Salvia divinorum (Salvia, Magic Mint) is a plant used for entheogenic purposes by the Mazatec people of Mexico. A relative of the common garden plant "scarlet sage" (Salvia splendens), S. divinorum contains several hallucinogens that include salvinorin A, the first non-nitrogenous agonist known for kappa opioid receptors (KOR).
I had known of salvinorin A since a highly-cited 2002 Proceedings of the National Academy of Sciences paper by Bryan Roth, Richard Rothman and colleagues (full text here). At that time, I had read several anecdotal reports (that I cannot locate now) that the hallucinations rendered by Salvia ingestion or smoking were so bizarre and disturbing that 8 of 10 first-time users declared they would not use it again. Hence, I never really thought that Salvia would become much of a public health problem or be embraced by recreational hallucinogen enthusiasts.
However, just Google "Salvia" and take a gander at the ads on the right sidebar.
I'm still not certain if Salvia is enough of a public health problem to warrant legislation but we just learned this week that North Carolina will join 13 other US states in criminalizing possession and use of the plant or extracts made thereof:
A bill that would outlaw the psychoactive herb Salvia divinorum has passed the state Senate, prompting consumers to rush to buy it legally.
Senate Bill 138, sponsored by Sen. Bill Purcell, D-Laurinburg, would prohibit the "manufacture, sale, delivery, or possession" of Salvia divinorum. The law calls for a fine for the first two offenses and misdemeanor charges for subsequent offenses. Purcell stressed that North Carolina's law would not be as strict as those of 13 states, which made Salvia divinorum a drug on par with heroin. Read the rest of this post... | Read the comments on this post...... Read more »
Roth, B. (2002) Salvinorin A: A potent naturally occurring nonnitrogenous kappa opioid selective agonist. Proceedings of the National Academy of Sciences, 99(18), 11934-11939. DOI: 10.1073/pnas.182234399
Shu Kobayashi (University of Tokyo) and coworkers
have developed a safe, effective protocol for synthesizing
carbonyl molecules, which are foundational chemical entities in
molecular synthesis, using molecular oxygen as the oxidant.
This news feature was written on June 11, 2009.... Read more »
Wang, N., Matsumoto, T., Ueno, M., Miyamura, H., & Kobayashi, S. (2009) A Gold-Immobilized Microchannel Flow Reactor for Oxidation of Alcohols with Molecular Oxygen. Angewandte Chemie International Edition, 48(26), 4744-4746. DOI: 10.1002/anie.200900565
Peter Flynn (University of Utah) and coworkers
have demonstrated reversible, precise control over protein crowding
and confinement, two basic features of the cell interior,
in an artificial model system.
This news feature was written on June 10, 2009.... Read more »
Van Horn, W. D., Ogilvie, M. E., & Flynn, P. F. (2009) Reverse Micelle Encapsulation as a Model for Intracellular Crowding. Journal of the American Chemical Society, 131(23), 8030-8039. DOI: 10.1021/ja901871n
Kenjiro Taura is visting Manchester next week from the Department of Information and Communication Engineering at the University of Tokyo. He will be doing a seminar, the details of which are below:
Title: Large scale text processing made simple by GXP make: A Unixish way to parallel workflow processing
Date-time: Monday, 15 June 2009 at 11:00 AM
Location: [...]... Read more »
Miyao, Y., Sagae, K., Saetre, R., Matsuzaki, T., & Tsujii, J. (2008) Evaluating contributions of natural language parsers to protein-protein interaction extraction. Bioinformatics, 25(3), 394-400. DOI: 10.1093/bioinformatics/btn631
Crystals are generally rigid and brittle, but this paper describes microcrystals of dimethylamino trans azobenzene that bend into a semicircle when a light is shined on them. That the azobenzene molecule responds to light is no real surprize, but the fact that the whole crystal changes shape, and reversibly to boot, was pretty cool.Take a look at the video's of this that are provided, for free, in the supplemental information for the paper. The movie 002 shows the bending motion most clearly. This crystal is about 0.5 mm by 0.28 mm and 0.005 mm thick, so it is really tiny. A larger crystal probably would not do this.So what's going on? The N=N double bond can be in either the trans orientation or the cis orientation. The trans version is preferred - the cis version suffers from steric crowding as the two benzene rings bump into one another. By shining light with the proper wavelength on the molecule, you can convert the trans into the cis molecule. Turn off the light, and the molecule can revert back the the trans version.The authors were able to confirm that when they shine light on their crystals they convert about 1% of the molecules from the trans form to the cis form. This was readily apparent in proton NMR, but evidence could also be seen in changes in the UV-vis spectrum and the melting point of the crystals. After turning off the light source, the molecules in the crystal return slowly to all-trans.So, how does this cause the crystal to bend almost in half? It seems to have to do with the way the molecules arrange themselves in the crystal lattice. The trans molecules are flat and stack into a very regular herring-bone type of pattern. The cis molecules don't fit this pattern - in addition to the U-shape, the cis molecules have a twist in them to reduce some of the steric strain between the benzene rings. The twist make the molecules much bulkier than the flat trans form As a result the cis molecules don't fit into the crystal lattice and cause the unit cell to be longer than the unit cell for only the trans molecules.When the light source converts some of the molecules to the cis form, the side of the crystal nearest the light source appears to expand - because of the larger unit cell of the cis molecules. The side of the crystal away from the light source does not experience this and stays the same size. To accommodate the expanding surface facing the light source, the whole crystal bends away from the light source. When the light is turned off, the cis molecules slowly revert to the (more stable) trans form and the crystal un-bends.Koshima, H., Ojima, N., & Uchimoto, H. (2009). Mechanical Motion of Azobenzene Crystals upon Photoirradiation Journal of the American Chemical Society, 131 (20), 6890-6891 DOI: 10.1021/ja8098596... Read more »
Koshima, H., Ojima, N., & Uchimoto, H. (2009) Mechanical Motion of Azobenzene Crystals upon Photoirradiation. Journal of the American Chemical Society, 131(20), 6890-6891. DOI: 10.1021/ja8098596
Jin-Quan Yu (Scripps Research Institute, California)
and coworkers have developed an improved synthetic protocol
for a class of molecules that are finding much use in
modern pharmaceuticals, but are typically challenging to synthesize.
This news feature was written on June 9, 2009.... Read more »
Wang, X., Mei, T.-S., & Yu, J.-Q. (2009) Versatile Pd(OTf)2·2H2O-Catalyzed ortho-Fluorination Using NMP as a Promoter. Journal of the American Chemical Society, 131(22), 7520-7521. DOI: 10.1021/ja901352k
A recent publication indicates that more bias in the form of natural product scaffolds not yet synthesized could improve hit rates in screeningMost drug discovery projects are inaugurated by some kind of screening campaigns where millions of molecules are screened against a biological target. Even though the hit rate from High-Throughout Screening (HTS) can be quite low, HTS still provides one of the best starting points to discover interesting new structures that display biological activity. In spite of this, there is frequent disappointment at the low rates from HTS which could be as low as 0.05%.But instead of focusing on the low hit rate from HTS, what if we express surprise that this hit rate is actually high? This thought takes me into a slight digression. In his remarkable book The Black Swan, the author Nassim Nicholas Taleb talks about an "anti-library", the set of all books you have not read. The anti-library is in some ways more important than your library because it really tells you what you are ignorant about. Similarly we can define an "anti-question". The anti-question is a question opposite to one which we might usually ask. So instead of asking; "Why is this drug specific for this protein?", we could ask "Why is this drug not hitting other proteins?". The value of the anti-question is that it forces us to analyze and evaluate things that we otherwise may not and enables us to think outside the box. As the wise professor exhorts detective Sponer in "I Robot" to constantly get to the all-important right question, so it could be important to get to the right anti-question.In the context of HTS, the anti-question actually turns out to be logical. Instead of asking, "Why is the hit rate from HTS so low"?, one should ask "Given the number of small molecules in small-molecule space (~10*60) compared to the extremely low number typically screened in HTS campaigns (10*6), why should we get any hits from HTS at all?". Even narrowing down the unimaginably large small-molecule universe to more drug-like or lead-like entities, we still run into a numbers paradox since even this number is orders of magnitude greater than what is usually screened.In their most recent paper, Brian Shoichet and his team ask this important anti-question, and it leads them down an interesting road. Most campaigns that screen libraries focus on readily available commercial compounds and fragments that can be synthesized by organic chemists. This bias in turn reflects what has been more or less synthetically accessible through more than a hundred years of synthesis. Compared to this, the Kyoto Encyclopedia of Genes and Genomes (KEGG) contains metabolites whose structures are untainted by the minds of organic chemists. These are scaffolds among secondary metabolites and natural products that have simply been found.There is another set of structures; the Generated Database (GDB), a theoretical set which contains all possible molecules containing less than 11 heavy atoms consisting of first-row elements (C, O, N, F). This number is not as large as may be imagined and amounts to about 26 million. In the study the authors essentially compare the set of purchasable KEBB compounds found in their own annotated library called ZINC with the GDB. They use a similarity measure called a Tanimoto coefficient derived from 2D fingerprint comparison to accomplish this. 2D fingerprints use different kinds of protocols for breaking up a molecule into a bit string and then compare bit strings by distances and atom types.The comparison indicates something interesting; the compounds in the purchasable set are much more similar to the KEBB compounds than are the compounds from the rest of the GDB. In other words, purchasable compounds contain scaffolds that are biased towards those in the KEBB. This is a good thing, since metabolites are usually primed by nature to show at least some biological activity. Another noteworthy finding was that the bias also increased with molecular size, as compounds became more drug-like or lead-like in terms of size. However, the more surprising and useful observation was that there are hundreds of scaffolds in the KEBB that are notpresent in the commercial library. The authors also do this comparison for other popular commercial libraries designed specifically for screening and find a similar result. The bottom line; while synthesized commercial libraries of molecules show a bias toward natural products and metabolites, there are also several natural product scaffolds that are not found in these libraries.So what is the prescription? Introduce further bias! The compounds in the KEGG are more or less optimized for biological activity. If their scaffolds are not yet present in the commercial libraries, organic chemists should go ahead and focus on synthesizing these scaffolds and adding them to screening libraries. More such scaffolds could increase the hit rate in HTS by enriching libraries in biologically relevant scaffolds. Of course the usual caveats of false positives and promiscuous compounds should be kept in mind, and it's also not clear that proteins like kinases which are optimized to bind certain core scaffold structures would greatly benefit from these diverse scaffolds. But in terms of unmined drug space, introducing such further bias would be beneficial.This study again goes to show the possibilities for finding new stars in the constellations and galaxies of the drug universe. Hopefully the universe will keep on expanding.Hert, J., Irwin, J., Laggner, C., Keiser, M., & Shoichet, B. (2009). Quantifying biogenic bias in screening libraries Nature Chemical Biology DOI: 10.1038/nchembio.180... Read more »
One of my enduring memories of Oxford is sitting in the Chemistry School lecture theatre while a long-haired, leather-jacketed lecturer covered the blackboards in chalky organic reactions (the first time ever I heard about S~N~2 reactions; and a whole heap other stuff I have since forgotten) non-stop for an hour. One of the advantages of taking Biochemistry, instead of something less hardcore, say, is that I got to learn real science instead of just squishy biological stuff, which might surprise Henry ‘cell biologists are stronger than they look’ Gee.
I’ve also maintained contact with chemists of one flavour or another for several years subsequently, including some very clever people working at a drug discovery company based just outside Cambridge. And two of these chaps have written a rather splendid review on chemistry for the non-chemist (one of them was at my party a couple of weeks ago).
Derived from an in-house workshop The review explains nomenclature and concepts that even the squishiest biologist should be able to understand. The naming conventions for oxygen- and nitrogen- (and everything else-) containing compounds are explained, as well as stuff like solid support chemistry and a little bit on how medicinal chemists actually go about making new compounds for testing. And I learned something too. For example, I didn’t know — or had forgotten — ring numbering conventions. Aromatic rings are numbered to ensure heteroatoms (i.e. non-carbons in rings) bear the lowest possible number.
In the figure above, (a) is correct but (b) wouldn’t be because the nitrogen atom would end up with a higher than possible number.
There are some silly errors in the paper. Figure 5 is captioned as if it were Figure 4. The heterocyclic animation, I mean amination, in figure 7 isn’t.
spot the difference
Figure 9 comes before figure 7 and figure 8 is missing. The authors refer to “Laboratoy Equipment” (as if they don’t didn’t have access to a spill chequer).
But anyway. I want to see more of this sort of thing. I want to see a guide to physics for biology, and I’d quite like to co-write something the other way round: NMR or crystallography or squishy stuff, even genetics, for non-biologists.... Read more »
Jordan, A., & Roughley, S. (2009) Drug discovery chemistry: a primer for the non-specialist. Drug Discovery Today. DOI: 10.1016/j.drudis.2009.04.005
Henry Du, Svetlana Sukhishvili (Stevens Institute
of Technology, New Jersey), and coworkers have found that utilizing
a deoxygenated surface can improve the molecular detection limit of
surface-enhanced Raman spectroscopy by a factor of 100,000.
This news feature was written on June 5, 2009.... Read more »
Erol, M., Han, Y., Stanley, S. K., Stafford, C. M., Du, H., & Sukhishvili, S. (2009) SERS Not To Be Taken for Granted in the Presence of Oxygen. Journal of the American Chemical Society, 131(22), 7480-7481. DOI: 10.1021/ja807458x
The Open Biomedical Ontologies (OBO) are a set of reference ontologies for describing all kinds of biomedical data, see [1,2] for examples. Every year, users and developers of these ontologies gather from around the globe for a workshop. Following in from last year, the 2nd OBO workshop 2009 is fast approaching.
In preparation, I’ve been revisiting [...]... Read more »
Noy, N., Shah, N., Whetzel, P., Dai, B., Dorf, M., Griffith, N., Jonquet, C., Rubin, D., Storey, M., Chute, C.... (2009) BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Research. DOI: 10.1093/nar/gkp440
Côté, R., Jones, P., Apweiler, R., & Hermjakob, H. (2006) The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics, 7(1), 97. DOI: 10.1186/1471-2105-7-97
Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L., Eilbeck, K., Ireland, A., Mungall, C.... (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology, 25(11), 1251-1255. DOI: 10.1038/nbt1346
Smith, B., Ceusters, W., Klagges, B., Köhler, J., Kumar, A., Lomax, J., Mungall, C., Neuhaus, F., Rector, A., & Rosse, C. (2005) Relations in biomedical ontologies. Genome Biology, 6(5). DOI: 10.1186/gb-2005-6-5-r46
Bada, M., & Hunter, L. (2008) Identification of OBO nonalignments and its implications for OBO enrichment. Bioinformatics, 24(12), 1448-1455. DOI: 10.1093/bioinformatics/btn194
Ilona Hauber (Heinrich-Pette-Institute for Experimental
Virology and Immunology, Germany) and coworkers have discovered
that a molecule in green tea hinders the ability of a protein
aggregate to facilitate HIV transmission.
This news feature was written on June 2, 2009.... Read more »
Hauber, I., Hohenberg, H., Holstermann, B., Hunstein, W., & Hauber, J. (2009) The main green tea polyphenol epigallocatechin-3-gallate counteracts semen-mediated enhancement of HIV infection. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0811827106
Yong Cao (Fudan University, China) and coworkers
have developed a highly useful protocol for synthesizing
imine and oxime molecules, which are widely used in
pharmaceutical, agricultural, and other industries.
This news feature was written on June 2, 2009.... Read more »
Sun, H., Su, F.-Z., Ni, J., Cao, Y., He, H.-Y., & Fan, K.-N. (2009) Gold Supported on Hydroxyapatite as a Versatile Multifunctional Catalyst for the Direct Tandem Synthesis of Imines and Oximes. Angewandte Chemie International Edition, 48(24), 4390-4393. DOI: 10.1002/anie.200900802
One of the most painful parts in the book "A Beautiful Mind" narrates how the brilliant mathematician John Nash was admitted to a Trenton hospital and subjected to what was then one of the most fashionable treatments for schizophrenia- insulin shock therapy. The periodic administrations of large doses of insulin to induce convulsions and coma not only was embarrassing for the future Nobel Laureate and his family but it may have possibly damaged parts of his mind- and not just brain- beyond repair. It may have scarred a beautiful mind.But we had lobotomy, and we had insulin shock therapy. And then we evolved. The drugs chlorpromazine and reserpine revolutionized the treatment of schizophrenia in the 1950s (recall the movie "Awakenings"). Since then a variety of drugs have been used for mitigating the symptoms of this devastating disorder. However most of these drugs target what are called the "positive symptoms" of the disease, which include delusions, agitation and hallucinations. The "negative symptoms" include social withdrawal, depression and poverty of speech, symptoms not targeted by many drugs. More importantly, many of the early drugs had nasty side effects, termed "extrapyramidal symptoms" (EPS) which included involuntary twitching of facial and other muscles, part of what is termed tardive dyskinesia. A lot of focus has been put over the years on reducing these effects as well as in mitigating negative symptoms. Medicines supposed to achieve these goals have been traditionally termed "atypical antipsychotics"Now an article co-authored by Nobel Laureate Arvid Carlsson questions this widely accepted definition of atypical antipsychotics and suggests that the definition actually hampered the development of these drugs for more than 30 years. The article contains some rather technical commentary, but what I could get from it is the following: the most widely accepted hypothesis for the etiology of schizophrenia is the so-called "dopamine hypothesis", pioneered by Carlsson himself, that contends that high levels of dopamine in the brain are associated with psychoses. Drugs like clozapine are supposed to prevent dopamine metabolism by binding especially to the D2 family of dopamine receptors. These drugs bind to other receptors too but its their action at dopamine D2 receptors that's important in managing the symptoms of schizophrenia.Carlsson contends that the flaw in 30 years of antipsychotic therapy lies in searching for the perfect "atypical" antipsychotic which will tackle both positive and negative symptoms of schizophrenia as well as EPS. It was believed for many years that all these effects could not be disentangled from each other and necessarily went together. This led to the search for a "magic bullet", a single compound that could hit all symptoms. Carlsson says that recent studies on the action of antipsychotics suggests different mechanisms responsible for different symptoms, including mechanisms involving novel receptors that were not implicated before. The drugs also cause different levels of occupancy for D2 receptors in different tissues and parts of the brain, and thus provide the opportunity for designing multiple compounds that hit subtypes in different places. According to Carlsson, the "atypical" compounds used to treat psychoses should actually be called "typical" since they usually do a good job in treating the positive symptoms of the disease. The bottom line is that multiple avenues for treating the symptoms of schizophrenia arising from different molecular mechanisms should be explored, instead of focusing on a single compound that would encompass all features. Different compounds should be used for targeting positive and negative symptoms.To me this narrative reinforced what is becoming clear about CNS disorders and the accompanying therapy; that non-selective drugs targeting different mechanisms are often more beneficial than single, selective drugs targeting only one receptor, and that multiple pathways affect the development of a disease whose symptoms and side-effects may be classified into distinct categories only with deceptive convenience. The brain is the most complex structure known to man. Its manipulation and the treatment of its disorders deserves an approach that is not too less complex and nuanced.Gründer, G., Hippius, H., & Carlsson, A. (2009). The 'atypicality' of antipsychotics: a concept re-examined and re-defined Nature Reviews Drug Discovery, 8 (3), 197-202 DOI: 10.1038/nrd2806... Read more »
Gründer, G., Hippius, H., & Carlsson, A. (2009) The 'atypicality' of antipsychotics: a concept re-examined and re-defined. Nature Reviews Drug Discovery, 8(3), 197-202. DOI: 10.1038/nrd2806
Steven Taylor (Columbia University, New York)
and coworkers have worked towards developing a minimally invasive
device that can reliably and controllably release insulin, enabled by
This news feature was written on June 1, 2009.... Read more »
Taylor, S. K., Pei, R., Moon, B. C., Damera, S., Shen, A., & Stojanovic, M. N. (2009) Triggered Release of an Active Peptide Conjugate from a DNA Device by an Orally Administrable Small Molecule. Angewandte Chemie International Edition, 48(24), 4394-4397. DOI: 10.1002/anie.200900499
Uli Kazmaier, Rolf Muller, (Universitat des Saarlandes,
Germany), and coworkers have synthesized a simpler version of
the strongly inhibiting anti-cancer drug tubulysin D,
which will greatly aid efforts aimed at further enhancing
the efficacy of this class of molecules.
This news feature was written on June 1, 2009.... Read more »
Ullrich, A., Chai, Y., Pistorius, D., Elnakady, Y. A., Herrmann, J. E., Weissman, K. J., Kazmaier, U., & Müller, R. (2009) Pretubulysin, a Potent and Chemically Accessible Tubulysin Precursor from Angiococcus disciformis . Angewandte Chemie International Edition, 48(24), 4422-4425. DOI: 10.1002/anie.200900406
Dieter Lentz (Freie Universitat Berlin) and coworkers
have made progress towards applying hydrazine borane as a
highly effective hydrogen storage medium.
This news feature was written on June 1, 2009.... Read more »
Hügle, T., Kühnel, M. F., & Lentz, D. (2009) Hydrazine Borane: A Promising Hydrogen Storage Material. Journal of the American Chemical Society, 131(21), 7444-7446. DOI: 10.1021/ja9013437
Ayyalusamy Ramamoorthy (University of Michigan)
and coworkers have presented new evidence implicating the role
of individual protein molecules and small protein chains in
the damage done to pancreatic cells seen in type 2 diabetes.
This news feature was written on May 26, 2009.... Read more »
Soong, R., Brender, J. R., Macdonald, P. M., & Ramamoorthy, A. (2009) Association of Highly Compact Type II Diabetes Related Islet Amyloid Polypeptide Intermediate Species at Physiological Temperature Revealed by Diffusion NMR Spectroscopy. Journal of the American Chemical Society, 131(20), 7079-7085. DOI: 10.1021/ja900285z
George Schatz, Chad Mirkin
(Northwestern University, Illinois), and coworkers have expanded
the utility of surface-enhanced Raman scattering
for molecular detection by demonstrating that it is operable over
distances longer than 100 nanometers.
This news feature was written on May 24, 2009.... Read more »
Wei, W., Li, S., Millstone, J. E., Banholzer, M. J., Chen, X., Xu, X., Schatz, G. C., & Mirkin, C. A. (2009) Surprisingly Long-Range Surface-Enhanced Raman Scattering (SERS) on Au-Ni Multisegmented Nanowires. Angewandte Chemie International Edition, 48(23), 4210-4212. DOI: 10.1002/anie.200806116
Sangyong Jon (Gwangju Institute of Science and Technology,
South Korea) and coworkers have developed a practically-useful
assay for calcium ions, for disease diagnostics purposes.
This news feature was written on May 23, 2009.... Read more »
Kim, S., Park, J. W., Kim, D., Kim, D., Lee, I.-H., & Jon, S. (2009) Bioinspired Colorimetric Detection of Calcium(II) Ions in Serum Using Calsequestrin-Functionalized Gold Nanoparticles. Angewandte Chemie International Edition, 48(23), 4138-4141. DOI: 10.1002/anie.200900071
Karl Jorgensen (Aarhus University, Denmark) and coworkers
have developed an improved synthetic protocol for a class of
molecules that are otherwise particularly challenging to prepare,
which are of wide-ranging biochemical and pharmaceutical utility.
This news feature was written on May 22, 2009.... Read more »
Jiang, H., Falcicchio, A., Jensen, K. L., Paixão, M. W., Bertelsen, S., & Jørgensen, K. A. (2009) Target-Directed Organocatalysis: A Direct Asymmetric Catalytic Approach to Chiral Propargylic and Allylic Fluorides. Journal of the American Chemical Society, 131(20), 7153-7157. DOI: 10.1021/ja901459z
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