Avian Influenza Neuraminidase, Tamiflu and Relenza: Difference between revisions

<big>

This article was updated May 23, 2009.

</big>

 

Influenza <ref name="flu">[http://en.wikipedia.org/wiki/Influenza Influenza] (in Wikipedia).</ref> is a contagious disease caused by a virus. Influenza A<ref name="flu_a">See [http://en.wikipedia.org/wiki/Influenza#Types_of_influenza_virus Influenza A Types of Influenza Virus] (in Wikipedia).</ref> (one of several genera and species of influenza) is the most virulent form infecting humans. Largely by facilitating secondary bacterial pneumonias, influenza kills 500,000 people worldwide annually (including about 36,000 in the USA), mostly during seasonal [http://en.wikipedia.org/wiki/Epidemic epidemics] each year. Most people killed in the annual influenza epidemics are people whose immune defenses are weak, including the very young and the old. Influenza also kills large numbers of animals and birds, both domestic and wild<ref name="animals">[http://www.fao.org/avianflu/en/clinical.html Epidemiology of Avian Influenza] at the [http://fao.org Food and Agriculture Organization of the United Nations].</ref>. The influenza virus includes only eight proteins. Sequences of these proteins as obtained from numerous strains are available in the [http://www.ncbi.nlm.nih.gov/genomes/FLU/Database/select.cgi?go=1 NCBI Influenza Virus Resource]. For more about the structure and biology, including references for the points made here, please see [http://en.wikipedia.org/wiki/Influenza Influenza at Wikipedia].

*Each of the four protein chains in the tetramer has a catalytic site, indicated in <scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/2hu4_tetramer/3'>this scene</scene> by the positions of the bound <font color='red'>'''Tamiflu'''</font> inhibitors.

*The <scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/2hu4_tetramer/5'>substrate binding site</scene> involves only a single protein chain, being distant from neighboring chains.

*The <scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/2hu4_tetramer/6'>secondary structure</scene> is mostly beta, consisting of several beta sheets with three short alpha helices ({{Template:ColorKey_Strand}}, {{Template:ColorKey_Helix}}).

*The residues contacting the <font color='red'>'''Tamiflu inhibitory substrate analog'''</font> are <scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/2hu4_tetramer/7'>highly conserved</scene><ref>See [[Evolutionary Conservation]]. Coloring by ConSurf on chain A of 2hu4 based on 100 unique homologs using default conditions, done on September 23, 2008.</ref>.

*These highly conserved residues include some known to be crucial to binding sialic acid substrate: Arg 118, Arg 292 and Arg 371 bind the carboxylate; Arg 152 interacts with the acetamido substituent; and Glu 276 forms hydrogen bonds with the 8- and 9-hydroxyl groups of the substrate. These residues are <scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/2hu4_tetramer/8'>highlighted here</scene> in contact with the sialic acid substrate analog Tamiflu. In this scene, atoms and bonds in Tamiflu and the highlighted residues are colored by element: {{Template:ColorKey_Element_C}}, {{Template:ColorKey_Element_O}}, {{Template:ColorKey_Element_N}}.

On April 29, 2009, the World Health Organization (WHO) raised its pandemic alert to level five on a six point scale, indicating that a pandemic is imminent ([http://www.who.int www.who.int]). The CDC is maintaining frequent updates at [http://cdc.gov/h1n1flu cdc.gov/h1n1flu].  A preliminary [http://www.proteopedia.org/wiki/index.php/User:Michael_Strong/H1N1 proteopedia-based analysis of the 2009 H1N1 Swine Flu sequence polymorphisms] within the context of protein homology models is also available.

'''Vaccines''' are effective at preventing influenza, but only if they target the relevant viral subtypes. New vaccines against the annual epidemics of influenza A and B are prepared each year, separately in the northern and southern hemispheres. These are designed to target the subtypes predicted to be prevalent in any given flu season, but sometimes those predictions are wrong, leading to that year's vaccine being ineffective. A vaccine for a pandemic strain of H5N1 could not be prepared until after the pandemic began, because only then would the relevant subtype be known<ref>[http://en.wikipedia.org/wiki/Influenza#Vaccination_and_infection_control Vaccination for Influenza] at Wikipedia</ref>.

'''Drugs''' against influenza, stockpiled in advance of a panedmic, appear to be the best preparation, given the limitations of vaccines. Tens of billions of dollars have been spent on pandemic preparedness in the USA alone, and a large portion of these expenditures is for [http://en.wikipedia.org/wiki/Oseltamivir stockpiling of anti-influenza drugs]. Similar expenditures have been made in many developed countries. The World Health Organization is poised to distribute anti-influenza drugs at the first signs of an epidemic of H5N1.

[http://en.wikipedia.org/wiki/Amantadine Amantadine] and [http://en.wikipedia.org/wiki/Rimantadine Rimantadine] are an anti-viral drugs that work by blocking the [http://www.proteopedia.org/wiki/index.php/Proton_Channels M2 proton-channel] ([[3bkd]], [[1nyj]], [[2kad]], [[2rlf]], [[3c9j]]) that is required for viruses to infect cells. Ion-channel function appears to be required for uncoating during endocytosis. Amantadine was approved for anti-viral uses beginning in 1966 by the US FDA. Subsequent widespread use has selected amantadine-resistant influenza in humans and birds. By 2005-2006, the US CDC found 92% of H3N2 isolates were resistant, and 2 of 8 H1N1 isolates. In Asia, resistance is close to 100%. The most common mutation responsible for resistance is S31N in M2, which confers resistance to both amantadine and rimantadine<ref>[http://www.cdc.gov/mmwr/preview/mmwrhtml/mm5502a7.htm Report on amantadine resistance], CDC Morbidity and Mortality Weekly Reports, January 2006.</ref>. References for this paragraph will be found in the [http://en.wikipedia.org/wiki/Amantadine ''Amantadine'' article in Wikipedia].

[http://en.wikipedia.org/wiki/Oseltamivir Tamiflu (oseltamivir)] is an inhibitor of influenza neuraminidase that binds to the enzyme active site. (''Tamiflu'' is [http://en.wikipedia.org/wiki/Hoffmann-La_Roche Roche]'s trade name; oseltamivir is the [http://en.wikipedia.org/wiki/International_Nonproprietary_Name generic] name.) Tamiflu is a [[Transition state analog|transition state analog]], and was the first orally active neuraminidase inhibitor commercially developed. Because neuraminidase is required for the viral life cycle, its enzymatic active site is highly conserved, and Tamflu is effective on a range of neuraminidase subtypes. It is indicated both for prophylaxis and for treatment within two days of the onset of symptoms.

[http://en.wikipedia.org/wiki/Zanamivir Relenza (zanamivir)] is also an inhibitor of influenze neuraminidase that binds to the enzyme active site. (''Relenza'' is [http://en.wikipedia.org/wiki/GlaxoSmithKline GlaxoSmithKline]'s trade name; zanamivir is the [http://en.wikipedia.org/wiki/International_Nonproprietary_Name generic] name.) Unlike Tamiflu, which is given orally, Relenza is usually administered by '''inhalation, or can be injected'''.

Two common mutations that confer resistance to Tamiflu did not confer resistance to Relenza<ref name="collins2008" />.  At right is Relenza binding to the H274Y mutant of N1. This suggests that it would be prudent to stockpile Relenza in addition to Tamiflu, and that combination therapy might be the most effective weapon against a new pandemic, prior to development and deployment of a vaccine.

<applet load='2hty2hu4_j.pdb' size='500' frame='true' align='right' caption='Morph of N1 alone (2hty) to N1 complexed with Tamiflu (2hu4). The position where Tamiflu will bind is shown translucent except when bound in the empirically-determined model.' scene='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/Morph_2hty_to_2hu4/2' />

Tamiflu was designed to fit N2/N9, so it is serendipitous that it works on N1. In fact, when the structure of N1 was determined<ref name='Russell2006' />, the <font color='#e07000'><b>loop comprising residues 147-152</b></font> was not in a suitable position to participate in binding Tamiflu. However, the complex of N1 with Tamiflu revealed that this loop is pulled into proper contact with the drug in an [[Induced fit|induced fit]] manner<ref name='Russell2006' />. A [[Morphs|morph]] from N1 alone ([[2hty]]) to N1 complexed with Tamiflu ([[2hu4]])<ref>Chain A from [[2hty]] was morphed to chain A of [[2hu4]] by linear interpolation, inserting 6 intermediate interpolated frames, using the freely available [http://www.umass.edu/microbio/rasmol/pdbtools.htm#martz morph2 program].</ref> shows the change in position of this loop (<scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/Morph_2hty_to_2hu4/8'>replay initial morph</scene>).

The binding of Tamiflu to N1 pulls the sidechains of two conserved residues, <scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/Morph_2hty_to_2hu4/7'>Asp151, Glu119</scene>, closer to the inhibitor.

For technical reasons, the cavity cannot be shown yet in Jmol in Proteopedia. (We are working to resolve this problem.) However, it may be seen in View 2 of

of the [http://www.bioinformatics.org/jmol-tutorials/jtat/jtatdemo Jmol Tutorial-Authoring Template (JTAT) Demonstration Tutorial].