Will PTP1B be a new therapeutic option for T2DM and Obesity?


Insulin and Lectin are two hormones which play crucial roles in energy storage and peripheral energy uptake. Resistance to these hormones is a hallmark for both Type 2 Diabetes Mellitus (T2DM) and obesity1. Nearly 220 million people are living with diabetes and WHO projected the death due to diabetes would double between 2005 and 20302. The global epidemic nature of T2DM and obesity demand the need for new therapeutic approaches. PTP1B stands out in the PTP family as a negative regulator of insulin signal transduction pathway through its ability to dephosphorylate and inactivate the insulin receptor3. PTP1B also negatively regulates the leptin signalling pathway by dephosphorylating JAK2 (a phosphorylated tyrosine kinase) in the hypothalamus. Leptin is a key hormone directly associated with obesity that regulates food intake and energy expenditure4,11.

sri-1

Fig.1: PTP1B dephosphorylates the insulin receptor during its biosynthesis in the endoplasmic reticulum (ER)4

Natural products like prenylated xanthones, flavonoids, bromophenols, phenolic acids, cumarins, terpenes, steroids were isolated and tested to have potent PTP1B inhibition of 1.6-30.0 µmol/L5. These natural products have opened the gate to many small molecule inhibitors for PTP1B. However, carboxylates and phosphonates with nanomolar inhibition have failed to progress to the clinic due to poor membrane penetration6.

Many studies have postulated that existing anti-diabetic drugs belonging to the thiazolidinediones (TZDs) family, commonly known as glitazones (rosiglitazone7, pioglitazones etc.), could inhibit PTP1B8. Early competitive PTP1B inhibitors based on Vanadium compounds (vanadates and pentavanadates) have significant therapeutic values in human but they are not specific8,11. Series of benzofurans, benzothiophenes and phosphonates have been synthesised and patented as potential PTP1B inhibitors6,8. Unfortunately, none of them has made Phase II clinical trials9. Ertiprotafab from Wyeth, the first PTP1B inhibitor, was halted in Phase II due to data inconsistencies10.

Selectivity6,11 and bioavailability12 are the main challenges in developing potent PTP inhibitors. The PTP1B catalytic site shares structural motifs of other enzymes of PTP family and is highly charged. Consequently, highly charged inhibitors with very strong PTP1B inhibition lack biovailability11. Achieving selectivity against TC-PTP13 is the most challenging task for medicinal chemists. Many clinical trials, patent applications and drugs validation experiments proves that PTP1B has emerged as a novel target for the management, treatment of T2DM. However, the journey in the search for selective PTP1B inhibitors has been facing many pitfalls.

Interestingly, current phase II trial on Trodusquemine14 and PTP1B antisense oligonucleotides (IONIS-GCGRRX) by Ionis pharmaceuticals15 could be an alternate therapeutic option for T2DM and obesity.  At least one of the clinical candidates in Phase II studies will receive green signal from FDA in few years’ time

Blog by Srinivasan Natarajan

References

  1. D.Popov, Biochemical and Biophysical Research Communications, 2011, 410, 377-381

www.sciencedirect.com/science/journal/0006291X/410/3

  1. WHO diabetes fact sheet available from

http://www.who.int/mediacentre/factsheets/fs312/en/

  1. S.Koren and I.G Fantus., Best Practice & research Clinical Endocrinology & Metabolism, 2007, 21(4), 621-640

https://www.ncbi.nlm.nih.gov/pubmed/18054739

  1. J.Montalibet and B.P.Kennedy., Drug Discovery Today: Therapeutic Stragies, 2005, 2, 129-135.

www.sciencedirect.com/science/article/pii/S1740677305000069

  1. C.S JIANG, L.LIANG and Y GUO, Acta Pharmacologica Sinica (2012) 33: 1217–1245

https://www.ncbi.nlm.nih.gov/pubmed/22941286

  1. H.Cho Vitamins and Harmones, V 91, chapter 17, 2013, Elsevier Inc.,

https://www.ncbi.nlm.nih.gov/pubmed/23374726

  1. The antidiabetic drug rosiglitazone was withdrawn from European market since 2010 due to the increased risk of heart attack

https://en.wikipedia.org/wiki/Rosiglitazone

  1. Review by A.K Tamarkar and A.K. Rai, Expert Opin. Ther. Patents, 2014, 24(10), 1-15.

https://www.ncbi.nlm.nih.gov/pubmed/25120222

  1. Review by M.L.Tremblay et al., Crit.Rev.Biochem.Mol.Biol., 2013, 48(5), 430-445

https://www.ncbi.nlm.nih.gov/pubmed/23879520

  1. DV. Erbe et al. Molecular Pharmacology, 67(1), 69-77.

http://molpharm.aspetjournals.org/content/67/1/69

  1. S.Koren, I.G. Fantus, Best Practice & Research Clinical Endocrinology & Metabolism, 214, 621-640.

http://www.sciencedirect.com/science/article/pii/S1521690X07000814

Tonks N.K et al., Nature Chemical Biology, 2014, 10, 558-568

http://www.nature.com/nchembio/journal/v10/n7/abs/nchembio.1528.html

  1. H.Oh et al., Molecules, 2015, 20, 11173-11183

www.mdpi.com/1420-3049/20/6/11173/pdf

  1. T.Tcell PTP (TC-PTP) which linked to the development of several inflammatory disorder including type 1diabetes, Crohn disease and rheumatoid arthritis (J.Am.Chem.Soc.,2009, 131(36), 13072-79)

http://pubs.acs.org/doi/pdf/10.1021/ja903733z

  1. K.A. Lantz et al. Obesity, 2010, 18(8), 1516-1523.

https://www.ncbi.nlm.nih.gov/pubmed/20075852

  1. Phase II for IONIS-GCGRRX completed in January 2017. See the company website http://www.ionispharma.com/pipeline/

also see https://www.ncbi.nlm.nih.gov/pubmed/25197025  for anti -sense oligos for PTP1B

 

 

 

 

Making ‘Marvelous Medicines’ at the Brighton Science Festival


As part of the Brighton science festival the Sussex Drug Discovery Centre (SDDC) has participated for the last two years by doing an activity at the bright sparks event. The bright sparks weekend is aimed at 7-14 year olds and is the festival’s flagship event where there are over 50 stalls, stands and shows across the two days.

The SDDC activity aimed to do a journey though drug discovery called Making Marvelous Medicines. We did this by creating 4 stations of activity lasting 50 minutes. The 4 stations included: What are proteins, Designing Drugs, Synthetic Chemistry and Testing Drugs.

What Are Proteins ?

This station aimed to introduce the concept of proteins, by explaining their role as tiny machines doing millions of jobs that allow us to function healthily.james-1

To illustrate the “power of proteins” the enzyme catalase was used in liver to degrade hydrogen peroxide in our bubbly volcano experiment. An animated video of the motor protein kinesin was also used, and the use of ATP as protein food to give them energy was also introduced.

 

Designing Drugs

Now we introduced a ATP “eating” protein from tuberculosis, using molymods the children built molecules to fit into the ATP binding pocket of this protein. We then introduced a human ATP binding protein and tested the selectivity of the molecule.

Synthetic Chemistry

Participants were introduced to the concept of a chemical reaction using baking as an analogy: different reagents (“ingredients”) can be combined in order to make new chemical products e.g. a new medicine. The young people carried out their own reaction to make their “drug”  – we used the popular “golden rain” precipitation reaction between potassium iodide and lead nitrate https://www.youtube.com/watch?v=zJkv0HiqApo.

Gasps of awe and wonder came from the young scientists (and the adults with them) when two seemingly colorless solutions formed a bright yellow solid when mixed together.  The student demonstrators also recrystallized the products the children had formed in order to explain the importance of purifying medicines that are made in a lab.

  Testing Drugs

In the final stall, we aimed to simulate a biochemical assay to test our drugs effectiveness. This assay tuned blue for negative and pink for positive. The actual reagents used for this were Phenolphthalein and Thymolphthalein.

james-6

Feedback from parents and children was really positive and the audience grasped the key concepts. Parents were often just as interested as the children. At the end some children left comments on the white board.

james-7

Blog written by James Noble [PhD Student]

 

 

 

 

 

Synthesise a CNS drug that can cross the blood brain barrier?


Central nervous system (CNS) drugs include analgesics, sedatives, and anticonvulsants, with drugs being used to treat the effects of a wide variety of medical conditions such as Alzheimer’s disease, Parkinson’s disease, and depression. More than 1 billion people globally suffer from a CNS disease, with one in five Americans taking at least one psychiatric drug. In the US and Europe combined, the overall cost of the economic burden of CNS diseases is estimated to be more than $2 trillion, with that figure expecting to triple by 2030 (1). Whilst most pharmaceutical companies are patient centric, these figures are financially appealing. However, development of therapies for CNS diseases has lagged behind that for other therapeutic areas. CNS drugs can take more than 20 months longer to develop than other drugs, with attrition rates greater than 50%. These failures can be attributed to a number of reasons such as inadequate dosage to hit the therapeutic target, high placebo effect, high patient dropout rate, inaccuracies of preclinical disease models, and incomplete understanding of brain disease mechanisms. (1)

One of the challenges of working on a CNS drug discovery project is for the drug to traverse the blood-brain barrier (BBB). The BBB protects the brain from most pathogens, sheltering it from the systemic circulation. It also prevents most large molecule neurotherapeutics and more than 98% of all small molecule drugs reaching the brain from the bloodstream, the tight junctions of the endothelial cells lining brain capillaries restricting paracellular movement of substances across the BBB. The BBB serves roles other than that of blocking circulating substances from entering the CNS. It also facilitates and regulates the entry of many substances that are critical to CNS function and secretes substances into the blood and CNS. These extra-barrier functions allow the BBB to influence the homeostatic, nutritive, and immune environments of the CNS and to regulate the exchange of informational molecules between the CNS and blood. (3)

High attrition rates of preclinical and clinical drug candidates led Wager et al (4) to design a tool based on key physicochemical properties (clogP, clogD, molecular weight, topological polar surface area, hydrogen bond donors, and pKa) that would enable multiparameter optimisation (MPO) of druglike properties to accelerate the identification of drug candidates with optimal pharmacokinetic and safety profiles. After nearly 8 years of using this tool at Pfizer, Wager et al have reported a reduction in the number of compounds submitted to exploratory toxicity studies and an increase in the survival of the CNS MPO candidates through regulatory toxicology into first in human studies. (5) The tool has also been used outside of Pfizer to reduce attrition and improve compound quality in the design phase.

An understanding of the barrier and extra-barrier aspects of BBB physiology is also critical to developing drugs that can access the CNS. A recent CNS paper by Patel et al (6) discusses several key approaches for brain targeting including physiological transport mechanisms such as adsorptive-mediated transcytosis, inhibition of active efflux pumps, receptor-mediated transport, cell-mediated endocytosis, and the use of peptide vectors. Drug-delivery approaches comprise delivery from microspheres, biodegradable wafers, and colloidal drug-carrier systems (e.g., liposomes, nanoparticles, nanogels, dendrimers, micelles, nanoemulsions, polymersomes, exosomes, and quantum dots). These alternative approaches look promising.

The Canadian company Angiochem is using a physiological approach to gain entry across the BBB. They have engineered ANG1005, an Angiopep-2 paclitaxel conjugate to gain entry into the brain by targeting lipoprotein receptor-related protein (LRP-1), which is one of the most highly-expressed receptors on the surface of the BBB.  Once inside the brain, ANG1005 enters tumour cells using the same receptor-mediated pathway through LRP-1, which is upregulated in various cancer cells including malignant glioma and metastatic cancers in the brain. (7) Phase II data presented in October 2016 shows ANG1005 has demonstrated clinical benefit, both intracranially and extracranially in pre-treated breast cancer patients with recurrent brain metastases. (8)

Blog written by Kamlesh Bala

References

(1)www.parexel.com/files/4314/4113/4032/Venturing_Into_a_New_Era_of_CNS_Drug_Development_to_Improve_Success.pdf

(2) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC539316/

(3) https://bmcneurol.biomedcentral.com/articles/10.1186/1471-2377-9-S1-S3

(4) ACS Chem Neurosci. 2010 Jun 16;1(6):435-49

(5) ACS Chem. Neurosci. 2016, 7, 767−775

(6) Patel, M.M. & Patel, B.M. CNS Drugs (2017).

(7) http://angiochem.com

(8) http://angiochem.com/angiochems-ang1005-shows-clinical-benefits-and-prolonged-survival-breast-cancer-patients-brain

 

A powerful small molecule; believing in GABA


rosemary-1

GABA (γ-aminobutyrate) is the major inhibitory neurotransmitter in the mammalian brain. It contributes to the all-important excitatory-inhibitory balance of neuronal communication. Dysfunction of the GABAergic system is implicated in disease, such as epilepsy, insomnia, schizophrenia and anxiety disorders. The history of GABA, from when it was first discovered to when its power as an inhibitory neurotransmitter was accepted, is an interesting one. It is wrapped up in personal accounts of the scientists involved, and looking back at the winding path of acceptance is fascinating.[1],[2],[3]

The story starts with the discovery of a ninhydrin-reactive material in mouse brain tumours by Eugene Roberts and Sam Frankel in 1949.[4] GABA had been known since 1910, of course, and had been found in bacteria and fungi and potatoes.[5] Once the structure of this ninhydrin-reactive material was confirmed to be GABA by Sidney Udenfriend, Roberts scribbles “the brain is like a potato!” in his notebook, and sets about proving its biological significance. [6],[7]

Roberts and Frankel’s work was published in 1950 for a conference at which Jorge Awapara also reported the presence of an “unidentified amino acid” found only in the brain.[8] By the time of the conference Awapara had also recognised it was GABA. At the conference a room-shortage led these two into close proximity, and Awapara and Roberts apparently agreed that Roberts would continue working on metabolism of GABA, and Awapara would continue working on the metabolism of taurine.7b

Six years pass, and scientists were still questioning whether the presence of GABA in the brain meant it had a role in signal conductance.[9] It should be noted that the debate over whether synaptic transmission was electrical or chemical had only just reached its chemical conclusion.[10] Ernst Florey had found Factor I, a chemical of unknown composition, extracted from mammalian brain and which inhibited the crayfish muscle system amongst others.[11] With help from Merck scientist Alva Bazemore, they purified over 45 kg of cow brain, and, using over 450 L of acetone they managed to yield crystalline Factor I. It was GABA, obviously.[12] There were still things to clear up, however, as some of their earlier work on the spinal cord of cats was initially unrepeatable by David Curtis, a fact now anecdotally put down to the allosteric modulation by the barbiturates also used in the experiments, or contamination of glycine in Florey’s earlier samples.11, [13]

Evidence against GABA being a neurotransmitter was accruing. The fact that GABA was so widespread in the brain was a worry for many in the field. “It’s just a metabolic wastebasket” remarked one great neurochemist.7b Strychnine was known to inhibit transmission in the spinal cord, and yet did not compete with GABA, which was another point of confusion at the time. With hindsight we know it was the as-yet-undiscovered glycine receptors in the spine causing havoc here.

Some scientists remained convinced there was more to the story, and Eugene Roberts was one of them. “Stop bringing your GABA solutions to our labs,” pleaded biologists, daily. “They take up room, and we’re not going to test them.”

In 1959 a notable conference was convened to hear the latest research and clear up the confusion. This proceeding (the 1st Interdisciplinary Conference on GABA) at a nearby pub (City of Hope Research Institute) was attended by many of the leading people in the field. Excitement was in the air as scientists from Australia, Canada, England, France, Hungary, Japan, the United States and the former Soviet Union bustled together, spilling pints and talking Neuroanatomy. Most researchers had a top night, and left feeling like they had made life-long friends and collaborations from all over the world.

GABA itself, however, fared badly. It was not going to join the echelons of the neurotransmitters quite yet. Alongside everything else it was seen not to have a rapid, enzymatic degradation pathway, unlike the newly-discovered acetylcholine neurotransmitter. This was thought to preclude it from involvement in rapid on-off communication. GABA was a metabolite with some generalised depressant nature, but that was all.[14]

It was not until nearly ten years later that unequivocal proof was published by Krešimir Krnjević and Susan Schwartz in 1967 that GABA was shown to be the major inhibitory neurotransmitter.[15] Intracellular recordings, as well as pharmacological tests revealing selective block by picrotoxin and bicuculline, clearly demonstrated GABAergic transmission.[16] After this proof, there was an exponential growth in GABA research. Writing in 1974, Eugene Roberts says ‘In the 25 years since the discovery of GABA … the status of the compound has passed from that of a biochemical curiosity and physiological enigma to that of a major inhibitory transmitter.’[17] At fifty years GABA receptors are shown to have decisive roles in many diseases, and they become big targets in drug discovery, including big-hitting benzodiazepines and general anaesthetics.[18] At 67 years, there are a huge 74,000 references containing ‘gamma-aminobutyric acid’ on Scifinder Scholar.[19]

The mixture of personal and peer-reviewed literature accounts of how GABA came to be accepted is what makes it fascinating. It is useless to deny that the direction of any scientific progress is open to contemporary influences and personal preferences. Perhaps it just reminds us that, as Carl Sagan writes: “Nature is always more subtle, more intricate, more elegant than what we are able to imagine.” And that means the path to understanding this transmitter will never stop winding.

Blog written by Rosemary Huckvale

POST SCRIPTS

  1. Dr Eugene (Gene) Roberts died last year on 8th November 2016 at the age of 96. His obituaries can be found here.
  2. This blog hopes to relate only a small portion of the history surrounding the establishment of GABA as a major inhibitory transmitter. There will have been other important contributions not mentioned here.

REFERENCES

[1] Johnston, G.A.R, GABA Australis, some reflections on the history of GABA receptor research in Australia, Pharmacological Research, article in press, 2016.

[2] Avoli, M., Krnjević, K., The Long and Winding Road to Gamma-amino-butyric acid as neurotransmitter The Canadian Journal of Neurological Science, 43:219-226, 2016.

[3] Krnjević, K. How does a little acronym become a big transmitter? Biochemical Pharmacology, 68:1549-1555, 2004.

[4] a) Roberts, E. and Frankel, S. γ-aminobutyric acid in brain. Federation Proceedings 9:219, 1950. b) Roberts, E. and Frankel, S. γ-aminobutyric acid in brain: its formation from glutamic acid. Journal of Biological Chemistry 187:55-63, 1950.

[5] Steward FC, Thompson JF, Dent CE. γ-Aminobutyric acid. A constituent of the potato tuber? Science 110:439-440, 1949.

[6] Udenfriend, S. Identification of gamma-aminobutyric acid in brain by the isotope derivative method. Journal of Biological Chemistry 187:65-9, 1950.

[7] Roberts, E.. Gamma-aminobutyric acid, Scholarpedia, 2(10):3356, 2007. B) Roberts, E., The History of Neuroscience in Autobiography Volume 2, Edited by Squire, L.R, Academic Press, 350-395, 1999.

[8] a) Awapara, J. Detection and identification of metabolites in tissues by means of paper chromatography. Federation Procedings, 9:148, 1950. b) Awapara, J., Landua, A.J., Fuerst, R., and Seale, B. Free gamma-aminobutyric acid in brain. Journal of Biological Chemistry 187:35-9, 1950.

[9] Roberts E. Formation and utilization of γ-aminobutyric acid in brain. Edited by Korey S.R., and Nurnberger J.I., Progress in neurobiology. 1. Neurochemistry. New York: Hoeber-Harper, 1956;11-25.

[10] Eccles, J.C., The Synapse: From electrical to Chemical transmission, Annual Review of Neuroscience, 5:325-39, 1982.

[11] For overview see Florey, E., GABA: history and perspectives, Canadian Journal of Physiology and Pharamcology, 69(7):1049-56, 1991.

[12] Bazemore, A.W., Elliott, K.A.C., Florey, E., Isolation of Factor I, Journal of Neurochemistry, 1:334-9, 1957.

[13] Johnston, G.A.R, GABA Australis, some reflections on the history of GABA receptor research in Australia, Pharmacological Research, article in press, 2016.

[14] Bowery, N.G, Smart, T.G, GABA and glycine as neurotransmitters: a brief history. British Journal of Pharmacology, 147:109-119, 2006. And references therein.

[15] a) Krnjević, K. & Schwartz, S. Is γ-aminobutyric acid an inhibitory transmitter? Nature, 211:1372, 1966. b) Krnjević, K. & Schwartz, S. The action of γ-aminobutyric acid on cortical neurones. Experimental Brain Research, 3, 320–326, 1967.

[16] Curtis, D.R., Duggan, A.W., Felix, D., Johnston, G.A.R., GABA, Bicuculline and central inhibition., Nature, 226:1222-1225, 1970.

[17] Roberts, E., γ-aminobutyric acid and nervous system function – a perspective, Biochemical Pharmacology, 23:2637-2649, 1974.

[18] GABA in the Nervous System: The view at Fifty Years, Edited by Martin, D.L and Olsen, R.W., Lippincott Williams & Wilkins, 2000.

[19] Accessed Jan 2017.


A brief introduction to enzyme inhibitors -Nonspecific, Irreversible and reversible (competitive, uncompetitive and non-competitive) inhibitors


Enzyme inhibitors are molecules that bind to the enzyme and reduce the catalytic activity of enzymes. There are many types of inhibitors, including nonspecific, irreversible or reversible (competitive, uncompetitive and non-competitive inhibitors).

Non-specific inhibitors can inhibit multiple enzyme targets by forming the aggregate. One mechanism for this nonspecific interaction is the formation of colloidal aggregates by self-association of low molecular weight compounds in aqueous solutions. These aggregates tend to sequester protein, presumably by partially unfolding it and thus inhibiting its function.[1]

Irreversible inhibitors usually react with the enzyme by forming covalent bonds; thus dissociating very slowly from its target enzyme.[2, 3] There are some important drugs act as irreversible inhibitors to the enzyme. One example is penicillin, as a first discovered antibiotic, can covalently bind to the enzyme transpeptidase by mimic the normal substrate the D-Ala-D-Ala peptide. It is therefore preventing the synthesis of bacterial cell walls and killing the bacteria.[2] (Fig.1-2) It is very useful to identify if inhibitors are irreversible or not. One method is through dilution, namely measuring the recovery of enzymatic activity after a rapid and large dilution of the enzyme-inhibitor complex. [3, 4] (Fig.3)

tina-1

Figure 1. Transpeptidation Reaction. An acyl-enzyme intermediate is formed in the transpeptidation reaction leading to cross-link formation. Figure is from the following published study: Reference 2.[2]

tina-2

Figure 2. Conformations of Penicillin and a Normal Substrate. The conformation of penicillin in the vicinity of its reactive peptide bond (A) resembles the postulated conformation of the transition state of R-d-Ala-d-Ala (B) in the transpeptidation reaction. Figure is from the following published study: Reference 2.[2]

tina-3

Figure 3. Hypothetical time-courses for activity recovery after rapid dilution of enzyme-bound inhibitor into a solution containing saturating substrate concentration. C, Control sample having no inhibitor present; R, Reversible inhibitor bound as E$I complex at zero-time; SR, Slowly-reversible inhibitor bound as E$In complex at zero-time, but must isomerize through one or more intermediate states to form E$I complex, which then releases inhibitor; I, Irreversible inhibitor bound as E–I complex at zero-time. The actual time-scale for inhibitor release will depend to the transit time for isomerization of enzyme-inhibitor complexes to that enzyme species from which inhibitor is released. Figure is from the following published study: Reference 3.[3]

In contrast with irreversible inhibitors, reversible inhibitors have a rapid dissociation to the enzyme and bind non-covalently. [2, 3] Reversible inhibitors contain three types of inhibitors, competitive, uncompetitive and non-competitive, depend on whether the inhibitors compete with substrate binding to the enzyme or binding the enzyme-substrate complex.[3] (Fig.4) Competitive inhibitors can compete with substrate to bind the active site of the enzyme and this binding state can be relieved by increasing the substrate concentration. On the contrary, noncompetitive inhibitors can bind to the enzyme simultaneously with the substrate and this inhibition cannot be overcome by increasing the substrate concentration. Uncompetitive inhibitors can only bind to the enzyme-substrate complex, in which a binding site is formed.

tina-4

Figure 4. Three types of reversible inhibitors: A. competitive; B. noncompetitive; C. uncompetitive inhibitors. Figure is from the following published study: Reference 3.[3]

These three types of inhibitions can be determined by Michaelis-Menten kinetics. Since the competitive inhibition can be overcome by a sufficiently high concentration of substrate, Vmax can be maintained in the same value and Km value (Km = [S] at Vmax/2) is increased in the presence of a competitive inhibitor. Noncompetitive inhibitors inactive the enzyme, lower the concentration of functional enzyme, so Vmax is declined and Km is unchanged. Uncompetitive inhibitors work best when substrate concentration is high, both Vmax and Km values are therefore decreased.[2, 5](Fig.5)

tina-5

Figure 5. A. Competitive inhibition is characterized by an increase in Km for the substrate and no change of Vmax. B. Non-competitive inhibition is characterized by no change in the Km value and a decrease in Vmax. C. Uncompetitive inhibition is characterized by a decrease in the apparent Km value and a decreased Vmax. Figure is from the following published study: Reference 5.[5]

Among three types of reversible inhibitors, uncompetitive inhibitors are rare, but some potent drugs have been regarded as uncompetitive inhibitors to the enzyme.(Table.1) Many enzyme-substrate complexes are extremely short-lived in the enzyme-catalyzed reactions, so uncompetitive inhibitors have much less opportunities to bind the target than other two types of reversible inhibitors. [3] One example is about the first uncompetitive inhibitor-blebbistatin of myosin, binding at a site other than the nucleotide- or actin filament-binding sites, which opens and closes during the contractile cycle. Blebbistatin can stabilize the metastable or ‘transition’ state of myosin, representing a long-live complex of myosin with ADP and inorganic phosphate. [3, 6]

tina-6

Table 1. Several clinically useful uncompetitive inhibitors. Table is from the following published study: Reference

Blog by Tina(Xiangrong) CHEN


References

  1. Habig, M., et al., Efficient elimination of nonstoichiometric enzyme inhibitors from HTS hit lists. Journal of biomolecular screening, 2009. 14(6): p. 679-689.
  2. Berg, J.M., J.L. Tymoczko, and L. Stryer, Biochemistry New York. NY: WH Freeman, 2002.
  3. Purich, D.L., Enzyme kinetics: catalysis and control: a reference of theory and best-practice methods. 2010: Elsevier.
  4. Copeland, R.A., Evaluation of enzyme inhibitors in drug discovery: a guide for medicinal chemists and pharmacologists. 2013: John Wiley & Sons.
  5. Kenakin, T.P., Chapter 6 – Enzymes as Drug Targets, in Pharmacology in Drug Discovery. 2012, Academic Press: Boston. p. 105-124.
  6. Allingham, J.S., R. Smith, and I. Rayment, The structural basis of blebbistatin inhibition and specificity for myosin II. Nature structural & molecular biology, 2005. 12(4): p. 378-379.

 

 

Understanding Tuberculosis and the challenges ahead


Recently, I had the opportunity to meet one of my colleagues from Sussex University whose area of expertise and research is based in tuberculosis (TB), Dr. S. Wadell. This heightened my curiosity on the disease and I wanted to know more.

Thus I have chosen the paper in Expert Opinion on Drug Discovery by Anuradha, Kumar et al. [1].

TB is caused by the bacteria Mycobacterium tuberculosis in humans and Mycobacterium bovis in cattle and badgers, where it still an area of ardent discussion and where there is still lot of work to do [2]

TB is highly likely to spread in areas of poor sanitation, poor access to drugs and where patients have to be confined; it is treated with cocktails of up-to-4 antibiotic drugs over periods of time greater than 6 months.

Far from being an under-controlled disease as I initially thought, TB bacteria still possess a threat to humans due to:

  1. The nature of bacteria: stick-shaped cell with a highly lipophilic-rich cell membrane, slow growing and highly infectious organism which has to be dealt in a controlled environment.
  2. Its physiology: present in an active/ latent form, existing in multiple physiological states (explaining the length and combination of antibacterial drugs required for an effective treatment)
  3. The lack of animal models due to the difficulty to replicate the disease as it occurs in humans.
  4. Location: the bacteria can be found intracellular (eg. Macrophages) or extracellular in granulomas; or cavities, individually or as aggregates. Adding a second cell membrane to be crossed and making drug delivery and distribution a challenge.
  5. Drug-resistance as it has followed in other bactericidal-type diseases. Sometimes appears associated to HIV infection.
  6. Difficulty to identify the biological environment, small target space and mechanism of action
  7. Traditional approaches targeting biochemical assays have failed due to screening libraries of compounds based in Lipinski’s rule of 5 with a low number of compounds meeting the clogP > 5 requirement is matched [3].

In contrast, the whole-cell screening, although more successful, has highlighted promiscuous targets like MmpL3 and QcrB alerting that the development of new drugs will have to answer the need to have  multiple-target active compounds.

The use of TB infected macrophages has been used as valid source of new inhibitors, either from synthetic origin as well as based in natural products [4] – open the door to chemicals no covered in commercial screening libraries. This approach has later derived in obtaining semi-synthetically analogues from Rifamycin, where the common structure (inside the blue box) is kept and highlighted are the modifications in Fig 1.

jose

   Fig 1 Current therapeutic drugs derived from Rifamycin family discovered in the 1950s and its semi-synthetic analogues.

The synthesis of active analogues from natural products can be challenging but it has recently highlighted some potential leads to be further investigated [5]. Therefore, new active compounds could follow from the isolation of active substances based in their physiochemical properties (eg. high lipophilicity) from sub-fractions of natural product mixtures [6].

The authors emphasise that current techniques using metabolomics and genomics could be valuable tools in the design and understanding the synthesis of new active compounds. The use of Diversity-orientated synthesis (DOS) is pointed as a way to generate and explore the untargeted chemical space [7].

Clear progress and innovation from new emerging techniques have led to a better understanding in fighting the disease. The lack of compounds with specific physicochemical properties as well as suitable animal models, how to penetrate the TB lipophilic cell membrane, shorter and more efficient patient treatments and which targets to focus on are going to be the areas where it is anticipated more researching resources will be deployed.

Blog written by Jose Gascon

References:

[1] Anuradha Kumar, Somsundaram Chettiar & Tanya Parish, Expert Opinion in Drug Discovery, 2017, Vol

12, 1, 1-4

[2] https://www.theguardian.com/science/2012/nov/11/alice-roberts-bovine-tb-badgers ;

http://www.tbfreeengland.co.uk/faqs/

[3] Koul, A et al  The challenge of new drug discovery for tuberculosis Nature, 2011, Jan 27:469

(7331):483-490. DOI:10.1038/nature09657

[4] Cragg, GM et al  Natural products: a continuing source of novel drug leads. Biochim Biophys Acta,

2013, 1830, 6, 3670-3695.  DOI:10.1016/j.bbagen.2013.02.008

[5] Mdluli, K et al   Tuberculosis drug discovery and emerging targets. Ann N Y Acad Sci, 2014, Sep;1323:

56-75. DOI:10.1111/nyas.12459

[6] Wagenaar, MM et al  Pre-fractioned microbial samples-the second generation natural products library

at Wyeth Molecules, 2008; 13, 6, 1406-1426 ;  Camp, D. et al  Drug-like properties: guiding principles

for the design of natural product libraries J. Nat. Prod, 2012, 75, 1,72-81

[7] Galloway, WR et al  Diversity-orientated synthesis as a tool for the discovery of novel biological active

small molecules. Nat Commun. 2010, 2, 1, 80

 

 

 

 

2,3-Substituted Indole synthesis by Regioselective Electrophilic Trapping


The selective synthesis of indoles is an important area of organic chemistry, largely due to their prevalence in countless natural products, medicines, materials etc. Numerous methods have been described for the synthesis of substituted indoles, with many requiring the pre-instillation of functional groups by incorporating them within the initial starting material. Late stage functionalisation is also possible, but in order for this to be achieved additional steps are often required, with some involving harsh conditions or the use of expensive transition metal catalysts. With this in mind, the report described by Eiichi Nakamura from the University of Tokyo could be of interest to people wishing to make a small library of substituted indoles from one common building block.1

mark-1

Scheme 1

Within this communication, Nakamura describes the synthesis of indoles via dimetalated intermediates – although the synthesis via 2,3-dimetalloindoles has previously been reported, the selective introduction of electrophiles has, to the best of my knowledge, not previously been achieved. The problem of obtaining such selectively is shown in Scheme 2 – the dimetalated intermediates A and B react without selectivity, and so a mixture of isomers are obtained. In comparison to other dimetalated indoles,2 the Authors show that dizincioindoles are stable and relatively easily formed, suggesting a dimeric structure (shown in Figure 1) to rationalise this stability.

mark-2

Scheme 2

 

mark-3

Figure 1

The Authors show that when using of ZnCl2, electrophiles can be introduced at C-3 when simple electrophiles are used, but this can be switched C-2 when transition metals are introduced. When ZnPhBr is used, reactivity is generally more selective for C-3, unless a stannane is used, with differing reactivity probably due to a change in mechanism from simple nucleophilic reactions to that occurring through charge transfer (please see reference 1 for detailed substrate scope).

Although the above chemistry is not completely selective, it is certainly a good starting point for further investigation, as the selective synthesis of indoles remains and important task within many disciplines. I suppose the next question is – what other heterocyclic systems can this chemistry be applied to next?

Blog by Mark Honey

All Schemes and Figures were taken from J. Am. Chem. Soc. 2017, 139, 23-26

References

  1. J. Am. Chem. Soc. 2017, 139, 23-26
  2. Organometallics, 1998, 17, 2906

 

“Post-antibiotic era”


In 2013, the Centers for Disease Control and Prevention (CDC) published a report on the burden and threats of antibiotic-resistant germs (CDC, 2013a). Bacteria resistant to different classes of antibiotics rapidly emerge worldwide and endanger the efficacy of antimicrobial. This resistance crisis can mostly be attributed to the overuse and misuse of antibiotics, but also to the lack of innovation and new drug development. Antibiotic research is not any longer attractive to the pharmaceutical industry, higher profits are made with new anti-cancer therapies and with other chronic conditions such as diabetes. “If we’re not careful, we will soon be in a post antibiotic era” (CDC, 2013b). What are the reasons for the decline in this field of research and are there any advancements in antibiotic drug research and development?

The era of antibiotics started in 1928 with the discovery of penicillin by Sir Alexander Fleming (Fleming, 1929). They should revolutionize modern medicine and increase general life expectancy. However, shortly after the introduction of penicillin, penicillin resistance in bacteria emerged and should become a substantial clinical problem. Discovery of new beta-lactam antibiotics such as methicillin in the 1960s only temporarily restored confidence, as antibiotic related resistance developed shortly after; the first case of methicillin-resistant Staphylococcus aureus (MRSA) in 1962 in the UK. This mêlée of antibiotic introduction and antibiotic resistance should go on for decades to come and still is happening at present day.

Causes of antibiotic resistance are diverse. Mostly, they are a result of overuse and misuse. Often, wrong antibiotics are prescribed and duration of antibiotic therapy is faulty. Overuse of antibiotics in agriculture to promote growth of farm animals and to prevent infectious diseases additionally contributes to increased resistance. Unfortunately, we are standing against this resistance with only few new antibiotics. The development of new antibiotics by pharmaceutical companies and academia slowed over the past decade due to funding cuts and due to being considered unprofitable. While 19 new antibiotics were approved in between 1980 and 1984, only 6 were approved by the Food and Drug Administration (FDA) since 2010. Many big pharma companies pulled out of research and the companies left didn’t do much progress. Thus, a combination of poor prospect and profit, as well as difficulties in getting regulatory approval slowed down the field.

Nevertheless, there has been a recent revive in antibiotic R&D and several antibiotics are in the pipeline for clinical trials. These include a variety of classes of antibiotics such as aminoglycosides, tetracyclines and beta-lactamase inhibitors. But also new approaches are being investigated (e.g. inhibiting endotoxin production by germs), as well as new sources of natural antibiotics. Teixobactin for instance was isolated from Eleftheria terrae and represents a new class of antibiotic that inhibits cell wall synthesis (Ling et al., 2015).

References, recommended articles in bold

Blog written by Lucas Kraft Continue reading

Screening the DEC (DNA-encoded chemistry)


A 2016 paper by workers at GSK, published in J. Med. Chem., really grabbed my attention. GSK appear to have achieved the difficult feat of discovering a molecule that exhibits monokinase selectivity!  Intriguingly, the initial hit was discovered not through screening the GSK kinase inhibitor set, nor through the HTS screening of the GSK compound collection (~2 million compounds).  The novel benzoxazepinone series was actually found by screening GSK’s DNA-encoded library.[1]

In its simplest form a DNA-encoded library is constructed with chemical building blocks that are individually ‘tagged’ with DNA fragments.  The DNA serves as an amplifiable genetic barcode.  Millions (or billions) of compounds can be produced in weeks using ‘routine’ combichem approaches (Fig 1).  The resulting libraries can be screened in a single test tube against the target.  Hits are read/identified by PCR amplification of DNA barcodes – Fantastic!  A smart and efficient way of getting around the arduous deconvolution involved with combinatorial libraries.[2]

 scott-1

Figure 1 taken from a fantastic review of GSK’s contribution to the field of DNA-encoded libraries (Med. Chem. Commun., 2016 016, 7, 1898–1909)

An advantage of screening DNA-encoded libraries is that they enable a more thorough exploration of chemical space (4 – 5 orders of magnitude more!) than is achievable by traditional HTS methods.[3]  To give you an idea of the space explored, just one of the many DNA-encoded libraries that GSK screened to find the benzoxazepinone hit had a ‘total warhead diversity of approx. 7.7 billion’.[1] 

scott-2

Figure 2 taken from paper (J. Med. Chem. 2016, 59, 2163−2178)

 The benzoxazepinone series was selected for further investigation because it appeared to be far removed from what is perceived as the ‘same old’ kinase motif.  Fortunately for the team on the project, this line of enquiry furnished a novel chemotype with tractable SAR.  The initial hit matter was progressed to a lead that had desirable properties for a kinase inhibitor (i.e. excellent potency, exquisite kinase specificity, oral bioavailability etc. etc.) and also appears to be competitive with ATP whilst making no interactions with the hinge of the kinase at all! (a.k.a. Type III kinase inhibitor).  The atypical binding mode of the inhibitor was elucidated using a raft of techniques including photoaffinity labeling, hydrogen-deuterium exchange analysis and co-crystallography.[1]

DNA-encoded libraries are an accessible screening platform to both academic groups (whilst undertaking my Master’s project I saw the creation of (very similar) PNA-encoded libraries) and industry. The reason for an academic group to screen via this method is obvious – the combinatorial platform enables them to amass vast compound libraries that would have taken a substantial cash injection and multiple (hu)man hours to produce.  For industry, the DNA-encoded libraries represent another screening platform to churn out novel hit matter, casting the net deep into chemical space.

The construction and screening of DNA-encoded libraries is a relatively young field (~ 10 years). Reports of high-affinity hits for biological targets are becoming more common.[3] Ultimately the quality of the library and its output will depend on the diversity/novelty of each building block and the diversity of reactions employed in its construction.  For sure DNA-encoded libraries (and other encoded libraries) represent a step forward from the usual solid-phase mix and split OBOC libraries of the past.  Improvements in methodology (encoding and selection methods), library construction (arrays of 3D- and diverse building blocks, reaction diversity etc.), library curation and data analysis are all possible growth areas in the future.

GSK’s paper also serves as a useful reminder that choosing an unusual starting point – especially in the Kinase field where many privileged kinase motifs exist in the public domain – may guide you into hitherto unexplored chemical space.  The benefits of a proprietary starting point are obvious – the DNA-encoded library screening platform employed in this paper was critical to the discovery of novel, selective and potent hit matter.[1]

For recent reviews read [2], [3] and [4].

 Blog written by Scott Henry Henderson

References

[1] Harris et al., J. Med. Chem. 2016, 59, 2163

[2] Zimmermann and Neri., Drug Discovery Today. 2016, 21, 11, 1828

[3] Goodnow, Dumelin and Keefe., Nature Reviews Drug Discovery (2016) [doi:10.1038/nrd.2016.213]

[4] Arico-Muendel., Med. Chem. Commun., 2016 016, 7, 1898–1909

5 key points of a new drug for anxiety


In my previous blog on anxiety, I discussed how the treatments available for anxiety disorders have modest efficacy or severe side-effects. Furthermore many patients do not respond to first line pharmacological treatments (principally antidepressants). Psychological approaches (such as cognitive-behavioural therapy) are often limited in availability. As a result of this, benzodiazepines are frequently used for short-term management of anxiety symptoms. It can be argued that benzodiazepines are probably the most effective and well tolerated medications for anxiety; nevertheless, their long-term use is not recommended due to the unfavourable risk profile.

At the Sussex Drug Discovery Centre with the support of the Medical Research Council (MRC) we are currently studying a new generation of anxiolytic drugs.

These drugs, similarly to benzodiazepines, act as positive modulators of GABAA receptors, the main inhibitory mechanism in the mammalian brain, but are selective for the ‘anxiolytic’ subpopulation of the receptor. This approach may result in a drug with significantly less liabilities and ultimately improved risk-benefit profile.

I will focus on 5 key characteristics that a new ideal anxiolytic drug should possess to be superior to existing first-line treatments and benzodiazepines.

  1. Be active on all anxiety disorders and over the range of severity.The most common anxiety disorders are generalised anxiety disorder, social anxiety disorder, panic disorder, obsessive-compulsive disorder and post-traumatic stress disorder1. They all share common psychological and physical symptoms but differ in having characteristic features. The ideal drug should be active on all diseases and be effective in reducing both psychological and physical symptoms including the acute presentation of symptoms, which are common in all anxiety disorders.
  2. Have a rapid onset of action. Antidepressants, currently the first line treatment for anxiety, typically need 2 to 4 weeks to show benefits and this has obvious repercussions on the management of acute symptoms. On this point, the ideal anxiolytic drug should be similar to fast acting benzodiazepines which are effective in less than half an hour.
  3. Do not interfere with daily life. Antidepressants are associated with a number of physical side-effects: abdominal pain, weight gain, loss of libido, headache and nausea. Interestingly, anxiety is also included in the list of potential side-effects for antidepressants, in particular in the first weeks of treatment.                           Benzodiazepines at anxiolytic doses may induce sedation, dizziness and memory impairment. We believe that our approach which targets the anxiolytic subpopulation of GABAA receptors will result in a drug with a clean anxiolytic profile devoid of sedation side-effects2.
  4. Not be associated with the development of physical dependence or tolerance.  Problems upon discontinuation of treatment after long-term use are common to antidepressant and benzodiazepines. Up to a third of people who stop SSRIs and SNRIs have withdrawal symptoms which can last between 2 weeks and 2 months. These include a number of physical symptoms and additionally the possibility of developing rebound anxiety. Benzodiazepine long-term use has been associated with both physical dependence and tolerance (the need to increase the dose to obtain similar therapeutic effect). Sudden discontinuation from benzodiazepine treatment is even more problematic with a withdrawal syndrome that again includes rebound anxiety as a common symptom. The mechanism underpinning benzodiazepine dependence and tolerance is still a matter of discussion but there is general consensus that it probably involves some sort of neuroadaptation of the GABAergic synapses which constitute one-third of the synapses of the whole human brain. It has been argued that selective GABAA modulators may be superior in avoiding these neuroadaptation processes3, but in reality more studies are necessary to characterise selective modulators in models of dependence and tolerance.
  5. Not have a potential for addiction and abuse. It has been estimated that approximately 0.1–0.2% of the adult population abuse or are dependent upon benzodiazepines. Individuals with potential for abuse tend to cluster into two categories: alcohol or drugs-dependent outpatients and people suffering from anxiety disorders. Many studies – including drug self-administration models in several species and studies with human connoisseurs ‘familiar’ with recreational drugs – have indicated that selective GABAA modulators targeting only the anxiolytic subtype may again be superior in avoiding addiction and abuse4. Interestingly, studies on the neural bases of the addictive properties of benzodiazepines seems to confirm the results in animal models5.

 

 

Blog written by Alessandro Mazzacani

References

  1. Anxiety disorders, post-traumatic stress disorder, and obsessive–compulsive disorder, D. S. Baldwin et al., Medicine, 2016, 44 (11), pages 664–671.
  2. TPA023 [7-(1,1-Dimethylethyl)-6-(2-ethyl-2H-1,2,4-triazol-3-ylmethoxy)-3-(2-fluorophenyl)-1,2,4-triazolo[4,3-b]pyridazine], an Agonist Selective for α2- and α3-Containing GABAA Receptors, Is a Nonsedating Anxiolytic in Rodents and Primates, J. Atack et al., The Journal of Pharmacology and Experimental Therapeutics, 2006, 316(1), pages 410-422
  3. Mechanisms Underlying Tolerance after Long-Term Benzodiazepine Use: A Future for Subtype-Selective GABAA Receptor Modulators?, C. H. Vinkers and B. Oliver, Advances in Pharmacological Sciences, 2012, doi:10.1155/2012/416864
  4. Beyond classical benzodiazepines: novel therapeutic potential of GABAA receptor subtypes, Uwe Rudolph and Frédéric Knoflach, NATURE REVIEWS DRUG DISCOVERY, 2011, 10, pages 685-697
  5. Neural bases for addictive properties of benzodiazepines, M. Brown et al., NATURE, 2010, 463, pages 769-775