PDE1
Encyclopedia
PDE1 is a phosphodiesterase
enzyme
also known as calcium
- and calmodulin
-dependent phosphodiesterase. It is one of the 11 families of phosphodiesterase (PDE1-PDE11). PDE1 has three subtypes, PDE1A, PDE1B and PDE1C which divide further into various isoforms. The various isoforms exhibit different affinities for cAMP
and cGMP
.
and rat
brain respectively.. It has since been found to be widely distributed in various mammalian tissues
as well as in other eukaryotes. It is now one of the most intensively studied member of the PDE
superfamily of enzymes , which today represents 11 gene
families , and the best characterized one as well .
Further researches in the field along with increased availability of monoclonal antibodies
have shown that various PDE1 isozymes exist and have been identified and purified. It is now known that PDE1 exists as tissue specific isozymes.
PDEs and some yeast
enzymes. Class I enzymes all have a catalytic core of at least 250 amino acids whereas Class II enzymes lack such a common feature.
Usually vertebrate PDEs are dimers
of linear 50 – 150 kDa proteins. They consist of three functional domains
; a conserved catalytic core, a regulatory N-terminus and a C-terminus [3-5]. The proteins are chimeric
and each domain is associated with their particular function.
The regulatory N-terminus is substantially different in various PDE types.. They are flanked by the catalytic core and include regions that auto-inhibit the catalytic domains. They also target sequences that control subcellular localization. In PDE1 this region contains a calmodulin binding domain.
The catalytic domains of PDE1 (and other types of PDEs) have three helical subdomains: an N-terminal cyclin-fold region, a linker region and a C-terminal helical bundle. A deep hydrophobic pocket is formed at the interface of these subdomains. It is composed of four subsites. They are: a metal
binding site (M site), core pocket (Q pocket), hydrophobic pocket (H pocket) and lid region (L region). The M site is placed at the bottom of the hydrophobic pocket with several metal atoms. The metal atoms bind to residues that are completely conserved in all PDE family members. The identity of the metal atoms is not known with absolute certainty. However, some evidence indicate that at least one of the metals is zinc
and the other is likely to be magnesium
. The zinc coordination sphere
is composed of three histidines, one aspartate and two water molecules. The magnesium coordination sphere involves the same aspartate along with five water molecules, one of which is shared with the zinc molecule. The reputed role of the metal ions include structure stabilization as well as activation of hydroxide
to mediate catalysis
.
The domains are separated by ”hinge” regions where they can be experimentally separated by limited proteolysis.
The PDE1 isozyme family (along with the PDE4 family) is the most diverse one and includes numerous splice variant PDE1 isoforms. It has three subtypes, PDE1A, PDE1B and PDE1C which divide further into various isoforms.
Table 1. Various PDE1s location in tissues and within cells.
Most PDE1 isoforms are reported to be cytosolic. However, there are instances of PDE1s being localized to subcellular regions but little is known about the molecular mechanisms responsible for such localization. It is thought to be likely that the unique N-terminal or C-terminal regions of the various isoforms allow the different proteins to be targeted to specific subcellular domains.
and degrative activity of cyclic nucleotide PDE. The role of PDE1 enzymes is to degrade both cGMP and cAMP.
The various isoforms exhibit different affinities for cAMP and cGMP. PDE1A and PDE1B preferentially hydrolyse cGMP, whereas PDE1C degrades both cAMP and cGMP with high affinity. For example in airway smooth muscles of humans and other species, generic PDE1 accounts for more than 50% of the hydrolytic activity of cyclic nucleotides . It has been demonstrated that deletion and overexpression of PDE1 produces strong effects on agonist
-induced cAMP signalling but has little effect on the basal cAMP level.
regulation by Ca2+/calmodulin, PDE1s are believed to function as a mechanism for integrating cell signalling pathways mediated by cGMP and cAMP with pathways that regulate intracellular calcium levels. The precise function of PDE1 isozymes in various pathophysiological processes is not clear because most of the studies have been carried out in vitro. Therefore it is essential to direct further research to in vivo studies.
PDE1 has been implicated to play a role in a number of physiological and pathological processes:
PDE1A most likely serves to regulate vascular
smooth muscle concentration and has been found to be up-regulated in rat aorta in response to chronic nitroglycerin treatment. It is also possible that it plays a role in sperm
function.
PDE1B
knockout
mice have increased locomotor
activity and in some paradigms decreased memory and learning abilities. PDE1B
is also involved in dopaminergic
signalling and is induced in several types of activated immune cells. PDE1B
mRNA is induced in PHA or anti-CD3/CD28-activated human T-lymphocytes and participates in IL-13 regulation implicated in allergic diseases.
PDE1C has been shown to be a major regulator of smooth muscle proliferation, at least in human smooth muscle. Nonproliferating smooth muscle cells (SMC) exhibit only low levels of PDE1C expression
but it is highly expressed in proliferating SMCs. It can therefore be speculated that inhibition
of PDE1C could produce beneficial effects due to its putative inhibition of SMC proliferation, an event that contributes importantly to the pathophysiology of atherosclerosis
. Another likely roles of PDE1C is in olfaction
[4], to regulate sperm function and neuronal signaling.
to binding sites near the N-terminus stimulates hydrolysis of cyclic nucleotides. In intact cells, PDE1 is almost exclusively activated by Ca2+ entering the cell from the extracellular
space. The regulation of PDE1 by Ca2+ and CaM has been studied in vitro and these studies have shown that eight methionine
residues within the hydrophobic clefts of Ca2+-CaM are required for the binding and activation of PDE1. Mutations in the N-terminal lobe of CaM affect its ability to activate PDE1 so it is believed that the C-terminal lobe of CaM serves to target CaM to PDE1, while the N-terminal lobe activates the enzyme. The presence of an aromatic residue, usually a tryptophan
, in the CaM-binding region of Ca2+-CaM-regulated proteins may also be required for binding to PDE1.
Between different PDE1 isozymes there is a significant difference in affinity for Ca2+/CaM. In general, the PDE1 enzymes have high affinity for the complex but the affinity can be affected by phosphorylation. Phosphorylation
of PDE1A1 and PDE1A2 by protein kinase A and of PDE1B1 by CaM Kinase II decreases their sensitivity to calmodulin activation. This phosphorylation can be reversed by the phosphatase, calcineurin. The phosphorylation of the isozymes is accompanied by a decrease in the isozymes affinity towards CaM, as well as an increase in the Ca2+ concentrations required for CaM activation of the isozymes.
targets because of the basic pharmacological principle that regulation of degradation of any ligand
or second messenger can often make a more rapid and larger percentage change in concentration than comparable rates of synthesis
. Another reason is that PDEs do not have to compete with very high levels of endogenous
substrate to be effective since the levels of cAMP and cGMP in most cells are typically in the micromolar range.
The availability of high-resolution crystal structures of the catalytic domains of PDEs makes the development of highly potent and specific inhibitors
possible.
Many compounds reported as PDE1 inhibitors do not interact directly with the catalytic site of PDE1 but interact during activation, either at the level of calmodulin binding sites such as compound KS505a or directly on Ca2+/calmodulin such as bepril, flunarizine
and amiodarone
.
Those inhibitors that interact with the catalytic site occupy part of the active site, primarily around the Q pocket and occasionally close to the M pocket. A major point of interaction is a conserved hydrophobic pocket that is involved in orienting the substrate purine ring for interaction with a glutamine residue that is crucial for the catalytic mechanism of the PDEs.
The interactions of inhibitors can be split into three major types: interactions with the metal ions mediated through water, H-bond interactions with the protein residues involved in nucleotide recognition and most importantly the interaction with the hydrophobic residues lining the cavity of the active site. All known inhibitors seem to exploit these three types of interactions and hence these interactions should guide the design of new types of inhibitors.
Initially PDE1 inhibitors were claimed to be effective vascular relaxants. With availability of purified cloned enzymes, however, it is now known that such inhibitors are in fact equally active against PDE5. Those inhibitors include e.g. zaprinast
, 8-methoxymethyl IPMX and SCH 51866.
All therapeutically effective PDE inhibitors must be incorporated into the cell because all PDEs are localized in the cytoplasm and/or on intracellular membranes.
Today, there is no real and effective specific PDE1 inhibitor that can be used to assess the functional role of PDE1 in tissues .
(3,5-pyridinedicarboxylic acid, 1,4-dihydro-2,6-dimethyl-4-(3-nitrophenyl)-, 2-methoxyethyl 1-methylethyl ester ) is a dihydropyridine that antagonizes/blocks specifically L-type Ca2+-channel, and was first described as a PDE1 inhibitor. This effect is not related to its calcium antagonist property since it inhibits, in micromolar range, basal and calmodulin stimulated purified PDE1. Since nimodipine at lower concentrations blocks the L-type calcium channel, it can only be used to estimate PDE1 participation in tissue and cell homogenates .
Vinpocetine
was described as a specific inhibitor of basal and calmodulin-activated PDE1. This effect leads to an increase of cAMP over cGMP . It is mainly used as a pharmacological tool to implicate PDE1. Vinpocetine inhibits differently the various subtypes of PDE1 (IC50 from 8 to 50 µm) and it is also able to inhibit PDE7B. It can not be used as a specific tool to investigate the functional role of PDE1 due to its direct activator effects on BK (Ca) channels. Vinpocetine crosses the blood-brain barrier and is taken up by cerebral tissue. It has been hypothesized that vinpocetine can effect voltage dependent calcium channels.
IC224 inhibits PDE1 (IC50 = 0.08 µM) with a selective ratio of 127 (ratio of IC50 value for the next most sensitive PDE and for IC50 value for PDE1). It was developed by ICOS corporation. If IC224 similarly inhibits basal and calmodulin-activated PDE1 subtypes, this compound could be very helpful to characterize PDE1 activity and to clearly investigate the various roles of PDE1 in pathophysiology.
PDE1A2 has a potential role in neurodegenerative diseases e.g.:
Parkinsons
Axonal neurofilament
degradation
Motorneuronal degradation
Neuronal ischemia
Alzheimer’s disease
epilepsy
PDE1C could have a role in the regulation of insulin
release and may target proliferating smooth muscle cells in atherosclerotic lesions or during restenosis
.
Phosphodiesterase
A phosphodiesterase is any enzyme that breaks a phosphodiester bond. Usually, people speaking of phosphodiesterase are referring to cyclic nucleotide phosphodiesterases, which have great clinical significance and are described below...
enzyme
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
also known as calcium
Calcium
Calcium is the chemical element with the symbol Ca and atomic number 20. It has an atomic mass of 40.078 amu. Calcium is a soft gray alkaline earth metal, and is the fifth-most-abundant element by mass in the Earth's crust...
- and calmodulin
Calmodulin
Calmodulin is a calcium-binding protein expressed in all eukaryotic cells...
-dependent phosphodiesterase. It is one of the 11 families of phosphodiesterase (PDE1-PDE11). PDE1 has three subtypes, PDE1A, PDE1B and PDE1C which divide further into various isoforms. The various isoforms exhibit different affinities for cAMP
Cyclic adenosine monophosphate
Cyclic adenosine monophosphate is a second messenger important in many biological processes...
and cGMP
Cyclic guanosine monophosphate
Cyclic guanosine monophosphate is a cyclic nucleotide derived from guanosine triphosphate . cGMP acts as a second messenger much like cyclic AMP...
.
Discovery of PDE1
The existence of the Ca2+-stimulated PDE1 was first demonstrated by Cheung (1970), Kakiuchi and Yamazaki (1970) as a result of their research on bovine brainBrain
The brain is the center of the nervous system in all vertebrate and most invertebrate animals—only a few primitive invertebrates such as sponges, jellyfish, sea squirts and starfishes do not have one. It is located in the head, usually close to primary sensory apparatus such as vision, hearing,...
and rat
Rat
Rats are various medium-sized, long-tailed rodents of the superfamily Muroidea. "True rats" are members of the genus Rattus, the most important of which to humans are the black rat, Rattus rattus, and the brown rat, Rattus norvegicus...
brain respectively.. It has since been found to be widely distributed in various mammalian tissues
Biological tissue
Tissue is a cellular organizational level intermediate between cells and a complete organism. A tissue is an ensemble of cells, not necessarily identical, but from the same origin, that together carry out a specific function. These are called tissues because of their identical functioning...
as well as in other eukaryotes. It is now one of the most intensively studied member of the PDE
Phosphodiesterase
A phosphodiesterase is any enzyme that breaks a phosphodiester bond. Usually, people speaking of phosphodiesterase are referring to cyclic nucleotide phosphodiesterases, which have great clinical significance and are described below...
superfamily of enzymes , which today represents 11 gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
families , and the best characterized one as well .
Further researches in the field along with increased availability of monoclonal antibodies
Monoclonal antibodies
Monoclonal antibodies are monospecific antibodies that are the same because they are made by identical immune cells that are all clones of a unique parent cell....
have shown that various PDE1 isozymes exist and have been identified and purified. It is now known that PDE1 exists as tissue specific isozymes.
Structure of PDE1
The PDE1 isozyme family belongs to a Class I enzymes , which includes all vertebrateVertebrate
Vertebrates are animals that are members of the subphylum Vertebrata . Vertebrates are the largest group of chordates, with currently about 58,000 species described. Vertebrates include the jawless fishes, bony fishes, sharks and rays, amphibians, reptiles, mammals, and birds...
PDEs and some yeast
Yeast
Yeasts are eukaryotic micro-organisms classified in the kingdom Fungi, with 1,500 species currently described estimated to be only 1% of all fungal species. Most reproduce asexually by mitosis, and many do so by an asymmetric division process called budding...
enzymes. Class I enzymes all have a catalytic core of at least 250 amino acids whereas Class II enzymes lack such a common feature.
Usually vertebrate PDEs are dimers
Protein dimer
In biochemistry, a dimer is a macromolecular complex formed by two, usually non-covalently bound, macromolecules like proteins or nucleic acids...
of linear 50 – 150 kDa proteins. They consist of three functional domains
Protein domain
A protein domain is a part of protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and often can be independently stable and folded. Many proteins consist of several structural...
; a conserved catalytic core, a regulatory N-terminus and a C-terminus [3-5]. The proteins are chimeric
Fusion protein
Fusion proteins or chimeric proteins are proteins created through the joining of two or more genes which originally coded for separate proteins. Translation of this fusion gene results in a single polypeptide with functional properties derived from each of the original proteins...
and each domain is associated with their particular function.
The regulatory N-terminus is substantially different in various PDE types.. They are flanked by the catalytic core and include regions that auto-inhibit the catalytic domains. They also target sequences that control subcellular localization. In PDE1 this region contains a calmodulin binding domain.
The catalytic domains of PDE1 (and other types of PDEs) have three helical subdomains: an N-terminal cyclin-fold region, a linker region and a C-terminal helical bundle. A deep hydrophobic pocket is formed at the interface of these subdomains. It is composed of four subsites. They are: a metal
Metal
A metal , is an element, compound, or alloy that is a good conductor of both electricity and heat. Metals are usually malleable and shiny, that is they reflect most of incident light...
binding site (M site), core pocket (Q pocket), hydrophobic pocket (H pocket) and lid region (L region). The M site is placed at the bottom of the hydrophobic pocket with several metal atoms. The metal atoms bind to residues that are completely conserved in all PDE family members. The identity of the metal atoms is not known with absolute certainty. However, some evidence indicate that at least one of the metals is zinc
Zinc
Zinc , or spelter , is a metallic chemical element; it has the symbol Zn and atomic number 30. It is the first element in group 12 of the periodic table. Zinc is, in some respects, chemically similar to magnesium, because its ion is of similar size and its only common oxidation state is +2...
and the other is likely to be magnesium
Magnesium
Magnesium is a chemical element with the symbol Mg, atomic number 12, and common oxidation number +2. It is an alkaline earth metal and the eighth most abundant element in the Earth's crust and ninth in the known universe as a whole...
. The zinc coordination sphere
Coordination sphere
In coordination chemistry, the coordination sphere refers to a central atom or ion and an array of molecules or anions, the ligands, around.Molecules that are attached noncovalently to the ligands are called the second coordination sphere....
is composed of three histidines, one aspartate and two water molecules. The magnesium coordination sphere involves the same aspartate along with five water molecules, one of which is shared with the zinc molecule. The reputed role of the metal ions include structure stabilization as well as activation of hydroxide
Hydroxide
Hydroxide is a diatomic anion with chemical formula OH−. It consists of an oxygen and a hydrogen atom held together by a covalent bond, and carrying a negative electric charge. It is an important but usually minor constituent of water. It functions as a base, as a ligand, a nucleophile, and a...
to mediate catalysis
Catalysis
Catalysis is the change in rate of a chemical reaction due to the participation of a substance called a catalyst. Unlike other reagents that participate in the chemical reaction, a catalyst is not consumed by the reaction itself. A catalyst may participate in multiple chemical transformations....
.
The domains are separated by ”hinge” regions where they can be experimentally separated by limited proteolysis.
The PDE1 isozyme family (along with the PDE4 family) is the most diverse one and includes numerous splice variant PDE1 isoforms. It has three subtypes, PDE1A, PDE1B and PDE1C which divide further into various isoforms.
Localization
The localization of PDE1 isoforms in different tissues/cells and their location within the cells is as follows:| Isoform | Tissue/cellular localization | Intracellular localization |
|---|---|---|
| PDE1A | Smooth muscle, heart, lung, brain, sperm | Predominantly cytosolic |
| PDE1A1 | Heart, lung | Predominantly cytosolic |
| PDE1A2 | Brain | Predominantly cytosolic |
| PDE1B1 | Neurons, lymphocytes, smooth muscle brain, heart, skeletal muscle | Cytosolic |
| PDE1B2 | Macrophages, lymphocytes | Cytosolic |
| PDE1C | Brain, proliferating human smooth muscle, spermatids | Cytosolic |
| PDE1C1 | Brain, heart, testis | - |
| PDE1C2 | Olfactory epithelium | Cytosolic |
| PDE1C4/5 | mRNA is present in the testis | - |
Table 1. Various PDE1s location in tissues and within cells.
Most PDE1 isoforms are reported to be cytosolic. However, there are instances of PDE1s being localized to subcellular regions but little is known about the molecular mechanisms responsible for such localization. It is thought to be likely that the unique N-terminal or C-terminal regions of the various isoforms allow the different proteins to be targeted to specific subcellular domains.
Functional role
Intracellular second messengers such as cGMP and cAMP undergo rapid changes in concentration in a response to a wide variety of cell specific stimuli. The concentration of these second messengers is determined to a large extent by the relative synthetic activity of adenylate cyclaseAdenylate cyclase
Adenylate cyclase is part of the G protein signalling cascade, which transmits chemical signals from outside the cell across the membrane to the inside of the cell ....
and degrative activity of cyclic nucleotide PDE. The role of PDE1 enzymes is to degrade both cGMP and cAMP.
The various isoforms exhibit different affinities for cAMP and cGMP. PDE1A and PDE1B preferentially hydrolyse cGMP, whereas PDE1C degrades both cAMP and cGMP with high affinity. For example in airway smooth muscles of humans and other species, generic PDE1 accounts for more than 50% of the hydrolytic activity of cyclic nucleotides . It has been demonstrated that deletion and overexpression of PDE1 produces strong effects on agonist
Agonist
An agonist is a chemical that binds to a receptor of a cell and triggers a response by that cell. Agonists often mimic the action of a naturally occurring substance...
-induced cAMP signalling but has little effect on the basal cAMP level.
Pharmacology
Because of in vitroIn vitro
In vitro refers to studies in experimental biology that are conducted using components of an organism that have been isolated from their usual biological context in order to permit a more detailed or more convenient analysis than can be done with whole organisms. Colloquially, these experiments...
regulation by Ca2+/calmodulin, PDE1s are believed to function as a mechanism for integrating cell signalling pathways mediated by cGMP and cAMP with pathways that regulate intracellular calcium levels. The precise function of PDE1 isozymes in various pathophysiological processes is not clear because most of the studies have been carried out in vitro. Therefore it is essential to direct further research to in vivo studies.
PDE1 has been implicated to play a role in a number of physiological and pathological processes:
PDE1A most likely serves to regulate vascular
Blood vessel
The blood vessels are the part of the circulatory system that transports blood throughout the body. There are three major types of blood vessels: the arteries, which carry the blood away from the heart; the capillaries, which enable the actual exchange of water and chemicals between the blood and...
smooth muscle concentration and has been found to be up-regulated in rat aorta in response to chronic nitroglycerin treatment. It is also possible that it plays a role in sperm
Spermatozoon
A spermatozoon is a motile sperm cell, or moving form of the haploid cell that is the male gamete. A spermatozoon joins an ovum to form a zygote...
function.
PDE1B
PDE1B
Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B is an enzyme that in humans is encoded by the PDE1B gene.-Further reading:...
knockout
Knockout
A knockout is a fight-ending, winning criterion in several full-contact combat sports, such as boxing, kickboxing, Muay Thai, mixed martial arts, Karate and others sports involving striking...
mice have increased locomotor
Locomotor system
Locomotor system may mean:* Animal locomotion system* Human musculoskeletal system, also known simply as "the locomotor system"...
activity and in some paradigms decreased memory and learning abilities. PDE1B
PDE1B
Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B is an enzyme that in humans is encoded by the PDE1B gene.-Further reading:...
is also involved in dopaminergic
Dopaminergic
Dopaminergic means related to the neurotransmitter dopamine. For example, certain proteins such as the dopamine transporter , vesicular monoamine transporter 2 , and dopamine receptors can be classified as dopaminergic, and neurons which synthesize or contain dopamine and synapses with dopamine...
signalling and is induced in several types of activated immune cells. PDE1B
PDE1B
Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B is an enzyme that in humans is encoded by the PDE1B gene.-Further reading:...
mRNA is induced in PHA or anti-CD3/CD28-activated human T-lymphocytes and participates in IL-13 regulation implicated in allergic diseases.
PDE1C has been shown to be a major regulator of smooth muscle proliferation, at least in human smooth muscle. Nonproliferating smooth muscle cells (SMC) exhibit only low levels of PDE1C expression
Gene expression
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA , transfer RNA or small nuclear RNA genes, the product is a functional RNA...
but it is highly expressed in proliferating SMCs. It can therefore be speculated that inhibition
Enzyme inhibitor
An enzyme inhibitor is a molecule that binds to enzymes and decreases their activity. Since blocking an enzyme's activity can kill a pathogen or correct a metabolic imbalance, many drugs are enzyme inhibitors. They are also used as herbicides and pesticides...
of PDE1C could produce beneficial effects due to its putative inhibition of SMC proliferation, an event that contributes importantly to the pathophysiology of atherosclerosis
Atherosclerosis
Atherosclerosis is a condition in which an artery wall thickens as a result of the accumulation of fatty materials such as cholesterol...
. Another likely roles of PDE1C is in olfaction
Olfaction
Olfaction is the sense of smell. This sense is mediated by specialized sensory cells of the nasal cavity of vertebrates, and, by analogy, sensory cells of the antennae of invertebrates...
[4], to regulate sperm function and neuronal signaling.
Regulation
The distinguishing feature of PDE1 as a family is their regulation by calcium (Ca2+) and calmodulin (CaM). Calmodulin has been shown to activate cyclic nucleotide PDE in a calcium-dependent manner and the cooperative binding of four Ca2+ to calmodulin is required to fully activate PDE1 [2]. The binding of one Ca2+/CaM complex per monomerMonomer
A monomer is an atom or a small molecule that may bind chemically to other monomers to form a polymer; the term "monomeric protein" may also be used to describe one of the proteins making up a multiprotein complex...
to binding sites near the N-terminus stimulates hydrolysis of cyclic nucleotides. In intact cells, PDE1 is almost exclusively activated by Ca2+ entering the cell from the extracellular
Extracellular
In cell biology, molecular biology and related fields, the word extracellular means "outside the cell". This space is usually taken to be outside the plasma membranes, and occupied by fluid...
space. The regulation of PDE1 by Ca2+ and CaM has been studied in vitro and these studies have shown that eight methionine
Methionine
Methionine is an α-amino acid with the chemical formula HO2CCHCH2CH2SCH3. This essential amino acid is classified as nonpolar. This amino-acid is coded by the codon AUG, also known as the initiation codon, since it indicates mRNA's coding region where translation into protein...
residues within the hydrophobic clefts of Ca2+-CaM are required for the binding and activation of PDE1. Mutations in the N-terminal lobe of CaM affect its ability to activate PDE1 so it is believed that the C-terminal lobe of CaM serves to target CaM to PDE1, while the N-terminal lobe activates the enzyme. The presence of an aromatic residue, usually a tryptophan
Tryptophan
Tryptophan is one of the 20 standard amino acids, as well as an essential amino acid in the human diet. It is encoded in the standard genetic code as the codon UGG...
, in the CaM-binding region of Ca2+-CaM-regulated proteins may also be required for binding to PDE1.
Between different PDE1 isozymes there is a significant difference in affinity for Ca2+/CaM. In general, the PDE1 enzymes have high affinity for the complex but the affinity can be affected by phosphorylation. Phosphorylation
Phosphorylation
Phosphorylation is the addition of a phosphate group to a protein or other organic molecule. Phosphorylation activates or deactivates many protein enzymes....
of PDE1A1 and PDE1A2 by protein kinase A and of PDE1B1 by CaM Kinase II decreases their sensitivity to calmodulin activation. This phosphorylation can be reversed by the phosphatase, calcineurin. The phosphorylation of the isozymes is accompanied by a decrease in the isozymes affinity towards CaM, as well as an increase in the Ca2+ concentrations required for CaM activation of the isozymes.
PDE1 inhibitors and their function
PDEs have been pursued as therapeuticPharmacotherapy
Pharmacotherapy is the treatment of disease through the administration of drugs. As such, it is considered part of the larger category of therapy....
targets because of the basic pharmacological principle that regulation of degradation of any ligand
Ligand
In coordination chemistry, a ligand is an ion or molecule that binds to a central metal atom to form a coordination complex. The bonding between metal and ligand generally involves formal donation of one or more of the ligand's electron pairs. The nature of metal-ligand bonding can range from...
or second messenger can often make a more rapid and larger percentage change in concentration than comparable rates of synthesis
Chemical synthesis
In chemistry, chemical synthesis is purposeful execution of chemical reactions to get a product, or several products. This happens by physical and chemical manipulations usually involving one or more reactions...
. Another reason is that PDEs do not have to compete with very high levels of endogenous
Endogenous
Endogenous substances are those that originate from within an organism, tissue, or cell. Endogenous retroviruses are caused by ancient infections of germ cells in humans, mammals and other vertebrates...
substrate to be effective since the levels of cAMP and cGMP in most cells are typically in the micromolar range.
The availability of high-resolution crystal structures of the catalytic domains of PDEs makes the development of highly potent and specific inhibitors
Enzyme inhibitor
An enzyme inhibitor is a molecule that binds to enzymes and decreases their activity. Since blocking an enzyme's activity can kill a pathogen or correct a metabolic imbalance, many drugs are enzyme inhibitors. They are also used as herbicides and pesticides...
possible.
Many compounds reported as PDE1 inhibitors do not interact directly with the catalytic site of PDE1 but interact during activation, either at the level of calmodulin binding sites such as compound KS505a or directly on Ca2+/calmodulin such as bepril, flunarizine
Flunarizine
Flunarizine is a drug classified as a calcium channel blocker. Flunarizine is a non-selective calcium entry blocker with calmodulin binding properties and histamine H1 blocking activity. It is effective in the prophylaxis of migraine, occlusive peripheral vascular disease, vertigo of central and...
and amiodarone
Amiodarone
Amiodarone is an antiarrhythmic agent used for various types of tachyarrhythmias , both ventricular and supraventricular arrhythmias. Discovered in 1961, it was not approved for use in the United States until 1985...
.
Those inhibitors that interact with the catalytic site occupy part of the active site, primarily around the Q pocket and occasionally close to the M pocket. A major point of interaction is a conserved hydrophobic pocket that is involved in orienting the substrate purine ring for interaction with a glutamine residue that is crucial for the catalytic mechanism of the PDEs.
The interactions of inhibitors can be split into three major types: interactions with the metal ions mediated through water, H-bond interactions with the protein residues involved in nucleotide recognition and most importantly the interaction with the hydrophobic residues lining the cavity of the active site. All known inhibitors seem to exploit these three types of interactions and hence these interactions should guide the design of new types of inhibitors.
Initially PDE1 inhibitors were claimed to be effective vascular relaxants. With availability of purified cloned enzymes, however, it is now known that such inhibitors are in fact equally active against PDE5. Those inhibitors include e.g. zaprinast
Zaprinast
Zaprinast was an unsuccessful clinical drug candidate that was a precursor to the chemically-related PDE5 inhibitors, such as sildenafil , which successfully reached the market. It is a phosphodiesterase inhibitor, selective for the subtypes PDE5, PDE6, PDE9 and PDE11. IC50 values are 0.76, 0.15,...
, 8-methoxymethyl IPMX and SCH 51866.
All therapeutically effective PDE inhibitors must be incorporated into the cell because all PDEs are localized in the cytoplasm and/or on intracellular membranes.
Today, there is no real and effective specific PDE1 inhibitor that can be used to assess the functional role of PDE1 in tissues .
Common PDE1 inhibitors
NimodipineNimodipine
Nimodipine is a dihydropyridine calcium channel blocker originally developed for the treatment of high blood pressure...
(3,5-pyridinedicarboxylic acid, 1,4-dihydro-2,6-dimethyl-4-(3-nitrophenyl)-, 2-methoxyethyl 1-methylethyl ester ) is a dihydropyridine that antagonizes/blocks specifically L-type Ca2+-channel, and was first described as a PDE1 inhibitor. This effect is not related to its calcium antagonist property since it inhibits, in micromolar range, basal and calmodulin stimulated purified PDE1. Since nimodipine at lower concentrations blocks the L-type calcium channel, it can only be used to estimate PDE1 participation in tissue and cell homogenates .
Vinpocetine
Vinpocetine
Vinpocetine is a semisynthetic derivative alkaloid of vincamine , an extract from the periwinkle plant....
was described as a specific inhibitor of basal and calmodulin-activated PDE1. This effect leads to an increase of cAMP over cGMP . It is mainly used as a pharmacological tool to implicate PDE1. Vinpocetine inhibits differently the various subtypes of PDE1 (IC50 from 8 to 50 µm) and it is also able to inhibit PDE7B. It can not be used as a specific tool to investigate the functional role of PDE1 due to its direct activator effects on BK (Ca) channels. Vinpocetine crosses the blood-brain barrier and is taken up by cerebral tissue. It has been hypothesized that vinpocetine can effect voltage dependent calcium channels.
IC224 inhibits PDE1 (IC50 = 0.08 µM) with a selective ratio of 127 (ratio of IC50 value for the next most sensitive PDE and for IC50 value for PDE1). It was developed by ICOS corporation. If IC224 similarly inhibits basal and calmodulin-activated PDE1 subtypes, this compound could be very helpful to characterize PDE1 activity and to clearly investigate the various roles of PDE1 in pathophysiology.
PDE1 inhibitors in diseases
Nearly all the phosphodiesterases are expressed in the CNS, making this gene family an attractive source of new targets for the treatment of psychiatric and neurodegenerative disorders.PDE1A2 has a potential role in neurodegenerative diseases e.g.:
Parkinsons
Axonal neurofilament
Neurofilament
Neurofilaments are the 10 nanometer intermediate filaments found specifically in neurons. They are a major component of the cell's cytoskeleton, and provide support for normal axonal radial growth...
degradation
Chemical decomposition
Chemical decomposition, analysis or breakdown is the separation of a chemical compound into elements or simpler compounds. It is sometimes defined as the exact opposite of a chemical synthesis. Chemical decomposition is often an undesired chemical reaction...
Motorneuronal degradation
Neuronal ischemia
Ischemia
In medicine, ischemia is a restriction in blood supply, generally due to factors in the blood vessels, with resultant damage or dysfunction of tissue. It may also be spelled ischaemia or ischæmia...
Alzheimer’s disease
epilepsy
Epilepsy
Epilepsy is a common chronic neurological disorder characterized by seizures. These seizures are transient signs and/or symptoms of abnormal, excessive or hypersynchronous neuronal activity in the brain.About 50 million people worldwide have epilepsy, and nearly two out of every three new cases...
PDE1C could have a role in the regulation of insulin
Insulin
Insulin is a hormone central to regulating carbohydrate and fat metabolism in the body. Insulin causes cells in the liver, muscle, and fat tissue to take up glucose from the blood, storing it as glycogen in the liver and muscle....
release and may target proliferating smooth muscle cells in atherosclerotic lesions or during restenosis
Restenosis
Restenosis literally means the reoccurrence of stenosis, a narrowing of a blood vessel, leading to restricted blood flow. Restenosis usually pertains to an artery or other large blood vessel that has become narrowed, received treatment to clear the blockage and subsequently become renarrowed...
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