PDE5 drug design

This article is about the uses of phosphodiesterase 5 (PDE5) in drug design.

General

The human genome contains at least 21 genes involved in determining the intracellular levels of cAMP and cGMP by the expression of phosphodiesterase proteins or PDE’s. These PDE’s are grouped into at least 11 functional subfamiles, named PDE1-PDE11.^[1] PDEs are enzymes that hydrolyze cyclic adenosine 3,5-monophosphate (cAMP) and cyclic guanosine 3,5-monophospahate (cGMP), which are intracellular second messengers, into AMP and GMP. These second messengers control many physiological processes.^[2] The cAMP is formed from ATP by the enzyme adenylyl cyclase and cGMP is formed from GTP by the enzyme guanylyl cyclase which are either membrane bound or soluble in the cytosol. When soluble it functions as a receptor for nitric oxide (NO) (see figure 1).^[3] Formation of cGMP initiates several reactions in the body including influence on cGMP ion channels, cGMP binding proteins and protein kinase G (PKG). The effect on PKG reduces levels of calcium leading to relaxation of smooth muscles (see figure 2).^[4] The PDE5 enzyme is specific for cGMP which means it only hydrolyzes cGMP but not cAMP.^[5] The selectivity is mediated through an intricate network of hydrogen bonding which is favorable for cGMP but unfavorable for cAMP in PDE5.^[6] By inhibition of PDE5 enzyme the cGMP concentration will be raised and can therefore increase the relaxation of smooth muscles.^[4] PDE5 has only one subtype, PDE5A, of which there are 4 isoforms in humans called PDE5A1-4.^[5] The difference in PDE5A1-3 isoforms is only in the 5´ end of the mRNA and corresponding N-terminal of the protein.^[7]

Figure 1: Effect of PDE5 enzyme

Figure 2. Formation of cGMP and its effect in the body

Distribution of PDE5 in the body

In humans the distribution of PDE5A1 and PDE5A2 isoforms is the same and can be found in the brain, lung tissue, heart, liver, kidneys, [urinary bladder|[bladder]], prostate, urethra, penis, uterus and skeletal muscles. PDE5A2 is more common than PDE5A1. PDE5A3 is not as widespread as the other two isoforms, and is only found in smooth muscle tissues, it is found in the heart, bladder, prostate, urethra, penis and uterus,^[7][8] Exact distribution of PDE5A4 isoform was not found in the literature. PDE5 enzyme in humans has also been reported in platelets, gastrointestinal epithelial cells, Purkinje cells of cerebellum,^[9] corpus cavernosum,^[2] pancreas,^[10] placenta and colon,^[1] clitoral corpus cavernosum as well as vaginal smooth muscle and epithelium.^[8]

PDE Structure and SAR

PDE enzymes are composed of 3 functional domains: an N-terminal cyclin fold domain, a linker helical domain and a C-terminal helical bundle domain (see figure 3).^[6] The active site is a deep pocket at the junction of the 3 subdomains and is lined with highly conserved residues between isotypes of PDE.^[11] The pocket is approximately 15 Å deep and the opening is approximately 20 by 10 Å. The volume of the active site has been calculated to be between 875 and 927 ų.^[11] The active site of PDE5 has been described as subdivided into 3 main regions based on its crystal structure in complex with sildenafil:^[4]

• M site: contains both a zinc and magnesium ion. The role of the ions is to stabilize the structure and activation of hydroxide to mediate the reaction. Current PDE5 inhibitors do not interact with the metal ions, in contrast with cGMP. Direct or indirect interactions may improve the potency of future inhibitors.^[6]
• Q pocket: it is believed that the guanidine group of cGMP binds in this region as the Q pocket accommodates the pyrazolopyrimidinone group (see figure 4) of sildenafil. The pyrazolopyrimidinone of sildenafil mimics the that of the guanine in cGMP and has the same H-bond donor and acceptor features, forming a bidendrate H-bond with Q817. Card et al. describe the Q pocket as subdivided into 3 parts:^[11]
  • A saddle formed by the conserved glutamine (Q817 in PDE5A, Q443 in PDE4B and Q369 in PDE4D) and the P clamp (a hydrophopic clamp at the narrow side of the active sites pocket, formed of invariant purine-selective glutamine and a pair of conserved residues).^[11]
  • 2 narrow, hydrophobic pockets, Q1 and Q2, composed mainly of hydrophobic residues flanking the saddle.^[11]
• L region: the methyl piperazine group (see figure 4) of sildenafil is surrounded by Tyr 664, Met 816, Ala 823 and Gly 819 residues, and residues 662-664 form a lid over the pocket narrowing the entrance to the active site of PDE5.

Jeon et al.^[6] also describe a fourth pocket called the H pocket which is hydrophobic and accommodates the ethoxyphenyl group of sildenafil The 3 PDE5 inhibitors already on the market, sildenafil, tadalafil and vardenafil, occupy part of the active site, mainly around the Q pocket and sometimes the M pocket as well and all 3 interact with the active site in 3 important manners:

1. interaction between the metal ions mediated through water
2. hydrogen bonding with the saddle of the Q pocket
3. hydrophobic interaction with hydrophobic residues lining the cavity of the active site.^[11]

It has also been described that the hydrophobic interaction with the Q1 and Q2 pockets are important for inhibitor potency and differences between isotypes of PDE in the Q2 pocket can be exploited for selectivity between isotypes.^[11]

Figure 3: Vardenafil (yellow) is seen here in complex with PDE5. Violet: N-terminal domain, grey: linker domain, blue: C-terminal domain, magnesium and zinc ions can also be seen.^[6] Image produced by Cn3D12 from (http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?form=6&db=t&Dopt=s&uid=31153)^[12]

Figure 4: Sildenafil. Blue shows the methyl piperazine group, orange is the ethoxyphenyl group and orange and green together represent the pyrazolopyrimidinone group.

Role in diseases

Erectile dysfunction

Drugs that inhibit PDE5, sildenafil, tadalafil and vardenafil, have been used as treatment for erectile dysfunction.^[13] These inhibitors increase the cGMP, smooth muscle relaxation and consequentally cause penis erection^[6] during sexual stimulation.^[14]

Pulmonary hypertension

Pulmonary hypertension is the result of upregulation of PDE5 gene expression, causing vasoconstriction in the lung. PDE5 inhibitors are used as potent pulmonary vasodilators reducing Pulmonary hypertension^[4] and inhibiting vascular remodelling.^[15] Long-term treatment with a PDE5 inhibitor has been shown to enhance natriuretic peptide-cGMP pathway, downregulate Ca²⁺ signaling pathway and alter vascular tone in pulmonary arteries in rat models.^[6]

Future indications for PDE5 inhibitors

Premature ejaculation

Adding PDE5 inhibitors to SSRI drugs (e.g. paroxetine) for the treatment of premature ejaculation could result in better ejaculatory control according to recent studies.^[8] Possible mechanism is based on nitric oxide (NO)/cGMP transduction system as a central and peripheral mediator of inhibitory non-adrenergic, non-cholinergic nitrergic neurotransmission in the urogenital system.^[13]

Female sexual arousal disorder

PDE5 is expressed in clitoral corpus cavernosum and in vaginal smooth muscle and epithelium. Therefore it is possible that PDE5 inhibitors could affect female sexual arousal disorder but further research is needed. Increased levels of cGMP have been shown to occur in human-cultered vaginal smooth muscle cells treated with a PDE5 inhibitor suggesting involvement of the NO/cGMP axis in the female sexual response.^[8]

Raynaud's phenomenon

Sildenafil has been shown to be effective in treating severe Raynaud's phenomenon associated with systemic sclerosis and digital ulceration. When given sildenafil for 4 weeks subjects had reduced mean frequency and duration of Raynaud attacks and a significantly lowered mean Raynaud’s condition score. The capillary blood flow velocity also increased in each individual patient and the mean capillary flow velocity of all patients increased significantly. These results came without significant reductions of the systemic blood pressure.^[4]

Heart failure

Sildenafil has shown promise in the treatment of congestive cardiac failure. A study showed that effective treatment of pulmonary arterial hypertension with sildenafil improved functional capacity and reduced right ventricular mass in patients. The effects on right ventricular remodeling were significantly greater in comparison with the non-selective endothelia receptor antagonist bosentan.^[4]

Cardiovascular disease and systemic hypertension

Sildenafil has been shown to improve endothelial function in diabetes and congestive heart failure.,^[16][4] It has also been shown to reduce aortic pressure through vasodilation, reduced arterial stiffness and wave reflection and could be used in the management of systemic hypertension.^[4]

Vascular disease

Sildenafil has been shown to significantly improve neurovascular coupling without affecting overall cerebral blood flow by increasing brain levels of cGMP, evoking neurogenesis and reducing neurological deficits in rats 2 or 24 hours after stroke. This data suggest that PDE5 inhibitors may have a role in promoting recovery from stroke.,,^[4][8][6]

PDE5-inhibitors in clinical trials

Drug	Clinical trial status (2005)	Indication	Producer
UK357903	Phase II	Erectile dysfunction (second generation PDE5 inhibitor)[6]	Pfizer
Avanafil	Phase II	Erectile dysfunction and female sexual arousal disorder[6]	Tanabe
Udenafil (DA-8159)	Phase II	Endothelial dysfunction,[6] erectile dysfunction[6] and erectile dysfunction associated with obesity,[17] diabetes[16] and use of SSRIs[18]	Dong-A Pharmaceutical

See also

• Molecular modelling

References

1. ^ ^{a b} Bingham, J., Sudarsanam, S. & Srinivasan, S. (2006). "Profiling human phosphodiesterase genes and splice isoforms". Biochemical and Biophysical Research Communications 350, 25-32. 
2. ^ ^{a b} Jiang, W. Q. et al. (2004). "Profiling Synthesis and SAR of tetracyclic pyrroloquinolones as phosphodiesterase 5 inhibitors". Bioorganic & Medicinal Chemistry 12, 1505-1515. 
3. ^ Garrett (2002). Principles of biochemistry : with a human focus. Fort Worth. ISBN 0-03-097369-4. 
4. ^ ^{a b c d e f g h i} Ghofrani, H. A., Osterloh, I. H. & Grimminger, F. (2006). "Sildenafil: from angina to erectile dysfunction to pulmonary hypertension and beyond.". Nature Reviews Drug Discovery 5, 689-702. 
5. ^ ^{a b} Sung, B. J. et al. (2003). "Structure of the catalytic domain of human phosphodiesterase 5 with bound drug molecules.". Nature 425, 98-102. 
6. ^ ^{a b c d e f g h i j k l} Jeon, Y. H. et al. (2005). "Phosphodiesterase: overview of protein structures, potential therapeutic applications and recent progress in drug development.". Cmls-Cellular and Molecular Life Sciences 62, 1198-1220. 
7. ^ ^{a b} Lin, C. S. (2004). "Tissue expression, distribution, and regulation of PDE5.". International Journal of Impotence Research 16, S8-S10. 
8. ^ ^{a b c d e} Jackson, G., Gillies, H. & Osterloh, I. (2005). "Past, present, and future: a 7-year update of Viagra((R)) (sildenafil citrate).". International Journal of Clinical Practice 59, 680-691. 
9. ^ Blount, M. A. et al. (2004). "Binding of tritiated sildenafil, tadalafil, or vardenafil to the phosphodiesterase-5 catalytic site displays potency, specificity, heterogeneity, and cGMP stimulation.". Molecular Pharmacology 66, 144-152. 
10. ^ Lugnier, C. (2006). "Cyclic nucleotide phosphodiesterase (PDE) superfamily: A new target for the development of specific therapeutic agents.". Pharmacology & Therapeutics 109, 366-398. 
11. ^ ^{a b c d e f g} Card, G. L. et al. (2004). "Structural basis for the activity of drugs that inhibit phosphodiesterases.". Structure 12, 2233-2247. 
12. ^ Chen, J. et al. (2003). "MMDB: Entrez's 3D-structure database 10.1093/nar/gkg086.". Nucl. Acids Res. 31, 474-477. 
13. ^ ^{a b} McMahon, C. G., McMahon, C. N., Leow, L. J. & Winestock, C. G. (2006). "Efficacy of type-5 phosphodiesterase inhibitors in the drug treatment of premature ejaculation: a systematic review.". Bju International 98, 259-272. 
14. ^ Shinlapawittayatorn, K., Chattipakorn, S. & Chattipakorn, N. (2005). "Effect of sildenafil citrate on the cardiovascular system.". Brazilian Journal of Medical and Biological Research 38, 1303-1311. 
15. ^ Chung, K. F. (2006). "Phosphodiesterase inhibitors in airways disease.". European Journal of Pharmacology 533, 110-117. 
16. ^ ^{a b} Ahn, G. J. et al. (2005). "Chronic administration of phosphodiesterase 5 inhibitor improves erectile and endothelial function in a rat model of diabetes.". International Journal of Andrology 28, 260-266. 
17. ^ Yu, J. Y., Kang, K. K. & Yoo, M. (2006). "Erectile potentials of a new phosphodiesterase type 5 inhibitor, DA-8159, in diet-induced obese rats.". Asian Journal of Andrology 8, 325-329. 
18. ^ Ahn, G. J. et al. (2005). "DA-8159 reverses selective serotonin reuptake inhibitor-induced erectile dysfunction in rats.". Urology 65, 202-207.