding domain proteins DNA demethylation enzymes e.g. DNMT1
Histone acetylation Histone acetyltransferases (HATs) bromodomain proteins Histone deacetylases (HDACs)
tandem PHD finger proteins
pleckstrin homology domain proteins e.g. PHIP
Histone arginine methylation Protein arginine methyltransferases (PRMTs) tudor domain proteins Histone arginine demethylase JMJD6
WD40 domain proteins e.g. WDR5 peptidyl arginine deiminases (putative)
histone lysine methylation Histone lysine methyltransferases chromodomain proteins Histone lysine demethylases
tudor domain proteins
PHD finger domain proteins
MBT domain proteins
ZF-CW proteins
WD40 domain proteins
PWWP domain proteins
histone phosphorylation kinases (e.g. JAK2, ATM/ATR, PKC, PKA, Haspin, Aurora Kinase B, RSK2, AMPK, MSK, MEK) chromoshadow domain proteins (phosphoTyrosine) protein serine/threonine phosphatases
14.3.3 proteins (phosphoSerine) protein tyrosine phosphatases
inhibitor of apoptosis (IAP)/BIR domain proteins
BRCA1 C terminus (BRCT) domain proteins
histone ubiquitination ubiquitin E2 conjugases unknown deubiquitinating enzymes
ubiquitin E3 ligases

 

DNA methylation

Covalent addition of methyl (CH3) groups is performed by a family of enzymes called DNA methyltransferases (DNMTs), of which DNMT1, -3A and -3B are especially important for the establishment and maintenance of DNA methylation patterns. CH3 methylation marks are added to cytosine residues, and once in place project in to the major groove of DNA and inhibit transcription. Whilst DNMT1 seems to be required for maintaining established DNA methylation patterns, DNMT3A and -3B appear to mediate de novo DNA methylation patterns. In cancer cells DNMT1 and DNMT3B contribute to maintaining gene hypermethylation.

Histone modifications

Histone proteins can be modified in many ways, including lysine acetylation, lysine and arginine methylation, serine and threonine phosphorylation, and lysine ubiquitination and sumoylation. The unstructured N-termini of histones ('histone tails') are particularly highly modified. Of particular pharmacological relevance are the histone deacetylases (HDACs), which catalyze the hydrolytic removal of acetyl groups from histone lysine residues. HDAC inhibitors have been developed to coreect the imbalance in the equilibrium of histone acetylation that is associated with tumorigenesis and cancer progression. Vorinostat was the first HDAC inhibitor to receive regulatory approval (inhibits Class I, II and IV HDACs; approved for cutaneous T-cell lymphoma) and this has been followed by marketing authorisations for romidepsin (Class II HDAC inhibitor; approved to treat cutaneous T-cell lymphoma), belinostat (pan-HDAC inhibitor; approved for relapsed or refactory peripheral T-cell lymphoma) and panobinostat (pan-HDAC inhibitor; approved for multiple myeloma treatment).