The virtuous circle: Cultivating closer ties between academia and industry

Academia and industry always have a lot to gain from cultivating close ties with each other. As with any relationship, getting the balance right between give and take starts with a generous attitude from both parties.

Cresset develops software and services for small molecule discovery and design, primarily for the pharmaceutical R&D. We work with the global academic community in a number of ways, including collaborative projects, Knowledge Transfer Partnerships and commercialization of academic methods. We also invest in academic programs with the hope of shared benefits on several different timescales.

“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.”

Dr Daniel Barr, Assistant Professor of Biochemistry, Department of Chemistry and Biochemistry, Utica College, USA

A long-term investment of lecturing and training

We wholeheartedly believe that our methods shorten the path to new compounds. That by using Cresset computational software, more and better compounds will be discovered more efficiently. Therefore, we want to spread the word to the next generation of computational chemists, who are already far more computationally literate than any previous generation. We are actively involved in teaching and training the next generation of computational chemists.Here’s what we’re doing to support that goal:

  • Applied for a network grant with European Training Network ETN to help with training computational chemists at the Universities of Oxford, Southampton, Bristol, Portsmouth and Sussex
  • Mark Mackey, Cresset’s CSO, is a visiting lecturer at the University of London
  • A range of summer projects to A-level and undergraduate students
  • Successful Knowledge Transfer Partnerships with the University of Edinburgh and the University of Bristol.

By being closely associated with the up and coming generation of computational chemists, we’re also staying in touch with how our user base is growing and changing.

The traditional gap between medicinal chemists and computational chemists is becoming blurred. It is unthinkable that today’s medicinal chemist graduates will not use computers in their every-day work. They may not want to work with command line code, but they feel very at home with our chemistry software.

In response, we’re changing how we develop new tools in order to make them more accessible to a widening group of users. We continue to invest heavily in usability and good design, and we also continually review and add new tools that support workflow.

Collaboration for new scientific methods

Everyone who works in computational chemistry knows that the open source community develops many and varied methods, most of which are useful and some of which are outstanding.

Rather than viewing this as competition for commercial software, we see it as an opportunity for partnership. Rather than developing new methods, we can work with academics to build their excellent code into our computational chemistry environments.

But why would anyone pay for an open source method?

The answer is convenience, usability, validation and support. Some professionals working in industry find it difficult to adopt academic methods for their work since they’re not supported by their in-house IT policies. We put academic methods into a professional environment with a highly usable GUI and make sure it integrates with the rest of our software and complies with other protocols. We also offer a professional level of support.

In return, the academic authors may receive royalties, additional kudos from broader usage of their code, valuable links with industrial scientists, plus a broader user community contributes to the ongoing development of their methods.
For example, WaterSwap is a widely used, open source method implemented in SIRE. It was developed by Dr Chris Woods at the University of Bristol. Cresset collaborated with Dr Woods to license WaterSwap and include it in Flare, our structure-based design application.

WaterSwap in Flare
Figure 1: WaterSwap is a thermodynamic integration method for investigating ligand-protein energetics. Green residues show where the ligand is gaining the most energy from interaction. Red residues show where water binding is preferred and represents opportunities to improve ligand design.

“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.”

Dr. Prija Ponnan, Department of Chemistry, University of Delhi

Low cost software for academic research

One of the hurdles faced by many software vendors in validating their methods is the understandably high level of confidentiality associated with pharmaceutical R&D. To take one (anonymized) example. Two years ago Blaze, our virtual screening platform, was used to successfully identify a potential hit from the large compound libraries of a major organization. That compound is now going into clinical trials. However, the time scales are such that it could be ten years before anything is ever published about the methods used to discover the compound.

By contrast, academic groups using our software are extremely likely to report their results in papers, thus creating a healthy supply of citations. Our customers need proof that our software delivers results, and academia is an ideal source.

We offer significant reductions on software used for academic research, and we offer flexible licensing options for software used for teaching or PhD research.

Listening to and delivering what researchers want

Finally, we want to hear from opinion makers, and this can be the most mutually valuable exchange of all.

Our software needs to provide outstanding science and support changing workflows. As we develop and improve applications we need to keep listening to researchers about how they are working and what will help them stay on leading edge of research. Close relationships, sometimes over many years, encourages an open dialog that helps us to get our products right, and helps leading academics to get the software that will be of most use to them most in their research.

We want academics to be able to work as efficiently as possible to find compounds that will help in therapeutic areas of need. And we also want to provide the best possible tools to the broader market.

Access our software and work with us

See the licensing options for our ligand-based and structure-based applications. Or contact us for a free confidential discussion to find out how Cresset Discovery Services experts can add value to your project.

CEO end of year message 2018

Dr Robert Scoffin, CEO

As we near the end of the year I’ve been reflecting on the progress we’ve made. During 2018 we’ve seen major developments in Cresset Discovery Services, in software development, and in our application science team in particular, but wherever I look in the company there are exciting activities and new faces. Here are a few highlights of the past year.

Our landmark structure-based design tool, Flare™, has been expanded to include Electrostatic Complementarity™, ensemble docking and much more, making it a truly powerful design environment for medicinal chemists. Not forgetting our computational chemist audience, we’ve also added a Python API, making Flare a new playground for computational chemists, scripters and developers.

The year also saw us reveal an exciting new development project: a web-based platform for small molecule discovery. In case you missed the announcement, have a look at this sneak peek at next generation collaborative 3D design. This project, combined with our collaboration with Elixir Software, will deliver a platform that will radically increase the efficiency of drug discovery by managing, analyzing and reporting all processes within and between drug discovery projects. Further details will be announced next year.

One of the highlights of any year is always the many customer interactions we enjoy – not least at our annual Users’ Group Meeting. In June we were honoured to welcome delegates and presenters from all over the world to share their research progress and scientific successes. Even if you were not able to attend, many of the presentations are available online. As always, delegates expressed their appreciation of the science presented and the hands-on workshops. You are warmly invited to join us for the 2019 UGM on June 20-21 in Cambridge, UK.

As our software development and commercial activities increase, we’re delighted to have welcomed several new team members, including Dr Andy Smith who has joined Cresset Discovery Services as Discovery Services Scientist, based at BioHub, Alderley Park, UK.

I’d like to sincerely thank you, our customers, partners and the Cresset team, for all of your input and support. We look forward to delivering more outstanding applications to enhance your research in 2019 and beyond.

CEO end of year message 2017

Dr Robert Scoffin

Dr Robert Scoffin, CEO, Cresset

As 2017 draws to a close I’d like to take the opportunity to say a huge thank you to all of our customers, partners and staff for your support, collaboration and hard work. 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.

This was clearly demonstrated in the many success stories and by the record-breaking attendance at The Cresset User Group Meeting 2017 in Cambridge, UK in June. We welcomed attendees from all over the world, reflecting our growth in many different geographical markets, including Australia, Japan,  China, India and Russia.

This year, it felt to me that Cresset truly came of age. We successfully applied our principles of ‘innovative science delivered through intuitive software’ to launching Flare, a completely new product for structure-based design. We’re delighted with the positive feedback from our first Flare customers and are already working to deliver additional features in 2018.

Alongside Flare, our existing software is being continually developed and updated in response to customer requirements and scientific developments. In order to ensure that we continue to meet your workflow and scientific needs, we have welcomed two new members of staff this year. Dr Sylvie Sciammetta has joined our North American team as an applications scientist, and Dr Matthias Bauer has joined the Cambridge R&D team as a scientific developer.

Over this past year, Cresset Discovery Services has worked on customer projects with a diverse range of challenges and targets. We’ve had a number of particularly successful projects with academic spin-offs and early phase companies where we’ve worked to accelerate progress on developing their discovery platforms. Many of these projects make for particularly exciting science and we hope to be able to share more of our successes with you in future case studies and at our 2018 UGM.

We greatly value and appreciate all of your requests and feedback as we continue to work to advance the quality of our software, services and support. We look forward to working with you in 2018 to develop an even more exciting future for Cresset customers and the computational chemistry community.

Link prescriptions to medical conditions to pave the way for more repurposed drugs

david-cavalla

 
 
By David Cavalla, Numedicus Limited.

 
 
 

Repurposed drugs are often subject to off-label generic substitution, making them an unattractive development route for some pharmaceutical companies. Dave Cavalla 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.

On 6-7 November 2015, I attended the annual conference of the Action Duchenne charity. One of the key points of debate was the status of Translarna, an expensive new product for the rare muscle disorder Duchenne Muscular Dystrophy, which is currently being considered for reimbursement by the NICE, the UK body that approves NHS treatments.[1] The subject raises substantial ire among Duchenne sufferers and their families, due to the hesitation of NICE to fund the treatment, even though it is not a cure and is not the only highly priced product likely to be reviewed for this condition in the future.

At the same conference we heard about the potential to treat the condition with repurposed compounds like Viagra, tamoxifen and metformin; cheap alternatives that are based on small molecule generic products. These research programs are taken forward with public funds or charitable support, and in consequence are much slower to come to the market. If an alternative pricing structure were available to encourage pharmaceutical companies to pursue repurposing as a development strategy, it could mean that more and better drugs are brought to market faster for rare diseases such as Duchenne.

Rare diseases are relatively common

1 in 17 people will be affected by a rare disease at some point in their life. There are over 6,000 rare diseases, and new rare diseases are documented in the medical literature at a rate of 5 per week. Fewer than 5% of these conditions have an approved therapeutic option.

Despite this large cumulative effect, each rare disease, by EU definition, affects less than 5 in 10,000 of the general population. In order to obtain a return on investment for new medical treatments, companies have to charge very high prices to the few people who have the condition.

Drug repurposing makes development faster and cheaper

It is common for medicines to have multiple uses. Aspirin is a salient example: it was first used for pain, then as an antithrombotic and has recently been found to have important potential cancer preventative properties. We now believe that over 90% of existing drugs can be repurposed, in some cases more than once.

Drug repurposing has become increasingly adopted by charities and some small biotech companies as a means to decrease cost and time to market for drugs for rare diseases. The advantages are clear:

  • drug discovery time is reduced by two-thirds
  • the chance of developmental success is increased by 250%
  • the cost of R&D for new medicines is reduced by five-sixths.

Pharmaceutical companies still prefer NCEs

However, the return on investment (ROI) for repurposed compounds is not always clear, even with new use patents. Companies are concerned that generic drugs will be substituted for the branded repurposed medicine and they will be unable to recoup their costs.

This represents a tremendous lost opportunity.

Possible solutions to encourage patient-led research are to:

  • incentivise the pharmaceutical industry to invest in drug repurposing
  • facilitate the involvement of the not-for-profit sector
  • create a new pricing structure that links electronic prescriptions and pricing to medical condition.

An alternative pricing structure

I have worked in drug repurposing for as long as the strategy has had a name and I have considered this problem deeply. I recently wrote a book called ‘Off-Label Prescribing: Justifying Unapproved Medicine’[2], where I proposed that there should be an enhanced level of pricing for repurposed products. This would be imposed at the point of prescription and reimbursement, and operated for some years as an incentive to the repurposing innovator. Since the book was published, a very similar proposal was made by Prof Ben Roin, a respected policy strategist at Harvard/MIT, with respect to the US system of medicines.[3]

In the era of electronic prescribing, a dual pricing arrangement would not be difficult to implement. Moreover, it would dovetail with the founding principle of NICE, that therapeutic indication and reimbursement are intertwined.

This simple change, linking prescription to condition on an electronic platform with a dual pricing structure, would strengthen the value of mode-of-use patents for the pharmaceutical industry, thus promoting commercial investment into repurposing research.

Support repurposing through pricing

In the absence of a balanced framework of incentives for drug repurposing, pharmaceutical research will be slanted towards high-priced products that are ultimately unaffordable. Under the current system, the interests of pharmaceutical companies are not aligned with those of patients and healthcare providers. The need to make a profit currently takes companies towards difficult and lengthy research that can command a high price rather than easier and quicker research that is likely to have more effective patient outcomes, but which might be unprofitable. This is a lose-lose scenario for governments and taxpayers alike.

For the sake of patients, and especially for those with the thousands of rare conditions currently lacking any therapy, implementing a pricing policy to protect revenues from repurposed compounds are an option that should not be ignored.

 

[1] Translarna was recommended by NICE on 16 April 2016 in connection with a Managed Access Agreement (MAA) with NHS England for ambulatory patients older than 5 years old.

[2] Off-label Prescribing: Justifying Unapproved Medicine. David Cavalla. ISBN: 978-1-118-91207-2. 216 pages. March 2015, Wiley-Blackwell.

[3] Roin, B. Solving the Problem of New Uses http://dash.harvard.edu/bitstream/handle/1/11189865/Solving%20the%20Problem%20of%20New%20Uses%20.pdf Oct 13, 2015.

CEO end of year message 2016

seasons-greeting-2016

2016 has been a year of exciting developments for Cresset. We have been working hard on developing an outstanding new software tool for discovery, we have expanded our services offering and we have broadened our global network of customers and collaborators.

A new workbench for structure-based design

I am delighted to announce that our new workbench for structure-based design, will be released in 2017. The application offers outstanding 3D electrostatic and shape analysis of protein binding sites and is underpinned by the trusted and well validated XED force field.

It will be a significant addition to our range of software for discovery chemistry, and I am looking forward to seeing it in your hands and making a real difference to your projects.

Making the molecules that matter

In 2016 we are proud to say that Cresset Discovery Services has helped chemists to do less chemistry!

Our projects with multi-national corporations, small biotechs, academic and non-for profit groups and many more show time and again that the Cresset approach saves time and money by helping chemists to focus on the molecules that matter. There are three key elements to this:

  • Using modeling to maximize your knowledge of the protein-ligand system
  • Using virtual screening to rapidly assess chemical space to choose the subset that matters
  • Integrating this knowledge into the whole project, by working alongside project decision makers and medicinal chemists.

A second patent for Re-Pharm

In March, Re-Pharm was awarded its second patent for the anti-inflammatory, steroid-sparing properties we discovered in the re-purposed compound RP0217.

We already held a patent on its use for the treatment or prevention of respiratory and gastrointestinal inflammatory disorders. This second patent covered the use of RP0217 with and without co-formulated or co-administered steroids in topical ophthalmic indications. We look forward to the granting of similar US patents in 2017.

Welcome to the family

Over the year we have welcomed Mary Megan and Ken Stott to the development team, as well as Jay Lakhan to the sales team. Level 5 have been appointed as our distributors in Japan. We have also formed a new partnership with BioMolTech, the producers of the Lead Finder docking engine.

User Group Meeting in Cambridge, UK

In June 2017 I look forward to welcoming you to our global User Group Meeting in Cambridge, UK to share knowledge, ideas and successes.

Cresset was founded on the unique work of Dr Andy Vinter on the XED force field in the mid-1990s. At the 2017 UGM we will celebrate our 15th anniversary of trading as Cresset. Whether you are new to Cresset, or whether you have been with us from the beginning, I hope to see you there.

 

Thank you for your custom and support in 2016. We wish you a very happy and successful 2017.

Rob

 

 

 

 

 

 

Dr Robert Scoffin
CEO, Cresset

User Group Meetings 2016 review

The Cresset 2016 North American and European User Group Meetings combined presentations and workshops in Cambridge, MA and UK respectively. A large and diverse group of scientists gathered to share ideas and experiences in the latest computational approaches to the design and optimization of small molecules.

As well as talks from invited speakers from the pharmaceutical and agrochemical industries, plus academia, Cresset staff also gave updates on new developments, including a preview of the new Cresset protein tool, due for alpha release this summer. You can see the presentations we have permission to publish below.

Workshops ran in parallel streams, focusing on increasing and deepening understanding of Cresset software. You can see the content covered in the workshops below.

Feedback from delegates on the scientific program and workshops was excellent, and I particularly enjoyed the chance to catch up with familiar faces and meet new people. These were our largest User Group Meetings to-date and we are already looking forward to celebrating 15 years of Cresset in 2017 – I hope many of you will join us.

Photos from User Group Meetings

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CEO end of year message 2015

As we head towards the end of the year, I reflect that 2015 has seen many exciting and challenging changes. As a business we have developed and made progress in all directions.

New worldwide relations

As our business in India continues to grow, I am pleased to announce that we have appointed a new country manager and two regional distributors in Delhi and Kolkata so as to better serve this emerging market.

We recently signed an agreement with COSMOlogic to distribute their software in North America. I have just returned from a successful trade show in Utah promoting their tools for chemical engineers, providing users with highly accurate predictions of the thermochemical properties of pure compounds and complex mixtures. I am looking forward to opening new markets and achieving commercial success with them.

This year also marks the start of some exciting new international customer relationships. CTx in Australia are using Blaze to set up a new virtual screening service for Australian research groups. Our business in China continues to strengthen, with new customers at the Shenyang Pharmaceutical University. Cresset is also strengthening links with China by participating in the Lancaster University China Catalyst programme.

Cresset Discovery Services: A new breed of CRONew breed of CRO services_for web

Over the summer we considered how best to organise our resources to better serve our customers. As a result we have broadened and re-brand our services business as Cresset Discovery Services (CDS), offering a comprehensive set of solutions for discovery research. We launched CDS at the Boston Fall ACS meeting with the headline ‘A new breed of CRO’ and have received high levels of interest from new prospective customers.

New science driving new software components

A significant software development earlier this year was Activity Atlas, a new component for Forge enabling you to easily summarize complex SAR as a 3D visualization. Our R&D team are working hard on more exciting new developments for 2016 so subscribe to our newsletter to be amongst the first to hear this news.

Outstanding levels of customer service

A recent analysis of our support statistics showed that we have an exceptionally good record for response time. 80% of queries were resolved the same day they were raised, 90% were resolved in 24 hours and 95% were resolved in 48 hours, which includes weekend and Friday afternoon queries. I hope that your personal experience is reflected in these figures. We look forward to continuing this outstanding level of customer service in the years to come so don’t hesitate to contact our support team when needed.

Events

1_Cresset European User Group Meeting 2015Our User Group Meetings in North America and Europe (picture right) continue to provide an excellent opportunity to hear case studies from customers and learn about new science. I was delighted to receive many complimentary comments following these meetings. We are already building an impressive line-up of speakers for the 2016 meetings where I hope to see you: North America, June 1st; Europe June 16th-17th.

In the spring we continued a successful series of symposia, this time at the British Consulate, Cambridge, MA, USA.

Most recently, we hosted the autumn meeting of the UK QSAR Discussion Group at Duxford, UK.

The first drug discovery patent for Re-Pharm

Last month Re-Pharm, our daughter company, were granted their first drug discovery patent for the re-profiling of an existing marketed drug into a novel set of therapeutic indications for inflammatory conditions. We are excited about the prospects for its further development and eventual out-licensing.

Thank you to all of our valued and loyal customers for the work we’ve done together in 2015. I look forward to future innovations and successes in 2016.

All the best wishes of the season

Rob

Rob Scoffin
CEO

End of year message from Dr Robert Scoffin, CEO of Cresset

As we near the end of the year it is great to look back at how we have helped our customers deliver concrete results in 2014. Commercial R&D is highly competitive and customer confidentiality is of primary importance to our customers, and therefore also to us. This makes it all the more rewarding to be able to share these recent announcements:

2014 has seen a continued strengthening of Cresset’s staff. Dr Ritesh Chauhan (European Account Manager), Dr Paolo Tosco (Computational Chemistry Developer) and Dr Giovanna Tedesco (Product Manager) are recent recruits who are based in our European headquarters in Cambridge, UK. We have also acquired new office space in Cambridge, MA, USA in order to better serve our North American customers.

New-staff-Dec-newsletter-2014_Paolo-Ritesh-Giovanna_2
Left to right: Paolo Tosco, Ritesh Chauhan, Giovanna Tedesco.
At the same time, there has been an increased focus on the increasingly important Asian markets in China, Japan and India. We appointed Shanghai-based Cloud Scientific as our primary distributor for the China market. In November we hosted the International Symposium on Compound Design Technologies, a successful one-day meeting in Shanghai, along with our partners Optibrium and Cloud Scientific. I was very pleased with the enthusiastic response to our software from Chinese industry and academia. This symposium was a repeat of a similarly successful event held in Tokyo and Osaka, Japan, in March.

Shanghai_edited-1
Left to right: Andrea, Hu, Qi, Jack (Cloud Scientific), Prof Jun Xu (Sun Yat-sen University) and Rob (Cresset) at the ISCDT held at the British Consular offices in Shanghai.
In Japan, Cresset also participated in the Bio-Japan Conference and Exhibition as part of the EU-Japan Bio Cluster Mission, both to raise the profile of Cresset and identify new opportunities for the company. Working with our distributor, Hulinks, we were pleased to announce the addition of Nagoya University to our growing list of Japanese customers.

There has been a continued focus on India, with the country seeing growth in pharmaceutical, biotechnology, agrochemical and academic research. The Centre for Chemical Biology & Therapeutics (CCBT) at Institute for Stem Cell Biology and Regenerative Medicine in Bangalore, India, recently took a 3-year license agreement for Forge and Spark. Dr Kavitha Bharatham, who leads the computational chemistry team in CCBT, commented that, “The support I have received from Cresset staff has been excellent, and I am very pleased to introduce their computational tools to CCBT for our lead optimization and identification projects. I am confident that we will achieve our goals.”

Our North American and European user group meetings this year were a great chance to hear from customers old and new. If you missed these meetings you can see the presentations we have permission to publish here. The 2015 user meeting dates are June 3rd in Cambridge, MA, USA and June 18th – 19th in Cambridge, UK. I encourage everyone connected with Cresset to attend one of these informative meetings. They are a great opportunity to share ideas and innovations, receive hands on software training and to network with new contacts from industry and academia.

On behalf of the Cresset team, I wish you all the very best for a successful 2015. I look forward to meeting you at our user meetings or one of our other forthcoming events, and I hope to be able to share many more successes with Cresset’s customers around the world.

Rob
Dr Robert Scoffin
CEO

Cresset adds to scientific and commercial team in Cambridge

In response to our continued business growth we are delighted to announce that Paolo Tosco has joined us as a Computational Chemistry Developer and Ritesh Chauhan has joined us as Account Manager for UK and Europe.

Paolo was previously Assistant Professor in Medicinal Chemistry at the Department of Drug Science and Technology (University of Turin). He has also held positions at COSMOlogic and Novartis Institutes for Biomedical Research. Paulo has a Masters in Medicinal Chemistry and Pharmaceutical Technology plus a PhD in Drug Chemistry from the University of Turin.

Ritesh has previously held commercial roles with Charnwood Molecular Ltd and Johnson Matthey PLC. He has a PhD in Synthetic Organic Chemistry from Loughborough University and a MChem(Hons) in Chemistry from Nottingham Trent University.

“As you will have seen from our recent blog posts and newsletters, there is a lot happening at Cresset in terms of scientific activity and commercial growth. This has enabled us to enhance the Cresset team, in order to continue to provide our customers with the highest levels of quality in products and services. I extend a very warm welcome to both Paolo and Ritesh and I encourage you to take the opportunity to meet both of them at various events during the course of the year” said Dr. Robert Scoffin, Cresset CEO.

From virtual screening to real compounds

Managing the procurement process to deliver plated compounds to your door

Cresset consulting services runs computational experiments to help you understand your chemistry better. The usual result from a project is a list of compounds to make or purchase. However, we can also go further and manage your procurement process so that we deliver plated, assay-ready compounds to your lab.

Cresset optimizes the compound selection process so that you get the best possible selection of compounds delivered to the next stage in the discovery process. We work with best- in-class chemistry and shipping providers to provide you with a single point of contact so that you end up with not only the answers you want, but also the actual compounds.

This can be particularly helpful when choosing compounds to purchase after a virtual screening project.

An up-to-date 3D database of available screening compounds

Cresset’s virtual screening database contains over 10 million compounds from over 20 different vendors. It is kept continually up to date from the catalogues and is a comprehensive source of available screening compounds.

We load the compounds into the database in the form of SMILES strings or SD files. In order to make this database searchable using our virtual screening engine Blaze, each 2D compound is expanded to a set of 3D conformations. These are minimized, and up to 100 conformers are stored for each compound. Fields are added to each conformer, enabling it to be compared to the query molecule for a potential match.

Easing the logistic challenge of dealing with multiple vendors

This database gives our customers a very broad selection of chemistry, as opposed to screening compounds from only one vendor. The downside is that the final results of a virtual screen may be 500 compounds from 20 different vendors, possibly with only a handful of compounds coming from some vendors. This leads to bureaucratic and shipping overheads. Each vendor charges a fixed amount per compound, plus a flat rate shipping fee, therefore the more compounds sourced per vendor, the cheaper the final total.

Cresset can help to deal with logistic difficulties in two ways. The first is to compare the results and suggest the same or very similar compounds from alternative vendors in order to reduce the number of vendors in the final list of compounds. The second is for us to handle the procurement process for you.

Case study: from virtual screening to plated compounds

We recently worked with a customer who came to us with a known target. They had a number of published active compounds and were looking for some new chemistry for some assays they had booked with a biology CRO.

Our virtual screening work resulted in recommendations for 250 screening compounds. For additional diversity, we used Spark to do some bioisosteric replacements around the core of the known active compounds. We used these new bioisosteres for a further virtual screen and used these results to recommend a further 50 compounds.

We then did further work to optimize the selection of compounds by looking at both alternative vendors for the same compounds, and highly similar compounds from alternative vendors. Where we had found very few compounds from one vendor, we identified alternatives from larger suppliers. At the end of this process we reduced the number of vendors for the 300 compounds from about 10 to 6. Of those 300, approximately 200 were sourced from only 2 vendors.

The customer chose to completely outsource the procurement of these compounds to Cresset.

Cresset managed the process, using a dedicated chemistry provider and specialist shipping agents. The compounds were bought from the various vendors, weighted, dissolved, plated and delivered to the biology CRO to be screened. The compound procurement for this project was multi-national, including the UK, Europe, Eastern Europe and the US. The final delivery was to a California-based biology CRO.

Not only did we recommend new compounds, we delivered the final plates to the biology CRO.

Translating computational results into real compounds

Outsourcing your chemistry logistics to Cresset as part of a computational chemistry project eases logistic challenges and smooths your supply chain. We can deliver not only the answers, but also the actual compounds.

Contact us to enquire about outsourcing a computational chemistry project.