Commentary on the distinction between Cannabis and cannabinoids

The Cannabis plant is a natural product from which more than 100 apparently unique metabolites (cannabinoids) have been identified. Many of these have been found in human plasma following consumption of Cannabis preparations. The most well-recognised is tetrahydrocannabinol, THC, because of its well-documented psychotropic effects mediated through activating CB1 cannabinoid receptors. It has been used clinically as an anti-emetic and for treating glaucoma.

Cannabidiol, CBD, is also a prominent metabolite from the plant, which lacks the psychotropic effects of THC, since it is not an agonist at CB1 cannabinoid receptors. It is in advanced trials for treating childhood epilepsy, but may also have benefit in schizophrenia or post-traumatic stress disorder. The molecular mechanisms of action of CBD are not precisely defined, but may involve multiple targets.

A standardised combination of THC and CBD is available in many countries, including the UK as a licensed medicine for treating the symptoms of multiple sclerosis.

There is a lack of clear understanding of the biological effects of the majority of the other cannabinoid metabolites from the plant, which may have applications in inflammatory disorders, nausea and metabolic disorders, such as type II diabetes.

In many countries, Cannabis itself is licensed as a medicine for indications such as pain relief or the weight loss associated with terminal cancer or AIDS. However, preparations from Cannabis are highly variable in terms of the spectrum and concentrations of cannabinoid content, as well as other compounds present in the plant, such as the terpenoids, which have also been proposed to have independent bioactivity.

Commentary by Steve Alexander (@mqzspa) & Anthony Davenport

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Posted in Hot Topics, Uncategorized

GtoPdb: Database Status Reports

As some of our contacts may know, we hold hemi-annual meetings between IUPHAR, BPS the GtoPdb team, together with invited guests from our collaborators and NC-IUPHAR committee representatives. Covering ~ 2.5 days these usually take place in Paris or Edinburgh. One of the outputs from these rewarding gatherings is an extensive (i.e. ~ 20-25 pages) database report document. For interested parties these provide a usefully detailed snapshot of what we have collectively been up to for the preceding 6-month period.

The last three of these are now on-line (http://www.guidetopharmacology.org/download.jsp#db_reports).

The latest one (May 2018) also includes links to slide sets shown in the meeting that accompany the report, which are also available here:

Database Status Report: Core GtoPdb

Database Status Report: GtoImmuPdb

Linking GtoPdb, PubChem and PubMed

 

Posted in Database updates, Technical, Uncategorized

Hot topic (update): from double to triple whammy for BACE1 inhibitors

19 June 2018 update. Announced only about a week after the events described below,  yet a third clinical candidate, lanabecestat  (AZD-3293, LY3314814) has also bitten the dust (4).  The two PhIII trials were stopped because they were deemed unlikely to meet their primary endpoints. This bad news engendered yet another “In The Pipeline” commentary  If detailed reports are eventually published these will be curated as new references for the ligand entry.

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BACE1  (beta secretase 1, BACE-1 or BACE) has been a key target for Alzheimer’s disease (AD) for nearly two decades (1).  However, there was a major disappointment when the Phase III trials with the Merck inhibitor verubecestat failed unequivocally despite lowering A-beta levels.  The termination is reported both in NCT01739348  and the  May 2018  full paper on the trial results (2).  The gravity of this setback is underlined by the “In The Pipeline” commentary title “Merck’s BACE-Inhibitor Alzheimer’s Wipeout” wherein it is suggested that this brings the validation status of this target and, by definition, other inhibitors in late-stage development into doubt.  Thus, even glimmers of success for any mechanistic class of AD  therapy would seem to be currently extinguished.   There remains perhaps the slimmest of hopes from the recent report that the initial process of plaque formation might yet prove sensitive to therapeutic BACE1 inhibition (3).  However, there may be no diagnostic and/or biomarker specific enough to identify prospective asymptomatic patients this early in disease development.

The bad news for BACE1 inhibitors was compounded by a press release from Janssen in the same month. They reported serious liver enzyme elevations for some participants in Janssen’s atabecestat  (JNJ-54861911) Phase 2b/3 trial.  While this may be a chemotype liability for this series rather than a target-related issue, it does mean that yet another AD drug candidate has bitten the dust.  We would hope that a full clinical data report on this trial cessation could be pending,  However,  despite a number of early clinical reports, Janssen has not so far published any primary in vitro medicinal chemistry papers on this compound.  Comments about both these failures have also just  appeared in Nature Reviews in Drug Discovery

N.b. Our BACE1  target entry is in the process of being updated so a number of new inhibitors and curatorial comments will appear in database release 2018.3.  The technicalities of gathering these new structures, including unblinding JNJ-54861911, as well as what might still be progressing,  are described in this blog post.

Comments by Chris Southan (@cdsouthan)

1) Southan and Hancock  (2013) A tale of two drug targets: the evolutionary history of BACE1 and BACE2. Front Genet. Dec 17;4:293. doi: 10.3389/fgene.2013.00293.[PMID 24381583]

2) Egan et. al.  (2018)  Randomized Trial of Verubecestat for Mild-to-Moderate Alzheimer’s Disease. N. Engl. J. Med., 378 (18): 1691-1703, [PMID 29719179]

3) Peters et. al. (2018) BACE1 inhibition more effectively suppresses initiation than progression of β-amyloid pathology, Acta Neuropathol. May;135(5):695-710. doi: 10.1007/s00401-017-1804-9. [PMID 29327084]

4) Update on Phase 3 Clinical Trials of Lanabecestat for Alzheimer’s Disease (2918)  Eli Lilly and AstraZeneca press release [CUL 14602932]

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Database release 2018.2

Our second database release of the year, 2018.2, is now available. This update contains the following new features and content changes:

Content updates

GPCRs:
5-Hydroxytryptamine receptors
Adenosine receptors
Adrenoceptors
Histamine receptors
Opioid receptors
Lysophospholipid (S1P) receptors
Prostanoid receptors

NHRs:
Mineralocorticoid receptor
Peroxisome proliferator-activated receptors

Channels:
Transient Receptor Potential channels
Nav1.5

Enzymes:
Nitric oxide synthases
Cyclooxygenase
Phosphodiesterases, 3′,5′-cyclic nucleotide (PDEs)
Cyclin-dependent kinase (CDK) family
Mitogen-activated protein kinases (MAP kinases)
NADPH oxidases

Transporters:
Monoamine transporter subfamily

Others:
Heat shock proteins

New website features

Pharmacology Search Tool

In release 2018.1 we announced a new Pharmacology Search Tool allowing users to upload lists of target ids and find ligands to modulate them. We have now extended this tool to (optionally) search for other relevant ligands in ChEMBL v23. The ChEMBL data has been filtered according to the same rules we use for the ligand activity visualisation charts (see the help documentation for details) and as well as displaying the ChEMBL curated activity values, we also display their calculated -log pChEMBL value. An example of the results returned from this type of search is shown in Fig 1.

pharm_search_res

Figure 1. Example of results returned from a UniProt Accession search in the Pharmacology Search Tool, showing the top 3 GtoPdb and ChEMBL ligands. Results are ordered by total number of ligands in these databases that match search criteria.

New PDB ligand icon

As part of our increased emphasis on ligand structures (as seen with our synPHARM resource), we have introduced a new ligand icon for PDB entries. We display this on the ligand list and target interaction tables to indicate which ligands have PDB entries (orange circle with a white alpha helix across the centre), as shown in Fig 2.

PDB_icon_lig_list

Figure 2A. The ligand list showing the new PDB ligand icon in orange.

PDB_object_icon

Figure 2B. A target inhibitor table showing the new PDB ligand icon in orange.

Sponsored Tocris product links

We have collaborated with Tocris as a quality supplier of many of the ligands in GtoPdb by adding links from our ligand pages out to the matching Tocris products. An example, which can be found on the ligand page beneath the summary tab, is shown in Fig 3. In total there are links to 1198 Tocris products.

tocris_link

Figure 3. Ligand summary page showing a link to the Tocris product.

Other updates

BJP/BJCP linking

As an adjunct to our successful entity-linking initiative for the BJP and more recently BJCP, we have instigated a process whereby, on manuscript acceptance and their own marking-up of GtoPdb links, authors alert us directly to key entities from their studies that are not in our database. In most cases, we then add the missing ligands. This has the advantages for both the author and the journal of not only adding their reference into GtoPdb but also the paper gains PubChem PubMed reciprocal linking derived from our PubChem ligand submissions. Examples from this release include GS-458967 from BJP and esaxerenone from BJCP.

BACE1 in doubt as an Alzheimer’s drug target

The target entry for the Alzheimer’s drug target BACE1 underwent key updates. The first of these was to add a new reference for the full report published just last week on the Phase III failure of the lead Merck BACE1 inhibitor verubecestat. Unfortunately, this paper now casts doubt on the target validation status and thus the future for this entire class of compounds pursued intensively for over 18 years. Notwithstanding, several ligands on the BACE1 list may yet complete their clinical evaluation (these will be joined by the latest  development candidate from Pfizer as PF-06751979 in 2018.3)

SynPHARM article

We are pleased to report that an open pre-print version (i.e. pending changes compared to the eventually accepted journal version) of our manuscript describing our SynPharm resource is now on-line.

How-to-Guide 

We are also pleased to report the publication of  Accessing Expert‐Curated Pharmacological Data in the IUPHAR/BPS Guide to PHARMACOLOGY. It is not indexed in PubMed yet but note that the PDF is free to access until the end of May (so pull it down while you can! – but we could send you one if you miss the window).  It includes useful examples of how to use both GtoPdb and GtoImmuPdb as a supplement to our online help and FAQ.

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Posted in Database updates, Guide to Malaria Pharmacology

Hot topic: Cryo-EM structure of the adenosine A2A receptor coupled to an engineered heterotrimeric G protein

The A2A adenosine receptor is densely expressed in dopamine-rich areas of the brain and in the vasculature. It is the target of an adjunct medication for Parkinson’s Disease, istradefylline in Japan, an A2A receptor antagonist.

The A2A adenosine receptor is an example of a Gs-coupled receptor, activation of which in the cardiovascular system leads to inhibition of platelet aggregation and vasorelaxation. This new report (1) highlights the link between the receptor and the G protein to focus on areas of unexpected flexibility in the ligand binding region. Further, classical understanding of receptor:G protein interaction identifies a prominent role for the third intracellular loop and the proximal end of the C-terminus (in some GPCR, such as the beta2-AR, a fourth intracellular loop is formed by palmitoylation of an intracellular cysteine residue, which the A2A lacks). The model generated from this cryo-EM study with a nanobody suggests a potentially novel role for an interaction between the first intracellular loop and the Gbeta subunit.

Comments by Steve Alexander (@mqzspa)

(1) Garcia-Nafría J et al. (2018). Cryo-EM structure of the adenosine A2A receptor coupled to an engineered heterotrimeric G protein. eLife, 7. pii: e35946. doi: 10.7554/eLife.35946. [PMID: 29726815]

Posted in Hot Topics

Hot topic: Conformational plasticity in the selectivity filter of the TRPV2 ion channel

The TRPV2 ion channel is the less well-characterised relative of the TRPV1 or vanilloid receptor that is activated by capsaicin. TRPV2 channels have many similarities to the TRPV1 channels, in that they are homotetrameric and respond to some of the same ligands (natural products such as cannabinoids) as well as being triggered at elevated temperatures. This study (1) focusses on a different common feature of the whole Transient Receptor Potential family, which are often described as non-selective cation channels. Using comparative analysis of crystals structures in which calcium is bound with and without an agonist, resiniferatoxin, present. The authors suggest that this agonist evokes a symmetrical opening of a selectivity filter gate, which permits increased permeation of calcium ions and also larger organic cations, such as the dye Yo-PRO-1.

Comments by Steve Alexander (@mqzspa)

(1) Zubcevic L et al. (2018). Conformational plasticity in the selectivity filter of the TRPV2 ion channel. Nat Struc Mol Biol., 25:405-415. doi:10.1038/s41594-018-0059-z. [Abstract]

Posted in Hot Topics

Hot topic: 3D structure of the P2X3 receptor bound to a negative allosteric modifier, identifies a binding site that is a target for development of novel therapeutic agents

Negative allosteric modulators (NAMs) are of great interest in drug development because they offer improved scope for the production of receptor antagonists with enhanced subtype-selectivity. Indeed, many NAMs are already on the market or undergoing clinical trials. NAMs act by binding to sites within receptors that are distinct from the primary, orthosteric ligand binding site and can inhibit the structural rearrangements of a receptor that are induced by orthosteric agonist binding.

P2X receptors are ligand-gated cation channels for which ATP is the endogenous orthosteric agonist. They are expressed throughout the body and the evidence indicates that they have numerous functions, including in sympathetic and parasympathetic neurotransmission, perception of sound, taste and pain, and immune regulation. Seven P2X subunits have been identified, which form trimers, to produce at least twelve different receptor subtypes. A major issue within the field has been a lack of selective antagonists for most P2X subtypes. This is unsurprising given the amino acid sequence similarity within the ATP binding site. Several selective NAMs have now been developed, but little is known about where in receptors they act and how exactly they inhibit receptor activation.

AF-219 is small molecule NAM at P2X3 receptors that was reported to be effective in a phase II clinical trial for treatment of refractory chronic cough. Wang et al., (1) combined X-ray crystallography, molecular modelling, and mutagenesis, to identify the site and mode of action of AF-219. P2X3 receptors are composed of three subunits, each of which adopts a conformation that could be likened to the shape of a leaping dolphin. The tail represents the transmembrane-spanning regions, the upper body the bulk of the extracellular loop and the head the most distal part of the extracellular loop. Also attached to the body are three structurally-distinct elements: the dorsal fin, the right flipper, and the left flipper. As a trimer, the subunits wrap round each other to produce a structure that resembles a chalice.

The AF-219 binding site is formed by the lower body and dorsal fin of one subunit and the lower body and left flipper of an adjacent subunit. Mutational analysis identified which amino acid residues within this pocket are essential for AF-219 binding, whilst in silico modelling showed that the small molecule P2X3 NAMS, AF-353, RO-51, RO-3 and TCP 262, but not the large NAMS suramin and PPADS, also bind to the same site. Activation of P2X3 receptors by ATP closes the binding cavity, so by occupying it, AF-219 prevents the protein structural rearrangements that lead to opening of the P2X3 receptor ion pore.

This identification of the AF-219 NAM binding site in P2X3 receptors is an opportunity for rational, intelligent drug design. It enables virtual screening of compound libraries, with the aim of identifying potential new molecular core structures, which can then be modified in order to optimise the structure of a novel NAM. In addition, this site differs among P2X receptor subtypes, so it is highly possible that drugs with greatly enhanced subtype-selectivity can be developed.

Comments by Dr. Charles Kennedy, University of Strathclyde

(1) Wang J, Wang Y, Cui WW, Huang Y, Yang Y, Liu Y, Zhao WS, Cheng XY, Sun WS, Cao P, Zhu MX, Wang R, Hattori M, Yu Y. (2018). Druggable negative allosteric site of P2X3 receptors. Proc Natl Acad Sci U S A. 2018 pii: 201800907. doi: 10.1073/pnas.1800907115. [PMID:  29674445]

Posted in Hot Topics