Thursday, May 28, 2015

From Herb Garden To Medicine Cabinet: Developing A New Drug for Malaria

We live on a lush planet filled with over 290,000 species of plants. Herbs are a particular type of plant that lack a wooden stem, and humans have often sampled them with hopes of finding a new food or flavoring. Sometimes ingestion of an herb produces unwanted effects, such as death. But other herbs have medicinal qualities, such as the alleviation of fever.

Dichroa febrifuga, a medicinal herb that has been historically used to treat fever, is named for its active ingredient, febrifugine.
Dichroa febrifuga is one of the most important herbs in traditional Chinese medicine, used for millennia to treat ailments such as malaria. Malaria is caused by a unicellular parasite called Plasmodium that is transmitted by mosquitoes, and a high fever is one of the trademark symptoms.

Malaria has a complex life cycle. After the parasites (sporozoites) are injected via mosquitoes, they travel to the liver (merozoites) and then infect red blood cells. In blood cells, they gobble up the hemoglobin as a nutrient source for replication and development into sexual stages (gametocytes) that can be taken up by another mosquito, thereby spreading the parasite to a new victim.
Malaria continues to be a devastating disease, killing up to 1 million people each year, most of whom are children under the age of five in sub-Saharan Africa. There is an urgent need for new treatments since the parasite has developed resistance to most of our anti-malaria drugs.

While effective against malaria, febrifugine is not tolerated well. What is needed is a better understanding of how febrifugine works:  how does it kill the malaria parasite? If the natural product’s mechanism of action against malaria could be identified, it would pave the way for the development of refined derivatives that are more specific against the parasite and less detrimental to patients. Alas, this is not an easy task. Over 2000 years in the making, scientists have now identified an enzyme in the parasite that is inhibited by febrifugine. That enzyme is called prolyl-tRNA synthetase.

Prolyl-tRNA synthetase is critical for the production of proteins in a cell, a process known as translation. As shown in the figure below, messenger RNA (mRNA), which serves as the “middle man” conveying the information in genes to build proteins, is read by molecular machines called ribosomes. Another type of RNA molecule called transfer RNA (tRNA) recognizes specific nucleotide sequences in the mRNA, bringing the corresponding amino acid to the ribosome so it can be added to a growing protein sequence.

The production of proteins in the cell. Proteins are composed of amino acids (the colored balls) that are connected together in a specific order, as directed by the gene coding for it. The chain of amino acids then typically folds into a three-dimensional shape so that the protein can do its job in the cell.
Aminoacyl-tRNA synthetase enzymes are needed to “charge” the tRNA; in other words, they attach the correct amino acid to the correct tRNA. When prolyl-tRNA synthetase is blocked by febrifugine, the amino acid proline does not get attached to tRNA. This leads to a buildup of “uncharged” tRNA, which is interpreted as a sign of starvation by the cell (or by the single-celled malaria parasite in this case). Proline is a common amino acid needed to build many proteins, and when prolyl-tRNA synthetase isn’t able to do its job, protein production grinds to a halt.

Even better, this enzyme is required in multiple stages of the parasite’s life cycle, knocking out both the liver and the blood forms. But as mentioned above, humans do not tolerate febrifugine very well, probably because we also have a version of prolyl-tRNA synthetase and perhaps other proteins that febrifugine poisons. Having identified this drug target is helping researchers develop derivatives of febrifugine, such as halofuginol, that act more strongly against the parasite’s prolyl-tRNA synthetase with less toxicity in humans.

Halofuginol is chemically similar to febrifugine (see above), having potent activity against malaria but less adverse effects on the host.
So how did scientists figure out that febrifugine targets prolyl-tRNA synthetase? There are several ways to identify the molecular mechanism of drug activity. In this case, the group cultured malaria in the presence of drug, forcing the parasites to evolve or die. Those that lived were less sensitive to febrifugine, meaning that they accrued a genetic change (one or more mutations in their DNA) that allowed them to persist despite the presence of the drug. This process is very analogous to the development of penicillin-resistant bacteria.

Parasites that were able to grow better in febrifugine had their genomes sequenced. Such a feat would have taken years and millions of dollars not long ago, but today it has become routine. The genome sequence of the febrifugine-resistant parasites contained a common mutation in the gene encoding prolyl-tRNA synthetase, which signaled that this enzyme plays a critical role in the drug’s action. Understanding how the parasite develops resistance also helps scientists design compounds that act on the target differently. As you may surmise, we are in a constant “arms race” with these insidious microbes, but this discovery is a step towards a victory for us.

Two independent parasite lines that were resistant to febrifugine, HFGR I and II, contained mutations in their prolyl-tRNA synthetase gene. In drug-sensitive parasites (Dd2), an amino acid called leucine (leu) is present at position 1444, but in the mutant parasites, a DNA change led to a different amino acid that conferred resistance to the drug.
Contributed by:  Bill Sullivan
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Herman JD, Pepper LR, Cortese JF, Estiu G, Galinsky K, Zuzarte-Luis V, Derbyshire ER, Ribacke U, Lukens AK, Santos SA, Patel V, Clish CB, Sullivan WJ Jr, Zhou H, Bopp SE, Schimmel P, Lindquist S, Clardy J, Mota MM, Keller TL, Whitman M, Wiest O, Wirth DF, & Mazitschek R (2015). The cytoplasmic prolyl-tRNA synthetase of the malaria parasite is a dual-stage target of febrifugine and its analogs. Science translational medicine, 7 (288) PMID: 25995223

Thursday, May 14, 2015

Darwin Can Dance! The Evolution Of Pop Music

Why do most people over 40 hate today’s music? Why do your grandparents keep playing their “Malt Shop Memories” CDs? Why does your mom start dancing when she hears Wham! and your dad start nodding his head wildly when he hears Motley Crue? Why does your Uncle never shut up about how Nirvana was the greatest band ever because they "changed everything"? 

As evidenced by their song, "Do The Evolution", Pearl Jam appears to be well-versed in evolutionary theory. But was the advent of grunge the most radical change in the course of modern music history?
Despite the cliché, the song does not remain the same. Just like biological organisms, music evolves - and where there is evolution, there is science. The modern rock band, As I Lay Dying, sings it best: “The Only Constant Is Change”. 

As I Lay Dying is not the kind of music your parents are going to understand. You can hear them now as they cover their ears, “Turn off that racket! My ears are bleeding! You call that singing? He’s just screaming! Back in my day…” and so on.

Elvis Presley is commonly known as “The King of Rock and Roll” for popularizing a groundbreaking style of music in the 1950s that fused rockabilly, country, and rhythm & blues. To this day, he remains the best selling musical artist of all time, having sold in excess of 600 million records.

With this extraordinary popularity, you’d think that his type of music would still be going strong, but one look at today’s pop music chart and you’ll quickly see that there is little on there that resembles the music Elvis brought to the world. On the contrary, there are styles of music on the charts now that Elvis never could have imagined. At the time this article was written, the #1 song on the Top 100 Billboard chart is “See You Again”, which sounds nothing like the music that was popular prior to the 1990s.

While the reason remains debatable, there’s no question that music changes over time. However, our favorite music tends to be what was popular during the most impressionable years of our youth, between ages 12 and 22. Music heard during that window in our lives appears to get hardwired into our brain, forever serving as a powerful stimulus for dopamine release, a neurotransmitter that makes us feel pleasantly satisfied (perhaps "comfortably numb").

In a new study published in Royal Society Open Science, evolutionary biologists and computer scientists “come together” to advance our understanding of pop music’s evolution. The researchers analyzed 17,000 songs from the US Billboard Hot 100 charts from 1960 to 2010 in order to identify the greatest musical revolution in recent US music history. Was it the famous “British Invasion” led by the Beatles and the Rolling Stones in the 1960s?
Was it the rise of disco in the 1970s, led by the Bee Gees, Village People, and KC & the Sunshine Band, or maybe the earth-shattering hard rock of Led Zeppelin?

Could it be the rise of synth-pop and electronic music by the likes of Madonna, Duran Duran, or Howard Jones in the 1980s?

How about the meteoric rise of those late 80s hairbands like Bon Jovi, Poison, or Warrant?
Or maybe it was the gritty angst of grunge that blasted onto the scene with Nirvana, Alice in Chains, Pearl Jam, and Soundgarden?
None of the above is correct, at least according to the criteria used by the authors of the study, which employed “cutting edge methods from signal processing and text-mining to analyze the musical properties of songs. Their system automatically grouped the thousands of songs by patterns of chord changes and tone allowing researchers to statistically identify trends with an unprecedented degree of consistency.”

The biggest upheaval occurred in 1991, but not with grunge…it was with hip-hop. Starting in the mid-80s, rap and hip-hop began climbing a steady ladder to the mainstream, with the help of artists like Run-DMC, Beastie Boys, Salt-N-Pepa, and LL Cool J. But 1991 was a watershed year with huge breakthroughs for hip-hop artists like N.W.A., Ice Cube, Ice-T, 2Pac, TLC, and Public Enemy. The radical changes in lyrical content and delivery, arrangement, and the diversity of sounds culminated to make hip-hop one of the most innovative changes to music in recent history.

With these powerful tools to analyze how music has evolved over the past 50 years, one has to wonder if it is possible to predict how music might sound in 2065.

Contributed by:  Bill Sullivan


Matthias Mauch, Robert M. Maccallum, Mark Levy, Armand M. Leroi. The evolution of popular music: USA 1960–2010. Royal Society Open Science, May 2015 DOI: 10.1098/rsos.150081
Salimpoor, V., Benovoy, M., Larcher, K., Dagher, A., & Zatorre, R. (2011). Anatomically distinct dopamine release during anticipation and experience of peak emotion to music Nature Neuroscience, 14 (2), 257-262 DOI: 10.1038/nn.2726