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Cambridge MedChem Consulting

ChemBridge Macrocycle Library

Macrocycles offer a unique opportunity to address some of the more challenging drug targets and I've highlighted this on a couple of pages on the Drug Discovery Resources, here and here.

Macrocycles lie outside the usual "drug space" delineated by the Rule-of-5 and macrocycles can adopt different conformation in various media, hiding polar atoms or forming intramolecular hydrogen bonds, thus retaining good cell permeability and ADME properties

bRo5macrocycles

I recently got an email from ChemBridge highlighting a new 11,000 member Macrocyclic Library for screening. The general characteristics of compounds in the ChemBridge Macrocycle Library include:

  • Molecular weight range up to 800
  • Primary ring size ranging from 11 to 27 atoms
  • Heterocyclic primary rings
  • Scaffolds with and without peptidic backbone elements as part of the macrocyclic ring
  • Scaffolds with and without fused rings as part of the primary macrocyclic ring

Developing an assay for high-throughput screening

SULSA’s Assay Development Fund is actively recruiting innovative molecular targets for which there is a strong rationale for therapeutic potential.

Development of a high-throughput assay provide access to the various drug discovery initiatives that are available to the academic community, i.e. MRC DPFS, Bayer G4Targets, Wellcome Trust translational fund, the European Lead Factory, AZ innovation portal etc.

How many compounds do you select from virtual screening?

Whilst high-throughput screening (HTS) has been the starting point for many successful drug discovery programs the cost of screening, the accessibility of a large diverse sample collection, or throughput of the primary assay may preclude HTS as a starting point and identification of a smaller selection of compounds with a higher probability of being a hit may be desired. Directed or Virtual screening is a computational technique used in drug discovery research designed to identify potential hits for evaluation in primary assays. It involves the rapid in silico assessment of large libraries of chemical structures in order to identify those structures that most likely to be active against a drug target. The key question is then how many molecules do you select from your virtual screen?

Whilst virtual screening is certainly less expensive than high-throughput screening it is not free, even an in house academic cluster has an overhead (probably equating to > $10,000 per virtual screen). So with that investment how much would you invest in actual compounds?





Trust but verify

There is an article in Nature describing a collection of problems that have arisen from incorrect chemical structures in biological screens DOI. I'm slightly surprised that this is regarded as newsworthy, but I guess it serves as a timely reminder.

The data from screening campaigns invariably contains errors

  • It is often a single point assay
  • Quality and diversity of Sample Collection is variable
  • Compounds may interfere with the detection system
  • False positives due to aggregation
  • High density plates can result in cross contamination, edge effects

There is a very simple mantra you should adopt when analysing screening data "Trust but verify".

  • Check compounds that were found active against the selected target are re-tested using the same assay conditions used during the HTS.
  • Does a resynthesised (not repurchased) show the same activity
  • Dose response curve generation: an IC50 or EC50 value is then generated, does it have a reasonable slope? Uneffected by incubation time.
  • Are related analogues available, check for genuine Structure-Activity Relationships

elf

There is a strategy for the analysis of HTS data in the Drug Discovery Resources.

Virtual Screening Pages Updated

I've updated the pages describing virtual screening, in particular the docking section.

dockedligand

Heart on a chip

Cardiotoxicity is a major hurdle for all drug discovery programs and so I'm always interested in ways that any potential liabilities can be flagged without the need to go into whole animals. A recent publication highlights progress in developing a novel model system.

Human induced pluripotent stem cell-derived cardiomyocytes were cultured as a model system, and used to validate the platform with an excitation–contraction decoupling chemical. Preliminary data using the platform to investigate the effect of the drug norepinephrine are combined with computational efforts. This platform provides a quantitative and predictive assay system that can potentially be used for comprehensive assessment of cardiac toxicity earlier in the drug discovery process. DOI.

The European Lead Factory Works!

The European Lead Factory (ELF) is a collaborative public-private partnership aiming to deliver novel lead molecules for drug discovery programs. When the consortium was formed around 5 years ago there was a lot of scepticism about whether a group of 30 partners rating from large Pharma companies to small academic groups could ever agree on a legal framework that would allow the ELF to function. In a addition, in an industry where confidentiality was critical to maintaining intellectual property the idea that a group of large Pharma companies would share their sample collections often regarded as the "Crown Jewels" seemed impossible. However I was at the European Lead factory Stakeholder Meeting (24-25 April 2017) and it is clear that is has been a success.

Read More…

European Lead factory Newsletter

The latest issue of the European Lead Factory Newsletter has just been published.

Highlights include the European Lead Factory recently reached the milestone of having received over 1,000 chemical library proposals for consideration. To date, 143,529 novel compounds, out of the 200,000 prospected compounds for the Public Compound Collection, have been synthesized, which means that the ELF compound collection grows daily by approximately 250 novel compounds to eventually constitute the 500,000 Joint European Compound Library (JECL).

Parkinson’s UK and the University of Sheffield have launched a joint venture biotech company, Keapstone Therapeutics. Parkinson’s UK has allocated 1 million GBP over the next sixteen months to further develop compounds that boost the internal cellular defence mechanisms against oxidative stress. These compounds were discovered by European Lead Factory.

The Ecstasy and Agony of Assay Interference Compounds

There is an editorial in ACS Central Science DOI that I would encourage everyone involved in hit identification to read.

A couple of quotes will give you an idea of the content

Alarmingly, up to 80–100% of initial hits from screening can be artefacts if appropriate control experiments are not employed.

it is important to realize that no PAINS-containing drug has ever been developed starting from a protein-reactive PAINS target-based screening hit

They also emphasise the critical need for experimental validation for any screening hit.

Such validation experiments include classic dose response curves, lack of incubation effects, imperviousness to mild reductants, and specificity versus counter-screening targets. If a molecule is flagged as a potential PAINS or aggregator using published patterns but is well-behaved by these criteria, it may be a true, well-behaved ligand. Ultimately, genuine SAR combined with careful mechanistic study provides the most convincing evidence for a specific interaction. Covalent and spectroscopic interference molecules act via specific physical mechanisms, for which controls are known. Colloidal aggregation, fortunately, is readily identified by rapid mechanistic tests and by counter-screening.

In addition you need to consider compound identify and purity, reproducing the activity with an authentic sample is essential.

Whilst time-consuming this validation work will save a fortune in the future.

Peptidyl-Prolyl cis-trans Isomerase (PPIase) assays

Having worked wit Selcia on a number of projects I always keep an eye out for news on their work on Peptidyl-Prolyl cis-trans Isomerases (PPIase). These are very interesting class of enzymes whose principal function is to catalyse the cis-trans isomerisation of the X-Pro peptide bonds in polypeptide chains (where X is any amino acid). This transformation is thought to be a mechanism to modulate protein function.

PPIase

PPIase enzyme targets are of increasing interest in drug discovery due to the extensive potential of small molecule inhibitors in a range of therapeutic areas, including infection, inflammation, cancer and neuroprotection.

Selcia have now expanded the range of Peptidyl-Prolyl cis-trans Isomerase (PPIase) assays they can offer.

The SULSA Assay Development Fund:

I've worked with a couple of academic groups who have a very interesting target but no small molecule leads. Whilst there are several places offering high-throughput screening the stumbling block is often development of a robust screening assay running in a high density format. Most academic groups have little experience in developing such an assay and to be honest will need to do so very infrequently.

The SULSA Assay Development Fund: accelerating translation of new biology from academia to pharma DOI describes efforts to support the development of such assays, work carried out in collaboration with the European Lead Factory in Newhouse.

However, many scientifically interesting, novel molecular targets lack associated high-quality, robust assays suitable for hit finding and development. To bridge this gap, the Scottish Universities Life Sciences Alliance (SULSA) established a fund to develop assays to meet quality criteria such as those of the European Lead Factory. A diverse project portfolio was quickly assembled, and a review of the learnings and successful outcomes showed this fund as a new highly cost-effective model for leveraging significant follow-on resources, training early-career scientists and establishing a culture of translational drug discovery in the academic community.

European Lead Factory technical acceptance criteria

  • Minimally 384 wells (max 30 μl)
  • Homogenous assay (no washing steps)
  • Defined endpoint
  • Z-prime >0.6
  • Readout stability >1 h
  • S/B signal >3
  • Incubation times <4 h
  • DMSO tolerance: minimum 0.5%
  • All reagents minimally 8 h stable
  • Recombinant proteins(s) >80% pure

Perhaps this quote sums things up very nicely.

‘We only got so far in optimising our assay because in my opinion we do not have either the equipment or the personnel with the skill set required to do this efficiently. So being able to come and work at Newhouse where you are then surrounded by people who can identify quickly where assay improvements should be made and then pass on the knowledge of how to set about applying these changes (as well as gaining experience with various pieces of equipment) was invaluable.’

More details are available here http://www.sulsa.ac.uk/sites/sbsweb2.bio.ed.ac.uk.sulsa/files/downloads/SULSAassaydevelopmentfundguidancenotes4.pdf

The Wellcome Trust also provides Seed/Pathfinder awards that could cover similar projects.

Another European Lead Factory success

We are now starting to see some of the results of the screening of academic projects at the European Lead factory that was initiated in 2013.

Dr Mahlapuu’s group, based at the University of Gothenburg, first identified a new target which could be used to reverse metabolic complications in type 2 diabetes. With the help of the European Lead Factory experts, she then screened the Joint European Compound Library of the then 320,000 industry compounds and identified a set of selective and potent small molecules which interfere with this target.

They have now formed a spinout company to develop these leads. ScandiCure has received 1 MSEK from the 2016 SWElife program to continue the development of first-in-class anti-diabetic drug based on small molecule antagonists of a novel key mediator - serine/threonine protein kinase 25 (STK25).

ELF and antibiotic resistance programme

The latest news report from the European Lead Factory highlights work targeting antimicrobial resistance in collaboration with Professor Chris Schofield (University of Oxford). The high throughput screen of >300,000 compounds and initial triaging provided 50 qualified hits.

Multiple series of compounds were validated through resynthesis, biochemical and biophysical profiling at the European Screening Centre site in Newhouse, complemented with ligand–protein crystallography and antimicrobial evaluation at University of Oxford

Great to see projects like this move forward, demonstrates how important the ELF is in providing hits for academic groups/small companies.

European Lead Factory Update

The latest newsletter from the European Lead Factory has just been published and highlights a number of notable achievements.

As a result of the screening campaigns >3000 qualified hits have been awarded to private and public target owners. 72 public target programmes have been accepted, 48 high throughput screens finished and 41 hit lists with associated data reports handed over to the target owners. >150 bespoke assays have been developed in order to extract the most interesting hits for public programmes.

There are now 450,000 compounds in the compound library of which 120,000 are novel compound specifically synthesised for the ELF.

You can read more details here https://www.europeanleadfactory.eu/results/

The European Lead Factory is a collaborative public-private partnership aiming to deliver innovative drug discovery starting points. Having established the first European Compound Library and the first European Screening Centre, the EU Lead Factory aims to give free access to up to 500,000 novel compounds, a unique industry-standard uHTS platform, and much more.

We are now starting to see publications describing these endeavours..

https://www.europeanleadfactory.eu/results/publications/scientific-articles/

CO-ADD web portal

The CO-ADD web portal is now live You can now submit your free antimicrobial screening request, download all forms and access your primary screening, cytotoxicity, hit confirmation and hit validation reports online on the new secure CO-ADD user portal.

CO-ADD (Community for Open Antimicrobial Drug Discovery) is a not-for-profit initiative led by academics at The University of Queensland. Our goal is to screen compounds for antimicrobial activity for academic research groups for free. We aim to help researchers worldwide to find new, diverse compounds to combat drug-resistant infections.


Community for Open Antimicrobial Drug Discovery

A little while ago I mentioned The Community for Open Antimicrobial Drug Discovery effort to provide free compound screening against a variety of infective agents. .

Primary Screening of a 1mg sample Test against key ESKAPE pathogens, E. coli, K. pneumoniae, A. baumannii, P. aeruginosa, S. aureus (MRSA), as well as the fungi C. neoformans and C. albicans, at a single concentration.
Hit Confirmation:- Confirm activity with minimum inhibitory concentration and counterscreen for cytotoxicity and membrane interaction.
Hit Validation:- Test the positive hit against a broader panel of microbes and evaluate the basic drug qualities of actives. CO-ADD will screen your compounds for free and make no claim to IP. The linked flyer gives full details

You can also read more details in this Nature article DOI

It looks like they have achieved an important milestone!

Thanks to our research community we have received 100,000 compounds from 30 countries in 15 months! Make a difference: clear the fridge, empty the shelves and send through your compounds for free antimicrobial screening against 5 bacteria and 2 fungi. We would also like to acknowledge the contribution of the French National Chemical Library that has safely arrived in Brisbane last week!

So if you have compounds sitting in the back of cupboards why not send them to be tested



Drug Discovery Resources Update

I've updated the hit identification section of the Drug Discovery Resources. In particular I've added to the high-throughput screening analysis including more information on PAINS (Pan Assay Interference Compounds) first described by Baell et al DOI and subsequently summarised in an excellent Nature comment.

Academic researchers, drawn into drug discovery without appropriate guidance, are doing muddled science. When biologists identify a protein that contributes to disease, they hunt for chemical compounds that bind to the protein and affect its activity. A typical assay screens many thousands of chemicals. ‘Hits’ become tools for studying the disease, as well as starting points in the hunt for treatments.

These molecules — pan-assay interference compounds, or PAINS — have defined structures, covering several classes of compound. But biologists and inexperienced chemists rarely recognize them. Instead, such compounds are reported as having promising activity against a wide variety of proteins. Time and research money are consequently wasted in attempts to optimize the activity of these compounds. Chemists make multiple analogues of apparent hits hoping to improve the ‘fit’ between protein and compound. Meanwhile, true hits with real potential are neglected.

Also added a page on Aggregators. Promiscuous inhibition caused by small molecule aggregation is a major source of false positive results in high-throughput screening. To mitigate this, use of a nonionic detergent such as Triton X-100 or Tween-80 has been studied, which can disrupt aggregates, and is now common in screening campaigns DOI.

An Aggregation Advisor for Ligand Discovery

Aggregation is a regular concern when evaluating potential hits from screening and a recent paper "An Aggregation Advisor for Ligand Discovery" DOI attempts to provide an insight into this phenomenon, in addition they provide a useful web-based tool http://advisor.bkslab.org that provides a free service to advise whether molecules may aggregate under biological assay conditions.

aggre

Antibiotic Screening

A little while ago I mentioned The Community for Open Antimicrobial Drug Discovery effort to provide free compound screening against a variety of infective agents. I now have a few more details of what you might be able to access for a 1mg sample.

Primary Screening:- Test against key ESKAPE pathogens, E. coli, K. pneumoniae, A. baumannii, P. aeruginosa, S. aureus (MRSA), as well as the fungi C. neoformans and C. albicans, at a single concentration.
Hit Confirmation:- Confirm activity with minimum inhibitory concentration and counterscreen for cytotoxicity and membrane interaction.
Hit Validation:- Test the positive hit against a broader panel of microbes and evaluate the basic drug qualities of actives.

CO-ADD will screen your compounds for free and make no claim to IP

The linked flyer gives full details

European Lead Factory

p>The European Lead Factory has just announced that an additional 50,000 new compounds have been added to their screening collection. This brings the collection up to 350,000 compounds and sets them well on the way to their 500,000 target.

I've been involved in a couple of projects that have made use of this high-throughput screening facility and I've been impressed with the quality and diversity of the hits generated.

The European Lead Factory was established to promote the discovery of novel lead compounds, suitable for subsequent optimization either to drug candidates or to high‐quality pharmacological tools for the experimental validation of targets.

If you have a target you want to screen against you can submit a proposal online. For an academic or small company this is an interesting way to identify novel starting points for a medicinal chemistry program.

Protein-Protein Interactions

I’ve just added a section on Protein-Protein interactions.

These seem to be an increasingly popular target class and I’ hope to expand on it as we find out more.

And now for something completely different

In the last few updates I’ve concentrated on Fragment-Based-Screening, where by screening a small set of low molecular weight fragments it is possible to obtain hits that can then be expanded. The latest update highlights the use of encoded libraries, here vast libraries (>>1M compounds) can be screened the hits isolated and identified by virtue of a DNA tag.

From the early “proof-of-principle” peptide libraries this area has now extended into a variety of interesting chemistries.

European Lead Factory

I’m delighted to see the announcement about the European Lead Factory, hopefully this will be a huge asset for Drug Discovery. http://www.nature.com/news/europe-bets-on-drug-discovery-1.12372

Two sites shuttered by the pharmaceutical giant Merck, one in Scotland and one in the Netherlands, will soon be humming again with the work of drug discovery. But the hum will not be business as usual. It will be the sound of a public–private consortium placing a high-stakes wager: a nearly €200-million (US$271-million) bet that it can boost a languishing pharmaceutical sector by fusing academic innovation with industrial-scale screening, using robots to test chemicals for biological activity….Any academic group or company can also propose assays to test molecules in the library for biological activity. Lead-factory scientists will run these assays free of charge and confirm any promising results, working mainly in laboratory space closed by Merck in 2011 at Oss in the Netherlands. Follow-up work will be done at the University of Dundee in Scotland. Results will be provided confidentially to the groups that proposed the assays so that they can pursue further work and publications.

Building a Screening Collection

I’ve just updated the page on building a screening collection and added links to recent useful publications.

Broad Coverage of Commercially Available Lead-like Screening Space with Fewer than 350,000 Compounds, Jonathan Baell DOI
Metal Impurities Cause False Positives in High-Throughput Screening Campaigns, Johannes C. Hermann et al DOI

Directed and Virtual Screening

I’ve just started a section on Virtual Screening.

Malaria HTS results

Recently two groups have reported the results of screening campaigns, GlaxoSmithKline (GSK) published ( doi:10.1038/nature09107 ) the results of screening nearly 2 million compounds from their chemical library for inhibitors of P. falciparum, of which 13,533 were confirmed to inhibit parasite growth by at least 80% at 2 uM. The chemical structures and associated data were made public to encourage additional drug lead identification efforts and further research into this disease. In a second paper ( doi:10.1038/nature09099 ) a library containing 309,474 unique compounds, “designed at the scaffold level to provide diverse, comprehensive coverage of bioactive space”, was screened against Plasmodium falciparum strain 3D7 at a fixed concentration of 7 uM and afforded 1536 hits.

I thought I'd contribute to this generous effort by calculating a number of descriptors and properties for the molecules and then cluster the molecules in a variety of ways to help analysis and provide the data for download. You can read about it here.

Fragment-Based Screening

Updated the list of commercially available fragment libraries.

Frequent Hitters

I’ve just added a new section to the Drug Discovery Resources describing :-

Frequent Hitters, False Positives, Promiscuous Compounds

Site Updates

Details of Website updates Read More...