Structure-basedpredictive model for some benzimidazole inhibitors of hepatitis C virus NS5B polymerase
Supplementary data
1.Binding mode of indole-based NS5b inhibitors is summarized in this paragraph:
1-Mutation studies indicated that resistant mutations are localized at the top of thumb domain (Pro 495, Pro 496 and Val 499).(Beaulieu 2006)
2-Photoaffinity labeling experiments confirmed interaction of benzimidazole-based inhibitors with thumb domain through cross linking to the (word) finger loop residues in the vicinity of the resistant mutations.(Di Marco et al. 2005)
3-Isosteric indole scaffolds were the first to be disclosed with x-ray structures though .The discovery of N-acetamide-indole 6-carboxylic acid was followed by reports of Boehringer Ingelheim on the x-ray structure. (Beaulieu PL 2004)
4-Strucutral data confirmed binding of inhibitors in the allosteric site at the top of the thumb domain with indole-scaffold stacked against pro-495.(LaPlante et al. 2010)
5-The cyclohexyl substituent which is characterisitc of this class was found to reside in the well-defined hydrophobic- pocket which in the structure of the apoenzyme by leucine side chain of a (word) finger loop residue.
6- In the structure of the complex, the Λ1 finger loop is no longer visible, suggesting disruption of the interaction with the thumb domain and displacement upon inhibitor binding.
7- Another key inhibitor-protein interaction is a hydrogen bond or salt bridge between the carboxyl functionality in the 6-position of the scaffold and Arg503.
8-It is believed that inhibition of the polymerase by benzimidazole and indole carboxylic acid derivatives results from disruption of the interaction between the thumb domain and
the finger loops, preventing the formation of a closed,tunnel-like conformation of the active site.
Concerning the structural data of the benzimidazole inhibitors, these pdbs were deposited
1-3MWV
2-3MWW
These 2 pdbs were deposited in
Importance of ligand bioactive conformation in the discovery of potent indole-diamide inhibitors of the hepatitis C virus NS5B.(LaPlante et al. 2010)
3-2BRK:(Di Marco et al. 2005)
This was deposited in
Interdomain communication in hepatitis C virus polymerase abolished by small molecule inhibitors bound to a novel allosteric site.
4-3QOZ:(Zheng et al. 2011)
Syntheses and initial evaluation of a series of indolo-fused heterocyclic inhibitors of the polymerase enzyme (NS5B) of the hepatitis C virus.
5-2XWY:(Narjes et al. 2011)
Discovery of (7R)-14-Cyclohexyl-7-{[2-(Dimethylamino)Ethyl] (Methyl)Amino}vv-7,8-Dihydro-6H-Indolo[1,2-E][1,5] Benzoxazocine -11-Carboxylic Acid (Mk-3281), a Potent and Orally Bioavailable Finger-Loop Inhibitor of the Hepatitis C Virus Ns5B Polymerase
6-3QGD 3QGE 3QGF 3QGH 3QGI 3QOZ:(Gentles et al. 2011)
Investigation of the mode of binding of a novel series of N-benzyl-4-heteroaryl-1-(phenylsulfonyl)piperazine-2-carboxamides to the hepatitis C virus polymerase.
2.Application of the activity prediction model in optimization of JTK-109 class:
The model was applied in JTK-109 class optimization regarding pharmacokinetic properties. It was used to find new derivatives of benzimidazole which have good predicted activities and better physicochemical properties. This was done by applying the model as a screening tool on a focused library of benzimidazole derivatives generated in silico. This library was generated using fragment-hopping approach implemented in ReCore. ReCore is a de-novo drug design module in LeadIT( ligand optimization software by BioSolve IT) which can be used to generate new ligands based on two important inputs: structural-model of the ligand-protein complex and the essential pharmacophore features of the fragment to be hopped(Maass et al. 2007). Both requirements were fulfilled in this study. Reocre idea depends on disconnecting the ligand at some points and replacing a certain disconnected part with fragments which share the same pharmacophore features that are derived from the interaction with the protein (Figure 1).
Figure 1: (a) ReCore cutting points were made in the compound shown to serve as attachment points for the new fragments to be added to the main benzimidazole scaffold, (b) JTK109 inside the binding site with the essential features defined as a target pharmacophore for fragment hopping using the ReCore engine, namely the hydrogen bond acceptor and the phenyl system
ReCore was used to generate 2000 composites (composite in ReCore is the new ligand; consisting of the main scaffold and the new fragment attached to it). Out of which, 1114 composites could pass Lipinski filter with violation of molecular weight. They were first screened using the structure-based pharmacophore model while setting maximum omitted features to zero to give 381 hits. This criterion in screening was used in order to retain the most active compounds as mentioned before i.e. keep those compounds bearing the hydrogen bond acceptor feature on ring D. These hits were then docked using CDOCKER with pharmacophore restraints module in Accelrys discovery studio 2.5 and scored using PLP1 scoring function. The scored hits were evaluated in addition using OPS analysis (Optimum Predication Space) (Gombar March 14, 2000.)which can determine if the ligand lies in the model applicability domain. Only ligands within the model applicability domain (52 ligands) were selected. Table.1 shows the structures and the predicted activities of 10 of the best newly designed ligands. The designed ligands retained the hydrogen acceptor feature that is responsible for the high activity of this class. The solutions showed diverse acceptor features other than the carbonyl group originally present in the training set. On the other hand the halogen bearing phenyl ring responsible for the interaction with Trp 397 was replaced by various heterocyclic rings. Most of the best resulted compounds were from the composites keeping the phenyl ring bearing a fluorine atom confirming its importance for activity. The good physicochemical properties of these compounds can be attributed to the introduction of different heterocyclic rings substituents which can improve water solubility, Log P and other determining factors in the pharmacokinetic profiles of these compounds. The binding mode of the best compound together with its mapping to the pharmacophore is shown in (Figure 2).
Figure 2:(a) Binding mode of the highest score compound in the polymerase binding site. A furan ring acts as the hydrogen bond acceptor and a pyrimidine ring makes a pi-pi interaction, (b) Mapping of the same compound with the pharmacophore generated. The two Figures reflect the essential parts for the activity of these ligands.
Table 1:table showing the molecular structures, scores, Predicted activities and molecular properties of the top 10 designed molecules based on the model;
index / Molecular structure / PLP 1 / Predicted – Log IC50 / Alog P / M. wt / MPSA1 / / 119.13 / -0.75613 / 4.189 / 593.671 / 112.14
2 / / 104.41 / -1.74199 / 4.996 / 561.543 / 156.68
3 / / 101.99 / -1.90407 / 3.732 / 575.616 / 126.47
4 / / 101.6 / -1.93019 / 5 / 614.691 / 104.27
5 / / 101.18 / -1.95832 / 4.067 / 579.644 / 113
6 / / 99.84 / -2.04807 / 4.574 / 549.578 / 133.13
7 / / 98.95 / -2.10767 / 4.217 / 593.69 / 100.44
8 / / 98.35 / -2.14786 / 4.728 / 543.585 / 108.97
9 / / 97.53 / -2.20278 / 3.028 / 560.619 / 131.66
10 / / 97.18 / -2.22622 / 3.339 / 550.563 / 130.65
A detailed description of the structures which were generated using De-novo drug design is given in the following website:
References:
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