January 2018 newsletter

Spark V10.5 released

This new release of Spark, our scaffold hopping and bioisostere replacement tool, focuses on advanced workflows and improved database management. Giovanna Tedesco, Product Manager, details the highlights of this release and lists the many other new features and improvements.

Existing users are encouraged to upgrade to Spark  V10.5 at their earliest convenience and to download the Spark V10.5 keyboard shortcuts and Spark V10.5 Molecule Editor keyboard shortcuts.

If you’re not yet a Spark user, but are interested in advancing your research through R-group exploration, patent busting or scaffold hopping, please request a free evaluation.

Video tips and tricks

  • What’s new in Spark V10.5
    • View the highlights of this new release of Spark.
  • Interacting with structures in Flare
    • Learn how to interact with proteins, protein chains, water molecules and small molecule ligands in the Flare GUI.
  • Tagging by cluster using Activity Miner
    • Learn how to tag compounds in a Forge project by cluster membership, following a cluster analysis run with Activity Miner.

See these and more video tips and tricks.

Citations and editorial

Registration open for The Cresset User Group Meeting 2018

Register early to secure your space at The Cresset User Group Meeting. Confirmed speakers include: AbbVie Inc., USA; Cancer Therapeutics CRC, Australia; Novartis, Switzerland.

December 2017 newsletter

CEO end of year message

Dr Robert Scoffin, CEO, reviews 2017 and says, “It’s a real privilege to work with such scientifically dedicated people and to know that Cresset software and services make a real difference to your research and results.”

Software review 2017

Throughout the year we have published many more case studies and web clip tips and tricks. Users have published widely citing the use of Cresset software and our chapter, Lessons and Successes in the Use of Molecular Fields, has been published in Comprehensive Medicinal Chemistry III. The most recent news is that we’re delighted to announce Proximagen have added Flare to their medicinal chemists’ toolkit. See our newsletters for what else you may have missed.

Discovery Services review 2017

Cresset Discovery Services has worked on numerous projects for customers in 2017. Confidentiality prevents us talking in detail about the work we have undertaken, however, you can see examples of the specific services we offer and read case studies demonstrating how we can help you make the molecules that matter.

Student bursary for The Cresset User Group Meeting

Students have until January 12 to apply for a bursary to present at The Cresset User Group Meeting on June 21, 2018.

Upcoming events

  • March 18-22, 255th ACS National Meeting, New Orleans, LA, USA
  • April 2-6, Drug Discovery Chemistry, San Diego, CA, USA
  • April 11-12, UK QSAR and MGMS Structure-Activity Relationships, Cardiff, UK
  • June 21-22, The Cresset User Group Meeting, Cambridge, UK

See all events.

Proximagen enhances medicinal chemists’ toolkit with Flare for structure-based design

Cambridge, UK – 12 December 2017 – Cresset, innovative provider of software and contract research services for small molecule discovery and design, is pleased to announce that Proximagen, a drug discovery and development company, has licensed Flare.

“Flare will give our medicinal chemistry team rapid, hands-on access to structure-based design capabilities” says Dr Ed Savory, Head of Exploratory Research, Proximagen. “When combined with our use of Cresset’s Forge for SAR and design, and Spark for R-group exploration and scaffold hopping, our medicinal chemists have access to a wide range of easy to use modelling applications.”

“I’m delighted that Proximagen have chosen to enhance their toolkit by making Flare accessible to their medicinal chemists,” says Dr Tim Cheeseright, Director of Products, Cresset. “I’m confident that Flare will bring fresh insights into their protein-ligand analysis and design.”

November 2017 newsletter

Tversky similarity in field-based virtual screening

Tim Cheeseright, Director of Products, describes how Tversky similarity is used to perform substructure and superstructure type searches using Blaze.

Computational approaches to ion channel drug discovery

Martin Slater, Director of Consulting Services, makes a case for information based strategies and ligand centric techniques which pit the efficiency of rationality against blind trial and error.

Web clip tips and tricks

New Spark reagent databases

This month a small change is being made to the Spark reagent databases in that we now only include reagents that are in eMolecules’ Tiers 1, 2, and 3. These correspond to the most accessible reagents and should be a good source of inspiration for R-group design experiments in Spark.

Keyboard shortcut guides

The Cresset User Group Meeting • June 21-22, 2018

We are delighted to announce that the keynote lecture at The Cresset User Group Meeting in 2018 will be delivered by Dr Steve Djuric, Vice President Discovery, AbbVie Inc.

Bursary for students

Students have until January 12, 2018 to apply for a bursary to attend and present at the meeting.

October 2017 newsletter

Forge V10.5 released

With over 30 enhancements, V10.5 of Forge introduces new science, the new Conformation Explorer, and a large number of GUI and usability improvements.

Torch V10.5 released

The improved design workflow in V10.5 of Torch enables live updating of physicochemical properties and predicted activities while you design.

Web clip tips and tricks

Student bursary

Students are invited to apply for a bursary to attend and present at The Cresset User Group Meeting on June 21st – 22nd, 2018 in Cambridge, UK.

Cresset awarded French R&D tax credit accreditation

Up to 30% tax relief for French companies outsourcing projects to Cresset Discovery Services.

Student bursary: The Cresset User Group Meeting 2018

Students affiliated to a higher education institution are invited to apply for a bursary to attend, and present at, The Cresset User Group Meeting on June 21st, 2018 in Cambridge, UK.

To apply, submit an extended abstract, no more than 1 side of US letter/A4, on your proposed presentation about the application of Cresset software. Your submission should include your:

  • Course title/PhD title
  • Expected date of graduation
  • Principal investigator/PhD supervisor

Deadline for applications is January 12th, 2018. Award of the bursary will be announced in February 2018.


  • Only 1 submission per student
  • The bursary will be a maximum of £1,000
  • The bursary is awarded to the student submitting the abstract, and cannot be transferred
  • The successful applicant must present in person on June 21st, 2018 in Cambridge, UK
  • Decision of who the bursary is awarded to is made by Cresset and not open to discussion.

Up to 30% tax relief for French companies outsourcing projects to Cresset Discovery Services

Up to 30% tax relief for French companies outsourcing projects to Cresset Discovery Services

Cambridge, UK – 17th October 2017 – Cresset, innovative provider of software and contract research services for small molecule discovery and design, has been awarded French R&D tax credit (Credit d’Impot Recherche (CIR)) accreditation by the French Minister for Higher Education, Research and Innovation (MESRI).

Recognition of Cresset as an official Research Organization by the Ministry of Education and Research allows eligible organizations to claim up to 30% tax relief on projects outsourced to Cresset Discovery Services.

“This accreditation emphasizes Cresset’s commitment to helping companies make the molecules that matter, at the best possible price,” says Dr David Bardsley, Commercial Director at Cresset.

Find out how to get support for your R&D and innovation.

Jusqu’à 30 % d’allègement fiscal pour les entreprises françaises qui externalisent leurs projets auprès de Cresset Discovery Services

Cambridge, Royaume-Uni – le 17 octobre 2017 – Cresset, fournisseur innovant de logiciels et de services de recherche contractuelle pour la découverte et la conception de petites molécules, s’est vu décerner l’accréditation Crédit d’Impôt Recherche (CIR) par le Ministère français de l’Enseignement supérieur, de la recherche et de l’innovation (MESRI).

La reconnaissance de Cresset en tant qu’organisme de recherche officiel par le Ministère de l’Enseignement et de la recherche permet aux organisations remplissant les conditions requises de demander jusqu’à 30 % d’allègement fiscal sur les projets externalisés auprès de Cresset Discovery Services.

« Cette accréditation témoigne de la détermination de Cresset à aider les entreprises à fabriquer les molécules qui importent, au meilleur prix possible, » déclare le Dr David Bardsley, Directeur commercial chez Cresset.

Découvrez comment vous pouvez obtenir de l’aide pour vos projets de R&D et d’innovation.

September 2017 newsletter

Blaze V10.3 released for even better virtual screening

The latest version of Blaze™, our virtual screening platform is now available. V10.3 introduces pharmacophore constraints to enable you to find the best possible new hits and leads. Alongside pharmacophore constraints, we’ve added additional similarity metrics and updated the user interface.

Sneak peek at Forge V10.5

New versions (V10.5) of Forge™ and Torch™ are due out next month. This release offers new science and functionality and plenty of improvements that significantly enhance both applications. Here we offer a sneak peek at some of the new functionality in Forge.

Flare enhances the Cresset Discovery Services toolbox

What does Flare™, our new structure-based design application, offer Cresset Discovery Services that it didn’t have before?

Recent citations

  • 3D-QSAR studies on Maslinic acid analogs for Anticancer activity against Breast Cancer cell line MCF-7, Nature Scientific Reports
  • Development and evaluation of 4-(pyrrolidin-3-yl)benzonitrile derivatives as inhibitors of lysine specific demethylase 1, Bioorganic & Medicinal Chemistry Letters
  • Development of (4-Cyanophenyl)glycine Derivatives as Reversible Inhibitors of Lysine Specific Demethylase 1, Journal of Medicinal Chemistry
  • Thiazolidine derivatives as potent and selective inhibitors of the PIM kinase family, Bioorganic & Medicinal Chemistry Letters

Read these and more citations.

Back to school offer

Up to 25% off academic research licenses on all orders received by October 31, 2017.

Commercial Director to run 32nd half marathon

On October 1, 2017, David Bardsley, our Commercial Director will run his 32nd half marathon in Cardiff, UK. We’re delighted to sponsor David in raising funds for cancer research at Cardiff University.

August 2017 newsletter

Comparing ligand and protein electrostatics of Btk inhibitors

In this case study, protein interaction potentials implemented in Flare, Cresset’s structure-based design software, were used to calculate a detailed map of the electrostatic character of the protein active site of Bruton’s tyrosine kinase (Btk), and compared to ligand fields to get a detailed understanding of ligand binding and SAR.

Flare web clip tips and tricks

  • Visualizing protein-ligand interactions
  • Docking ligands with Lead Finder
  • Protein alignment and superposition

See these and more tips and tricks.

Empowerment of rare disease patients in modern healthcare delivery

Patients with rare conditions are using their collective power to get access to better medicines. David Cavalla describes how patient communities are campaigning on social media, forming charities and even starting their own drug companies.

Meet us in September

  • 6th, Cambridge Cheminformatics Network Meeting, Cambridge, UK
  • 10th – 13th, RSC/SCI Medicinal Chemistry Symposium, Cambridge, UK – find us on Stand E
  • 11th, BAGIM Panel on Cloud Computing for Molecular Modeling, Boston, MA, USA
  • 19th, Pharma ChemOutsourcing, Long Branch, NJ, USA
  • 29th, UK QSAR Autumn Meeting, Manchester, UK

See all events.

Empowerment of rare disease patients in modern healthcare delivery



By David Cavalla, Numedicus Limited.

If you’re fond of alliteration you’ll know that you can divide the stakeholders in modern healthcare into three ‘P’s: patients, payers and pharmaceutical companies, with physicians and pharmacists taking additional minor roles. Traditionally the patient has played a passive part, but over recent years the patient community has dramatically increased its involvement and influence in modern healthcare delivery, particularly in the rare disease sector.

Approved drugs do not exist for over 90% of the 7,000-8,000 rare diseases, and the commercialization of niche products for rare and orphan drugs has become the most favored growth opportunity over the conventional mass-market ‘blockbuster’. Repurposing is a common development option, but the development of drugs in these areas is dependent on access to patients in clinical trials.

Patients with rare conditions are increasingly organized into communities with a voice, and they are using their collective power to get what they want, namely access to better medicines.

Social media helps patients organize

Rare disease patients are much more likely to be ill as a child, and from inherited genes, than as an older person. This leads to highly motivated communities consisting of patients and their friends and relatives. Social media makes it possible for self-organizing communities to further the aims of rare disease patients.

Pharma companies are keen to form alliances with patient groups to further their case for payers to reimburse expensive medicines.

A key demand of patient groups is that that healthcare resources are allocated to the patients, even when such resources are scarce. The charity Action Duchenne, recently parked the wheelchairs of over 100 teenage boys outside the UK parliament to campaign for reimbursement of the first approved drug for the condition.

Some of the carers of rare disease patients and the patients themselves go to great lengths to educate themselves about the relevant condition. From this position, it is an easy step for them to ask themselves a simple question – what more can a patient or carer do to improve therapy?

Patient groups founding drug companies

John Crowley has two children with a severe neuromuscular lysosomal storage disease called Pompe Disease. He started a foundation to raise money for the condition, then took a job with Bristol Myers Squibb in order to learn all he could about the pharmaceutical business.

His next step was to found Novazyme Pharmaceuticals to develop an enzyme replacement therapy for his daughters’ condition. This was subsequently acquired by Genzyme corporation and the treatment was brought to market.

Later, John Crowley became CEO of Amicus Therapeutics which is also engaged in lysosomal storage disorder research for Pompe and Fabry diseases. His story featured in a book, and in 2010 was made into a film called Extraordinary Measures starring Harrison Ford.

This story is exceptional, but there are many other examples of patient- and carer-motivated drug development.

Charities taking on drug development

The Cure Parkinson’s Trust is a leading charity aiming to slow the progression, stop or even to reverse Parkinson Disease, the progressive neurodegenerative condition characterised by rigidity, tremor and bradykinesia.

The trust has rapidly acquired interests into the study of a wide range of potential therapeutic interventions, and is currently connected with over 50 pharmaceutical companies and associated with nearly 3,000 investigators. They are carrying out a number of advanced clinical trials, including a Phase III trial of the calcium L-type blocker isradipine; drug repurposing features frequently in the work they do, with studies underway on exenatide and liraglutide (GLP-1 agonists), simvastatin (HMG-CoA inhibitor) and N-acetyl cysteine (antioxidant).

They place particular emphasis on a network of key opinion leaders with interests in investigating novel mechanisms in the condition, and are led by Dr Richard Wyse, a former lecturer in various London hospitals as well as medical director at two biotech companies.

Another example of this is Dr Pan Pantziarka of the ReDO project (Repurposing Drugs in Oncology), which was formed from the AntiCancer Fund and Global Cures. This organization has 5 trials underway, mostly drug repurposing combinations such as metformin (antidiabetic)/zoledronate (anti-osteoporosis)/sirolimus (transplant rejection medicine).

A particular focus is on the treatment of the rare cancer angiosarcoma with propranolol. Dr Pantziarka has a personal reason for his interest in cancer, but is also scientifically trained. ReDO are looking at putting in place a regime of tax incentives from the UK Government for the development of generic repurposed drugs.

The wider scope for development models

These examples point out the complex ways in which charities are becoming integrated into the drug R&D landscape, far beyond their original role in fundraising and care support for their conditions, patients can be medical experts, drug developers and clinical investigators. This is particularly the case for rare diseases, but in the future the changes will almost certainly extend into more common diseases too.

For the larger charities, this is not an entirely new phenomenon: Cancer Research UK supports a lot of research activity already – in 2015/6, amounting to £376 million, including nearly £120 million into the biology of cancer. The British Heart Foundation, too, spends over £100 million per annum, mostly on basic research. The focus on drug repurposing as a more efficient translational strategy is likely to grow, however, because of the cost and time advantages which characterise this approach, and it will be interesting to see what changes accrue when some of the larger charities adopt it to the same degree as some of the examples cited above.