Cresset User Group Meeting 2018 to showcase new science, customer case studies and hands-on software workshops

Helping chemistry teams design the best molecules

Cambridge, UK – 15 May 2018 – Cresset, innovative provider of outstanding software for molecular discovery, is pleased to announce the scientific program for its User Group Meeting on 21st – 22nd June in Cambridge, UK.

“Leading chemists from industry and academia will present scientific case studies and insights into how computational chemistry has helped transform their research,” says Dr Robert Scoffin, Cresset CEO. “In addition, Cresset scientists will present our latest scientific developments and will showcase upcoming applications to help chemistry teams design the best molecules as efficiently as possible. Whether you are new to Cresset, have been with us from the beginning, or are just intrigued to find out more about the solutions we offer, we invite you to join us.”

Registration is open to computational, medicinal and synthetic chemists, and those wanting to design the best molecules efficiently.

June 21 • Scientific program

Cresset presentations:

  • Sneak Peek at Next Generation Collaborative 3D Design
  • Real Time 3D Design in 2D!
  • Customizing and Scripting in Flare 2.0: Introducing the New API
  • Predicting Activity Using the Electrostatic Complementarity TM of Protein-ligand Complexes
  • New Science and Improved Workflows in Cresset Ligand-based Applications

Invited presentations:

  • Keynote lecture: Acceleration of Drug Discovery Through the Judicious Application of Enabling Chemistry Technology, AbbVie, USA
  • Molecules in 5D: Experiences with Peptidic Macrocycles, Novartis, Switzerland
  • Indole Regulation of Cytoplasmic pH makes E. coli More Resilient to Antibiotic Stress, University of Cambridge, UK
  • Exploring the Potential of Indirect Inhibition of GTPase Driven Oncogenesis via ICMT Inhibition, Cancer Therapeutics CRC, Australia
  • Identifying Pharmaceutical Molecules with a Chemotyping Approach, Sun Yat-sen University China
  • Progress of Compound Library Design Using In-silico Approach for Collaborative Drug Discovery, Keio University, Japan
  • Pushing the Boundaries of Computational Binding Free Energy Prediction Methods, University of Edinburgh, UK

 June 22 • Hands-on software workshops

  • Introduction to Flare for computational, medicinal and synthetic chemists
  • Python in Flare
  • Advanced Spark
  • 3D-QSAR in Forge
  • Forge SAR
  • Library design with Cresset nodes in KNIME

END

 

April 2018 newsletter

A sneak peek into Flare V2: Python API and new science

As promised, Flare V2, due for release next month. Giovanna Tedesco gives a sneak peek into the new Flare Python API, new science and significant improvements to functionality and usability.


In the Cresset lab: Molecular design re-imagined

Tim Cheeseright describes how project TorchWeb will enable medicinal chemists to make the best, most informed decision at every stage of the discovery process.


The Cresset User Group Meeting, Cambridge, UK

June 21 • Scientific program

  • AbbVie, Novartis and UCB will be presenting in our strongest ever scientific program
  • Cresset scientists will present for the first time our new approach to rapid activity prediction, introduce our web based collaboration platform for new molecule design and showcase updates to our ligand-based applications.

June 22 • Hands-on software workshops – spaces filling fast

  • Introduction to Flare
  • Python in Flare
  • Advanced Spark
  • 3D-QSAR in Forge
  • Forge SAR
  • Library design with Cresset nodes in KNIME

If you require accommodation on-site please book soon as there is limited availability left.

Find out more and register.


Pharmacophore constraints – when should they be used?

New pharmacophore constraints developed by Cresset are useful for more than just virtual screening. Mark Mackey explains how, and the effect adding constraints has on the probability of a successful ligand alignment.


Flexible academic licensing

Academic customers tell us that our applications help them communicate ideas, give new insight, and are easy to learn and use. See the flexible licensing options available to academics.


Review of the CCPBioSim training week

Matthias Bauer reviews the Collaborative Computational Project for Biomolecular Simulation (CCPBioSim) training week hosted by the University of Bristol.


Recent citations

  • Computer-aided drug design, synthesis and identification of disulfide compounds as novel and potential allosteric PAK1 inhibitors, RSC Adv., 2018,8, 11894-11901.
  • Activity and selectivity cliffs for DPP‐IV inhibitors: Lessons we can learn from SAR studies and their application to virtual screening, Medicinal Research Reviews

See these and other citations.


Upcoming events

  • 26 April, 29th Symposium on Medicinal Chemistry in Eastern England, Hatfield, UK
  • 29 April – 2 May, 36th National Medicinal Chemistry Symposium, Nashville, TN, USA
  • 4 May, NESACS: 7th Advances in Chemical Structures, Cambridge, MA, USA
  • 14 May, Kinase 2018, Cambridge, UK
  • 14 – 18 May, Workshop on Free Energy Methods, Kinetics and Markov State Models in Drug Design, Boston, MA, USA
  • 27 – 31 May, 11th International Conference on Chemical Structures, Noordwijkerhout, The Netherlands

See all events.


Compliance with the General Data Protection Regulation

We have always complied with data protection and have recently updated our privacy policy in accordance with the General Data Protection Regulation (GDPR) that comes into effect on May 25, 2018. Cresset has been sending newsletters every month for at least the last 6 years and we have always given the opportunity to opt-out. As you have not previously opted-out you continue to receive this newsletter under GDPR Legitimate Interest. You will always have the opportunity to opt-out at any time.

Flexible academic licensing

Are you a:

  • PhD student or postdoctoral researcher
  • Course tutor
  • Principal investigator
  • Department head?

Did you know that:

  • You can access Cresset ligand-based desktop applications through a variety of flexible licensing options
  • If you publish work which used Cresset technology, and you cite the applications used, we will promote your work through our website and newsletter?

Apply Cresset to your research

Academic customers tell us that our applications help them communicate ideas, give new insight, and are easy to learn and use. Below are just a few examples of how you can apply Cresset technology to your research.

Active design using electrostatics

Torch’s ligand-centric view enables 3D design whether or not you have a protein crystal structure. It makes it easy for you to focus on the designs that work and have good physicochemical properties.

Electrostatic and shape descriptors provide a rich informed view to help you understand the effects of chemical changes and eliminate designs that are unlikely to be active.


Figure 1: A change on one side of the molecule can often influence a distal region, especially if the systems are electronically linked through π-systems. This simple change has multiple effects due to the increased electron-withdrawing character of the new heteroatom and the addition of an aromatic ring: (A) the boundary of negative electrostatic potential extends further; (B) the shape and size of the negative π-cloud is significantly altered; (C) the size and extents of the positively charged aromatic edge are increased; and (D) there is a small increase in the positive potential associated with the aromatic hydrogens of the pyrimidine nucleus at the other end of the molecule.

Find and understand activity and selectivity cliffs in your SAR

Activity Miner, a component of Torch and Forge, helps you find and understand critical regions in complex SAR. Using the concepts of activity cliffs and matched molecular pairs, you can link activity changes to electrostatic and shape changes. Since selectivity is often as important as activity, Activity Miner makes it easy for you to compare multiple end points. The design process in Torch enables you to apply this knowledge to progress your project.

Activity Miner top pairs
Figure 2: Pinpoint the most significant changes to your molecules using the sortable top pairs table. Find critical points in the SAR and understand how they relate to changes in physicochemical properties.

Powerful models to interpret your data

Forge uses the Cresset patented ligand alignment algorithm to generate realistic, interpretable relationships between your molecules. It includes an impressive range of SAR models that combine robust analysis with customizable parameters, ease of use and intuitive visualization. For SAR analysis, there is no need to look any further than Forge.


Figure 3: QSAR models in Forge decipher complex SAR and inform the design of new molecules.

New SAR insights form novel methods


Figure 4: Activity Atlas is a novel, qualitative method that generates three distinct maps of the electrostatic, shape and hydrophobic properties around your molecules. It can be used with small or large data sets and is particularly useful for projects where traditional 3D-QSAR approaches fail.

Find biologically equivalent alternatives to escape IP and toxicity traps

Customers tell us that Spark is the best scaffold hopping and bioisostere replacement tool they have ever used. The easy to use interface quickly generates a range of novel molecules from an initial structure. Profiling and scoring help you choose the most innovative and tractable leads with the properties you need.


Figure 5: Spark workflow.

Request an academic license

Testimonials

Molecular visualization makes it easier to communicate ideas

“Working with Cresset tools has helped me generate new ideas for my projects in various disease areas. The molecular visualization has made it easier to communicate my ideas to my experimental collaborators, both chemists and biologists.”

New insight

“Cresset’s software gives new insight to projects I’ve been working on for the past three to four years. I specifically use it to see how proteins, DNA and molecules interact and bind to each other. If we can design drug molecules that will bind to DNA the same way proteins do, we can open up whole new lines of therapy. Cresset is supportive of academic research and they’ve been wonderful to work with to get everything up and running.”

Easy to learn and use

“Our students who use the Cresset systems in their projects tend to gain an affinity with a number of med-chem concepts far earlier than those who do strictly organic projects, for example using Spark to identify new frameworks that possess favorable properties and which can then be synthesized in the lab via a novel reaction. Compounds can be tracked within a TorchLite template and the student can invoke field patterns and orbital coefficients to explain changes to NMR spectra.”

 “My students and I are very grateful for providing us with the educational license and thus an opportunity to explore Cresset’s software in our lectures. Cresset provides marvelous software, easy to learn, easy to use, pleasant looking and its structure is logical and educational. The program manuals are great.”

 “Considering the absence of an experimental structure, the field based concept was a perfect match for our work. It helped us obtain bioactive conformations of ligands based on a validated pharmacophore. The software provided by Cresset is user easy and user friendly, creative and flexible for a new starter to an experienced researcher to use.”

“Visualizing the inhibitor/substrate binding site of protein crystal structure in Cresset using field points calculated by XED force field is very informative. The protocols for all the modules in Cresset are very quick and easy to use. Forge and Spark are excellent programs for LBDD. The radial plots obtained from alignment methods implemented in Forge provide a visual inspection of results and could be effectively used for simultaneously comparing any number of physical properties for the compounds in the dataset. I strongly believe that Cresset software is an important inclusion in the spectrum of software programs used for Computer Aided Drug Discovery paradigm.”

 

March 2018 newsletter

Flare: Accessible structure-based design

Tim Cheeseright, Director of Products, describes how a balance of usability and flexibility, with a focus on design and accessible methods, have contributed to accessible structure-based design with Flare™.


New Spark databases released

The release of Spark™ V10.5 in February brought completely new Spark databases. Derived from molecules in ZINC, eMolecules’ Screening Compounds and ChEMBL 23, they include over 3 million unique entities.


Full speaker line-up announced for The Cresset User Group Meeting

With speakers representing 7 countries across 4 continents, the scientific program for The Cresset User Group Meeting will give attendees insight to the use of computational chemistry in industry and academia.


Recent presentation, poster and citations

See all citations.


Review of 255th American Chemical Society Meeting

Martin Slater, Director of Consulting Services, reviews his first experience of ACS. From fragrances, food and cheminformatics to GPCRs it proved to be both exhilarating and enlightening.


Upcoming events

  • April 2-6: Drug Discovery Chemistry, San Diego, CA, USA Meet us on stand 502 and see our poster: Deciphering Kinase SAR using Electrostatics
  • April 5: Applied Pharmaceutical Chemistry, Boston, MA, USA See our poster: Deciphering Kinase SAR using Electrostatics
  • April 9-13: CCPBioSim Training Week, Bristol, UK We are proud to be supporting CCPBioSim is their drive to improve and integrate biomolecular simulation software
  • April 11-12: UK QSAR and MGMS Structure-Activity Relationships, Cardiff, UK Meet us on stand 5 in the exhibit hall
  • April 26: 29th Symposium on Medicinal Chemistry in Eastern England, Hatfield, UK See our poster: Deciphering Kinase SAR using Electrostatics
  • April 29: 36th National Medicinal Chemistry Symposium, Nashville, TN, USA Meet us in the exhibit hall

See all events.


Cresset Commercial Director to run 19th marathon

On April 29, David Bardsley will run his 19th marathon in Newport, Wales, UK. David is fundraising for DEBRA, a charity that supports individuals and families affected by Epidermolysis Bullosa – a painful genetic skin blistering condition.

Parkinson’s UK, Selcia, and Cresset collaborate to discover new drug candidates for Parkinson’s

London, Ongar and Cambridge, UK – 8 March 2018 – A new collaboration in the efforts to find a new drug candidate to combat Parkinson’s has been announced in the UK today.

The collaboration, formed by leading charity Parkinson’s UK, contract innovation and research organization, Selcia (part of Eurofins), and computational chemistry software and services provider, Cresset Discovery Services, is centred on creating novel molecules that could stop or slow the progression of the condition.

By modulating gene transcription, the collaboration aims to create molecules that increase the activity of a selection of genes which have the potential to both increase dopamine synthesis to ease symptoms, and boost the production of proteins which have neuroprotective effects. Parkinson’s UK is set to fund the £1.2million project, which will take place over 12 months.

This collaboration represents an expansion of Parkinson’s UK’s Virtual Biotech programme of work, which allows the charity to provide leadership and critical funding to early drug development in partnership with a range of other organisations that have the facilities and staff to carry out scientific work on a contract basis.

Dr Arthur Roach, Director of Research at Parkinson’s UK, said: “It’s fantastic to be working in partnership with these organisations, which have an exceptional range of skill and expertise in drug discovery. We’re also very excited to be working to identify a novel candidate that will not only be dopaminergic but also neuroprotective. Should initial studies go well, we could be looking at a new drug that has the potential to help millions of people with Parkinson’s across the world.”

Dr Vicky Steadman, Director of Discovery at Selcia, commented: “We are delighted that our proposal to Parkinson’s UK translated into the initiation of a collaboration that could lead to novel treatments for people with Parkinson’s. Selcia has an enviable track record in delivering pre-clinical candidates from lead optimization projects, and considerable expertise in designing drug candidates that cross the blood-brain barrier.”

Dr Martin Slater, Director, Cresset Discovery Services, said: “The combined strengths of the collaborating partners enables us to efficiently address the very difficult challenge of finding new medicines for this neurodegenerative condition. Cresset Discovery Services will provide unique cutting edge molecular modelling capability, our extensive AI capabilities and in silico expertise, to aid in the discovery of the most appropriate starting points for this program.”

ENDS

For further information, contact:

Parkinson’s UK: Kirsty Callingham, Senior Media and PR Officer, kcallingham@parkinsons.org.uk +442079 639311

Cresset: Sue Peffer, Marketing Manager, news@cresset-group.com, +44 1223 858890.

Selcia: Vicky Steadman, Director, Discovery Vicky.steadman@selcia.com 01277 367042.

About the partners

Parkinson’s UK

Parkinson’s UK is the UK’s leading charity supporting those with the condition. Its mission is to find a cure and improve life for everyone affected by Parkinson’s through cutting edge research, information, support and campaigning. For more information, visit www.parkinsons.org.uk

Selcia Ltd

Selcia Ltd is a UK-based provider of integrated drug discovery services with a worldwide client base. Founded in 2001, its workforce comprises industry experienced medicinal chemists, biologists and ADME scientists as well as 14C radiolabeling experts. Selcia announced its acquisition by Eurofins earlier this year.

Cresset Discovery Services

Cresset Discovery Services manages and delivers outsourced computational chemistry programs. Experienced scientists work alongside your chemists to solve problems, provide fresh ideas, remove roadblocks and add direction and insight. Cresset Discovery Services helps their customers reach their milestones faster and more cost effectively. For more information, please visit www.cresset-group.com/discovery-services

Eurofins

Eurofins – a global leader in bio-analysis believes it is the world leader in food, environment and pharmaceutical products testing and that it is also one of the global independent market leaders in certain testing and laboratory services for agroscience, genomics and discovery pharmacology and for supporting clinical studies. In addition, Eurofins is one of the significant emerging players in specialty clinical diagnostic testing in Europe and the USA.

As one of the most innovative and quality oriented international players in its industry, Eurofins is ideally positioned to support its clients’ increasingly stringent quality and safety standards and the expanding demands of regulatory authorities and healthcare practitioners around the world.

The shares of Eurofins Scientific are listed on the Euronext Paris Stock Exchange (ISIN FR0000038259, Reuters EUFI.PA, Bloomberg ERF FP).

February 2018 newsletter

Case study: Using Spark to design macrocycle BRD4 inhibitors

Macrocyclization of pharmaceutical compounds plays an increasing role in drug discovery. Macrocycles can provide several advantages such as favorable drug-like properties, and increased selectivity and binding affinity. Dr Matthias Bauer, Computational Chemist at Cresset, presents a case study of designing macrocyclization strategies for reported BRD4 inhibitors with Spark, Cresset’s bioisostere replacement and scaffold hopping tool.

Resurrection of the covalent inhibitor?

Martin Slater and Sylvie Sciammetta explore the revival of interest in covalent inhibitors. This has culminated in a growing list of diverse proteins that have been successfully targeted, that are outside the well-trodden protease area.

Video tips and tricks

  • Macrocyclization using Spark: How to use Spark to macrocyclize a molecule.
  • Ligand growing with Spark: How to grow a starter molecule into a new space, guided by existing ligands, mapping a different regions of the same active site.

See all web clips.

Workshop sessions announced for The Cresset User Group Meeting

Computational, medicinal and synthetic chemists can register for hands-on software workshops, which will take place on June 22 in Cambridge, UK.

The scientific program will be held on June 21. Presenters from the following companies are confirmed: AbbVie Inc., USA; Cancer Therapeutics CRC, Australia; Novartis, Switzerland; Sun Yat-Sen University, China; UCB Biopharma SPRL, Belgium; University of Cambridge, UK; University of Edinburgh, UK.

Upcoming events

  • March 18-22: 255th ACS National Meeting, New Orleans, LA, US
    • Using molecular fields to understand molecular determinants of the olfaction process (CINF; Fragrances, food and cheminformatics; Oral)
    • Adding pharmacophores to shape and electrostatics – too much of a good thing? (COMP; Poster)
  • April 2-6: Drug Discovery Chemistry
    • Meet us on stand 502
  • April 9-13: CCPBioSim Training Week, Bristol, UK
    • We are proud to be supporting CCPBioSim is their drive to improve and integrate biomolecular simulation software

See all events.

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.