Vioxx redux

Simulated Docking of Oseltamivir with the 2009
Pandemic Strain Influenza A/H1N1
Neuraminidase Active Site
Abstract
Influenza neuraminidases are glycoproteins that facilitate the transmission of the influenza virus from cell
to cell. Oseltamivir is the most widely used neuraminidase inhibitor. Here I provide a computational
docking analysis of oseltamivir with the active site of the neuraminidase of the 2009 Influenza A/H1N1
strain. The computed inhibitor/receptor binding energy suggests that oseltamivir would be effective
against that strain.
Keywords: Influenza, H1N1, neuraminidase, oseltamivir

1.0 Introduction
dimensional structure from that of group-2 enzymes. The differences lie in a loop of amino acids known as the "150-loop", which glycoproteins that facilitate the transmission of the influenza virus from cell to cell. conformation that opens a cavity not present Oseltamivir ((3R,4R,5S)-4-(acetylamino)-5- amino-3-(pentan-3-yloxy)cyclohex-1-ene-1- loop contains an amino acid designated Asp carboxylic acid; [4]) is the most widely used 151; the side chain of this amino acid has a carboxylic acid that, in group-1 enzymes, points away from the active site as a result of the 'open' conformation of the 150-loop. The side chain of another active-site amino related sero-subtypes, and these subtypes correspond at least roughly to differences in conformation in group-1 enzymes compared with the group-2 neuraminidases (8]).
neuraminidases. The subtypes fall into two groups ([3]): group-1 contains the subtypes acid side chains form critical interactions conformation” 150-loop, the side chains the group-1 N1, N4 and N8 neuraminidases inhibitors tightly ([8]). The active site ([1]) reveal that the active sites of these ([4]) using AutoDock Tools v 4.2 (ADT, differences in amino acids that lie outside docking of oseltamivir to the receptor. More the active site. This means that an enzyme inhibitor for one target will not necessarily have the same activity against another with the same active-site amino acids and the same overall three-dimensional structure. A/California/04/2009(H1N1)) is an atypical group 1 NA with some group 2-like features extracted. (3TI3 identifies the active site of in its active site (lack of a 150-cavity) ([4]). Chain A as 15 amides: ARG118, GLU119, ASP151, ARG152, ARG156, TRP178, 2.0 Method
torsions in the ligand and active site were assess the binding energy of the active site of crystallized A/California/04/2009(H1N1)) otherwise noted, all processing described in to be flexible wherever that assumption is Inspiron 545 with an Intel Core2 Quad CPU physically possible, was auto-docked to the active site, assumed to be rigid, using the RAM, running under the Windows Vista Lamarckian genetic algorithm implemented configuration from the analysis was saved, and the distances between the receptor and is a structural description of most of the ligand in 3TI3, and those computed here, docking are shown in Figure 1. Most values are, or are a consequence of, ADT defaults. 22 February 2011. A PDB description of
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autodock_parameter_version 4.2 # used by autodock to validate parameter set
outlev 1 # diagnostic output level
intelec # calculate internal electrostatics
seed pid time # seeds for random generator
ligand_types C HD OA N # atoms types in ligand
fld 3TI3_active.maps.fld # grid_data_file
map 3TI3_active.C.map # atom-specific affinity map
map 3TI3_active.HD.map # atom-specific affinity map
map 3TI3_active.OA.map # atom-specific affinity map
map 3TI3_active.N.map # atom-specific affinity map
elecmap 3TI3_active.e.map # electrostatics map
desolvmap 3TI3_active.d.map # desolvation map
move oseltamivir.pdbqt # small molecule
about 0.5292 81.1637 109.1143 # small molecule center
tran0 random # initial coordinates/A or random
axisangle0 random # initial orientation
dihe0 random # initial dihedrals (relative) or random
tstep 2.0 # translation step/A
qstep 50.0 # quaternion step/deg
dstep 50.0 # torsion step/deg
torsdof 7 # torsional degrees of freedom
rmstol 2.0 # cluster_tolerance/A
extnrg 1000.0 # external grid energy
e0max 0.0 10000 # max initial energy; max number of retries
ga_pop_size 150 # number of individuals in population
ga_num_evals 2500000 # maximum number of energy evaluations
ga_num_generations 27000 # maximum number of generations
ga_elitism 1 # number of top individuals to survive to next
generation
ga_mutation_rate 0.02 # rate of gene mutation
ga_crossover_rate 0.8 # rate of crossover
ga_window_size 10 #
ga_cauchy_alpha 0.0 # Alpha parameter of Cauchy distribution
ga_cauchy_beta 1.0 # Beta parameter Cauchy distribution
set_ga # set the above parameters for GA or LGA
sw_max_its 300 # iterations of Solis & Wets local search
sw_max_succ 4 # consecutive successes before changing rho
sw_max_fail 4 # consecutive failures before changing rho
sw_rho 1.0 # size of local search space to sample
sw_lb_rho 0.01 # lower bound on rho
ls_search_freq 0.06 # probability of performing local search on
individual
set_psw1 # set the above pseudo-Solis & Wets parameters
unbound_model bound # state of unbound ligand
ga_run 10 # do this many hybrid GA-LS runs
analysis # perform a ranked cluster analysis

Figure 1. ADT parameters for the docking in this study
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3.0 Results
processor (with occasional bursts to 40% of peak), and required a constant 2.9 GB of memory. which assumes familiarity with the general oseltamivir/receptor energy and position neuraminidase "landscape", took about 20 minutes in ADT; the docking proper, about energy of binding under these conditions is ~ -8.5 kcal/mol; the estimated inhibition monitor suggested that the calculation was more or less uniformly distributed across the four processors at ~25% of peak per

MODEL 8
USER Run = 8
USER Cluster Rank = 1
USER Number of conformations in this cluster = 10
USER
USER RMSD from reference structure = 146.946 A
USER
USER Estimated Free Energy of Binding = -8.49 kcal/mol [=(1)+(2)+(3)-(4)]
USER Estimated Inhibition Constant, Ki = 603.08 nM (nanomolar) [Temperature =
298.15 K]
USER
USER (1) Final Intermolecular Energy = -10.57 kcal/mol
USER vdW + Hbond + desolv Energy = -6.89 kcal/mol
USER Electrostatic Energy = -3.68 kcal/mol
USER (2) Final Total Internal Energy = -1.06 kcal/mol
USER (3) Torsional Free Energy = +2.09 kcal/mol
USER (4) Unbound System's Energy [=(2)] = -1.06 kcal/mol
USER
USER
USER
USER DPF = 3TI3_oseltamivir.dpf
USER NEWDPF move
oseltamivir.pdbqt
USER NEWDPF about 0.529200 81.163696 109.114304
USER NEWDPF tran0 30.119561 14.578922 -20.694645
USER NEWDPF axisangle0
0.665691 -0.552718 0.501357 -102.866417
USER NEWDPF quaternion0
0.520492 -0.432160 0.392002 -0.623427
USER NEWDPF dihe0 168.80 -157.63 -177.46 -10.23 -55.65 -0.70 28.39
USER
USER x y z vdW Elec q RMS
ATOM 1 C2 G39 A 800 29.602 13.195 -22.935 -0.22 +0.06 +0.091 146.946
ATOM 2 C3 G39 A 800 31.208 13.233 -22.632 -0.25 +0.00 +0.050 146.946
ATOM 3 C4 G39 A 800 31.725 14.395 -21.669 -0.22 -0.05 +0.209 146.946
ATOM 4 C5 G39 A 800 30.777 14.481 -20.473 -0.19 +0.03 +0.143 146.946
ATOM 5 C6 G39 A 800 29.308 14.818 -20.993 -0.17 +0.05 +0.147 146.946
ATOM 6 C7 G39 A 800 28.741 13.977 -22.105 -0.21 +0.03 +0.049 146.946
ATOM 7 O7 G39 A 800 28.408 14.858 -19.795 -0.01 -0.25 -0.379 146.946
ATOM 8 C8 G39 A 800 27.326 15.852 -19.571 -0.24 +0.09 +0.121 146.946
ATOM 9 C9 G39 A 800 27.103 16.932 -20.666 -0.40 +0.01 +0.027 146.946
ATOM 10 C91 G39 A 800 26.896 18.375 -20.179 -0.45 +0.01 +0.007 146.946
ATOM 11 C81 G39 A 800 26.079 15.023 -19.329 -0.28 +0.02 +0.027 146.946
ATOM 12 C82 G39 A 800 25.448 14.581 -20.611 -0.36 +0.00 +0.007 146.946
ATOM 13 N5 G39 A 800 31.316 15.593 -19.600 -0.06 -0.14 -0.352 146.946
ATOM 14 H5 G39 A 800 31.504 16.508 -20.010 +0.10 +0.01 +0.163 146.946
ATOM 15 C10 G39 A 800 31.552 15.389 -18.289 -0.28 +0.19 +0.214 146.946
ATOM 16 C11 G39 A 800 32.087 16.540 -17.517 -0.30 +0.11 +0.117 146.946
ATOM 17 O10 G39 A 800 31.350 14.297 -17.682 -0.76 -0.42 -0.274 146.946
ATOM 18 N4 G39 A 800 33.088 14.075 -21.248 -0.18 +0.04 -0.073 146.946
ATOM 19 H42 G39 A 800 33.671 13.752 -22.021 -0.11 -0.43 +0.274 146.946
ATOM 20 H41 G39 A 800 33.480 14.890 -20.776 +0.18 -0.03 +0.274 146.946
ATOM 21 H43 G39 A 800 33.133 13.232 -20.676 -0.27 -0.24 +0.274 146.946
ATOM 22 C1 G39 A 800 29.038 12.409 -24.007 -0.24 +0.29 +0.177 146.946
ATOM 23 O1B G39 A 800 27.789 12.427 -24.260 -1.03 -1.58 -0.648 146.946
ATOM 24 O1A G39 A 800 29.818 11.689 -24.695 -0.96 -1.48 -0.648 146.946
TER
ENDMDL

Figure 2. ADT's oseltamivir energy and position predictions.
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Figure 3 is a rendering of the active-site/inhibitor configuration computed in this study.
Figure 3. Rendering of oseltamivir computationally docked with the active site of PDB
3TI3. The molecular surface of the receptor is shown in white; the inhibitor, in stick form
in grey. Only the interior, inhibitor-containing region of the molecular surface of the active
site can be compared to in situ data: the surface distal to the interior is a computational
artifact, generated by the assumption that active site is detached from the rest of the
receptor.
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computation were within 10% of each other. assumes that the receptor is rigid. This assumption is appropriate for the binding 4.0 Discussion
However, the calculation does not reflect what receptor "flexing" could contribute to the interaction of the ligand with native in this study (~603 nanoMolar at ~298 K) is Sections 2.0 and 3.0 assumes receptor is in a much smaller than the inhibition constant of crystallized form. In situ, at physiologically normal temperatures (~310 K), the receptor clinically effective ([10], [11], [13], [14], [15]) against several H1N1 genotypes. This suggests that oseltamivir would be effective therefore, may not be identical to their conformation in the crystallized form. and functional analysis of laninamivir and its octanoate prodrug reveals group specific genetic algorithm used in this work could be [5] Butler D. Avian flu special: The flu models could be applied to this problem, and pandemic: were we ready? Nature 435 (26 its own active site. The work described in this paper was performed on Chain A only. highly similar to the Chain A active site. Future work will assess the ligand/receptor Summary: Interim Recommendations for the Use of Influenza Antiviral Medications in the Setting of Oseltamivir Resistance among Circulating Influenza A (H1N1) Viruses, 5.0 Acknowledgements
2008-09 Influenza Season. 19 December 2008. http://www.cdc.gov/flu/professionals/antivir [8] Luo M. Structural biology: antiviral drugs fit for a purpose. Nature 443 (7 6.0 References.
[1] Russell RJ et al. The structure of H5N1 opportunities for drug design. Nature 443 (6 the accounts: global mortality of the 1918- 1920 "Spanish " influenza pandemic. Bulletin of the History of Medicine 76 efficacies of RWJ-270201, zanamivir, and [3] World Health Organization. A revision oseltamivir against H5N1, H9N2, and other of the system of nomenclature for influenza avian influenza viruses. Antimicrobial viruses: a WHO memorandum. Bulletin of Agents and Chemotherapy 45 (2001), 2723- the World Health Organization 58 (1980), AutoDock 4 with AutoDock Tools: A M, Liu Y, Gao F, Liu J, Feng E, He J, Wang J, Liu H, Jiang H, and Gao GF. Structural neuraminidase active site. Proceedings of the 2011 International Conference on Relationship between the inhibition constant Genetic and Evolutionary Methods. CSREA (Ki) and the concentration of inhibitor which causes 50 per cent inhibition (I50) of an Pharmacology 22 (December 1973), 3099– site. Proceedings of the 2011 International Conference on Genetic and Evolutionary oseltamivir with the 1918 pandemic strain Methods. CSREA Press. pp. 136-142.

Source: http://www.worldcomp-proceedings.com/proc/p2012/BIC2208.pdf