CMDT Coursework - CW,N,NNNK PDF

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CW,N,NNNK...

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UP896787 Introduction The crystal structure of the N2 subtype of the neuraminidase flu virus was a key piece of information in the development of the Relenza drug. The active site of the neuraminidase enzyme was analysed by Mark von Itzstein et al. using the GRID software program.

(1)

Computational chemistry methods were designed to probe the

neuraminidase active site in order to produce DANA (deoxy-dehydro-N-acetyl neuraminic acid) derivatives that were modified structurally and could tightly bind to amino acids in the catalytic site; the compounds would hence prove to be potent and specific neuraminidase inhibitors. From this software, they were able to determine energetically favourable interactions between many different functional groups and residues at the catalytic site.

(1)

The data from the GRID software program

highlighted a negatively charged zone in the neuraminidase active site, which was complementary to the C4 DANA hydroxyl group. (1) Molecular Docking Molecular docking predicts the ligand-receptor complex structure from the use of computational methods. Ligand conformations in the active site need to be sampled and ranked by using a scoring function.

(2)

There are 2 approaches to molecular

docking: simulation approach and shape complementary approach.

(3)

Simulation

approach involves initially separating the ligand and target and then allowing the ligand to bind to the groove present on the target after a ‘definite number of moves’ in the ligands conformational space.

(3)

On the contrary, the shape complementarity

approach is much faster, whereby shape matching illustration is used to identify the complementarity between two surfaces in order to find the ligand complementary groove.

(3)

The shape complementarity approach allows thousands of ligands to be

scanned in seconds so as to determine the potential binding possibilities of the ligands on a target surface. (3)

Relenza Development

UP896787 The influenza virus sialidase had an initial crystal structure that was limited in structure-based drug design value. However, many sialidase crystal structures became further refined in the Neu5Ac complex and in Neu5Ac2en inhibitor using XRays, allowing computational docking techniques to create more potent, structurally modified Neu5Ac2en derivatives that would bind to the sialidase active site.

(4)

GRID

software was able to identify interactions between many functional groups that were energetically favourable, as well as residues in the binding sites that were present in sialidases across all influenza A and B strains.

(4)

This meant that ligands could target

all variations of the influenza virus effectively. From functional group testing on the GRID software system, replacing the hydroxyl group from the Neu5Ac2en derivative with a basic group was believed to result in a higher affinity for the sialidase active site than the Neu5Ac2en compound - this was due to a salt-bridge formation with the Glu119 amino acid. (4) However, further functional group analysis determined that the conserved Neu5Ac2en C-4 hydroxyl group-binding domain would be able to withhold a larger basic functional group, which led to the substitution of the C-4 hydroxyl group with guanidyl group to produce 4-deoxy-4-guanidino-Neu5Ac2en.

(4)

This was believed to further increase sialidase enzyme affinity for the ligand, because of the interactions of two conserved C-4 binding domain amino acids (Glu119 and Glu227) and the basic C-4 guanidyl group. (4)

Both 4-deoxy-4-guanidino-Neu5Ac2en and 4-amino-4-deoxy-Neu5Ac2en were formed and were determined as competitive inhibitors and, most importantly, highly potent virus replication inhibitors for all influenza A and B virus strains. 4-amino-4deoxy-Neu5Ac2en inhibited sialidase by 100 times more effectively than its derivativeNeu5Ac2en

(4-amino-4-deoxy-Neu5Ac2en).

4-deoxy-4-guanidino-

Neu5Ac2en was more potent, with a 10,000-fold higher affinity than Neu5Ac2en (4deoxy-4-guanidino-Neu5Ac2en), as was predicted. (4)

X-ray crystallographic structure confirmed the GRID software determination of the binding mechanisms in both 4-amino-4-deoxy-Neu5Ac2en and 4-deoxy-4-guanidinoNeu5Ac2en; the 4-amino group present in 4-amino-4-deoxy-Neu5Ac2en was shown to form a salt bridge with Glu119, and 4-deoxy-4-guanidino-Neu5Ac2en showed the predicted lateral binding between the guanidyl nitrogens and the Glu227 carboxylate. (4)

UP896787 4-deoxy-4-guanidino-Neu5Ac2en was found to be highly selective for sialidase and displayed much lower affinity for other sialidases from other sources, and was hence selected as the lead drug candidate as zanamivir, later named Relenza. (4)

Recent Neuraminidase Inhibitor Developments

In more recent times, molecular docking methods have been used to optimise structures of neuraminidase inhibitors to therapeutically target the influenza A virus H1N1 subtype. One study used Schrodinger docking software to optimise acyl thiourea pharmacophore in order to identify potent anti-viral derivatives. (5)

The docking software predicted the ligands would all be located in the same pocket of neuraminidase enzyme binding site containing Arg 118, Arg 152, Arg 292, Arg 371 Asp 151, Asn 294, Glu 227, Glu 277, Ser 246 and Tyr 406 amino acids, which took place experimentally.

(5)

This indicates that the newly derived compounds

demonstrated a strong binding affinity with the neuraminidase binding site.

(5)

This

strong binding affinity is defined by the hydrogen bond interaction with various arginine residues and electrostatic interaction with various glutamic acid residues (observed in R-7, R-8, R-9 and R-10 molecules), two structural necessities for selective neuraminidase inhibition.

(5)

This was proved from the hydrogen bonding

observed in the reference standard inhibitors Oseltamivir, Relenza and Peramivir with Arg 152, Tyr 406, Arg 371 and Arg 118. The Schrodinger software determined that either –NH2, H+ or –COOH bonding with a carboxyl group of glutamic acid made these interactions possible. R10 had the strongest hydrogen bond with Arg 292 amino acid, bound with a carboxyl functional group. (5) From these findings, further analysis is currently ongoing to determine the validity of the findings as well as the steps taken in the optimisation for a selective neuraminidase inhibitor derived from acyl thiourea pharmacophore. (5)

References

UP896787 1. Flu drugs - pathway to discovery [Internet]. Rsc.org. [cited 2021 May 11]. Available

from:

https://edu.rsc.org/feature/flu-drugs-pathway-to-

discovery/2020145.article 2. Meng X-Y, Zhang H-X, Mezei M, Cui M. Molecular docking: a powerful approach for structure-based drug discovery. Curr Comput Aided Drug Des. 2011;7(2):146– 57. 3. Dar AM, Mir S. Molecular docking: Approaches, types, applications and basic challenges. J Anal Bioanal Tech [Internet]. 2017;08(02). Available from: http://dx.doi.org/10.4172/2155-9872.1000356 4. von Itzstein M. The war against influenza: discovery and development of sialidase inhibitors. Nat Rev Drug Discov. 2007;6(12):967–74. 5. Inamdar P, Bhandari S, Sonawane B, Hole A, Jadhav C. Structure optimization of neuraminidase inhibitors as potential anti-influenza (H1N1Inhibitors) agents using QSAR and molecular docking studies. Iran J Pharm Res. 2014 Winter;13(1):49– 65....