Navigation Links
UC Irvine study points to new approach to influenza's antiviral resistance
Date:7/13/2011

Researchers from the University of California, Irvine, with assistance from the San Diego Supercomputer Center at UC San Diego, have found a new approach to the creation of customized therapies for virulent flu strains that resist current antiviral drugs.

The findings, published online this week in Nature Communications, could aid development of new drugs that exploit so-called flu protein 'pockets.'

Using powerful computer simulations on SDSC's new Trestles system, launched earlier this year under a $2.8 million National Science Foundation (NSF) award, UCI's Rommie Amaro and Robin Bush together with SDSC's Ross Walkercreated a method to predict how pocket structures on the surface of influenza proteins promoting viral replication can be identified as these proteins evolve, allowing for possible pharmaceutical exploitation.

"Our results can influence the development of new drugs taking advantage of this unique feature," said Amaro, an assistant professor of pharmaceutical sciences and computer science at UCI. Prior to joining UCI in 2009, Amaro was a postdoctoral fellow in chemistry at UC San Diego.

The search for effective flu drugs has always been hampered by the influenza virus itself, which mutates from strain to strain, making it difficult to target with a specific pharmaceutical approach. The most common clinical flu treatments are broad-based and only partially effective. They work by interrupting the action of an enzyme in the virus called neuraminidase, which plays a critical role in viral replication.

In 2006, scientists discovered that avian influenza neuraminidase (N1) exhibited a distinctive, pocket-shaped feature in the area pinpointed by clinically used drugs. They named it the 150-cavity.

Amaro and Bush, associate professor of ecology and evolutionary biology, conducted research using resources at the San Diego Supercomputer Center, as well as the National Institute for Computational Sciences (NICS) to learn the conditions under which the pockets form. They created molecular simulations of flu proteins to predict how these dynamic structures move and change, as well as and where and when the 150-cavity pockets will appear on the protein surface.

This sequence analysis method could be utilized on evolving flu strains, providing vital information for drug design, Amaro said. "Having additional antivirals in our treatment arsenal would be advantageous and potentially critical if a highly virulent strain, for example, H5N1, evolved to undergo rapid transmission among humans or if the already highly transmissible H1N1 pandemic virus was to develop resistance to existing antiviral drugs," she added.

Walker, an assistant research professor who runs the Walker Molecular Dynamics Lab at SDSC, developed a customized version of the AMBER software, a widely used package of molecular simulation codes, to run these specific simulations on Trestles under the NSF's TeraGrid Advanced User Support System. That included detailed performance tuning including hard-coding atom counts, atom types and parameters, and being able to use Trestles for uninterrupted two-week runs that together consumed more than one million SUs (single processor hours).

"We initially used the Athena supercomputer at NICS, which provided us with all the initial comparison data before Trestles came online earlier this year," said Walker, who is also an adjunct assistant professor in UC San Diego's Department of Chemistry and Biochemistry. "We had Trestles all ready to go as soon as the first H1N1 protein structure was available, and using the earlier work we did on Athena, we were able to put Trestles immediately to work to conduct simulations of the structure as part of this research."


'/>"/>

Contact: Jan Zverina
jzverina@sdsc.edu
858-534-5111
University of California - San Diego
Source:Eurekalert

Related medicine news :

1. UC Irvine Medical Center honors 9 for nursing excellence
2. UC Irvine Medical Center recognized for heart failure program
3. UC Irvine Medical Center is recognized for its commitment to organ donation
4. VOICE study will continue as it considers what action to take after results of 2 trials
5. Pivotal study in Africa finds that HIV medications prevent HIV infection
6. UAB researchers present a study on the psychological adaptation of adopted children
7. Bed Sores Afflict More Blacks in Nursing Homes Than Whites: Study
8. More U.S. Men Die From Cancer Than Women: Study
9. Older Women at Greater Risk for Common STD, Study Suggests
10. Bladder Cancer Patients Not Getting Recommended Care: Study
11. Fast Food Is King of the Neighborhood, Study Reports
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:2/24/2017)... ... , ... With ProGlass Prism users now have the ability to simulate prism ... position, rotation, distortion, edge softness, edge blur, chromatic aberration, individual glass position offset, anchor ... Prism users are given the tools and effects to generate a fractal prismatic ...
(Date:2/24/2017)... ... ... Indiana Fiber Network (IFN) President and CEO Kelly C. Dyer recently announced that he ... of the Management Committee when IFN was originally formed in 2002 where he was ... development of the business plan. He became the first paid employee of IFN ...
(Date:2/24/2017)... ... 24, 2017 , ... Castle Farms, the celebrated Northern ... with the winning couple announced on Feb. 14, 2017, on Facebook. The free ... vendors: A Matter of Taste, Ryan Rousseau Enterprises, A Touch of Spring and ...
(Date:2/23/2017)... ... 2017 , ... The Lymphoma Research Foundation (LRF) – the ... the lymphoma community through a comprehensive series of education programs, outreach initiatives and ... Beach to host its Swirl: Miami Wine Tasting Event on March 28, 2017. ...
(Date:2/23/2017)... ... 2017 , ... Hamlin Dental Group and Dr. Hamid Reza, dentist in ... the month of February, patients who visit Hamlin Dental Group will receive a ticket ... two at the Cheesecake Factory. , Tickets are available for routine dental visits ...
Breaking Medicine News(10 mins):
(Date:2/24/2017)... Research and Markets has announced the addition ... 2016" report to their offering. ... The latest research Urinary Incontinence Drugs Price ... in the global Urinary Incontinence market. The research answers the ... drugs marketed for Urinary Incontinence and their clinical attributes? How are ...
(Date:2/23/2017)... Research and Markets has announced the addition ... - 2016" report to their offering. ... The latest research Autism Spectrum Disorder ... and benchmarks in the global Autism Spectrum Disorder market. The ... are the key drugs marketed for Autism Spectrum Disorder and their ...
(Date:2/23/2017)... , Südkorea, 23. Februar 2017 LG ... für Sterilisationsaufgaben vorgestellt. Die Sterilisationsleistung beträgt das 1,5-fache des ... ultraviolette Strahlung im Bereich zwischen 200 und 280 nm und ... von Bakterien, indem es ihre DNA zerstört. Das Produkt ... ...
Breaking Medicine Technology: