Tumor Necrosis Factor-α (TNF-α) Novel Inhibitors Discovery Using Molecular

Docking And 3D-QSAR Models

Dr.Samad N. Ebrahimi

Mohammad Bayati

Jul 2019
Applied screening protocol for the identification of TNFα Inhibitors

Get Protein from PDB(2E7A) Pubchem-NP(~570 Molecules)

Protein Preparation(Maestro)

Ligand Preparation(Maestro)
Create Site Map for
Putative Binding Pocket

Glide Grid Generation

Glide-SP-Docking

Glide-XP-Docking for
10% of SP Poses

QSAR for Activity of Molecules

QikProp
Introduction

Tumor necrosis factor-α (TNF-α) is a multifunctional cytokine that acts as a central biological
mediator for critical immune functions, including inflammation, infection, and antitumor
responses. It plays pivotal role in auto-immune diseases like rheumatoid arthritis (RA).

The synthetic antibodies etanercept,infliximab, and adalimumab are approved

drugs for the treatment of inflammatory diseases bind to TNF-α directly.

These biologics causes serious side effects such as triggering an

autoimmune anti-antibody response or the weakening of the body's
immune defenses.

Compared to protein drugs, small molecule drugs are normally

orally available and less expensive.
Materials and Methods

Protein Preparation

 Side chains and loops were fixed  DOI: 10.2210/pdb2E7A/pdb

 Classification: CYTOKINE
 Hydrogen atoms were added
 Organism(s): Homo sapiens
 Disulfide bonds were created
 Method: X-RAY DIFFRACTION
 Protonation states of amino acids
at physiological pH 7.4 using PROPKA  Resolution: 1.8 Å
 PDB ID : 2E7A
using PrepWizard with OPLS3 forcefield  https://www.rcsb.org/

 Protein was prepared using Protein Preparation tool of Maestro suite (Maestro version 10.2, 2015)
Site Map
5
 SiteMap was used to identify potential binding pockets in protein
 Druggable sites were identified according the sitescore

Site Map Site Score Size

5 1.066 67
1 1.059 386
1
 (> 1.0 siteScore is considered as Druggable)
Materials and Methods

Ligand Preparation

 All compounds were downloaded from Pubchem Database (573 Natural

compounds)(https://pubchem.ncbi.nlm.nih.gov/)
 All compounds were prepared using LigPrep of Maestro suite with OPLS3
forcefield

Glide Grid Generation

 Receptor grid size(Å): 30x30x30

Site Map 5 X Y Z
9.36 1.68 10.38

Site Map 1 X Y Z
-2.05 -9.23 0.62
Docking Analysis

For the docking analysis of all compounds, “Glide” was used

SP (Standard Precision)
Glide consisted of
XP (Extra Precision) Top 10% of SP poses

Results of Positive Control Docking : Ezetimibe

SiteMap 2D Structure pIC50 Docking score CNS molMW QPlogPo/w DonorHB AcceptHB QPPCaco
(μM) (Kcal/mol) (Da) (nm/s)

Site5 5.374 -9.333 -1 409.4 5.044 2.00 4.450 806.062

Site1 5.410 -8.306 -1 409.4 4.974 2.00 4.450 592.152

Ligand interaction

Ezetimibe

Site1 Site5
Pubchem 2D structure pIC50 Docking score CNS molMW QPlogPo/w DonorHB AcceptHB QPPCaco
ID (μM) (Kcal/mol) (Da) (nm/s)

9807916 5.755 -9.594 -2 492.3 -1.516 6.00 14.50 0.138

10100906 5.744 -9.514 - - - - - -

46906103 5.955 -9.169 -2 639.5 -6.099 10.00 29.60 0.003

5355255 5.716 -8.852 -2 414.3 -3.212 2.00 9.25 0.183

222515 5.283 -8.652 -2 286.2 -2.627 4.00 3.75 165.996

Results of SP Docking : Site Map 5

Pubchem 2D structure pIC50 Docking score CNS mol MW QPlogPo/w DonorHB AcceptHB QPPCaco
ID (μM) (Kcal/mol) (Da) (nm/s)

5.955 -14.888 -2 639.5 -5.892 10.00 29.60 0.006

46906103

5.744 -14.760 - - - -
10100906 - -

5.755 -13.704 -2 492.4 -1.383 6.00 14.50 0.196

9807916

134264 5.310 -12.321 -2 565.6 -0.740 7.00 20.75 58.815

134693083 5.201 -11.519 -2 492.4 -1.417 5.00 12.30 0.667

Results of XP Docking : Site Map 5

Ligand interaction

46906103
Pubchem 2D structure pIC50 Docking score CNS mol MW QPlogPo/w DonorHB AcceptHB QPPCaco
ID (μM) (Kcal/mol) (Da) (nm/s)

5.190 -10.207 -2 976 -4.712 14.00 38.00 0.01

5281233

137185914 5.787 -9.769 -2 910 -3.686 13.00 30.25 0.017

46906103 5.955 -9.744 -2 639 -6.043 10.00 29.60 0.002

9807916 5.755 -9.570 -2 492 -1.400 6.00 14.50 0.204

134693083 5.201 -9.498 -2 462 -0.190 5.00 12.30 0.878

Results of SP Docking : Site Map 1

Pubchem 2D structure pIC50 Docking score CNS mol MW QPlogPo/w DonorHB AcceptHB QPPCaco
ID (μM) (Kcal/mol) (Da) (nm/s)

5.754 -16.924 -2 - - -
10100906 - -

5.772 -15.446 -2 910.8 -3.735 13.00 30.25 0.01

137185914

9807916 5.781 14.307 -2 492.4 -1.615 6.00 14.50 0.09

134693083 5.201 -14.055 -2 462.3 -0.137 5.00 12.30 1.303

46906103
5.955 -13.765 -2 639.5 -6.005 10.00 29.60 0.004

Results of XP Docking : Site Map 1

Ligand interaction

10100906
Product description

 Synonym name: Delphin; Hyacin; Delphoside.

 Formula: C27H31O17+

 Mol Weight: 627.527

 Botanical Source: Salvia patens, Elythranthera, Eucalyptus, Anemone spp.,

Punica granatum (pomegranate), Wisteria brachybotrys, Wisteria
floribunda and numerous other plants

10100906 Delphinidin 3,5-diglucoside

QSAR analysis

 Maestro's LigPrep module was used to prepare all the known inhibitors

 3D QSAR analysis was performed by randomly dividing compounds into 70% training and 30%
test sets using PHASE of maestro suite.
Highest pIC50 (6.67) 1i
 Which have <50 μM binding affinities
Lowest pIC50 (4.36) EJCM-1

EJCM-1
1i
Statistical Parameters of Generated QSAR Models

factors SD 𝑹𝟐 F-Value RMSE 𝑸𝟐 Person-r

1 0.4496 0.6362 40.2 0.68 -0.0377 0.2451
2 0.2453 0.8964 95.2 0.59 0.2141 0.4672
3 0.1732 0.9507 135.0 0.62 0.1453 0.4067

 Correlation graph between experimental and predicted activities of

the training (A) and test (B) set compounds

A B
QSAR Visualization

Hydrophobic/Non-polar

H-bond donor Electron-withdrawing

References
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