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Antimalarial drugs in the pipeline

25 May 2010 - Pharmacochemistry

A gloomy report in the May 14 issue of Science asserts that antimalarial drug research is as good as dead. The most common malaria agent plasmodium falciparum has built up resistance to the well known drug chloroquine and even the drug of last resort artemisinin is under threat. In 2009 the global malaria death toll was over 800,000 people. According to Timothy Wells of the Medicines for Malaria Venture There are plenty of new leads, but none of them are even in phase I safety studies and they would take at least 7 or 8 years to get to the market.

Luckily new leads have been described in two articles in the May 20 issue of Nature. The first is by researchers from GlaxoSmithKline (Gamo et al. DOI) who in a very generous mood have shared the results of antimalarial testing of over 2 million organic compounds with the rest of the world. In their introduction the authors cite intrinsic difficulties in discovering and developing new antimicrobials, as well as a relative lack of public and private resource commitment towards antimalarial research as reasons for the lack in drug development progress. Another plausible reason one can think of is the poorly perceived profitability of antimalarial drugs by pharmaceutical companies because the usually third-world victims are expected to have little to spend.

Assembling over two million little labeled bottles each containing a promising drug is quite a logistical undertaking but fortunately from then on robots can take over. The experimental details are as we are known to expect from biochemical research are fuzzy but in simple terms the process starts by filling each well on a microtiter plate with a solution of falciparum infected red blood cells that apparently you can buy someplace. The drug is added and the mix is incubated. An effective drug kills the parasite and cell health is monitored by so-called LDH activity. An LDH developing solution containing a lactate is added which LDH if present converts to a pyruvate. In this process a NAD+ analog also present is reduced to the NADH analog which proton then migrates to nitro blue tetrazolium (also present) forming a bright-red formazan. In each plate the effective drugs can then be visually detected as distinct red spots. In this way more than 8,000 compounds were found to have activity against a particular multidrug resistant strain (at IC50).

In the second Nature article a collective of over 30 scientists from several non-profit institutions (Guiguemde et al 2010 DOI) accomplish a similar feat. Here the library contained over 300,000 chemical compounds with a yield of 561 compounds at EC50. The detection method used (this blog guesses) measures the activity of the polymerase chain reaction in healthy cells by adding SYBR Green I which only shows fluorescence when bound to double stranded DNA.
antimalarial drugs screening

The molecular robot

15 May 2010 - Making it move part IV

themolecularrobot.jpgThis blog has a frequent topic called Making It Move that has been featuring thus far floating camphor boats, synchronized swimming droplets and brave droplets taking on a maze. Thanks to a group of researchers from Arizona State University / University of Michigan /Caltech / Columbia University we can now add to our list molecular DNA robots moving around on a DNA platform (Lund et al. DOI). The robot in question looks like a spider with a streptavidin body and three deoxyribozyme legs derived from a DNAzyme called 8-17 DNA (used often in DNA computing).

The robot arena is made from a single strand of DNA (7200 nucleotides) origami folded into a 2-dimensional platform measuring 65 nm x 390 nm x 32 nm with the aid of staple strands. Each spider leg on contact with a substrate site (a oligonucleotide) at the platform , catalytically cleaves it at the ribose unit. As each leg has higher substrate affinity than product affinity it will favor spots on the platform not yet trampled upon and a walking movement ensues.

The staple strands are fitted with probes that stick out from the surface serving special purposes: they form START (complementary to the TRIGGER), TRACK (substrate) and STOP (uncleavable substrate analogs) sites. A TRIGGER oligonucleotide sets the spiders in motion with an average speed of 180 nanometer per hour. The article is accompanied by a set of very fuzzy AFM images revealing the spider movements that could just as easy be taken as evidence for the Loch Ness monster. Also included are position-time trajactories obtained from total internal reflection fluorescence microscopy which required fluorophore labeling of spiders and STOP sites.
There is always the possibility that a spider dissociates all three legs simultaneously and makes a jump to a new section of the platform. As no spiders were found at so-called CONTROL sites (a STOP site well off a track) we should be reassured this does not happen.

Charge shifting protobranches

10 May 2010 - Computational chemistry

Carl Kemnitz has been paying attention to the Gronert vs Wodrich&Schleyer debate on the origin of stability in branched alkanes and protobranching as reported on in this blog in 2009 (DOI). In a nutshell, branched alkanes are more stable (more favorable heat of formation) than their linear counterparts thanks to protobranches (attractive 1,3 alkyl alkyl interactions) if you believe Wodrich or despite repulsive steric HCH, HCC or CCC interactions if you side with Gronert. No wonder Kemnitz labels the debate as controversial with diametrically opposed explanations. There is obviously work to be done.

No evidence was found for Gronerts physical model based on steric repulsions although his heat of formation group additivity method continues to hold. Kemnitz notes that on going from n-butane (1 PB, 8HCH, 14 HCC, 2CCC) to isobutane (3PB, 9 HCH, 12 HCC, 3 CCC) for every protobranch you add you also gain one HCH interaction, one CCC interaction and lose 2 HCC interactions. All aliphatic hydrocarbons share this property and Kemnitz was able to compute the energies involved arriving at 32 kcal/mol for CCC, 22 kcal/mol for HCC and 15 kcal/mol for HCH interactions. Adding a protobranch then involves an energy gain of 15+32-2*22 = +3 kcal/mol meaning that the contributions are destabilizing after all.

That leaves the protobranching model. Interestingly Wodrich never supplied his theory with a physical model (protobranches stabilize, that's it) but Kemnitz has developed one of its own or rather two. NBO calculations (natural bond orbitals see Goldbook) indicate stabilization through delocalization of electrons more precisely by sigma-sigma(star) excitation which this blog guesses is something like hyperconjugation with electrons in a sigma - carbon-carbon bond also occupy the empty sigma star orbital of the adjacent C-C bond. In another approach similarities are noted between protobranching and the charge-shift (CS) bond concept, the brain child of Shaik & Hiberty (DOI). CS bonds result from fluctuations in charge density and when applied to propane pure covalent bonding only accounts for 49% to the total picture and ionic contributions make up the rest. Specifically two 1,3-ionic structures H3C+ CH2 -H3C and H3C- CH2 + H3C make up 9% , require a protobranch and lower the total energy by 1.6 kcal/mol, a value close to the stabilization energy per protobranch.

Containing the spill

07 May 2010 - Deepwater Horizon

klik hier voor de afbeelding op ware grootteAs reported by Wired and C&EN and many others BP is trying to contain the damage done in the Deepwater Horizon oil spill by adding huge amounts of surfactant at the disaster site. The surfactant should emulsify the oil into tiny droplets making it degrade faster or at least make it disperse in the ocean and even sink to the bottom. Luckily the oil from the spill is high in asphaltene , a compound class that promotes emulsification (according to C&EN). The entire cleanup effort could explain why the disaster has not yet produced the familiar television images of black-caked beaches and smeared bird life even after two weeks. It does explain the bright orange glow produced by the (emulsified) oil when floating on water.

Question for this blog: what exactly is this miracle surfactant called Corexit EC9527A produced by Nalco. The material safety data sheet issued by the United States Environmental Protection Agency is not helpful but according to the one issued by Nalco the formula contains on average 45% 2-butoxyethanol, 15% of a proprietary organic sulfonic acid salt and 3% polyethylene glycol. This MSDS incidentally is published on, a website maintained by a bunch of oil companies carrying the slogan keeping the Americas clean since 1977 ..ahum.

According to Wired BP could also have opted for the more effective and less toxic formulation called dispersit produced by the company Polychemical (MSDS here). Patent number 6,261,463 (1999) reveals what is in it: water 17%, the sulfonic acid of dodecyl benzene 5%, triethanol amine 5%, dipropylene glycol methyl ether 20% (compound similar to 2-butoxyethanol?), ethoxylated tall oil fatty acid 5%, the amide of coconut oil 5% ethoxylated tallow amine 8%, sodium petroleum sulfonate 6%, an amine oxide surfactant 9%, aromatic phosphated ester 9%, tall oil 5%, another coco amide 5%, an ethoxylated secondary alcohol, 0.5% and another amine oxide 0.5%.

RCM vs ROM in triquinane synthesis

04 May 2010 - Organic chemistry

A novel DA - RCM - ROM Cascade reaction was described recently giving easy access to a group of complex tricyclic molecules called triquinanes (Nguyen et al. 2010 DOI). Reaction of alkyl tosylate 1 with cyclopentadiene and sodium hydride gives tetra-alkene 2 as a mixture of 2 isomers. The first step in de cascade is a high-temperature intramolecular Diels-Alder reaction of 2a to 3. No direct DA pathway exists for 2b because the formed double bond would violate Bredt's rule but isomerisation to 2a (T=210°C) is the alternative.

The second step in the cascade an olefin metathesis to 4 using Grubbs' catalyst and ethylene with both a ROM and a RCM component and the question arises: which one is first?. Nguyen settles for a mechanism in which the ruthenium alkylidene attacks the allyl double first, the key Ru complex shows up in low-temperature NMR and in an competition experiment n-hexene beats norbornadiene 6 to 1. This result is counter-intuitive (hence the exclamation mark in the publication's title) because initial attack of the Ru complex on the norbornene alkene would be driven by release of ring-strain.