!20151113  3D crystal structure automatically determined - now obvious?

In this PATNEWS, I turn again to the impact of the growing sophistication of automated drug discovery tools that eventually could make many new chemicals obvious inventions of PHOSITAs. Today's PATNEWS, a Nature article on a huge success in automatically determining the 3D crystal structure from 2D chemical structure maps. But first, some other IP news.

Gene Amdahl dies at 92.   One of the giant designers of mainframe computers, Gene Amdahl, has died at the age of 92 in Palo Alto. Amdahl was one of the chief designers of the IBM System/360 mainframe family of computers (almost as cool as Digital Equipment Corporation's VAX family of computers :-). He later left IBM to form Amdahl Corporation in 1970, probably the first computer clone company (they made mainframes that could run IBM software). The obituary ends with rightly putting him with three of the great designers, the other two being Seymour Cray and Steve Wozniak. New York Times obituary at: http://www.nytimes.com/2015/11/13/technology/gene-amdahl-pioneer-of-mainframe-computing-dies-at-92.html.

Will Orrin Hatch kill the Trans-Pacific Partnership?   President Obama was able to achieve success with 12 Pacific Rim countries in getting all to agree to the Trans-Pacific Partnership pact, which now needs approval by legislatures in all 12 countries. During negotiations, Senator Orrin Hatch provided much help to President Obama, no surprise given his huge role in (making a mess of) IP over the decades. But now, it could be that Hatch helps defeat approval of the TPP pact. Why? The pharmaceutical industry does not like the lack of support for protection for biologics (industry wants 12 years of protection, they only got a minimum of five to eight years). And on pharma issues, the pharma industry owns Hatch. As does the dietary supplements industry (which is why nothing in GNC is regulated by the FDA, though that now helps me :-). New York Times article at: http://www.nytimes.com/2015/11/13/us/politics/utah-senator-crucial-ally-for-the-pacific-rim-trade-deal-is-now-its-main-hurdle.html.

Law clinic helps small company fight huge Nautica over trademarks.   Nautica is a huge fashion company that fiercely protects its brands and marks. Some years ago, a start-up in Washington state, NautiGirl, start producing boating gear and other nautically-themed articles catering to women's fashion and user needs, with the trademark: "NautiGirl - Dare to be Naughty". They applied for a trademark. And of course, Nautica petitioned the USPTO to deny the trademark to NautiGirl. Something Nautica had done to over 100 other small businesses. But in NautiGirl's corner was the IP Clinic of Suffolk Law School in Boston. And with the help of the IP Clinic, NautiGirl won the fight and got their trademark. Article at: http://bostinno.streetwise.co/2015/11/03/startup-legal-help-suffolk-ip-clinic-nautica-trademark-suit/.

---    3D crystal structure automatically determined - now obvious?

      The growing sophistication of automated drug discovery tools continues unabated. Latest development - the successful prediction of the 3D shape of a chemical given its 2D mapping (for example, H-O-H as a 2D map for water). Given the 3D shape, this is much chemistry that can be determined about the chemical, without having to do the experiments. And thus makes it easier to finds uses for the chemical (like will the chemical bind to something interesting in a cell to achieve a useful result). But this is a notoriously difficult problem for large molecules, given the zillions of possible arrangements in 3D of the atoms, and then how the molecules are packed together in clumps.

      But now, there is increasingly becoming automated. The most recent challenge hosted by the Cambridge Crystallographic Data Centre has resulted in a combination of two teams being able to completely automatically determine the 3D structure of complex chemicals - "... this blind test has shown that the problem of organic crystal structure prediction [note: KSR prediction?] has been solved."

      As I said in a talk last December, the curve of the coherency of 103 caselaw continues to drop, while the curve of the power of automated drug discovery tools continues to increase. At some point in the next 20 years, the curves cross, and many new chemicals become unpatentably obvious. Or not. Much like the utter idiocy of all things 101 caselaw, increasingly all things 103 caselaw are becoming as idiotic. [Note to patent bar - I obviously have no idea what I am talking about, so feel free to ignore this issue as well]. [Note to insurance industry - I do know what I am talking about and am designing two insurance policies, one to protect and one to attack, so we can make some good monies]. [Note to self: stop writing notes] But do no fool yourself, this issue is one of increasing risk for chemical patenting.

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---    Software predicts slew of fiendish crystal structures
Chemists succeed at forecasting how complex molecules will assemble in 3D.

      by Elizabeth Gibney, Nature, 03 November 2015

Sketch the structure of an organic molecule on a napkin and it may not be apparent that there are millions of possible ways that it could assemble as a 3D crystal. Now, a collaboration of dozens of chemists and computer programmers has successfully predicted the crystal structure of five, complex, ‘drug-like’ organic molecules — using nothing but a 2D map showing which atoms connect to which.

The achievement, announced on 27 October at a workshop in Cambridge, UK, paves the way for software that would cut the cost of the design and manufacture of drugs and other chemical products, as well as further our understanding of fundamental chemistry.

A molecule’s crystal structure determines its properties (see ‘Crystal challenge’). In 1998, the US pharmaceutical firm Abbott Laboratories learned this the hard way when it had to pull production of the capsule form of the HIV treatment ritonavir because the drug had started switching to an unexpected structure during manufacture. The crystal structure that a molecule adopts is generally the one with the lowest energy, but predicting what this is for any particular molecule is “fiendishly difficult”, says Colin Groom, executive director of the Cambridge Crystallographic Data Centre (CCDC).

Even when chemists know which atoms are connected to which, the atoms can still be in different orientations because the bonds that connect them can bend and rotate in myriad ways. There are also multiple options for how molecules can pack together. “It is like looking for a needle in an unimaginably big haystack,” says Anthony Reilly, a structural chemist at the CCDC.

Since 1999, the CCDC has organized six challenges known as the Blind Test of Organic Crystal Structure Prediction Methods. Rather than a contest, organizers see the challenge as a large collaborative attempt to compare the strengths of the latest techniques. “The groups participating represent pretty much the entire crystal-structure prediction community, and the methods used are the very best developed,” says Groom.

The challenge typically takes place over a year, and sets two major problems. First, teams must come up with a list of all possible arrangements in which the molecules could form a crystal. Some teams do a rough calculation of the energy of each to whittle down the list, burning up hundreds of thousands of hours of computing time; others start with pure guesses and iteratively ‘breed’ the most stable to derive possible candidates more quickly. In the second stage, teams take the shortlists — sometimes assembled by a different group — and do more-precise calculations of the energy of each, producing a ranking of the candidates.

The latest challenge, which included a record 25 teams — ten more than the previous contest in 2010 — brought a “massive improvement”, says Groom. The molecules selected were “nasty, real-life systems” of the size and complexity to be interesting to drug companies. Previous challenges had included molecules that were flexible or made from multiple parts. This year’s challenge combined such features in the same molecules and for one target, asked participants to predict not just one stable structure, but all its many stable forms, known as polymorphs.

Problem solved

The teams rose to the challenge: at the Cambridge workshop, the CCDC announced that each of the five targets, and their polymorphs, appeared in at least one of the shortlists produced by the various methods. A paper with the full results will be published in a special issue of Acta Crystallographica Section B.

Moreover, one team, led by Marcus Neumann at the German company Avant-garde Materials Simulation in Freiburg, included the correct solution in each of its shortlists. Had the team combined its efforts with those of a group — led by theoretical chemist Alexandre Tkatchenko at the Fritz Haber Institute in Berlin — that got a perfect score in the ranking phase, the two would together have achieved a perfect score for both rounds and across all targets. Such a result has never occurred in the history of the contest. “With what you have seen from me, and what you have seen from Tkatchenko,” says Neumann, “it is fair to claim that to a large extent, this blind test has shown that the problem of organic crystal structure prediction has been solved.”

More so than in previous blind tests, teams including both Neumann’s and Tkatchenko’s took into account how quantum mechanical interactions would contribute to the energy of structures. In particular, Tkatchenko used a method published just last year that encompassed these interactions over longer ranges than has been done previously. And Neumann says that his program was unique because it made every decision by itself; most others required human decisions once the computer had returned its calculations. “We have finally kicked the user out of the equation,” Neumann says.

Although others agree that the joint feat is a milestone, they stop short of declaring the problem of crystal structure prediction solved. “This does not mean that they would have cracked the problem of predicting all organic crystal structures,” says Sally Price, a theoretical chemist at University College London.

And some are frustrated that Neumann has refused to release his computer code: “The day I have a pension plan, I will talk about this freely,” he told the workshop. That will make it hard for others to build on his team’s breakthrough. “We don’t really have a sense of how it works,” says challenge participant Claire Adjiman, a chemical engineer at Imperial College London. “But I understand why he doesn’t tell us more.”

Tkatchenko and Neumann now plan to work together. “My own interest is to understand polymorphism and be able to offer tools to people,” says Tkatchenko. “His interest is more commercial, but I’m sure we can find the middle ground.”

Both Price and Neumann, meanwhile, are already working with industry on how to use their prediction calculations in drug development.

Greg Aharonian
Internet Patent News Service
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