• F1000 Research, and our poster!



    Felix and I in the group do the occasional piece of work for F1000, and we've put up one of our posters on F1000Research (well Felix's, my only addition was too throw a fit when my name wasn't on their first time ;) ). This is fully Open, etc. At the moment it's on the front page, so check it out!

  • GPCR Structure: Muscarinic M2 receptor



    Another GPCR structure this week in Nature, this time, human muscarinic M2 receptor, complexed with an antagonist - 3-quinuclidinyl-benzilate - a controlled military incapacitation agent (CHEMBL12980); a link to the paper is here. A key difference to previously known structures is the large channel-like binding site. Coordinates are here PDBe:3uon


                              10        20        30        40        50  
    3uon  (  20 )    tfevvfivlvagslSlvTiigNilVmvSIkvnrhLqtvnnyflfSLAcAD
                        aaaaaaaaaaaaaaaaaaaaaaaaaaaa 333  aaaaaaaaaaaaa
    
                              60        70        80        90        100 
    3uon  (  70 )    liiGvfSMnlytlytvigyWplgpvvÇdlWlalDYvVSNAsVmNLliiSf
                     aaaaa aaaaaaaaaa       aaaaaaaaaaaaaaaaaaaaaaaaaaa
    
                              110       120       130       140       150 
    3uon  ( 120 )    dryfcvtkpltypvkrttkmAgmmiaaAwvlSfilwapaIlfwqfivgvr
                     aaaaaaa     333  aaaaaaaaaaaaaaaaaaaaaaaaaaaaaa   
    
                              160       170       180       190       200 
    3uon  ( 170 )    tVedgeÇyIqffsnaavtfgtAiaaFylpviiMtvlywhisrasksri p
                              3333 aaaaaaaaaaa aaaaaaaaaaaaaaaaaa      
    
                              210       220       230       240       250 
    3uon  ( 378 )    ppsrekkvtrtilaIllaFiitWapYNvmVlintfçapçipntvwtiGyw
                           aaaaaaaaaaaaaaaaaaaaaaaaaaaaa      aaaaaaaaa
    
                              260       270       
    3uon  ( 428 )    lCYinstiNpacYalcnatFkktfkhllm
                     aaaa   aaaaaaaaa aaaaaaaaaa  
    
    
    A K. Haga
    A A.C. Kruse
    A H. Asada
    A T. Yurugi-Kobayashi
    A M. Shiroishi
    A C. Zhang
    A W.I. Weis
    A T. Okada
    A B.K. Kobilka
    A T. Haga
    A T. Kobayashi
    %T Structure of the human M2 muscarinic acetylcholine receptor bound to an antagonist
    %J Nature
    %V 482
    %P 547-551
    %O http://dx.doi.org/10.1038/nature10753
    %D 2012
    

    I only found the GPCR Network website today (doh!), there is a great tracking chart of ongoing structural programmes - so bring on the S1P and kappa opioid structures! (The picture above summarises their target selection)

  • New Drug Approvals 2012 - Pt. VI - Tafluprost (ZioptanTM)



    ATC code S01EE05
    Wikipedia Tafluprost

    On Feb 13th, 2012 FDA approved Tafluprost (trade name Zioptan) for treatment of elevated intraocular pressure in patients with open-angle glaucoma or ocular hypertension.
    Tafluprost had been already available under the trade name Taflotan in Germany and Denmark from 2008, and under the trade name Saflutan in the United Kingdom and Spain from 2009.

    Glaucoma is an eye disease associated with increased fluid pressure in the eye, eventually causing permament damage to the optic nerve, impairing the field of vision and ultimately leading to blindness. Glaucomas can be sub-classified as open-angle glaucoma (OAG) and closed-angle glaucoma (CAG), with OAG being a slowly progressive disease responsible for ~90% of glaucoma cases in the US, and CAG being an acute disease with rapid progression. Alongside various surgical forms of treatment, management of OAG usually consists of medication to lower intraocular pressure.

    Tafluprost is a prostaglandin analogue (more specifically, a fluorinated analogue of prostaglandin F, acting as a prostaglandin receptor agonist) acting by increasing outflow of aequous humor. Similar dugs in the same class include Latanoprost, Bimatoprost and Travoprost. Alternative drug classes used for glaucoma include beta blockers which decrease aequous humor production. Tafluprost is dosed topically, i.e. as eye drops, and, unlike other prostaglandin analogs, is preservative-free, i.e. it does not contain benzalkonium chloride which may be harmful to sensitive eyes.

    The molecular target of Tafluprost is the Prostaglandin F2-alpha receptor (UniProt:P43088, PTGFR), which is a rhodopsin-like GPCR (Pfam:PF00001).


    >PF2R_HUMAN Prostaglandin F2-alpha receptor
    MSMNNSKQLVSPAAALLSNTTCQTENRLSVFFSVIFMTVGILSNSLAIAILMKAYQRFRQ
    KSKASFLLLASGLVITDFFGHLINGAIAVFVYASDKEWIRFDQSNVLCSIFGICMVFSGL
    CPLLLGSVMAIERCIGVTKPIFHSTKITSKHVKMMLSGVCLFAVFIALLPILGHRDYKIQ
    ASRTWCFYNTEDIKDWEDRFYLLLFSFLGLLALGVSLLCNAITGITLLRVKFKSQQHRQG
    RSHHLEMVIQLLAIMCVSCICWSPFLVTMANIGINGNHSLETCETTLFALRMATWNQILD
    PWVYILLRKAVLKNLYKLASQCCGVHVISLHIWELSSIKNSLKVAAISESPVAEKSAST




    Tafluprost (PubChem 6433101) is a prodrug and derived from the natural product prostaglandin scaffold. It is an ester prodrug, for which cornea permeation is facilitated; esterases in the eye convert it to the active form, an acid. It has a molecular weight of 452.5 Da and is practically insoluble in water (computed logP (alogP): 4.33).
    Its systematic name is isopropyl (5Z)-7-{(1R,2R,3R,5S)-2-[(1E)-3,3-difluoro-4-phenoxybut-1-en-1-yl]-3,5-dihydroxycyclopentyl}hept-5-enoate.
    InChI=1S/C25H34F2O5/c1-18(2)32-24(30)13-9-4-3-8-12-20-21(23(29)16-22(20) 28)14-15-25(26,27)17-31-19-10-6-5-7-11-19/h3,5-8,10-11,14-15,18,20-23, 28-29H,4,9,12-13,16-17H2,1-2H3/b8-3+,15-14+.
    Canonical Smiles=CC(C)OC(=O)CCC\C=C/C[C@H]1[C@@H](O)C[C@@H](O)[C@@H]1\C=C\C(F)(F)COc2ccccc2.

    Zioptan contains 0.015 mg/mL tafluprost and is provided in single-use containers of 0.3 mL for once per day use, containing ~10 μmol of active ingredient per dose per eye, about 1% of which is absorbed by the eye. Mean plasma Cmax is around 26-27 pg/mL, and mean plasma AUC is around 394-432 pg·min/mL.
    Common side effects include hyperaemia (i.e. red eyes), eye irritation or pain, headache, changes of pigmentation of the iris, eyelids, and eyelashes, and changes of length, thickness, shapes, and number of eyelashes. This side effect has led to off-label use of drugs of this class for primarily cosmetic purposes (there is now an approved PGF2R agonist for cosmetic use - Latisse).

    Zioptan is marketed by Merck.

    The product website can be found here, and the full prescribing information, here.

  • USAN Watch - February 2012

    The USANs for February 2012 have just been published.

    USAN Research Code StructureDrug ClassTherapeutic classTarget
    aladorian, aladorian sodiumS44121-1, ARM-036, S36    synthetic small moleculetherapeuticRyR
    avatrombopag, avatrombopag maleateE-5501, AKR-501synthetic small moleculetherapeuticTPOR
    balugrastimCG-10639proteintherapeuticGCSFR
    baricitinibLY-3009104, INCB-028050    synthetic small moleculetherapeuticJAK1 JAK2
    blisibimodA-623proteintherapeuticBAFF-R
    brexipiprazoleOPC-34712   synthetic small moleculetherapeuticD2R
    clazakizumabBMS-945429, ALD-518    mabtherapeuticIL-6
    enobosarmGTx-024synthetic small moleculetherapeuticAR
    ertugliflozinPF-04971729-00 synthetic small moleculetherapeuticSGLT2
    firtecan pegolEZN-2208synthetic small molecule conjugate prodrugtherapeutictopo 1
    giminabantsynthetic small moleculetherapeuticCB2
    ibrutinibPCI-32765, CRA-032765, PCI-32765-00    synthetic small moleculetherapeuticBTK
    lipefilgrastimXM-22proteintherapeuticGCSFR
    momelotinibCYT-387synthetic small moleculetherapeuticJAK1 JAK2
    omarigliptinMK-3102 (?)synthetic small moleculetherapeuticDPP-IV
    oprozomibONX-0912synthetic small moleculetherapeuticproteasome
    nivolumabMDX-1106, BMS-936558mabtherapeuticDR1
    placulumabCEP-37247, ART-621, PN-0621    mabtherapeuticTNFa
    quisinostatJNJ-26481585   synthetic small moleculetherapeuticHDAC
    saridegib, saridegib hydrochlorideIPI-926, FIN-5natural product-derived small moleculetherapeuticsmoothened
    technetium Tc 99m etarfolatideEC-20synthetic small moleculeimaging agentFolate receptor
    vocimagene amiretrorepvecTOCA-511viral vectortherapeutic

    If anyone can confirm the MK- number for omarigliptin, or knows the MK- number for giminabant that would be great, as would the sequences for clazakizumab, nivolumab, placulumab.

  • For The One You Love?



    Q. What was Marvin Gaye's favorite noble gas ?

    A. Sexual Helium !

  • New Drug Approvals 2012 - Pt. V - Ivacaftor (KalydecoTM)





     
      ATC code R07AX02 
    Wikipedia Ivacaftor

    On January 31st, FDA approved Ivacaftor (previously known as VX-770, trade name Kalydeco) as a first-in-class oral drug for the treatment of a rare form of Cystic Fibrosis in patients aged 6 or older, caused by a G551D mutation of the CFTR gene.

    Cystic Fibrosis (OMIM 219700) is an autosomal recessive genetic disease caused by a mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, resulting in a defective CFTR protein, an ABC-class chloride-ion transporter in epithelial cell membranes. Cystic Fibrosis (CF) most typically affects the lungs, leading to the secretion of thick mucus, consequent breathing difficulties and eventual secondary bacterial airway infections in an age-dependent manner, i.e. early infections with Staphylococcus aureus which eventually are replaced by Pseudomonas aeruginosa as disease progresses. Traditionally, management of the symptoms involves mechanical removal of mucus, assisted breathing by ventilators, and antibiotic treatment of the secondary infections.

    Ivacaftor is the first drug directly targeting CFTR rather than CF symptoms alone. It is estimated that about 1 in 20 to 1 in 25 people unsymtomatically carry one allele of the defective gene, with about 1 in 2000 to 1 in 3000 newborns being homozygous for defective CFTR. Numerous mutations may cause disfunctional products of the CFTR gene. More than two thirds of cases are caused by ΔF508, the deletion of Phenylalanine at position 508 of the CFTR protein (UniProt P13569), leading to failure of targeting the protein to the plasma membrane. The G551D mutation Ivacaftor is approved for less than 5% of CF cases (about 1,200 patients in the United States). With this mutation, the protein is transported to the plasma membrane correctly, but ion transport is impaired. Ivacaftor improves ion transport, and is therefore a CFTR potentiator. Currently, Vertex are developing a further compound, VX-809  targeting the ΔF508 mutation (currently in phase 2), and Ataluren, targeting nonsense mutations, is in phase 3 clinical trials.
    Ivacaftor (C24H28N2O3, PubChem 16220172) is a synthetic small molecule achiral drug with a molecular weight of 392.49 Da. It has 4 rotatable bonds, a calculated logP (alogP) of 4.516, 3 hydrogen bond acceptors and 3 hydrogen bond donors and is thus fully Ro5 compliant. IUPAC name: N-(2,4-ditert-butyl-5-hydroxyphenyl)-4-oxo-1H-quinoline-3-carboxamide InChi: InChI=1S/C24H28N2O3/c1-23(2,3)16-11-17(24(4, 5)6)20(27)12-19(16)26-22(29)15-13-25-18-10-8-7-9-14(18)21(15)28/h7-13, 27H,1-6H3,(H,25,28)(H,26,29) Canonical Smiles: CC(C)(C)C1=CC(=C(C=C1NC(=O)C2=CNC3=CC=CC=C3C2=O)O)C(C)(C)C Ivacaftor is dosed as 150 mg tablet twice daily (an equivalent of about 0.38 mM of active incredient per single dose), or less often in patients with renal impairment or patients taking CYP3A inhibitors (see below).

    Peak plasma concentrations (Tmax) occur at about 4 hours post administration with a Cmax of 768 ng/mL and mean apparent volume of distribution of 353 L. The main route of clearance of Ivacaftor is fecal with an apparent terminal half-life (t1/2) of 12 hours for a single dose. Ivacaftor is known to interact with drugs that inhibit CYP3A, such as ketoconazole and fluconazole, both antifungal agents, and grapefruit juice, or drugs inducing CYP3A, such as the bactericidal antibiotic rifampin. Ivacaftor has not been tested in pregnant or nursing populations, infants younger than 6 years, or geriatric populations (CF being a disease mostly affecting young adults).

    Ivacaftor has been developed by Vertex Pharmaceuticals (which it is also marketed by), and the Cystic Fibrosis Foundation.

    The product website can be found here, and the full prescribing information, here.

  • Some truly frightening costs of drug development


    Came across a link on Google+ to a post to a Forbes article (via Greg Landrum) and thought I would post a link here. It's a simple economic analysis of the costs of Large Pharma drug discovery. Very simple, money in vs. drugs out. There is however a lot of complexity behind the numbers, for example - quite a few of the drugs will have been licensed in, the transaction costs for these in-licensing events have probably been factored in, but what about all the other burnt capital in the biotech companies that supplied the in-licensed compounds - this will inflate the numbers further. Of course the majority of these costs are incurred on the failed projects, the wrong targets, the wrong compounds, or the wrong trials.

    To put the AstraZeneca number of $11.8 billion per drug in some national context (equivalent to £7.5 billion) - this is almost 17 years of the entire BBRSC budget (£445 million in 2011), or only two drugs from the entire investment portfolio of the mighty assets of the Wellcome Trust (~£14 billion in 2011) - that's right, not two drugs from their annual research budget, but two drugs by shutting down the investment fund and putting it all into drug discovery and development (at Astra Zeneca ROI levels).

    Scary numbers, eh?

    Are public funding agencies up to the task? Do we really know what to do differently?

    There's also a post on the same Forbes article on the In The Pipeline blog.

  • Course: Practical Aspects of Small Molecule Drug Discovery: At the interface of biology, chemistry and pharmacology


    This course aims to give researchers of any discipline a broad introduction to the theoretical, practical and organisational aspects of small molecule drug discovery. Each topic will include a lecture together with discussion sessions or case histories to develop key aspects highlighted in the lectures. In addition there will be practical sessions to illustrate the beginnings of drug discovery programmes, including the production of target product profiles, project plans and milestones, compound progression criteria and scientific strategy. The course is subsidised by the Wellcome Trust and limited bursaries covering up to 50% of the course fee are available (awarded on merit). Course applications and bursary requests must be received by Monday 5 March. Full details are on the website.

    Topics will include:
    • Project management and organisation of multi-disciplinary projects
    • Target discovery and validation
    • Hit discovery options
    • Screening set selection, storage and quality control
    • Screening cascades, assay development and quality control
    • Data mining
    • Principles of compound optimisation and case histories
    • Introduction to pharmacokinetics
    • In silico approaches to drug design
    • Intellectual property strategy
    • Regulatory bodies requirements
    • Data packages required for out licensing and partnering
    • An introduction to preclinical and clinical development