Biowebtronics Biotech, startups, web development and internet of things.

In silico drug discovery Co.s

This is a post of some notes I made in an attempt to aggregate companies where in silico drug discovery is a main part of their business. Most of the text about the companies is straight from the company website.

Many thanks to @simonbayley, @rowan_UK and @rscoffin for the suggestions.

If you have anymore let me know on twitter @bennmiles

Cheers,

-B

Nimbus US

Nimbus Discovery harnesses cutting-edge computational technologies to uncover breakthroughs in small molecule pharmacology. Nimbus focuses on medically important and highly sought-after disease targets that have proven inaccessible to traditional industry approaches. Nimbus’ robust pre-clinical pipeline includes novel agents for the treatment of cancer, metabolic disease and inflammation. Founded in 2009, Nimbus partnered with Schrödinger to invent and apply a physics-based approach that establishes a new standard for rational drug design.

http://www.nimbusdiscovery.com/

Molplex UK

Molplex is a new class of pharmaceutical company, using its innovative technology to identify and optimise novel treatments for infection, cancer and other serious diseases.

Its pipeline of small-molecule therapeutics is driven by our proprietary platform for drug optimisation, Optiplex - a highly scalable system combining automated decision-making with laboratory automation. Optiplex delivers safer and more effective drugs at radically lower cost.

Molplex aims to discover novel treatments quicker and more effectively, improving the health of patients around the globe.

http://www.molplex.com/

Domainex UK

Domainex is a drug discovery company with a reputation for speed and innovation built on an exceptional track record of drug candidate delivery. It has a world class discovery team with an unrivalled track record of 5 Candidate Drugs delivered in 5 years.

Domainex reduces industry average drug discovery timelines by as much as 30% through the application of novel proprietary technologies and a highly focussed and integrated approach to medicinal chemistry andcomputational chemistry. These technologies and Domainex’s approach also enable it to successfully tackle a greater range of drug target classes, such as kinases, proteases, ion channels, proteins involved in epigenetics and protein-protein interactions.

Domainex has applied its unique technologies and focussed discovery approach to enable it to develop its own pipeline of oncology drugs, including inhibitors of the kinases IKKε/TBK1 and a number of epigenetics related lysine methyltransferases.

http://www.domainex.co.uk/

Biofocus UK

Collaborating with BioFocus' computational team puts leading informatics, molecular modeling and QSAR expertise at your fingertips. Working closely with our colleagues in screening, structural biology, FBDD, medicinal chemistry and with a leading position in the design of our fragment and SoftFocus libraries, our capabilities are available as part of hit identification, hit expansion, hit-to-lead and lead optimization programs.

In addition to contributing to client programs carried out at BioFocus we are able to provide computational chemistry consultancy to troubleshoot and contribute fresh ideas to your projects.

http://www.biofocus.com/

Evotec Switzerland / 600 employees…

Evotec is a drug discovery alliance and development partnership company focused on rapidly progressing innovative product approaches with leading pharmaceutical and biotechnology companies. We operate worldwide providing the highest quality stand-alone and integrated drug discovery solutions, covering all activities from target-to-clinic. The Company has established a unique position by assembling top-class scientific experts and integrating state-of-the-art technologies as well as substantial experience and expertise in key therapeutic areas including neuroscience, pain, metabolic diseases as well as oncology and inflammation.

http://www.evotec.com/

Cresset Group UK

Cresset’s consultants work with a wide range of therapeutically relevant targets and also in many disease areas in which the biological target is unknown. The majority of these projects involve ligand focused virtual screening.

Virtual screening is an effective means of switching chemical series to identify new intellectual property. It is also a fast and cost effective way of testing several different hypotheses.

http://www.cresset-group.com/

Molecular-weightJS

My web application for the chemistry department is really focused on delivering an enjoyable user experience to the researcher, rather than the usual barely functional, ugly as hell software that we get to use.

With this in mind I wanted the app to calculate the molecular weight of a compound for the user, I think it would be a nice thing to see after you just enter the chemical formula, the app just does a bit of magic and does the sum for you.

Due to the app being javascript all the way through the stack, the code for calculating molecular weight based on a given properly formated chemical formula string looks like so:

mass = {
  "H":  1.00794,
  "He": 4.002602,
  "Li": 6.941,
  "Be": 9.012182,
  "B":  10.811,
  "C":  12.011,
  "N":  14.00674,
  "O":  15.9994,
  "F":  18.9984032,
  "Ne": 20.1797,
  "Na": 22.989768,
  "Mg": 24.3050,
  "Al": 26.981539,
  "Si": 28.0855,
  "P":  30.973762,
  "S":  32.066,
  "Cl": 35.4527,
  "Ar": 39.948,
  "K":  39.0983,
  "Ca": 40.078,
  "Sc": 44.955910,
  "Ti": 47.88,
  "V":  50.9415,
  "Cr": 51.9961,
  "Mn": 54.93805,
  "Fe": 55.847,
  "Co": 58.93320,
  "Ni": 58.6934,
  "Cu": 63.546,
  "Zn": 65.39,
  "Ga": 69.723,
  "Ge": 72.61,
  "As": 74.92159,
  "Se": 78.96,
  "Br": 79.904,
  "Kr": 83.80,
  "Rb": 85.4678,
  "Sr": 87.62,
  "Y":  88.90585,
  "Zr": 91.224,
  "Nb": 92.90638,
  "Mo": 95.94,
  "Tc": 98,
  "Ru": 101.07,
  "Rh": 102.90550,
  "Pd": 106.42,
  "Ag": 107.8682,
  "Cd": 112.411,
  "In": 114.82,
  "Sn": 118.710,
  "Sb": 121.757,
  "Te": 127.60,
  "I":  126.90447,
  "Xe": 131.29,
  "Cs": 132.90543,
  "Ba": 137.327,
  "La": 138.9055,
  "Ce": 140.115,
  "Pr": 140.90765,
  "Nd": 144.24,
  "Pm": 145,
  "Sm": 150.36,
  "Eu": 151.965,
  "Gd": 157.25,
  "Tb": 158.92534,
  "Dy": 162.50,
  "Ho": 164.93032,
  "Er": 167.26,
  "Tm": 168.93421,
  "Yb": 173.04,
  "Lu": 174.967,
  "Hf": 178.49,
  "Ta": 180.9479,
  "W":  183.85,
  "Re": 186.207,
  "Os": 190.2,
  "Ir": 192.22,
  "Pt": 195.08,
  "Au": 196.96654,
  "Hg": 200.59,
  "Tl": 204.3833,
  "Pb": 207.2,
  "Bi": 208.98037,
  "Po": 209,
  "At": 210,
  "Rn": 222,
  "Fr": 223,
  "Ra": 226.0254,
  "Ac": 227,
  "Th": 232.0381,
  "Pa": 213.0359,
  "U":  238.0289,
  "Np": 237.0482,
  "Pu": 244,
  "Am": 243,
  "Cm": 247,
  "Bk": 247,
  "Cf": 251,
  "Es": 252,
  "Fm": 257,
  "Md": 258,
  "No": 259,
  "Lr": 260,
  "Rf": 261,
  "Db": 262,
  "Sg": 263,
  "Bh": 262,
  "Hs": 265,
  "Mt": 266,
};

var mW = function (chem) {
    var s = chem.match(/([A-Z][a-z]?)(\d*)/g, chem);
    var compoundWeight = 0;
    for (var i = 0; i < s.length; i++) {
        var element = s[i].match(/([A-Z][a-z]?)/g);
        var count = s[i].match(/([0-9]*)\d/g) || 1;
        compoundWeight += mass[element] * count;
        }
    return compoundWeight
};

It first creates an object of all the atomic masses. The mW function splits up each element and quanity into different strings in an array. Then a loop iterates over each string which extracts the letters to do the look up in the atomic mass object and then it looks for the number to do the multiplication, finally the compundWeight variable is incremented.

You can find the repo on Github if you would like to contribute any changes or improvements.

I like doing code for chemistry and biology. Lets do more!

-B

Venture capital - providing value beyond capital

What follows is a brief message I provided to one of my friends in Life Science venture. It is on the topic of providing value to the community regardless of whether you are working with the member of the community or not.

Providing value = building a positive relationship.

37 Signals is a software company that makes a project management tool called Basecamp.

They regularly blog, sharing knowledge and experience on subjects such as business and software engineering. They also write books.

Here is an excerpt from one:

As a promotional technique, education is a soft way to get your name – and your product’s name – in front of more people. And instead of a hard sell “buy this product” approach, you’re getting attention by providing a valuable service. That creates positive buzz that traditional marketing tactics can’t match. People who you educate will become your evangelists. Education can come in many forms. Post tips and tricks at your site that people will want to share with others. Speak at con- ferences and stay afterwards to meet and greet with attendees. Conduct workshops so curious fans can learn more and talk to you in the flesh. Give interviews to publications. Write articles that share helpful information. And write books.

Now the value provided by 37 Signals is relevant to customers and non-customers alike. And they are happy to do this because if the value is good non-customers, eventually when they need a project management tool they sure as hell head straight to 37Signals because they have a relationship with them.

Let’s go over to venture and see how this works there…

Google ventures, a VC firm that educates.

Google Ventures, the corporate investment arm of Google primarily invests in tech but also have approximately 2 or 3 pharmaceutical companies and DNA data processing companies.

If you look at the GV portfolio it covers everything from coffee shops to cancer therapeutics, I think this comes from a desire to pursue businesses that are not just good opportunities but the mission of the companies is to shift away from the status quo.

So as an entrepreneur looking at GV how do they provide value to me even though I’m not part of their portfolio?

Well just like 37 Signals they provide education and entertainment.

Firstly there is the library section covering: design, hiring, leadership, marketing, engineering etc.

Second there is foundation.bz, founder interviews. My two favourites are Elon Musk and Hossain Rahman these are genuinely fascinating interviews that provide value to the entrepreneur in terms of education and entertainment.

What is available in Life Science?

So already GV is building a positive relationship with an entrepreneur without the entrepreneur even having met one of the team at GV.

But this is tech, tech entrepreneurs aren’t the same as life science entrepreneurs. There are 4 sources that I think are the closest.

  • Obviously Mr Drug Baron is first, he provides the best content
  • Second is Bruce Booth
  • Nature Biotech's first rounders podcast
  • Maybe pharmaTV? (I find this a little “stuffy”)

The problem is these are disparate sources and entrepreneurs don’t necessarily associate one with being for entrepreneurs.

Benefit to your venture firm

So what would be the benefit of your life science arm providing value to potential investments through education and entertainment?

Library: Where does one go to read about experiences of picking a CRO for trials, or compound screening? I have no idea, surely this is somewhere you could provide tons of value.

How do you do hiring right in a drug discovery platform company? I don’t know any resources for this.

I could go on.

However for every bit of knowledge that you share you provide value to an entrepreneur or a future entrepreneur and not only are you providing value you are turning them into a better entrepreneur and potentially a better investment!! And providing value builds a relationship.

Founder interviews: What was it like to found CAT? I would have no idea except I had the chance to ask Sir Greg Winter at the end of a lecture. This would be an amazing interview. Your firm could be the one to tell all these stories just like GV are the ones telling the stories of these great tech company founders.

Life science co. stories are so infrequently shared and hardly ever documented.

In summary

Education and entertainment provides value to the entrepreneur, and providing value leads to building a positive relationship. Through providing resources on your website you can provide value passively (i.e. providing value to 300 people with one video as apposed to meeting 50 people at an event).

Entrepreneurs will perceive venture firms by the value that it provides them rather than the press releases of deals it makes. This builds a relationship between the venture firm and entrepreneur and ultimately drives quality opportunities your way.