February 2017 newsletter

Case study: Conduct ligand-protein docking

Find out how we conducted ligand-protein docking to narrow down a 50k compound library to the best 1.5k compounds at a fraction of the cost of buying and screening the entire 50k library.


RDKit molecular simulations through OpenMM

Paolo Tosco describes how RDKit is used in Cresset software and presents preliminary work on boosting RDKit molecular simulations through OpenMM.
 
 


Web clip tips and tricks

  • Changing preferred alignments
  • Importing pre-existing conformations
  • Using Tags to organize data sets

See more tips and tricks.


Flexible licensing terms for academics

Cresset support the academic community through flexible licensing terms. Licenses have been created specifically to facilitate academic research and teaching within a university.


Cresset User Group Meeting, 29-30 June – workshop spaces limited

The day after the scientific program we will hold hands-on software workshops – spaces are limited so early registration is encouraged.

January 2017 newsletter

New visual identity for Cresset

Today we unveil our new visual identity. This reflects a new structure for our growing business and the different markets we serve: Cresset software, Cresset Discovery Services and Re-Pharm.


Call for beta testers for Flare, our new structure-based design application

Flare provides new insights for structure-based design by integrating cutting edge approaches from Cresset with significant open source and commercial methods. Flare will be available for beta testing in early February.


Case studies from Cresset Discovery Services

Outsourced computational chemistry projects come with an incredibly varied range of scope and focus. These case studies give an idea of the breadth and flexibility of our client projects.


Registration open for Cresset User Group Meeting, 29-30 June

Scientific program features an excellent line-up of speakers from 4 continents – each of who we are delighted will present in person. Hands-on software workshops exploring Cresset applications for computational, medicinal and synthetic chemists.
Find out more and register.

Cresset corporate rebrand reflects new structure for growing company

Cambridge, UK – 25 January 2017 – Cresset, innovative provider of software and contract research services for small molecule discovery and design, is pleased to announce a corporate rebrand, reflecting a new structure for this growing business.

“Cresset has grown dramatically since I joined as CEO in 2010, with a tripling of annual income over this period” says Dr Robert Scoffin, CEO of Cresset. “This new visual identity formalizes our structure into three divisions, reflecting the markets we serve and creating the conditions for even greater future growth.”

Cresset software: innovative science • intuitive software

The world’s leading research organizations use Cresset software on a daily basis to solve challenges in small molecule discovery, design and optimization.

“Our innovative science is delivered in a range of intuitive software for computational and medicinal chemists,” says Dr Tim Cheeseright, Director of Products. “Our passion for the continual development of the Cresset science and technology is reflected in the loyalty of our customers and strong business growth. Our software delivers results that our customers rely on.”

Cresset Discovery Services: make the molecules that matter

Cresset Discovery Services manages and delivers fully integrated outsourced computational chemistry programs from early to late stage discovery. In the last decade they have delivered hundreds of projects to clients ranging from small biotechs to pharmaceutical giants.

“We help chemists to understand as much as possible about the systems they are working on,” explains Dr David Bardsley, Commercial Director. “This enables our clients to save time and money by directing their scientific resources in the direction most likely to succeed and towards the molecules that matter.”

Re-Pharm: smarter drug re-profiling

Re-Pharm combines expert scientific insight with proven computational technology to identify and progress existing compounds that are suitable candidates for re-profiling against new disease indications.

“Re-Pharm demonstrates the power of Cresset software for rapidly identifying compounds, such as RP0217, that are likely to be active against disease targets.” says Dr Robert Scoffin, CEO of Re-Pharm and Cresset. “We have been granted patents on and are currently licensing  RP0217 for respiratory and ophthalmic indications.”

 

Cresset Discovery Services case studies

Cresset Discovery Services manages and delivers outsourced computational chemistry programs. We work alongside chemists to solve problems, provide fresh ideas, remove roadblocks and add direction and insight. We work on:

  • Lead generation and optimization
  • Creating, broadening or protecting IP
  • Supporting grant funding applications
  • Accelerating the commercialisation of assets.

What we actually do depends on the client project, which is usually confidential. Our case studies give an idea of the breadth and flexibility of our work and include some anonymized examples of client projects.

November & December 2016 newsletter

CEO end of year message

Rob Scoffin reviews 2016 which has been an exciting year of developments for Cresset.

Docking Factor-Xa ligands with Lead Finder

In this case study, two different Lead Finder docking modes (standard and extra precision) were used in docking studies on a small number of Factor-Xa (FXa) protein-ligand complexes originally used in the CSAR 2014 benchmark exercise.

Spark reagent databases

The November release of the Spark reagent databases derived from eMolecules is now available.

Elucidating binding mode and molecular interaction of new class of anti-fungal drugs

Dr Martin Slater, Director of Cresset Discovery Services, describes how modeling work was critical to predicting the binding mode of the inhibitor and important interacting amino acid residues.

Pave the way for more repurposed drugs

David Cavalla, Numedicus, argues that linking prescriptions to medical conditions would make it easier for companies to re-coup costs and open the way to market for repurposed compounds for rare diseases.

The Cresset User Group Meeting – June 29-30, 2017 – Cambridge, UK

  • June 29: Scientific program featuring invited speakers from 4 continents. Cresset in-house experts will present the latest software developments, including a showcase of our new structure-based design tool.
  • June 30: Hands-on software workshops.

Dr Scoffin, Cresset CEO, chairs and presents at International Congress of Medichem, Nanjing, China, 16-19 November 2016

Cambridge, UK – 15th November 2016 – Cresset, innovative provider of software and contract services for small molecule discovery and design, is pleased to announce that this week, Dr Robert Scoffin, CEO, will chair the ‘Sym 203: Pioneering Screening Technologies for Lead Compounds’ session at the Annual Congress of Medichem in Nanjing, China. Dr Scoffin will also present an overview of virtual screening methods for drug discovery.

The virtual screening of molecules is a commonly used technique within pharmaceutical drug discovery, and has many applications including the selection of compounds for ‘wet screening’ and the design of novel libraries of compounds.

“Cresset is a market leader in virtual screening,” says Dr Scoffin. “Blaze is an effective ligand-based virtual screening platform used by pharmaceutical companies globally. Blaze is also used by Cresset Discovery Services who carry out virtual screening in many consultancy projects. I am looking forward to sharing the various methods employed within a virtual screening cascade, including 2D methods, 3D ligand-based methods and 3D structure-based methods, and describing how each of these contributes to the overall value of the virtual screening process.”

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Dr Robert Scoffin

3D-RISM: Better water positions through improved electrostatics?

Professor Dr Paolo Tosco presented 3D-RISM: Better water positions through improved electrostatics? at the German Chemoinformatics Conference, Fulda, Germany. on 7th November.

Abstract

The Reference Interaction Site Model (RISM) is a modern approach to solvation based on the integral equation theory of liquids[1]. It has seen increasing use as a method to analyse the structure of water in and around protein active sites. The position and energetics of water molecules in and around the active site is known to be of crucial importance in understanding ligand binding, and in particular knowledge of which water molecules are tightly bound and which are energetically unfavourable can give valuable insights into structure-activity relationships.

The accuracy of 3D-RISM depends on the closure used and the functions used to compute the intermolecular potential between the protein and water molecules. In practise, the potential function consists of van der Waals interactions and electrostatic interactions. Increasing the accuracy of electrostatic calculations should therefore give more accurate 3D-RISM water placements and energies.

To date, 3D-RISM has been applied using traditional force fields such as AMBER[2] which utilise simple unpolarised atom-centred charges to represent electrostatic potentials. We have investigated whether a more accurate electrostatic model, XED[3], which provides both polarizability and electronic anisotropy, improves the effectiveness of the 3D-RISM method. As water energetics around a protein active site are not in general experimentally observable, we have in the first instance concentrated on computing water positions and energetics around a range of small molecule model systems, and validated these using DFT calculations with ONETEP[4] and interaction statistics from the CSD. Polarization and electronic anisotropy are found to be particularly important when assessing water structure around carbonyl groups, and the results from AMBER are found to be noticeably unrealistic in many cases. This has important implications for the accuracy of 3D-RISM calculations on protein active sites.

Read about progress in structure-based design at Cresset.

[1] Skyner, R.; McDonagh, J. L., Groom, C. R., van Mourik, T., Mitchell, J. B. O.; Groom, C. R.; Van Mourik, T.; Mitchell, J. B. O. A Review of Methods for the Calculation of Solution Free Energies and the Modelling of Systems in Solution. Phys. Chem. Chem. Phys 2015, 17 (9): 6174.

[2] J.A. Maier; C. Martinez; K. Kasavajhala; L. Wickstrom; K.E. Hauser; C. Simmerling. ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB. J. Chem. Theor. Comput. 2015, 11:3696-3713

[3] J.G. Vinter Extended Electron Distributions Applied to the Molecular Mechanics of some Intermolecular Interactions. J. Comput.-Aided Mol. Des. 1994, 8: 653-668

[4] C.-K. Skylaris; P. D. Haynes; A. A. Mostofi; M. C. Payne Introducing ONETEP: Linear-scaling density functional simulations on parallel computers. J. Chem. Phys. 2005, 122:084119


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Professor Dr Paolo Tosco, Cresset, Presenting at the German Chemoinformatics Conference
(Photo courtesy of Wendy Warr)

Review of Cresset seminar at the Chem-Bio Informatics Society Annual Meeting 2016, Japan

 Over 60 delegates attended this seminar, hosted by Cresset and Level Five (Cresset’s distributor in Japan) during the CBI Annual Meeting 2016, Tokyo, October 25th-27th.

Dr Giovanna Tedesco presented presented A picture tells a thousand words: Using activity cliffs maps to understand SAR. She focused on the combined use of activity cliffs analysis, as implemented in Activity Atlas and Activity Miner, as a useful method to analyze the Structure-Activity Relationships (SAR) of data sets of different size and complexity.

Summarizing SAR into simple, interpretable maps

Activity Atlas is a novel, qualitative method available in Forge, Cresset’s powerful workbench for ligand design and SAR analysis. It uses a probabilistic approach to take a global view of the data in a qualitative manner, analyzing the SAR of a set of aligned compounds as a function of their 3D electrostatic, hydrophobic and shape properties. Results are displayed as highly visual 3D activity cliffs summary maps that give an overview of the SAR landscape, focusing on the prevalent SAR signals.

Rapid navigation of complex SAR, highlighting key activity changes

Activity Miner, a module of Forge (and optional module in Torch), enables rapid navigation of activity cliffs. It can be used to drill down into the Activity Atlas maps and understand subtle molecule-to-molecule structure-activity changes, identifying potential outliers and giving concrete examples of changes that generate the summary.

The information derived from these analyses is an invaluable aid for drug discovery projects that help to inform design decisions and prioritize new molecules for synthesis.

Case studies

The application of the methods presented was illustrated on example data sets of different size and complexity taken from the literature. The case studies shown include:


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Cresset seminar at Chem-Bio Informatics Society Annual Meeting 2016, Japan
cresset-stand-at-the-chem-bio-informatics-society-annual-meeting-2016-japan
Cresset stand at Chem-Bio Informatics Society Annual Meeting 2016, Japan

October 2016 newsletter

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Progress in structure-based design at Cresset

We have made great strides towards our new product in the last six months. Find out more about our progress and what is left to do ahead of our planned beta release in early 2017.
 


docked_syk_ligands

What’s great about Lead Finder?

Mark Mackey, Cresset CSO, explains why we chose Lead Finder as our preferred docking engine for structure-based design and to expand our virtual screening capabilities.
 
 


End of year offer: Ligand-protein docking – 3 months free

Send us your purchase order for an annual license for Lead Finder by 31st December 2016 and we will issue a 15 month license, which means you get 3 months free. Try a free evaluation.


New updated Spark reagent databases now released monthly

From October 2016, Spark users will benefit from monthly releases of updated eMolecules derived reagent databases. The rolling updates are intended to provide the very best availability information on the reagents that you wish to employ.


Cresset Discovery Services: Business case studies


Recent news and citations


The Cresset User Group Meeting

June 29-30, 2017 • Cambridge, UK

Save the date in your diary to hear speakers from the following industry leading orgnaizations, with more still to be confirmed:

  • AbbVie, US
  • Bayer Pharma, Germany
  • Cancer Therapeutics CRC, Australia
  • Eli Lilly Open Innovation Drug Discovery, US
  • Evotec, UK
  • Redx Oncology, UK

September 2016 newsletter

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What’s in the Cresset Discovery Services virtual screening toolbox?

By combining the strengths of Blaze for ligand-based work with Lead Finder for docking, CDS now has the most comprehensive virtual screening capabilities available anywhere in the industry.


Inspiration through examples: A round-up of our case studies

See a selection of case studies that represent our larger body of work with selections taken from recent, most popular and historical studies.


Academic licensing

We actively support academic research through flexible licensing terms. Licenses have been created specifically to facilitate internal academic research within a university.


Recent presentations

See the presentations from our Symposia on Innovative Software for the Discovery and Design of Novel Compounds, Bangalore and Pune, India.


The Cresset User Group Meeting: June 29-30, 2017

Our 2017 User Group Meeting will take place in Cambridge, UK on June 29-30, 2017. Note this date in your diary – further details will be announced soon. In addition to the scientific meeting, we will celebrate 15 years since Andy Vinter founded Cresset.


Citations

The following publications have recently cited Cresset technology. View these and other citations.

  • The molecular shape and the field similarities as criteria to interpret SAR studies for fragment-based design of platinum(IV) anticancer agents. Correlation of physicochemical properties with cytotoxicity, Journal of Molecular Graphics and Modelling
  • Multi-layer graphene oxide alone and in a composite with nanosilica: preparation and interactions with polar and nonpolar adsorbates, Applied Surface Science