Posted on by Dr. Francis Collins
The recent COVID-19 outbreak of a novel type of coronavirus that began in China has prompted a massive global effort to contain and slow its spread. Despite those efforts, over the last month the virus has begun circulating outside of China in multiple countries and territories.
Cases have now appeared in the United States involving some affected individuals who haven’t traveled recently outside the country. They also have had no known contact with others who have recently arrived from China or other countries where the virus is spreading. The NIH and other U.S. public health agencies stand on high alert and have mobilized needed resources to help not only in its containment, but in the development of life-saving interventions.
On the treatment and prevention front, some encouraging news was recently reported. In record time, an NIH-funded team of researchers has created the first atomic-scale map of a promising protein target for vaccine development . This is the so-called spike protein on the new coronavirus that causes COVID-19. As shown above, a portion of this spiky surface appendage (green) allows the virus to bind a receptor on human cells, causing other portions of the spike to fuse the viral and human cell membranes. This process is needed for the virus to gain entry into cells and infect them.
Preclinical studies in mice of a candidate vaccine based on this spike protein are already underway at NIH’s Vaccine Research Center (VRC), part of the National Institute of Allergy and Infectious Diseases (NIAID). An early-stage phase I clinical trial of this vaccine in people is expected to begin within weeks. But there will be many more steps after that to test safety and efficacy, and then to scale up to produce millions of doses. Even though this timetable will potentially break all previous speed records, a safe and effective vaccine will take at least another year to be ready for widespread deployment.
Coronaviruses are a large family of viruses, including some that cause “the common cold” in healthy humans. In fact, these viruses are found throughout the world and account for up to 30 percent of upper respiratory tract infections in adults.
This outbreak of COVID-19 marks the third time in recent years that a coronavirus has emerged to cause severe disease and death in some people. Earlier coronavirus outbreaks included SARS (severe acute respiratory syndrome), which emerged in late 2002 and disappeared two years later, and MERS (Middle East respiratory syndrome), which emerged in 2012 and continues to affect people in small numbers.
Soon after COVID-19 emerged, the new coronavirus, which is closely related to SARS, was recognized as its cause. NIH-funded researchers including Jason McLellan, an alumnus of the VRC and now at The University of Texas at Austin, were ready. They’d been studying coronaviruses in collaboration with NIAID investigators for years, with special attention to the spike proteins.
Just two weeks after Chinese scientists reported the first genome sequence of the virus , McLellan and his colleagues designed and produced samples of its spike protein. Importantly, his team had earlier developed a method to lock coronavirus spike proteins into a shape that makes them both easier to analyze structurally via the high-resolution imaging tool cryo-electron microscopy and to use in vaccine development efforts.
After locking the spike protein in the shape it takes before fusing with a human cell to infect it, the researchers reconstructed its atomic-scale 3D structural map in just 12 days. Their results, published in Science, confirm that the spike protein on the virus that causes COVID-19 is quite similar to that of its close relative, the SARS virus. It also appears to bind human cells more tightly than the SARS virus, which may help to explain why the new coronavirus appears to spread more easily from person to person, mainly by respiratory transmission.
McLellan’s team and his NIAID VRC counterparts also plan to use the stabilized spike protein as a probe to isolate naturally produced antibodies from people who’ve recovered from COVID-19. Such antibodies might form the basis of a treatment for people who’ve been exposed to the virus, such as health care workers.
The NIAID is now working with the biotechnology company Moderna, Cambridge, MA, to use the latest findings to develop a vaccine candidate using messenger RNA (mRNA), molecules that serve as templates for making proteins. The goal is to direct the body to produce a spike protein in such a way to elicit an immune response and the production of antibodies. An early clinical trial of the vaccine in people is expected to begin in the coming weeks. Other vaccine candidates are also in preclinical development.
Meanwhile, the first clinical trial in the U.S. to evaluate an experimental treatment for COVID-19 is already underway at the University of Nebraska Medical Center’s biocontainment unit . The NIH-sponsored trial will evaluate the safety and efficacy of the experimental antiviral drug remdesivir in hospitalized adults diagnosed with COVID-19. The first participant is an American who was repatriated after being quarantined on the Diamond Princess cruise ship in Japan.
As noted, the risk of contracting COVID-19 in the United States is currently low, but the situation is changing rapidly. One of the features that makes the virus so challenging to stay in front of is its long latency period before the characteristic flu-like fever, cough, and shortness of breath manifest. In fact, people infected with the virus may not show any symptoms for up to two weeks, allowing them to pass it on to others in the meantime. You can track the reported cases in the United States on the Centers for Disease Control and Prevention’s website.
As the outbreak continues over the coming weeks and months, you can be certain that NIH and other U.S. public health organizations are working at full speed to understand this virus and to develop better diagnostics, treatments, and vaccines.
 Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Wrapp D, Wang N, Corbett KS, Goldsmith JA, Hsieh CL, Abiona O, Graham BS, McLellan JS. Science. 2020 Feb 19.
 A new coronavirus associated with human respiratory disease in China. Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, Hu Y, Tao ZW, Tian JH, Pei YY, Yuan ML, Zhang YL, Dai FH, Liu Y, Wang QM, Zheng JJ, Xu L, Holmes EC, Zhang YZ. Nature. 2020 Feb 3.
 NIH clinical trial of remdesivir to treat COVID-19 begins. NIH News Release. Feb 25, 2020.
Coronaviruses (National Institute of Allergy and Infectious Diseases/NIH)
Coronavirus (COVID-19) (NIAID)
Coronavirus Disease 2019 (Centers for Disease Control and Prevention, Atlanta)
NIH Support: National Institute of Allergy and Infectious Diseases
Posted on by Dr. Francis Collins
Tropical medicine has its share of wily microbes. Among the most clever is the mosquito-borne protozoan Plasmodium falciparum, which is the cause of the most common—and most lethal—form of malaria. For decades, doctors have used antimalarial drugs against P. falciparum. But just when malaria appeared to be well on its way to eradication, this parasitic protozoan mutated in ways that has enabled it to resist frontline antimalarial drugs. This resistance is a major reason that malaria, one of the world’s oldest diseases, still claims the lives of about 400,000 people each year .
This is a situation with which I have personal experience. Thirty years ago before traveling to Nigeria, I followed directions and took chloroquine to prevent malaria. But the resistance to the drug was already widespread, and I came down with malaria anyway. Fortunately, the parasite that a mosquito delivered to me was sensitive to another drug called Fansidar, which acts through another mechanism. I was pretty sick for a few days, but recovered without lasting consequences.
While new drugs are being developed to thwart P. falciparum, some researchers are busy developing tools to predict what mutations are likely to occur next in the parasite’s genome. And that’s what is so exciting about the image above. It presents the unprecedented, 3D atomic-resolution structure of a protein made by P. falciparum that’s been a major source of its resistance: the chloroquine-resistance transporter protein, or PfCRT.
In this cropped density map, you see part of the protein’s biochemical structure. The colorized area displays the long, winding chain of amino acids within the protein as helices in shades of green, blue and gold. These helices enclose a central cavity essential for the function of the protein, whose electrostatic properties are shown here as negative (red), positive (blue), and neutral (white). All this structural information was captured using cryo-electron microscopy (cryo-EM). The technique involves flash-freezing molecules in liquid nitrogen and bombarding them with electrons to capture their images with a special camera.
This groundbreaking work, published recently in Nature, comes from an NIH-supported multidisciplinary research team, led by David Fidock, Matthias Quick, and Filippo Mancia, Columbia University Irving Medical Center, New York . It marks a major feat for structural biology, because PfCRT is on the small side for standard cryo-EM and, as Mancia discovered, the protein is almost featureless.
These two strikes made Mancia and colleagues wonder at first whether they would swing and miss at their attempt to image the protein. With the help of coauthor Anthony Kossiakoff, a researcher at the University of Chicago, the team complexed PfCRT to a bulkier antibody fragment. That doubled the size of their subject, and the fragment helped to draw out PfCRT’s hidden features. One year and a lot of hard work later, they got their homerun.
PfCRT is a transport protein embedded in the surface membrane of what passes for the gut of P. falciparum. Because the gene encoding it is highly mutable, the PfCRT protein modified its structure many years ago, enabling it to pump out and render ineffective several drugs in a major class of antimalarials called 4-aminoquinolines. That includes chloroquine.
Now, with the atomic structure in hand, researchers can map the locations of existing mutations and study how they work. This information will also allow them to model which regions of the protein to be on the lookout for the next adaptive mutations. The hope is this work will help to prolong the effectiveness of today’s antimalarial drugs.
For example, the drug piperaquine, a 4-aminoquinoline agent, is now used in combination with another antimalarial. The combination has proved quite effective. But recent reports show that P. falciparum has acquired resistance to piperaquine, driven by mutations in PfCRT that are spreading rapidly across Southeast Asia .
Interestingly, the researchers say they have already pinpointed single mutations that could confer piperaquine resistance to parasites from South America. They’ve also located where new mutations are likely to occur to compromise the drug’s action in Africa, where most malarial infections and deaths occur. So, this atomic structure is already being put to good use.
Researchers also hope that this model will allow drug designers to make structural adjustments to old, less effective malarial drugs and perhaps restore them to their former potency. Perhaps this could even be done by modifying chloroquine, introduced in the 1940s as the first effective antimalarial. It was used worldwide but was largely shelved a few decades later due to resistance—as I experienced three decades ago.
Malaria remains a constant health threat for millions of people living in subtropical areas of the world. Wouldn’t it be great to restore chloroquine to the status of a frontline antimalarial? The drug is inexpensive, taken orally, and safe. Through the power of science, its return is no longer out of the question.
 World malaria report 2019. World Health Organization, December 4, 2019
 Structure and drug resistance of the Plasmodium falciparum transporter PfCRT. Kim J, Tan YZ, Wicht KJ, Erramilli SK, Dhingra SK, Okombo J, Vendome J, Hagenah LM, Giacometti SI, Warren AL, Nosol K, Roepe PD, Potter CS, Carragher B, Kossiakoff AA, Quick M, Fidock DA, Mancia F. Nature. 2019 Dec;576(7786):315-320.
 Determinants of dihydroartemisinin-piperaquine treatment failure in Plasmodium falciparum malaria in Cambodia, Thailand, and Vietnam: a prospective clinical, pharmacological, and genetic study. van der Pluijm RW, Imwong M, Chau NH, Hoa NT, et. al. Lancet Infect Dis. 2019 Sep;19(9):952-961.
Malaria (National Institute of Allergy and Infectious Diseases/NIH)
Fidock Lab (Columbia University Irving Medical Center, New York)
Video: David Fidock on antimalarial drug resistance (BioMedCentral/YouTube)
Kossiakoff Lab (University of Chicago)
Mancia Lab (Columbia University Irving Medical Center)
Matthias Quick (Columbia University Irving Medical Center)
NIH Support: National Institute of Allergy and Infectious Diseases; National Institute of General Medical Sciences; National Heart, Lung, and Blood Institute
Posted on by Dr. Francis Collins
Credit: Adapted from Jones et al. ChemRxiv.org
Over the past few years, there’s been a great deal of excitement about the power of cryo-electron microscopy (cryo-EM) for mapping the structures of large biological molecules like proteins and nucleic acids. Now comes word of another absolutely incredible use of cryo-EM: determining with great ease and exquisite precision the structure of the smaller organic chemical compounds, or “small molecules,” that play such key roles in biological exploration and drug development.
The new advance involves a cryo-EM technique called microcrystal-electron diffraction (MicroED). As detailed in a preprint on ChemRxiv.org  and the journal Angewandte Chemie , MicroED has enabled researchers to take the powdered form of commercially available small molecules and generate high-resolution data on their chemical structures in less than a half-hour—dramatically faster than with traditional methods!
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