October 2018 newsletter

Sneak peek: PickR to select electrostatically diverse monomers for libraries

PickR will be a new command line application to generate diverse R-groups for library design. Tim Cheeseright takes a peek at the results from using PickR to cluster 1000 amino side chains.


Make the molecules that matter

Watch our short video to see how Cresset Discovery Services works alongside your chemists to solve problems, provide fresh ideas, remove roadblocks and add direction and insight.


RDKit User Group Meeting review

Paolo Tosco reviews the RDKit UGM – one of his favorite scientific events of the year. From his presentation about the integration of RDKit in Flare, our structure-based design tool, and in particular on its usage from Python through the built-in Jupyter Notebook interface, to what’s new in RDKit, GSoC RDKit-MolVS integration, open source programs built on the RDKit, RDKit in the modern biotech and cheminformatics problems – Paolo discusses them all.


Introducing Andy Smith, Discovery Services Scientist

Andy Smith has joined Cresset Discovery Services, where he will work on customer projects. Read about his computational chemistry journey so far, including work on GPCRs, structure-based design, anti-infectives, oncology and crop protection.


Recent news


Citations

  • In Silico Discovery of a Small Molecule Suppressing Lung Carcinoma A549 Cells Proliferation and Inducing Autophagy via mTOR Pathway Inhibition, Mol. Pharmaceutics, Article ASAP, DOI: 10.1021/acs.molpharmaceut.8b00996
  • A Structure- and Ligand-Based Virtual Screening of a Database of “Small” Marine Natural Products for the Identification of “Blue” Sigma-2 Receptor Ligands, Marine Drugs. 2018; 16(10):384
  • Synthesis, Anti-Inflammatory Activity, and In Silico Study of Novel Diclofenac and Isatin Conjugates, International Journal of Medicinal Chemistry, vol. 2018, Article ID 9139786, 11 pages, 2018

See these and other citations.


Upcoming events

November 2018

  • 31 October-2 November, AusBiotech 2018, Brisbane, Australia
    • Meet us at booth 45
  • 1-4, Informatic Tools in Drug Discovery and Delivery, Patiala India
    • Workshop: Electrostatic Complementarity™ as a New Approach to Visualize and Predict Activity
  • 11-13, 14th German Conference on Chemoinformatics, Mainz, Germany
    • Poster: Predicting Activity Using the Electrostatic Complementarity™ of Protein-ligand Complexes
  • 20, Innovative Software for Molecular Discovery and Design, Lucknow, India
  • 22, Innovative Software for Molecular Discovery and Design, Hyderabad, India
  • 30, MGMS Young Modellers’ Forum, London, UK

2019

See all events.

Cancer Research UK Manchester Institute enhances toolkit for computational and medicinal chemists with Flare for structure-based drug design

Cambridge, UK – 18th October 2018 – Cresset, innovative provider of software and contract research services for small molecule discovery and design, is pleased to announce that Cancer Research UK Manchester Institute (CRUK MI), has licensed Flare for fresh insights into structure-based drug design.

“Putting easy-to use and visually driven structure-based design software in the hands of our medicinal chemists will empower them to deliver the next generation of cancer therapeutics more efficiently,” says Professor Caroline Springer, Director of the Drug Discovery Unit, CRUK MI. “These tools provide a common interface to further integrate our medicinal and computational chemistry expertise, and we are particularly excited that we will be able to gain immediate feedback on where to optimise the ligand-protein interactions by visually assessing how protein and ligand electrostatics complement each other.”

“Having licensed our ligand-focused applications, Spark™, Forge™ and Torch™, to CRUK MI for a number of years, we are delighted that this leading research institute, has added Flare™ for structure-based design,” says Dr David Bardsley, Commercial Director, Cresset.

Cresset’s innovative Electrostatic Complementarity TM maps and scores provide rapid feedback on new molecule designs. Green: good electrostatic complementarity. Red: electrostatic clash.

 

Cresset and Elixir collaborate to deliver efficiencies to the Design Make Test Analyze (DMTA) Cycle

Cambridge, UK – 15th October 2018 – Cresset, innovative provider of software and contract research services for small molecule discovery and design, and Elixir Software, provider of real-time workflow tracking applications, have formed an alliance whereby the combination of their technologies will form the basis of a new groundbreaking application, which will radically increase the efficiency of drug discovery by managing, analyzing and reporting all processes within and between projects.

“The modern paradigm in drug discovery is highly collaborative, both internally and externally, with design partners and CRO’s for instance. Key to making this paradigm efficient is effective real-time communications and the ability to manage and track all aspects of the Design, Make, Test, Analyze (DMTA) process.”, says Dr Robert Scoffin, CEO, Cresset.

“Elixir bring their cloud-based chemTraX platform to the collaboration; a highly visual DMTA workflow application for hypothesis capture, compound design prioritization and synthesis tracking. This will deliver improved/increased efficiencies wherever new molecule discovery is carried out.”, says Dr Paul Faulder, CEO, Elixir Software.

“Cresset bring a wealth of experience and expertise in the analysis and design of novel chemical entities. By combining these technologies, it is our ultimate vision to create a platform that enables efficient, modern drug discovery on a global scale and focusing on interactive communication and seamless collaboration amongst members of the discovery team.”, says Dr Tim Cheeseright, Director of Products, Cresset.

September 2018 newsletter

Integrating Jupyter Notebook into Flare

Take a sneak peak at Paolo Tosco’s work to integrate the Jupyter Notebook into Flare including the example workflow that he presented at the 7th RDKit user meeting.


Using Python in Flare to find common contacts in Flare

Tim Cheeseright takes a look at using Flare to automatically highlight the difference in binding site residues for two PDE5 ligands.


See Flare V2 new science and functionality in action

Following the launch of Flare V2 in June, this video demonstrates the fully featured science driven application which enables you to learn more about your protein-ligand systems.


Spark reagents databases

Monthly updates to the Spark reagent databases give you access to the latest reagent availability information, helping you make informed choices between Spark results. Download the latest version using the Spark Database Updater. Command line options are also available.


Artificial Intelligence and machine learning: Where’s the intelligence?

Andy Smith, Discovery Services Scientist, discusses the distinction between AI and machine learning, mining big data in drug discovery, prediction and understanding for small data sets, and how the real intelligence lies with the operator.


Review of XXV EFMC International Symposium on Medicinal Chemistry

With three separate scientific tracks: Therapeutic Areas, Technologies and Chemical Biology, it was impossible for the 800 plus delegates to see everything, but the busy schedule meant that there was something for everybody. Martin Slater reviews first disclosures, GPCRs and other highlights.


Citations

  • Structure–Activity Relationship and Molecular Docking of Natural Product Library Reveal Chrysin as a Novel Dipeptidyl Peptidase-4 (DPP-4) Inhibitor: An Integrated In Silico and In Vitro Study, Molecules 2018, 23, 1368.

See this and other citations.


Upcoming events

October

  • 8th-9th, 3rd RSC BMCS Medicinal Chemistry Symposium on Macrocycles, Stevenage, UK
    • Poster: Rapid and Accessible In-silico Macrocycle Design: Application to BRD4
  • 9th-10th, ELRIG Drug Discovery for Small and Large Molecules, London, UK
  • 9th-11th, Chem-Bio Informatics Society, Tokyo, Japan
    • Seminar: Predicting Biological Activity Using the Electrostatic Complementarity of Protein-ligand Complexes
    • Poster P2-06: Rapid and Accessible In-silico Macrocycle Design
  • 10th-12th, Bio Japan, Yokohama, Japan
  • 18th, Symposium on Streamlining Drug Discovery, Cambridge, MA, USA
  • 23rd, Symposium on Streamlining Drug Discovery, San Diego, CA, USA
  • 24th, Synthesis in Drug Discovery and Development Symposium, Alderley Edge, UK
  • 25th, Symposium on Streamlining Drug Discovery, San Francisco, CA, USA
  • 31st-2nd November, AusBiotech, Adelaide, Australia

Date for your diary

  • Cresset User Group meeting 2019, June 20th-21st

See all events.

August 2018 newsletter

Investigating the SAR of XIAP ligands with Electrostatic Complementarity maps and scores

In this case study, we used the Electrostatic Complementarity maps available in Flare to investigate the protein-ligand electrostatic interactions and the SAR of a set of inhibitors of the X-linked IAP (XIAP)-caspase protein-protein interaction. Electrostatic Complementarity scores calculated with Flare were used to quantitatively model XIAP-BIR3 pIC50.


Outstanding new 3D graphics in Spark V10.5.5

A new patch level release of Spark™, our scaffold hopping and bioisostere replacement application, is now available. Spark 10.5.5 includes improvements to the look and feel, rendering and performance of the graphics of the 3D window. Customers will receive the download link soon. If you’re not currently a Spark customer, request your free evaluation.


Modeling ‘big’: Applying the XED force field to biologics

Cresset is well known for powerful and accurate ligand-centric modeling, and Flare has established our methods for protein-ligand interactions. Work on GPCR modeling and viruses demonstrates the effectiveness and potential of Cresset technology for protein-protein interactions. Martin Slater, Director of Consulting Services, discusses the successes and challenges of modeling ‘big’ – applying Cresset’s XED force field to biologics.


Presentation from 256th ACS National Meeting

See the Rapid and accessible in silico macrocycle design presentation Rob Scoffin presented in the COMP Division at the 256th ACS National Meeting.


Citations

  • Exploring Modifications of an HIV-1 Capsid Inhibitor: Design, Synthesis, and Mechanism of Action, Journal of Drug Design and Research
  • Field Template-based Design and Biological Evaluation of New Sphingosine Kinase 1 Inhibitors, Breast Cancer Research and Treatment
  • Identification of Potentially Potent Heme Oxygenase 1 Inhibitors through 3D‐QSAR Coupled to Scaffold‐Hopping Analysis, ChemMedChem
  • Kinetic Characterization of Novel HIV-1 Entry Inhibitors: Discovery of a Relationship between Off-Rate and Potency, Molecules

See all citations.


Upcoming events

September

  • 2nd-6th, XXV EFMC International Symposium on Medicinal Chemistry, Ljubliana, Slovenia
    • Meet us on stand 32 and see our poster ‘Rapid and Accessible In-silico Macrocycle Design-Application to BRD4’
  • 10th-12th, 7th RSC/SCI Symposium on GPCRs in Medicinal Chemistry, Verona, Italy
    • Meet us in the exhibit area and see our poster ‘Summarizing and Understanding SAR and Activity Cliffs in GPCRs’ (P33)
  • 16th-20th, 22nd European Symposium on Quantitative Structure-Activity Relationship, Thessaloniki, Greece
    • Oral: Predicting Activity Using the Electrostatic Complementarity of Protein-ligand Complexes
    • Poster: Can I Make This Into a Macrocycle? Effective Methods for Fragment Growing, Joining and Cyclization
  • 17th-18th, Medicinal Chemistry Summit, Boston, MA, USA
  • 19th-21st, RDKit User Group Meeting, Cambridge, UK
  • 26th, The Best of Both Worlds: Innovation, Collaboration and Synergy between CROs and their Client Partners, Stevenage, UK
    • Poster: Predicting Activity Using the Electrostatic Complementarity™ of Protein-ligand Complexes
  • 26th, UK QSAR Fall Meeting, Oxford, UK
  • 28th, BioCap, Alderley Park, UK

October

  • Symposium on Streamlining Drug Discovery
    • 18th, Cambridge, MA, speakers from: AbbVie, AstraZeneca, Cresset, Elixir Software, Intellegens, Novartis, Optibrium, Takeda
    • 23rd, San Diego, CA, speakers from: Cresset, Elixir Software, Intellegens, Lilly, Optibrium, Retrophin, Takeda
    • 25th, San Francisco, CA, speakers from: Cresset, Elixir Software, Intellegens, Lilly, Novartis, Optibrium

See all events.

July 2018 newsletter

Launch of Cresset Python extensions for Flare

Python scripts that extend the functionality of FlareTM, our structure-based design platform, are now available for download from GitLab. This includes scripts written by Cresset that extend the functionality of Flare, scripts that use pyflare to create command line workflows and example scripts for developers.


Flare V2 keyboard shortcuts

See at a glance the keyboard shortcuts for V2 of Flare and the Flare Molecule Editor.


Spark reagent databases

Access the latest information on reagent availability to refine your SparkTM results. Download the updated version of the Spark reagent databases, based on the eMolecules Building Blocks collection.


We’re hiring!

We’re recruiting for a European Application Scientist, based in the UK. The successful applicant will provide scientific support to our existing customer base and commercial team.


Symposium on Streamlining Drug Discovery

These one day symposia, delivered by Cresset, Optibrium and Elixir, will highlight new approaches and technologies being applied to the search for future therapeutics.

Free to attend, these events are aimed at scientists from pharmaceutical, biotechnology, agrochemical, flavor and fragrance organizations, not-for-profits and academia who wish to get a broad appreciation of the latest advances in drug discovery delivered by key scientists and thought leaders from leading organizations.


Upcoming events

August 19-23: 256th ACS National Meeting, USA

August 19: MEDI poster: Rapid and Accessible In-silico Macrocycle Design: Application to BRD4

August 21: COMP oral: Rapid and Accessible In-silico Macrocycle Design; COMP poster: Deciphering Kinase SAR Using Electrostatics

September 2-6: XXV EFMC International Symposium on Medicinal Chemistry, Slovenia

  • Meet us on stand 32 and see our poster ‘Rapid and Accessible In-silico Macrocycle Design – application to BRD4′

See all events.

June 2018 newsletter

Flare V2 released: New science and functionality

Giovanna Tedesco introduces the new science and functionality in Flare V2, including: Electrostatic ComplementarityTM, enhanced protein surface coloring, ensemble docking, enhanced ligand-design functionality, Python API.


Flare API: A new playground for computational chemists and developers

The Python API in Flare enables both high-level access to scientific functionality with the aim to automate tasks, and low-level access to the graphical user interface and internal processes, thus enabling the implementation of own algorithms and customization of the interfaces through addition of user-defined controls. Paolo Tosco describes the different ways to deal with Python code in Flare, ranging from plain execution of Python scripts through the interpreter to the highly interactive Jupyter QtConsole and Notebooks.


Review of 11th International Conference on Chemical Structures

Paolo Tosco captures the highlights of talks he found most inspiring at the 11th International Conference on Chemical Structures, even though the list could indeed be much longer.


Presentations from the Cresset User Group Meeting

The excellent feedback from delegates who attended the Cresset User Group Meeting last week reflect our own view that this was an excellent forum for great science and collaborative discussion in a wonderful atmosphere. Thanks are extended to the speakers and exhibitors who contributed to the meeting and who have given permission for us to share their presentations.

Date for your diary: Cresset User Group Meeting 2019 on 19-20 June, Cambridge, UK.


Upcoming events

  • 4-6 July: RICT, Strasbourg, France
    • Meet us at booth 25
    • See our poster: Rapid and Accessible In-silico Macrocycle Design: Application to BRD4
  • 19-23 August: 256th ACS National Meeting
    • 19th August:
      • MEDI poster: Rapid and Accessible In-silico Macrocycle Design: Application to BRD4
    • 21st August:
      • COMP oral: Rapid and Accessible In-silico Macrocycle Design
      • COMP poster: Deciphering Kinase SAR Using Electrostatics

See all events.

Flare™ V2 heralds next generation of structure-based design with Electrostatic Complementarity™ scoring and new Python® API

Cambridge, UK – 20 June 2018 – Cresset, innovative provider of software for molecular discovery, is pleased to announce the release of Flare V2. Introducing major enhancements to ligand design and activity prediction in a modern, extensible, scriptable interface, Flare V2 raises the bar in structure-based design.

Make rapid activity predictions using Electrostatic Complementarity™

“Our commitment to innovation sees the introduction of Electrostatic Complementarity (EC) to Flare. This ground-breaking new technique promises a radical change in new molecule design,” says Dr Mark Mackey, CSO at Cresset.

EC scores and maps provide rapid activity prediction with visual feedback on new molecule designs. Chemists will better understand ligand binding, structure-activity relationships and the ranking of new molecule designs. Based on Cresset’s polarizable XED force field, the EC calculation is fast and predictive.

New Python® API makes Flare massively extensible

“The new Python® API enables chemists to create their own workflows and automate common tasks making Flare easy to customize and extend,” says Dr Tim Cheeseright, Director of Products at Cresset.

The Python API gives full access to all of Flare’s capabilities, including the RDKit cheminformatics toolkit, plus Python modules for graphing, statistics, Jupyter® notebook integration and other features.

Major enhancements to workflow and usability

Flare V2 includes over 200 new and improved features covering usability, multi-parameter scoring, ensemble docking and more.

Computational, medicinal and synthetic chemists are encouraged to request a free evaluation of Flare.

Flare V2 makes advanced structure-based design techniques, such as Electrostatic Complementarity, multiparametric scoring and Python scripting, accessible through an intuitive GUI.

The healing potential of tango for people living with Parkinson’s: Upcoming events

Cambridge, UK – 14 June 2018 – Cresset, innovative provider of outstanding software for molecular discovery, is pleased to announce its support for ‘Parkinson’s and the Tango Effect’, a book written by Kate Swindlehurst, a tango dancer living with a diagnosis of Parkinson’s. It is being crowd-funded through the publisher Unbound.

‘Parkinson’s and the Tango Effect’ began with a tango lesson and grew into an exploration of the healing potential of tango. The book builds on research on the impact of dance on Parkinson’s symptoms and takes it a stage further, with a behind-the-scenes record of private lessons and contributions from tango teachers. It documents the emotional and social benefits of the dance and its impact on the quality of life for people living with Parkinson’s.

Kate will be talking about the book and her experiences in three upcoming events:

May 2018 newsletter

Last chance to register for Cresset User Group Meeting, 21-22 June

With just four weeks until the Cresset User Group Meeting scientific program, we encourage you to secure your registration no later than 6th June.

  • Scientific program, June 21: Stevan W Djuric, AbbVie will deliver the keynote lecture, with additional invited presentations from Novartis, Cancer Therapeutics CRC, University of Cambridge, Sun Yat-sen University, Keio University, University of Edinburgh, and Cresset will present latest science and showcase upcoming applications.
  • Workshops, June 22: Very limited spaces remain on these hands-on software workshops: Introduction to Flare, Python in Flare, Advanced Spark, 3D-QSAR in Forge, Forge SAR, and Library design with Cresset nodes in KNIME.

A sneak peek into Flare V2: A major advancement for structure-based design with Flare

Flare V2 is in the final rounds of testing, which means the release announcement is imminent. Ahead of the user group meeting, where we will be presenting this major advancement, this post takes a sneak peek at some of the new features in this version.

Review of 8th RSC/SCI symposium on kinase inhibitor design

Martin Slater’s review of Kinase 2018 focuses on talks discussing lipid kinases, kinase activators and kinase inhibitors for the CNS.

Upcoming events

  • 4-7 June, BIO International 2018, Boston, MA, USA
  • 7-8 June, 19th Annual Drug Discovery Summit, Berlin, Germany
  • 7-8 June, New Frontiers in Ocular Therapeutics 2nd Edition, Dublin, Ireland
    • Mark Mackey, CSO, presenting on ‘In silico virtual screening to provide new candidates for drug discovery’
  • 7-10 June, 2nd Worldwide Chinese Computational Biology and Molecular Simulation Conference, Guangzhou, China
  • 21-22 June, Cresset User Group Meeting 2018, Cambridge, UK

See all events.

Parkinson’s and the Tango Effect

Through our corporate social responsibility, we are delighted to support Kate Swindlehurst who is promoting the healing potential of dance for those with Parkinson’s.