Re: [DIYbio] Re: civil disobedience and diybio

I think synthetic organelles could help increase the specificity of
the chemistry. Synthetic organelles and a shuttling system.

On Tue, May 28, 2013 at 6:10 PM, matt harbowy <hbergeronx@gmail.com> wrote:
> In poking around to support my response to this, I came across an excellent
> example of why this is not just a political or regulatory problem.
>
> In my head, I started to go through a "use case analysis" of a hypothetical
> research project. I wanted to come up with something practical, that might
> even be a project someone here is willing to take on. So I chose diabetes as
> the problem, and settled on galegine, a natural anti-diabetic found in
> galega officianalis. or French lilac.
> http://en.wikipedia.org/wiki/Galega_officinalis. Not surprisingly, after a
> little searching on publicly accessible journals, I found a link to "Furman
> and Coxon et al"- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2438274/ and,
> according to the article, pure galegine is hard to get but is "easily
> synthesized" from "benzyl amine" and 2-methylpseudourea sulphate, both
> available from Sigma.
>
> But wait- I thought galegine was also known as N-dimethylallyl guanidine: I
> woundered how they could have gotten an allyl from a benzene, which if you
> have synthetic chemistry experience is a huge red flag. So I managed to find
> a non-free publication, "Coxon and Furman et al"-
> http://www.ncbi.nlm.nih.gov/pubmed/19422230 which correctly shows the rather
> complicated synthesis of galegine. I quote:
>
> 1-(3-Methylbut-2-enyl)guanidine Hemisulfate 1 (Galegine) and General
> Procedure for Synthesis of Guanidine Hemisulfates.
>
>
> A mixture of 4-bromo-2-methyl-2-butene (19.4 g, 1.0 equiv, 130 mmol) and
> potassium phthalimide (29.8 g, 1.2 equiv, 161 mmol) were suspended in DMF
> (200 mL) and stirred at 120 C for 1 h before heating to 160 C and stirring
> for a further 18 h. The mixture was poured over ice and washed with
> dichloroethane (5 × 50 mL), and the organic phases were separated and
> combined before washing with sodium hydroxide solution (0.1 N) (2 × 100 mL)
> and water (2 × 50 mL). The organic extracts were separated, dried over
> anhydrous magnesium sulfate, filtered, and concentrated to leave a crude
> solid that was crystallized from cold ethanol to give the intermediate
> 2-(3-methylbut-2-enyl)isoindoline-1,3-dione (25.6 g, 93%) as a white solid;
> mp 100-101C
>
>
> A mixture of 2-(3-methylbut-2-enyl)isoindoline-1,3-dione (10 g, 1.0 equiv,
> 46.6 mmol), ethanol (100 mL), and hydrazine hydrate (85%) (2.9 mL, 1.2
> equiv, 51.1 mmol) were stirred under reflux for 1 h, cooled, hydrochloric
> acid (1M) (5.2 mL, 1.2 equiv, 51.1 mmol) added, and then refluxed for a
> further 1 h. The mixture was allowed to cool, filtered, and the residue
> washed with cold water (100 mL) before reducing the filtrate under vacuum to
> give the intermediate 3-methylbut-2-en-1-amine hydrochloride (4.4 g, 78%) as
> a white solid; mp 95-97C
>
> 2-Methylthiopseudourea sulfate (6.95 g, 1.0 equiv, 150 mmol) and
> 3-methylbut-2-en-1-amine (9.1 g, 2.0 equiv, 100 mmol) were dissolved in
> water (100 mL) and ethanol (100 mL). The mixture was stirred at reflux for
> 18 h, connected to a series of bleach traps, before cooling and reducing
> under vacuum to give a white crude solid. The compound was suspended in
> water (30 mL) and heated until it barely dissolved before allowing to slowly
> cool upon which a white solid began to form. After allowing the formation of
> the solid to continue overnight, it was collected by filtration and dried in
> the oven to give the title compound (5.4 g, 62%) as a white solid; mp
> 216-218C
>
>
>
> It turns out that you get a related compound, N-benzylguanidine. The class
> of all the compounds has been patented
> http://www.google.com/patents/US5373008 but this patent is now expired and
> the entire class of compounds should be free of patent, including the
> leading indication and first line therapy, metformin
> http://en.wikipedia.org/wiki/Metformin.
>
> So why do I mention this? Let's start off thinking about some of the
> research plans someone might take toward finding "open source" diabetes
> drugs. They might just be tempted to hack the minimal procedure from
> "F&Cetal" instead of following the correct procedure of "C&Fetal". The
> lingering doubt I have about this work is, what if the paper principally
> authored by Furman actually studied benzylguanidine instead of galegine?
> What is the differences of approach between Furman's lab and Coxon's lab
> that results in the difference in reported experimental procedure? Who
> edited and checked these papers? By simply following published research, it
> would be so easy to fool yourself when synthesizing drugs.
>
> At least with synthetic chemistry, I can fall back on the methods of
> chemistry to give myself at least some confidence that what I think I have,
> I can be sure I have, because proton and carbon NMR and mass spec and
> melting point and FTIR, while they all have flaws, eventually suss out the
> truth.
>
> Now move on to bioengineering: let's say you engineer a recombinant cell
> line to produce galegine. As with the chemical synthesis, actually
> recovering the free base is not easy, and when you add up all the possible
> side reactions that might make various contaminants, it could be really
> difficult to isolate the multigram quantities of any compound you would need
> to do a study n=1. You might just get a mixture. You might get poison. You
> don't know- and even if you are successful, the next person you give the
> drug to might die of lactic acidosis because you "happen" to have a gene
> that prevents that side effect. Who knows? Although we know metformin
> inhibits a particular enzyme(s?) involved in gluconeogenesis, we don't
> really know what giving somebody metformin does to the body, or why some
> people react so badly to it. As much as we don't know about metformin, we
> know even less about galegine, except that every animal reacts slightly
> differently to it.
>
> So, even in a pure libertarian utopia, drug research is fraught with
> difficulties on where to start and tons of conflicting theories on what we
> know. That's not to say doing some basic investigation in a DIY lab couldn't
> do some of the groundbreaking early stage research that might gain us some
> critical insights into the why and how of diabetes. There are GREAT projects
> to be had. But DIY medicine is more than just bad politics: hacking ceases
> to be science when you stop following scientific best practices. N=1
> experiments are interesting and all, but they're not science. The politics
> and regulation is, in large part, a way to shut down random people from
> poisoning each other, as happened all the time at the turn of the 20th
> century. For the chemical example, google "elixir sulfanilamide". For the
> biohack example, google "a horse named Jim", the ultimate in N=1 biohacked
> medicine and a case study on where biohacking could go very, very wrong.
>
> Do you really want to get your medical care from "a horse named Jim?"
>
> -matt
>
>
>
>
>
> On Monday, May 27, 2013 3:45:05 PM UTC-7, Reason wrote:
>>
>>
>> http://www.fightaging.org/archives/2013/05/civil-disobedience-and-diybio.php
>>
>> From a point of view of materials and time it is not costly to set up a
>> home
>> laboratory for the purposes of synthesizing chemical compounds or even
>> perform simple procedures in biotechnology - raising bacteria, assaying
>> genes in lower animals, and so on. It is, however, illegal to just forge
>> ahead and do this in most US states or in much of Europe due to the many
>> prosaic, stupid laws that encrust the body politic....
>>
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>



--
-Nathan

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