TMEM16A: A new road or a secret gate?


As ion channels go, TMEM16A are busy ones. As one of a number of channels responsible for chloride conduction at the cell surface, their activity has implications for both water movement and transmembrane potential. They are found in the cells of epithelial and smooth muscle tissue throughout the body, and their functional diversity encompasses secretion, cell proliferation, cardiac excitability, smooth muscle contraction and the prevention of polyspermy. With such a broad range of locations and potential functions, it stands to reason that their control mechanism might be complex. Indeed, if you look them up in the ion channel and receptor guide published by the BJP, they are not readily categorised as either ‘ligand-gated’ or ‘voltage-gated’, but languish under the heading ‘other’ alongside several other recent additions to the chloride channel family (ClC, CFTR and volume-regulated channels). Since their molecular identification in 2008, investigation into their gating control has generated a complex and sometimes confused picture involving both ligand and voltage mechanisms. A recent paper by Contreras-Vite and colleagues2 attempts to integrate experimental evidence gained over the last 8 years in the proposal of an updated model of TMEM16A gating.

Factors at play in TMEM16A activation

There are several well-established factors controlling the conduction of chloride ions through TMEM16A channels. Primarily:

  1. TMEM16A is a chloride channel, activated directly by intracellular calcium
  2. Activation by calcium is strongly influenced by membrane potential
  3. Speed of opening/closing is influenced by the concentration and nature of the permeant anion

 

These first two factors are inextricably linked. Under ‘resting’ physiological conditions of intracellular Ca2+ concentration (0.1 uM) and membrane potential (-40 to -60 mV, for example), these channels appear to be closed despite the presence of calcium.  Depolarisations above the chloride equilibrium potential begin to elicit a TMEM16A current, conduction increasing with increasing depolarisation, giving TMEM16A its classic ‘outward-rectifier’ profile. However, when intracellular calcium concentration increases beyond 1 uM, voltage sensitivity appears to be lost, and TMEM16A conduction is seen at negative and positive membrane potentials alike. There is also evidence to suggest that the intracellular side of the channel has the capacity to bind 2 Ca2+ ions. In terms of gating speed, both fast and slow gating kinetics have been seen (whole-cell and patch recordings) depending on the duration of membrane depolarisation. This speed also appears to be influenced by the level of extracellular chloride, with the slow component most markedly affected (slowed further) by increasing extracellular chloride levels from 30 to 140 mM. More permeant anions (SCN, I, NO3) promote/accelerate opening and slow channel closure when applied extracellularly.

So how do you bring these factors together in order to model TMEM16A gating? In the present study2, Contreras-Vite and his colleagues look at their own experimental findings combined with published information, presenting for example the novel observation that in zero intracellular calcium, TMEM16A conduction is still possible, but requires strong depolarisations beyond +100 mV. They also show that reducing extracellular chloride reduces channel open probability, and any ‘fast’ gating kinetics are entirely lost when the channel is maximally activated by high levels of intracellular calcium, and state that intracellular chloride level appears to have no effect on channel activation.

They use these findings to calculate the open-probability of the channel under the influence of these different factors, and define the rate constants governing the transitions between discreet ‘open’ (O) and ‘closed’ (C) states when 0, 1 or 2 Ca2+ ions are bound to the channel in the presence or absence of 1 external Cl ion. By using these to simulate steady-state activation properties and comparing these to their experimentally-derived activation and closure (tail-current) data, they came up with the following 12-state Markov chain model:

sarahq

Essentially, ‘open’ channel states are represented in the right half of the model, ‘closed’ in the left, concentric levels represent calcium binding – from the outer level in which both putative Ca2+ binding sites are occupied, the centre representing the channel with no calcium bound; each state being linked by a rate constants representing parameters listed fully in the paper, most of which are voltage-dependent, some being fast and some being slow (indicated in the diagram key).

Using this model, the authors demonstrate that they can reproduce the activation and deactivation kinetics shown by their experimental data, although they themselves admit that the quality of the fit begins to decrease under extreme levels of intracellular calcium and voltage. They do, however, successfully use it to predict that calcium binding affinity does not change with varying extracellular chloride. They then show experimentally that this does appear to be the case.

The basis of this latest gating model comes from evidence which is only briefly summarised here. There are, of course, other factors which have been proposed to influence TMEM16A channel activity under physiological conditions, such as the binding of calmodulin and inhibition of activation by intracellular protons. Whether this model proves to be correct, time will tell. But in targeting drugs to this channel, knowing how stable and long-lasting some of these conformations may be under various physiological conditions might lead to more efficient, state-dependent drug pharmacology.

Blog written by Sarah Lilley

References:

  1. “Still round the corner there may wait, A new road or a secret gate.” J R R Tolkein
  2. Contreras-Vite JA, Cruz-Rangel S, De Jesús-Pérez JJ, Figueroa IA, Rodríguez-Menchaca AA, Pérez-Cornejo P, Hartzell HC, Arreola J. (2016) Revealing the activation pathway for TMEM16A chloride channels from macroscopic currents and kinetic models. Pflugers Arch. 2016 May 2. [Epub ahead of print]
  3. Cruz Rangel S, De Jesús Pérez JJ, Contreras Vite JA, Pérez Cornejo P, Hartzell H, Arreola J (2015) Gating modes of calcium-activated chloride channels TMEM16A and TMEM16B. JPhysiol 24:5283–98. doi:10.1113/JP271256, PMID: 2672843
  4. Ni YL, Kuan AS, Chen TY (2014) Activation and inhibition of TMEM16A calcium-activated chloride channels. PLoS One 9:e86734. doi:10.1371/journal.pone.0086734, PMID:24489780
  5. Ferrera L, Caputo A, Galietta L. (2010) TMEM16A protein: A new identity for Ca2+-dependent chloride channels. Physiology. 2010, DOI: 10.1152/physiol.00030.2010, PMID: 21186280

Fragment Screen to Market Approval


Here (http://www.fda.gov/NewsEvents/Newsroom/PressAnnouncements/ucm495253.htm) is a landmark announcement from the FDA approving a new drug, Venclexta, for the treatment of patients with chronic lymphocytic leukaemia (CLL). Venclexta (Venetoclax) is a first in class BCL-2 inhibitor, but it is no ordinary small molecule. Not only is it the first example of a small molecule inhibitor of a protein-protein interaction designed from a fragment screen to reach FDA approval, but it also possesses physicochemical properties a long way from classical Lipinski space for an oral drug. This recent article in Nature reviews (http://dx.doi.org/10.1038/nrc.2015.17) provides a timely perspective on translating studies on the mechanisms of cell apoptosis into novel chemotherapeutics, and the challenges facing the drug discovery project team at AbbieV to bring Venetoclax to the market.

Clinical data for ABT-263, an earlier first generation inhibitor, was reported in 2010. Much has been published about the discovery of ABT-263, but it is still worth reflecting on the many achievements of the drug discovery team. With its origins in early fragment based drug discovery, the work stands as an unrivalled example of the power of fragment screening.

darren1

The molecule was assembled from linking together two small fragments in proximal ligand binding sites that were identified from a pioneering 15N HSQC NMR fragment screen of a 10,000 fragment library. The hits had weak affinity that could not be measured by biochemical assays, so the team pioneered the use of NMR to develop structure activity relationships for fragment optimisation. The work culminated in the discovery of ABT-737 and then finally after further optimisation, ABT-263. It is fascinating to see the guidelines for discovering orally bioavailable drug candidates to be so completely disregarded; a Mw of 974, a Log P of <<5, three basic centres, an aniline, two sulfonyl groups including an acyl sulphonamide and a phenyl thiol.  The acidity of the acyl sulphonamide should further impede permeability, though this may be tempered by the existence of a zwitterionic species formed from the morpholine and piperazine groups. Surely a compound with this profile would struggle to penetrate the lipid membranes of cells, let alone permeate the GI tract and survive oxidative metabolism in the liver! Surprisingly the compound has potent cellular activity, albeit several fold lower than the activity measured in the biochemical assay. But not only that, the compound achieved a successful clinical outcome in phase I human trials in respect to compound exposure and clinical efficacy.

Unfortunately, not everything went the teams way. Dose limiting toxicity of Navitoclax (ABT-236) prevented escalation to levels of exposure required for maximal efficacy. The compound is unselective against BCL-XL, another member of the BCL family highly expressed in platelets and crucial for their survival. Preclinical studies highlighted the potential of thrombocytopenia caused by BAX and BAK mediated platelet cell death that was confirmed in clinical studies, with the MTD limited to substantially below the predicted efficacious dose. After 25 years of research the team had to go back to the drawing board and design a selective BCL-2 inhibitor over BCL-XL.

This would seem a daunting task but for a fascinating observation in the X-ray crystal structure of a close analogue of ABT-263. The work published in this nature paper (http://www.nature.com/nm/journal/v19/n2/full/nm.3048.html) shows the X -ray crystal structure of an analogue of ABT-263 bound to BCL-2 with an intercalating tryptophan (shown in purple) from a neighboring BCL-2 molecule undergoing a p-p stacking interaction with the aryl sulfonamide, while at the same time hydrogen bonding to an aspartic acid residue. Essential to the observation was that the aspartic acid was one of thedarren few residues that differed between BCL-2 and BCL-XL, with the latter having a glutamic acid. The strategy was to attach the indole to the scaffold in such a position as to mimic the intercalating tryptophan on the X-ray crystal structure with the hope of achieving selectivity. Incredibly this was achieved with an azaindole linked via an ether to the central benzamide ring to give ABT-199 that was 1000 fold selective for BCL-2 over BCL-XL in a TR-FRET completion binding assay, albeit reducing to 65 fold in a cellular assay.

ABT-199 was granted break through therapy designation in 2015. In fact the compound was so efficacious in the phase I clinical trial that apoptotic cell death of cancer cells lead to tumour lysis syndrome in some patients, so the dose escalation schedule had to be adjusted to slow the onset of the drug.

The FDA approval brings to the market a first in class medicine to CLL patients that directly targets the apoptotic programme. Of the many achievement of this programme, it is the bravery of the medicinal chemists to push against all the boundaries, guidelines and rules in drug design and yet still reach market approval that gets my admiration. If anything, it clearly emphasises that there are no rules in the design of new drugs, just guidelines.

Blog writted by Darren Le Grand

 

The remyelination dogma


The myelin sheath is a major component of the white matter of the vertebrate brain and spinal cord.  It serves as an electrical insulator along nerve axons that accelerates conduction and enables higher brain function [1].  This specialised lipid-rich structure maintains axonal integrity by providing metabolic and trophic support, whilst allowing for efficient nerve conduction by minimising energy consumption [1].  However, characteristic to a number of CNS disease states is the process of demyelination [2].  For example, in Multiple Sclerosis (MS), where white and grey matter brain lesions occur throughout the brain and spinal cord, there is defective saltatory signal conduction and axonal damage, which then manifests itself in clinical symptoms such as motor weakness [3].  Interestingly though, in the adult CNS a quiescent pool of precursor cells exists which can differentiate into new oligodendrocytes capable of replacing lost myelin sheath [4].  In fact remyelination is a natural repair mechanism believed to protect against progressive axonal damage in MS.  Therefore, the focus of current therapeutic research has recently shifted from preventative to reparative in respect to existing white matter lesions.

The beneficial effects of remyelination are functional recovery via the restoration of both axonal conduction and trophic axonal support [5], and the additional neuroprotective properties of reducing the cell’s energy consumption.  This is done via recruitment of resident precursor cells to generate new oligodendrocytes [6].  However, the extent of this regeneration is limited. Although in vivo models to study MS show efficient and extensive remyelination, myelin sheaths generated in the adult brain of MS patients are generally thinner with shorter internodes. In MS, the process of remyelination is insufficient in about 80% of lesions and fails to counteract the accumulation of permanent axonal damage [7].  Successful remyelination may require the existence of oligodendrocytes, but initially needs the necessary factors that allow for the sufficient migration and differentiation of these precursor cells [8].  It is these factors that are thought to limit its success in the MS brain, although the underlying cellular and molecular mechanisms remain poorly understood.

But even so, do therapies focusing on enhancing this remyelination process inevitably incur neuroprotection?  One example which suggests they may not be so intimately related is the drug Fingolimod, approved by the FDA in 2010 to treat relapsing-remitting MS (RRMS).  Although this drug has been shown to reduce brain atrophy in RRMS patients [9], The Lancet this year reported that the INFORMS study, which used this drug in primary-progressive MS (PPMS) patients, failed to show any improvement in the neurodegenerative process [10].  So, why are we failing to find treatment for PPMS?  Is remyelination really the answer?  There is evidence from animal studies which shows that remyelination and neuroprotection may actually occur independently of each other.  After completion of remyelination the mice showed initial recovery of locomotor performance; however 6 months post completion, performance then began to decline compared to age-matched controls [11].  These studies highlighted that axonal damage continues long after remyelination, and can still accumulate over time to result in functional impairment.  Remyelination alone cannot compensate for the stress that demyelination has on a neuronal cell, and therefore neuroprotective strategies that do not rely solely on restoration of myelin must be explored.

Translating both remyelinating and neuroprotective strategies from bench to bedside, however, relies on appropriate in vitro and in vivo experimental settings for the development of new drug targets.  Focusing on remyelination in MS, the most commonly used animal models are toxin models, whereby a focal injection or systemic administration of a toxin, for example lysolecithin or cuprizone respectively, induces demyelination and successive remyelination [12].  A benefit of these models is that they exhibit endogenous remyelination with a predictable spatial and temporal distribution.  However, because remyelination is certain in these models, they are unsuitable for accessing the ability of a pharmaceutical compound to induce remyelination and can only be used to study the acceleration of it.  Additionally, the lesions in these models do not develop much, if any, autoimmune reaction, and inflammation is one reason thought to be behind the failure of remyelination in the MS brain.  This may be one reason behind some of the discrepancies that are seen between lab and clinic.  Having said that, remyelination in both the lysolecithin and cuprizone model is hampered in aged animals the chronic EAE model exhibits limited remyelination and a substantial input from the immune system [12].  These paradigms may provide a way of better studying the induction of remyelination in a compromised environment.

In conclusion, two factors must be addressed for research in this are to proceed: firstly the experimental setting most appropriate to study drug targets for remyelination; and secondly, the simultaneous neuroprotective strategies that should be employed to prevent the accumulation of irreversible grey matter damage.

Blog written by Victoria Miller

 

Bibliography

  1. Morrison.B, “Oligodendroglia: metabloic supporters of axonsTrends in Cell Biology, vol. 23, pp. 644-651, 2013.
  2. Bercury.K, “Dynamics and mechanisms of CNS myelinationDevelopmental cell, vol. 32, pp. 447-458, 2015.
  3. Chang.A, “Cortical remyelination: a new target for repair therapies in multiple sclerosisAnnual of Neurology, vol. 346, pp. 165-173, 2012.
  4. R. F.-C. C. Franklin, “Remyelination in the CNS: from biology to therapy,” Nature Reviews: Neuroscience, vol. 9, pp. 839-855, 2008.
  5. Honmou.O, “Restoration of normal conduction properties in demeylinated spinal cord axons in the adult rat by transplantation of exogenous Schwann cellsJounral of Neuroscience, vol. 16, no. 10, pp. 3199-3208, 1996.
  6. ElWaly.B, “Oligodrendogenesis in the normal and pathological central nervous systemFrontiers Neuroscience, vol. 8, p. 145, 2014.
  7. Frischer.J, “Clinical and pathological insights into the dynamic nature of the white matter multiple sclerosis plaqueAnnual of Neurology, vol. 78, pp. 710-721, 2015.
  8. Kuhlmann.T, “Differentiation block of oligodendrogial progenitor cells as a cause for remyelination failur in chronic multiple sclerosisBrain, vol. 131, pp. 1749-1758, 2008.
  9. Ingwersen.J, “Fingolimod in multiple sclerosis: mechanisms of action and clinical efficacyClinical Immunology, vol. 142, pp. 15-24, 2012.
  10. Lublin.F, “Oral Fingolimod verus placebo in primary progressive multiple sclerosis: results of INFORMS, a large phase III, randomised, double-blind, placebo-controlled trialLancet, 27 January 2016.
  11. Manrique-Hoyos.N, “Late motor decline after accomplished remyelination: impact for progressive multiple sclerosisAnnual of Neurology, vol. 19, pp. 227-244, 2012
  12. Blakemore.W, “Remyelination in experimental models of toxin-induced demyelinationCurrent Topics in Microbiological Immunology, vol. 318, pp. 193-212, 2008.

Smuggling drugs into the brain: old and new tricks


AM1

Figure 1. Proposed mechanisms of transport across the blood-brain barrier

Every medicinal chemist involved in neuroscience drug discovery has experienced the joys and pains of the blood brain barrier (BBB), classically defined as the system of tight junctions between the epithelial cells of the brain capillaries that strictly regiment the access of molecules into the CNS.

As medicinal chemists, we usually picture the BBB as a more impenetrable version of other biological interfaces and consequently we design our CNS-penetrant molecules applying more rigid physicochemical filters. Additionally, we use in vitro brain permeability models that tend to focus only on passive diffusion and efflux.

In reality big and polar molecules, antibodies and viruses have the ability of crossing or eluding the BBB using a number of ‘side entrances’.

In the last 30 years the understanding of the BBB mechanisms has increasingly gained clarity and accordingly many new opportunities for drug delivery into the brain have been tested. These new opportunities usually exploit existing mechanisms utilised by endogenous molecules that need to gain access to the brain (e.g. nutrients, aminoacids, regulatory blood proteins) or tricks invented by pathogens. Old and new ways of crossing the BBB have been recently reviewed by William A. Bank in the April issue of Nature Reviews Drug Discovery (doi:10.1038/nrd.2015.21).

Some of the most interesting and overlooked pathways include:

Access via influx (blood-to-brain) transporters – this is an old strategy for drug delivery (e.g. L-dopa, gabapentin which use transporters for neutral aminoacids). More recently this mechanism has been considered for selective delivery to targeted areas of the brain.

‘Trojan Horse strategies  –  where a therapeutic agent (cargo) is conjugated to a ligand (Trojan Horse) of a particular influx transporter expressed on the luminal membrane (blood-side). The complex in usually routed on the abluminal membrane (brain-side) by transcytosis.

Absorptive transcytosis – another vesicle-based pathway often used by penetrating peptides and antibodies fragments.

Extracellular pathways or functional leaks – these are anatomically defined areas of the brain that are deficient in blood brain barrier and as such allow controlled access to small amount of serum proteins including albumin and immunoglobulins. It has been suggested that antibodies – with low volume of distribution and high circulating half-life – can enter the CNS using this way.

Many small molecules and biologics that exploit these or similar tricks are being validated in the clinic.

Nevertheless, these mechanisms are quite difficult to predict and permeability models available to medicinal chemists for rational design are unfortunately still very rudimental…

 

Figure 1 adapted from: Smuggling Drugs into the Brain: An Overview of Ligands Targeting Transcytosis for Drug Delivery across the Blood–Brain Barrier; Julia V. Georgieva et al. Pharmaceutics 2014, 6, 557-583; doi:10.3390/pharmaceutics6040557

 

Blog written by Alessandro Mazzacani

Autistic Spectrum Disorder – Nature or Nurture? Aware or beware?


Since April was ‘Autism awareness month’ internationally, this blog is a little different, aiming to raise awareness of autism and how adults with autism and its associated disorders might differ from the neurotypical.

In March 2014, the US government released figures estimating the prevalence of autism as being 1 in 68 boys and 1 in 189 girls (thus creating a ratio of male:female prevalence of almost 3:1)1. This means that in most communities and workplaces, there will be at least one member who has been diagnosed as being ‘on the spectrum’, due to the expression of a ‘complex behavioural phenotype’, which now includes atypical disorders such as Asperger’s Syndrome or High Functioning Autism (those with an IQ higher than 80 and with good verbal skills).

The Nature-nurture debate

It is now commonly accepted that autistic traits run in families. It has even been argued that such traits are cumulative, resulting in children that are more autistic than their parents1. Recent studies have centred on mutations contained within nonsense DNA, that is to say, DNA which does not code for protein-coding genes, per se, but rather molecular modulators of gene expression. Such modulators include ‘enhancers’, of which more than 100 are now known to be present more in the brain than other tissues of the body, resulting in a significant influence over brain development in utero. Traditional gene studies, which focussed upon protein-coding genes, would actually miss more than 95 % of the human genome, therefore it’s of little wonder that our understanding of developmental pathways in neurological disorders lags behind that of more physically symptomatic diseases such as heart disease, or cancer. This is partly due to the phenomenon of ‘environmental fixation’, whereby families (particularly mothers) were blamed for their child’s autistic traits, to the extent of being branded ‘refrigerator mothers’, alluding to the alleged coldness with which they raised their children2. Furthermore, Harlow (1972) described behaviours in his rhesus monkeys, deprived of maternal contact, that were concordant with those of the autistic children carefully described by Kanner3, perpetuating the theory that families were to blame for the atypical behaviour of their child.  Thus, the pendulum of scientific opinion has swung between the two extremes of ‘nature’ versus ‘nurture’. Current models propose that multiple genetic, epigenetic and environmental factors may contribute to the etiology of autism, with the last decade of research revealing a significant genetic heterogeneity4. In summary, no two individuals diagnosed with ASD or Asperger Syndrome are the same!

The vast majority of studies into autism focus on children, as do the strategies designed to enable those diagnosed on the spectrum to cope with ‘day-to-day life’. However, children become adults, raising the challenge of both adaptation to an environment designed for neurotypical adults and also diagnosis for those adults who form the ‘lost generation’, people who were previously excluded from a diagnosis of classic autism either through ‘camouflage strategies’ (particularly prevalent in girls who are more likely to copy peers and thus appear ‘neurotypical’ to the untrained eye) or adaptation strategies, whereby an individual copies the actions of a neurotypical colleague, learning social rules as one might study a recipe, or protocol. A school friend of mine was such a case. She wore the same clothes as her best friend, did the same hobbies and was academically outstanding. Yet she failed to progress in her chosen career and was diagnosed with Asperger’s Syndrome aged 41. Her career choice of course was influenced by that of her peers, rather than her strengths.

So are HFAs and Aspies always doomed to failure in the workplace? Much is made of the drawbacks of HFA/Asperger’s Syndrome – appearing dissociated or uninterested, difficulties with social interaction, inappropriate conversation and lack of eye contact leading to perceptions of not telling the truth or being disinterested in a particular task or employment role to mention but a few – but shouldn’t we focus more on what autism has to offer?

For example, they may have the ability to focus intensely and for long periods on a difficult problem. There is often an enhanced learning ability, although this often is not applied to subjects they are uninterested in – and therefore it may be necessary to play to the strengths of employees or students, rather than attempting to counter-act weaknesses. HFAs and Aspies often present no problems in a supportive, well-resourced educational institution and often do well academically if they can be stimulated by good teachers. People with HFA and Asperger’s often have intense and deep knowledge of an obscure or difficult subject and a passion for pursuing it in an organized and scholarly manner. This makes them more likely to excel in ‘niche’ topics, particularly neglected areas of research. They are usually intelligent, gifted, honest, hard workers when interested in a task and excellent problem solvers. People with high-functioning autism are thought to become excellent scientists and engineers or enter other professions where painstaking, methodical analysis is required.

So should we beware of Autism? Or accept what it has to offer? Besides, what exactly is normal?

Blog written by Diane Lee, who has recently moved to the School of Veterinary Medicine at the Universityof Surrey.

1 Sylvie Goldman, MD, Albert Einstein College of Medicine, Opinion: Sex, Gender and the Diagnosis of Autism – A Biosocial View of the Male Preponderance (p.1-2) http://www.sciencedirect.com/science/article/pii/S1750946713000317

2Judith Miles: Autism spectrum disorders—A genetics review; Genetics in Medicine (2011) 13, 278–294; doi:10.1097/GIM.0b013e3181ff67ba

3Kanner L. (1949). Problems of nosology and psychodynamics of early infantile autism. Am. J. Orthopsychiatry 19, 416–426

4Geschwind D. H. (2008). Autism: many genes, common pathways? Cell 135, 391–39510.1016/j.cell.2008.10.016

The rise of reaction diversity …. or not


A recent article from Scientists from Novartis and NextMove Software gives a very interesting overview of the reactions described in US patents over the last 40 years. The authors analysed over 200,000 US patents since 1976 and extracted over 1 million unique reactions. The data was analysed breaking down each patent into a larger number of reaction types, reaction yields, product properties over time, etc.

Similarly as in one of our previous blogs, this short summary is far from an exhaustive review of the article which is rich in data that should excite any organic chemists but an invitation to look more deeply in what medicinal chemists have been making these last 40 years.

The largest set of reactions extracted from the dataset is made of ‘heteroatom alkylations and arylations and acylation’, representing 27.8% of the classified reactions over 40 years, followed by ‘acylations and related processes’ (21.3% of the data) (Figure 1).MPX1

Figure 1

Looking more deeply into the data for the larger set of alkylations and arylations, some reactions such as the Williamson ether synthesis and chloro N-alkylations that were very popular in the mid 70s and 80s have fallen out of favour over the years. Similarly, as much of medicinal chemistry revolves around amide bond formation, the popular Schotten-Baumann acylation of the 70s and 80s has now been largely superseded by the advent of modern activated coupling reagents, now representing just over 50% of all acylation reactions (Figure 2).

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Figure 2

The publication also covers the evolution of deprotections as a main class of reactions and how, since the mid 90s, the commercialisation of (Boc)2O has led to N-Boc as the nitrogen protecting group of choice. This reaction trend increase goes hand in hand with the sharp growth of amide bond formation depicted in Figure 2.

The analysis would not be correct if it did not capture the rise of the C-C bond formation and the ever increasing evolution toward a flatter molecular landscape. This class of reaction is very interesting as the sharp growth of C-C bond formation since the early 90s (Figure 1) is directly linked to the advent of transition metal catalysis and in particular to the Suzuki cross coupling reactions (Figure 3). Almost all non-Suzuki reaction type for the formation of C-C bonds since the 2000s have decreased in popularity, presumably linked to the increase in commercially available and stable boronic acids and extensive research efforts to improve on the Suzuki reliability and high yields.

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Figure 3

Other trends are reviewed in the article, including a heatmap of the evolution of oxidations over time. The analysis clearly shows a move toward environmentally friendly oxidative reagents from the early 2000s, replacing the classic and highly toxic chromium-based Jones and Collins oxidations.

The authors have also analysed the yields of each reaction over time from the patent set. Overall, there is a clear decline in the median yield of all the reactions analysed. The authors associated this reduction of yields with the increasing popularity of flash purification and HPLC purification and library/array production to feed the ever increasing miniaturisation of screening techniques.

Finally, the authors also looked at the trend in the properties of novel compounds reported in US patents over the last 40 years (Figure 4). cLogP has climbed steadily over the last 40 years, peaking around 2005, whilst molecular weight has also been increasing and started to level off around 2010 at around 410 – 420 Da. Another clear trend of molecular properties of novel compounds over the last 40 years is the significant drop in rotatable bond count since the mid 90s, which is likely to be associated with the rise of the mighty Suzuki cross coupling reactions.

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Figure 4. Evolution of physicochemical properties over time

The article reflects that although the modern medicinal chemist has a wide range of chemical reactions available to use in the design novel drugs, it seems that with the advent of modern acylation coupling reagents and palladium catalysed cross coupling, the modern medicinal chemist may be limiting himself to a very narrow range of reactions. The trend does not suggest this will change any time soon.

Blog written by Michael Paradowski