The structural relationship of sialidase to the influenza virus surface

Drug Design Strategies to Avoid Resistance in Direct-Acting Antivirals and Beyond

Drug resistance is prevalent across many diseases, rendering therapies ineffective with severe financial and health consequences. Rather than accepting resistance after the fact, proactive strategies need to be incorporated into the drug design and development process to minimize the impact of drug resistance. These strategies can be derived from our experience with viral disease targets where multiple generations of drugs had to be developed to combat resistance and avoid antiviral failure. Significant efforts including experimental and computational structural biology, medicinal chemistry, and machine learning have focused on understanding the mechanisms and structural basis of resistance against direct-acting antiviral (DAA) drugs. Integrated methods show promise for being predictive of resistance and potency. In this review, we give an overview of this research for human immunodeficiency virus type 1, hepatitis C virus, and influenza virus and the lessons learned from resistance mechanisms of DAAs. These lessons translate into rational strategies to avoid resistance in drug design, which can be generalized and applied beyond viral targets. While resistance may not be completely avoidable, rational drug design can and should incorporate strategies at the outset of drug development to decrease the prevalence of drug resistance.

Molecular Basis for Differential Patterns of Drug Resistance in Influenza N1 and N2 Neuraminidase

Neuraminidase (NA) inhibitors are used for the prevention and treatment of influenza A virus infections. Two subtypes of NA, N1 and N2, predominate in viruses that infect humans, but differential patterns of drug resistance have emerged in each subtype despite highly homologous active sites. To understand the molecular basis for the selection of these drug resistance mutations, structural and dynamic analyses on complexes of N1 and N2 NA with substrates and inhibitors were performed. Comparison of dynamic substrate and inhibitor envelopes and interactions at the active site revealed how differential patterns of drug resistance have emerged for specific drug resistance mutations, at residues I222, S246, and H274 in N1 and E119 in N2. Our results show that the differences in intermolecular interactions, especially van der Waals contacts, of the inhibitors versus substrates at the NA active site effectively explain the selection of resistance mutations in the two subtypes. Avoiding such contacts that render inhibitors vulnerable to resistance by better mimicking the dynamics and intermolecular interactions of substrates can lead to the development of novel inhibitors that avoid drug resistance in both subtypes.

Antiviral adhesion molecular mechanisms for influenza: W. G. Laver's lifetime obsession

Infection by the influenza virus depends firstly on cell adhesion via the sialic-acid-binding viral surface protein, haemagglutinin, and secondly on the successful escape of progeny viruses from the host cell to enable the virus to spread to other cells. To achieve the latter, influenza uses another glycoprotein, the enzyme neuraminidase (NA), to cleave the sialic acid receptors from the surface of the original host cell. This paper traces the development of anti-influenza drugs, from the initial suggestion by MacFarlane Burnet in 1948 that an effective 'competitive poison' of the virus' NA might be useful in controlling infection by the virus, through to the determination of the structure of NA by X-ray crystallography and the realization of Burnet's idea with the design of NA inhibitors. A focus is the contribution of the late William Graeme Laver, FRS, to this research.

Antiviral drugs for influenza: Tamiflu® past, present and future

Two antiviral drugs that are currently available for the treatment of influenza are effective against all strains of the virus, if used correctly. These are the neuraminidase inhibitors, zanamivir (Relenza®) and oseltamivir (Tamiflu®). These drugs are the result of basic research performed over a 60-year period by many people around the world. They were deliberately synthesized from a knowledge of the x-ray crystal structure of influenza virus neuraminidase. This article provides a brief historical account of some of the scientific events that lead to their creation.

Pandemic influenza: its origin and control

A "new" influenza virus will appear at some time in the future. This virus will arise by natural processes, which we do not fully understand, or it might be created by some bioterrorist. The world's population will have no immunity to the new virus, which will spread like wild-fire, causing much misery, economic disruption and many deaths. Vaccines will take time to develop and the only means of control, at least in the early stages of the epidemic, are anti-viral drugs, of which the neuraminidase inhibitors currently seem the most effective.

Sequence and crystallization of influenza virus B/Beijing/1/87 neuraminidase

Influenza B/Beijing/1/87 neuraminidase heads were isolated from virus via trypsin digestion and characterized by PAGE, N-terminal sequencing, electron microscopy, and enzyme activity. The heads were crystallized into two crystal forms; tetragonal plates, like other neuraminidase crystals described before, that diffract to medium resolution (3 A) and a new form consisting of trigonal prisms or needles that diffract to high resolution (at least 2 A). The gene segment coding for neuraminidase was sequenced and compared with the neuraminidase sequence of B/Lee/40. The deduced amino acid sequences for neuraminidase showed only a 7% difference, whereas those for the NB proteins differed by 20%.

Characterization of influenza virus neuraminidase with hemagglutinin activity and its comparison with that of viral neuraminidase

The neuraminidase associated with the bifunctional protein, hemagglutinin-neuraminidase, of influenza virus has been characterized. The enzyme has a pH optimum of 4.5, does not require Ca2+ and is inactivated (98%) by incubation at 50 degrees C. The enzyme has a Km of 2.00 X 10(-3) M and 0.06 X 10(-3) M with the substrates 2-(3-methoxyphenyl)-N-acetylneuraminic acid and fetuin, respectively. The Ki is 400 X 10(-6) with the inhibitor 2-deoxy-2,3-dehydro-N-acetylneuraminic acid. The incorporation of labeled cysteine, valine and leucine in the hemagglutinin-neuraminidase protein is different from that of viral neuraminidase. A comparison of the properties of the neuraminidase associated with protein hemagglutinin-neuraminidase with that of viral neuraminidase or sialidase showed that the former is biochemically different and an antigenically distinct enzyme. The unique feature of the new enzyme is that it has the hemagglutinin activity as well. The two biological activities could not be separated from each other in all systems used. Apparently, protein hemagglutinin-neuraminidase is genetically transferable and it is detectable in a laboratory recombinant virus E-2971 (H3 Aichi X N7). These results suggest that protein hemagglutinin-neuraminidase is a unique surface protein of the influenza virus A/Aichi/2/68 (H3N2).

Influenza virus neuraminidase with hemagglutinin activity

Isolated intact influenza virus neuraminidase (NA) molecules of the N9 subtype have been found to possess hemagglutinin (HA) activity which, at equivalent protein concentration, was fourfold higher than that of isolated hemagglutinin molecules of the H3 subtype. The amino-terminal sequence of the N9 NA is the same as in neuraminidases of the eight other influenza A virus NA subtypes previously reported. Viruses possessing N9 NA therefore have two different HA activities and antibody to either HA or NA alone was incapable of inhibiting hemagglutination by the virus. However, antibody to the HA of an H1N9 virus neutralized its infectivity as effectively as it neutralized H1N1 or H1N2 viruses whose neuraminidases have no HA activity. (Antibodies to N9 NA did not neutralize the infectivity of viruses with N9 neuraminidase). 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid inhibited N9 NA activity but had no effect on the HA activity of the isolated N9 NA. One interpretation of this result would be that the HA and NA activities are located in separate sites. Pronase-released N9 NA heads form crystals suitable for X-ray diffraction studies and preliminary data to 2.9 A establish the space group as cubic, I432 with cell dimension a = 184 A. Data extend to beyond 1.9 A resolution, and these will be collected in the future.

Preparation-conditioned changes of the antigenicity of influenza virus neuraminidases

The influenza virus strains A/Sing/1/57 (H2N2), A/Bel/42 (H0N1) and A/Bel/42 (HO)-A/Sing/1/57 (N2) were treated with bromelain under reducing conditions and with reducing agent alone, and the antigenicity of the neuraminidase (NA) of intact virus and of the split products was tested comparatively. It was found that the antigenicity of NA was influenced quantitatively and qualitatively by the preparation procedure. Antineuraminidase (AN) antibodies obtained after vaccination of guinea pigs with intact virus and with split products differed in their cross-reactivity with heterologous neuraminidases. In several cases, the quantity of AN antibody formation depended on the hemagglutinin (HA) dose present in the vaccines. The N2 NA on the recombinant virus was significantly more sensitive to treatment with reducing agent than was the N2 NA on the parent virus. AN antibodies directed against N2 NA on the recombinant differed qualitatively from that directed against N2 NA of parent virus. The results warrant the conclusion that the antigenicity of isolated NA or of NA on recombinant virus can differ from that of the NA on intact homologous virus and that such alterations could influence the determination of antigenic relationship between neuraminidases.

Serological studies with purified neuraminidase antigens of influenza B viruses

Neuraminidase (N) can be extracted from virus particles of influenza B strains by treatment with trypsin, in a form which is free from the viral HA and has specific immunological activity. The N antigen of B/LEE/40 behaves differently from that of 1965-6 strains in gel diffusion and enzyme inhibition tests with animal antisera raised by infection or by artificial immunization with the homologous or heterologous strains. The frequency and titres of NI antibody detected in human sera by B/LEE antigen are different from those found with antigen from B/Eng/13/65. The latter antibody appears to contribute to the effect of serum HI antibody in protecting volunteers exposed to a deliberate intranasal challenge infection of the B/Eng/13/65 strain.

Thermal inactivation of Newcastle disease virus. I. Coupled inactivation rates of hemagglutinating and neuraminidase activities

The thermal stability of Newcastle disease virus has been characterized in terms of the rate constants for inactivation of hemagglutinating activity (HA), neuraminidase activity (NA), and infectivity. Inactivation of HA results in the concomitant loss of NA. Infectivity, however, is much more thermolabile. Disintegration of the virus particle is not responsible for the identical rate constants for inactivation of HA and NA, nor is their parallel inactivation uncoupled in envelope fragments produced by pretreating the virus with phospholipase-C. The data indicate that a common envelope factor(s) can influence the thermal stability of both activities.

The chemical reactions of the haemagglutinins and neuraminidases of different strains of influenza viruses. 3. Effects of proteolytic enzymes

The action of trypsin and pronase on the haemagglutinins and neuraminidases of eight strains of influenza virus has been examined.The haemagglutinins of all the strains were highly susceptible to digestion by pronase but there were great variations in resistance to trypsin.The neuraminidases of the eight strains were of three types. The neuraminidases of the A 1 strains and the DSP strain of virus A were highly susceptible to destruction by both enzymes. The neuraminidases of the PR 8 and Swine strains showed partial resistance especially to trypsin, while the A 2 strains and the LEE strains of virus B possessed neuraminidases that were completely resistant to both trypsin and pronase.Proteolytic enzymes released free neuraminidases from the A 2 and LEE viruses the morphology of which was different from that of neuraminidases released by detergent treatment.

Isolation of hemagglutinin and neuraminidase subunits of hemagglutinating virus of Japan

When purified hemagglutinating virus of Japan (HVJ) was treated with trypsin, two major surface antigens were released from the virus. The "hemagglutinin" subunits obtained by this method were reactive with homologous hemagglutination-inhibition antibody and could be detected by an antibody-blocking test. They adsorbed to but did not agglutinate red cells and thus appeared to be "monovalent." The neuraminidase subunits were obtained in fully active form and did not adsorb to red cells. This finding suggests that these two activities of HVJ are associated with different subunits of the virus particle. The hemagglutinin and neuraminidase subunits could be partially separated by zonal rate centrifugation or gel filtration on Sephadex G-200. The molecular weights estimated for these subunits were approximately 124,000 and 114,000, respectively. After treatment with trypsin, virus-associated hemagglutinin and neuraminidase activities were both reduced significantly. The electron micrographs of such trypsinized virus particles showed complete or partial loss of surface projections. These results suggested that the subunits obtained by this method seemed to be those projections liberated from the virus by the action of trypsin.

The chemical reactions of the haemagglutinins and neuraminidases of different strains of influenza viruses. II. Effects of reagents modifying the higher order structure of the protein molecule

The results of treatment of influenza virus strains with chemical reagents acting on the higher-order structure of protein molecules shows that both the haemagglutinating and enzymic activities are susceptible to these agents but there are considerable differences between the different strains and the neuraminidase activity is more sensitive than the haemagglutinating activity.

The neuraminidase activity of A and A1strains is destroyed by urea, guanidine, urea+dithiothreitol and mercuric chloride. The haemagglutinin of the PR 8 and SWINE strains is resistant to urea and mercuric chloride but destroyed by guanidine and by urea+dithiothreitol. The haemagglutinin of the DSP strain of virus A and the A1strains is resistant to urea, guanidine and mercuric chloride but is destroyed by urea+dithiothreitol.

The neuraminidase activity of the A2strains is more resistant than that of the A and A1strains. It is resistant to mercuric chloride and partially resistant to urea but is destroyed by guanidine and by urea+dithiothreitol. The A2haemagglutinin is resistant to urea, urea+dithiothreitol, and mercuric chloride but is destroyed by guanidine.

The LEE virus neuraminidase is resistant to urea and partially resistant to guanidine but is destroyed by urea+dithiothreitol and mercuric chloride. The LEE haemagglutinin is resistant to urea, guanidine and mercuric chloride but is destroyed by urea+dithiothreitol.

It is suggested that the surface projections of the virus particle are protein polymers each made up of three or four monomers which are the components of the V antigen complex. Antigenic activity is a function of the primary or secondary structure of the monomers, haemagglutinin activity is a function of the tertiary structure of the monomers, while neuraminidase activity is a function of the quaternary structure of the polymer.

From studies of the chemical reactions of their haemagglutinins and neuraminidases strains of influenza virus A can be classified into groups. These groups are very similar to but not precisely identical with groupings made by serological methods.