Org Prep Daily

October 29, 2012

Uroboros

Filed under: industry life — milkshake @ 6:56 am

I have been making water-soluble polymers with biomedical applications for the last 16 months and it is quite satisfying: Our macromolecules are usually well behaved – they extract into organic phase. They precipitate as a snow-white fluffy crystalline solid, on a kilo scale. They even have beautiful NMR spectra. Unfortunately, such was not the case with the frothy mixture in the picture. I had to isolate the material from a solution in concentrated HCl (0.3L), with extra sludge of inorganic salts and assorted gunk that included gram quantity of dimethyl sulfide.

The usual process would be: dilute, filtrer, dialyze. But dialysis is a slow and rather frustrating business and we don’t even have bags giant enough for removing few mols of salts and HCl. So I was delighted to learn that ultrafiltration is a turbo-alternative to a dialysis – instead of steeping a swollen dialysis sausage bag (that can burst overnight) for days and waiting for the diffusion to run its course, an ultrafiltration setup visibly labors for you: the pump pushes the mixture against a semi-permeable membrane, water and other small molecular weight material leak out, the macromolecular fraction stays in. The purification is done in few hours.

The peristaltic pump in the picture circulates the crude mixture at moderate pressure and high flow rate (20 psi, 1.7 L/min) from the beaker to bottom of the column; the stuff that flows out at the top is fed back into the beaker in a closed loop. The column consist of a bunch of spaghettini-like capillaries that are coated with a semipermeable membrane. The spaghettini are housed in a plastic pipe casing. It is inside these capillaries that the mixture rushes through at high speed over and over again – water and small molecule material that leaks out through the walls of the capillaries collect in the casing and flow into waste (the sidearm and the transparent bottle). One has to keep adding water into the beaker quite often because with a good column + pumping rate/pressure the mixture gets concentrated rather quickly.

The time to end the purification is when chromatography (GPC) can no longer detect small-molecular weight impurities. Of course with a whopping excess of HCl at the beginning, one doesn’t need to run GPC to confirm that all low-molecular weight material is gone – a pH paper will tell you that. (A sniff test for dimethylsulfide presence is also fast … and revolting…)

November 19, 2011

Medchem Immigrant in the Polymer Republic

Filed under: industry life — milkshake @ 2:30 pm

Five months on – and there is no looking back. With potassium metal freshly cut, with the glassware, solvent and monomer lines pumped down overnight to 20 mTorr, ready or not, macromolecules, here I come.

September 6, 2011

A taste of their own medicine

Filed under: industry life — milkshake @ 1:51 pm

 Credit: Jirí Slíva

I got an e-mail from a patent litigation attorney representing a major pharma company, a company that puts beautiful ads on TV almost every night and whose name rhymes with “Mergers and Massacres”. Turns out, they have a problem with one of their drugs: the drug is selling just over a billion a year and a key patent covering this drug is being challenged by two generic companies. And since I am on the patent (with ten other authors), the company lawyers were eager to prepare me in case I get subpoenaed by the other companies challenging the patent. They offered a free legal representation during the hearings and they proposed to pay me as a consultant (“at my usual rate”).

They mentioned that they are trying to piece together the exact timeline of the project – I suppose questions like who proposed/synthesized what and when are important to the defense. And they are having problems: just one person from the original team is currently employed with the company.

This does not surprise me. I was laid off like everyone else when our research site was closed. (Also, our chemistry director was forced out just before the site closure and I heard that the company has brought some heavy investigation down on him). In the end, only a handful of employees got re-hired by our company and moved to other research sites. I suppose tracking down the patent inventors and interviewing them is somewhat difficult now – and it is possible that not everyone wants to be interviewed…

I did not call the company’s patent lawyers as they urged me to but we had a cordial e-mail exchange and I shared some of the impressions and experiences that I had while being (briefly) a part of their company – from the time they acquired us until they shut us down. I also reminisced on the class-action lawsuit that my ex-colleagues brought against the company because the company tried to cut their severance payments after the layoff. (The class action suit was settled out of court when the company paid in full – about 2 years late.)

I also reached out to the two generic companies involved in this litigation and let them know about this approach from my former employer;  I offered to answer questions about the history of this drug discovery and I gave them names of the few key inventors on the patent who could perhaps assist them more than I can. Then I wrote back to the legal team of my former employer to inform them that I contacted the other two companies involved in the litigation. I explained that I do not want money but maybe they could re-evaluate how they are going to treat the R&D inventors in the future. You know, in case they need them again.

June 23, 2011

Last post

Filed under: industry life, Uncategorized — milkshake @ 12:57 am

Today is my first day with a small privately held biotech company that is developing self-assembling polymers for targeted drug delivery. The group and the projects are awesome – and as much as I am excited about the research and the company, for obvious reasons I shouldn’t be writing about it. So there will be nothing new to add here. This is it – thank you for visiting!

April 22, 2009

blockbuster drugs

Filed under: industry life, lit highlights — milkshake @ 7:12 pm

I would like to direct the readers here to the excellent project-and-career story from Bruce Maryanoff in the most recent J. Med. Chem ASAP. It is very illuminating on how the drug discovery and development works, and it describes in some detail what a bright chemist can hope to achieve in this profession -with the necessary motivation and a decent employer (and tremendous amounts of luck).  

It is also an illuminating story on how the process does not work. For example, the currently most popular, target-driven rational-design-based approach can be pretty futile in CNS drug projects . The author also suggests that the management mantra about focusing on the discovery of the next “blockbuster drug” actually bankrupts the industry – financially and scientifically; his drug Topiramate (which has been making 2 billions a year for the company) would have not been discovered or developed under the management methods currently prevalent in the industry. Few things stand out: 1) It seems that having a blind luck and testing the compounds in a realistic animal model is more important than having a correct mechanistic understanding how the drug candidate actually works.  2) Few independent-minded individuals in their pharmacology and chemistry have made a good use of their lucky break. They stubbornly kept the research program going – even as their managers were lukewarm and would not support the compound development for a long time. It also goes to the credit of the management that allowed their researchers to pursue this as their hobby. The story shows that the progress in pharma research does not really happen by imposing some management-theory-derived reporting structure on the research department, by drafting the flowcharts and aligning the teams. For medchem research to succeed, the projects should be allowed to self-organize around the bright individuals rather than being planed out from top down, with red tape and micromanagement.

In this context it is entertaining to read rather disingenuous remarks made by the Merck chief strategy officer Merv Turner at the pharma management conference. He explained that they are currently sacking lots of people in research because  “Seventy-five cents of every dollar we spend on R&D goes to fund failure” and “the future results must come at a lower cost”.  

The actual drug discovery cost makes only few percent of the final drug development cost. By far the most expensive part is the clinical trials and namelly the late-stage clinical trials. What the Merck management poseurs do not tell in public is that it was the Merck top management decisions that cemented their company’s commitment to these “the next blockbuster” projects –  which eventually led to a string of stunningly expensive late-stage failures. When the top executives receive massive stock option bonuses, they become mercenaries of the stock prices. Their wishful thinking baloney percolates from top down through the management layers, etc.

There are many parallels between the state of pharma industry and the recent financial sector collapse, and it is always the executives who run their companies to the ground that are rewarding themselves most obscenely. Remember this whenever the pharma companies claim that the freedom to price their drugs is essential for the innovation.

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Update:  Here are additional two great articles from Bruce Maryanoff on the subject

August 11, 2008

The Road to Boredom (and back)

Filed under: industry life — milkshake @ 6:41 am

Derek Lowe of the Pipeline wrote a very insightful column in the last Chemistry World issue, about the narrow repertoire of synthetic methods used in medchem projects. His take is that the need for cranking out compounds for testing (=as many as possible) drives the chemists towards fool-proof reactions with a good functional group compatibility and building block commercial availability. The narrow choice often leads to insoluble series with poor oral availability and PK problems and insufficient structural diversity. More serious still is the turn-off effect on the chemists:

…For one thing, skills do need to be kept sharp, and running a variety of different chemistries is the best way to do that. And safety seminars aside, medicinal chemists do not actually have limitless capacities for boredom. Running yet another long line of palladium coupling reactions or amine displacements begins, after a while, to feel like working at a sawmill. The blade takes longer to cut through some of the logs than others, but the boards all come out looking about the same.

I think the problem of poor solubility and ugly design became more serious with the advent of kinase projects; the kinase slit-like binding sites typically extend far enough to accommodate ligands consisting of multiple aryl rings put together like beads on a string. Gleevec, Lapatinib, Dasatinib have this sort of structure – but then again, various ugly molecules are used in cancer treatment; I am unsure if this design will work for other therapeutic areas also.  (I have been making kinase compounds for a good part of this decade and I still like the smaller + more compact molecules better).

I met a number of chemists in the industry that already gave up on reading journals – their argument was that there were too many journals and too many articles and most of it was not very useful to them and whenever they needed to find a reaction the Scifinder and Beilstein-Crossfire search engines did adequate job. (Which is true). But I noticed that one typically loses his chemistry interest about the same time when he stops reading the literature; I don’t know what is the cause and the effect here.

More than 90% of synthetic chemistry is routine stuff – and frequently frustrating one, too. There are easier and healthier professions to chose from. I believe that most people got into synthetic chemistry because they experienced a sense of wonder, and they just kept coming back for more. Mixing up obscure, dangerous chemicals to obtain shiny crystals at the end is a pretty awesome and esoteric way to make living. Designing your own experiments and figuring out their problems, inventing tricks to make the chemistry work, trying your nutty ideas (to see if they translate into good compounds) is enormously gratifying experience. If the curiosity is quenched and the excitement is taken away all what’s left is shaking the sep funnels, putting flasks on the rotovap and analyzing fractions as they come off the column…

___________________________________________________________________________________________

There are various non-chemistry reasons why someone stops enjoying his particular project (personal-life problems, the lack of support, evil boss, problems with biology, the bureaucracy and politics, etc.) and the way to go about those difficulties is obvious. Instead I have few chemistry-related suggestions what to try, when the boredom and frustration takes over and the project becomes unsufferable:

1. Scaling-up. When chemistry does not work try some easy reliable procedure. Pushing through bulk material such as a commonly-used building block or an essential reagent that you made before helps to boost your self-confidence in times when your other chemistry failed you. Making a flask full of bright-yellow crystals is deeply satisfying and when you filter them, dry them and put them in a  bottle with a pretty label, when the NMR is clean, at least you don’t feel like a hack anymore. Besides if the material is useful to your group passing it selflessly around will make you popular.

2. Fluorine chemistry: Too many chemists opt to buy the fluorine-containing pieces without worrying how these molecules are made. There is a growing number of organofluorine building blocks available, companies like Apollo have a fat catalog full of them – but many important pieces are not available and easy chemistry to prepare them exists. Medicinal chemists shouldn’t be exhorted to work with F2 or anhydrous HF – but reagents like Deoxyfluor, Selectfluor, (PhSO2)2NF, NEt3.3HF are commercial, affordable, and are not too difficult to use (if the necessary precautions are taken). Many people are simply unaware that metabolically-stable difluoromethoxy group is readily introduced on a phenol OH by alkylating it with difluorocarbene (which is produced from chlorodifloroacetic acid) or that ArCF2CO2Et is easily made from Aryl iodides, BrCF2CO2Et and activated copper metal in DMSO under mild conditions, that CF3 group can be introduced  on aryl iodides with equal ease with catalytic CuI and sodium trifuloroacetate, that difluorocarbene in presence of PPh3 produces a Wittig reagent (that converts aldehydes to useful 1,1-difluoroalkenes), that trifluoromethyl anion generated from TMSCF3 adds to imines and aldehydes with ease etc.  There is a whole continent of a strange organofluorine chemistry and a medicinal chemist would do well to make himself familiar with these methods because apart from the nastiness of some HF-generating reagents these reactions tend to be well-behaved and predictable.

3. Metallation: Thanks to Schlosser and others there is a body of literature on position-selective lithiations of heterocycles, like pyridines and pyridimines, and there is also older literature on use of ortho-directing groups in benzene metellations. Very often these reactions are done with common reagents like BuLi, LDA, LiTMP, at simple conditions like THF -78C.  The functional group tolerability is not as great but this aryl CH-lithiation can be a powerful way of accessing simple building blocks with a special substitution pattern – a great help when changing the centerpiece ring in the series and run into the availability problem. 

Mg and Zn chemistry: Knochel is developing beautiful systems, for halogen-metal exchange, and many of his transmetallation reactions using secBu-Grignard and zinc reagents has been promptly adopted by process groups but medicinal chemists are lagging behind.  One can easily generate Grignards with ester ot even nitro group in the molecule, by transmetallation, and zinc reagents can provide much cleaner Negishi coupling than their Suzuki boronic acid counterparts.

Schwarz reagent, BBN-H borane: hydrometallation and hydroboration is a great way to access commercially-unavailable building blocks for Pd(0) catalysed cross-coupling reactions. BBN boranes do Suzuki-like sp3-carbon coupling with aryl, vinyl halides.

4. Cyclopropanation: Cyclopropyl substituents are of a great interest to a medicinal chemist on their own but they are great also for ring-opening reactions (they behave as a 3-carbon analog of C=C bond). In my opinion the enormously easy-to-use zinc promoted reactions (CH2I2 with ZnEt2)  and titanium-promoted cyclopropanation reactions (Cp2TiCl2 with Grignard) are neglected in medchem projects.

5. Asymmetric methods: There are so many of good ones and yet any medicinal chemist will always look first into buying the chirality – perhaps this has to do with the inconvenience of setting up a chiral column for analysis of the product ee. (One does not have this sort of excuse with chiral auxiliaries).  And some of the reactions are exceptionally easy to run, with commercial catalysts and and great functional group tolerance: Noyori Ru-TsDPHEN transfer hydrogenation of ketones, CBS reductions, Sharpless allyllic epoxidation, dihydroxylation and aminohydroxylation, Jacobsen asym epoxidation and epoxide hydrolysis kinetic resolution. There are Rh and Ru-phosphine C=C hydrogenation that go at modest pressures (50psi) and thus can be set on a Parr shaker. There is a whole field of organocatalysis, with simple catalysts like proline, doing great feats on simple aldehyde substrates – several stereocenters at once.  I think its mostly the laziness that medicinal chemists do not adopt these reactions more frequently even as most of them get trained to use them in grad school; as soon as they join pharma they learn to weed out the chiral centers from their molecules. Nature is chiral and even as it takes more time and effort to employ the asymmetric methods the methodology investment can be well worth the trouble – with a functional-group tolerant method like Noyori transfer hydrogenation, the development work needs to be done only once – and from then on the chemistry is just as easy to perform as a borohydride reduction. 

6. Making your own heterocycles. When you buy a boronic acid piece and slap it onto your molecule you make your final compounds faster – but often it is worth looking into how a particular ring system is made. The chemistry used may be ancient or completely new (Padwa is my hero), one can make everything from TOSMIC, etc. You would be amazed how many 5-membered rings are easily available from aldehyde or carboxylic acid.

7. Screening the ligand/solvent/base etc. Even the robust Pd(0)-catalysed reaction can become finicky for a particular class of substrates. There is the base, Pd-source, ligand, and solvent to choose  (apart from the temperature, concentration and time) and if you get one parameter wrong the reaction usually fails or stops at low conversion. Sometimes little time spent on methodology optimization pays off handsomely.

You should care about the chemistry methodology and do things not just to crank out the final compounds to fill up the testing queue. Your boss perhaps lost all his chemistry interest already and maybe he is unnerved about the project progress and pushes people hard –  but while you try not to get fired you don’t necessarily want to think like your boss (and end up wretched). If you continue to look at your research project with curiosity and do things also for the sake of your chemistry interest you are likely to be more original because thinking about the methodology will suggest new directions in your medchem project.  You may get acused of playing with chemistry and going off-tangent but you will likely remain more content and productive and you will continue to live your life in the lab – which could be a good or bad thing depending on the marriage situation.

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