| Literature DB >> 31435158 |
Palak Shukla1, Ravina Khandelwal1, Diksha Sharma1, Anindya Dhar1, Anuraj Nayarisseri1,2,3, Sanjeev Kumar Singh3.
Abstract
Juvenile idiopathic arthritis (JIA) is a heterogeneous disease characterized by the arthritis of unknown origin and IL6 is a known target for JIA. 20 known inhibitors towards IL-6 were screened and Methotrexate (MTX) having PubChem ID: 126941 showed high binding capacity with the receptor IL-6. The similarity searching with this compound gave 269 virtual screened compounds. The said screening presented 269 possible drugs having structural similarity to Methotrexate. The docking studies of the screened drugs separated the compound having PubChem CID: 122677576 (re-rank value of -140.262). Toxicity and interaction profile validated this compound for having a better affinity with the target protein. Conclusively, this study shows that according to ADMET profile and BOILED-Egg plot, the compound (PubChem CID: 122677576) obtained from Virtual Screen could be the best drug in future during the prevention of juvenile idiopathic arthritis. In the current study, the drug CID: 122677576 is a potent candidate for treating JIA. The pharmacophore study revealed that the drug CID: 122677576 is a non-inhibitor of CYP450 microsomal enzymes and was found to be non-toxic, similar to the established drug Methotrexate (CID: 126941). It has a lower LD50 value of 2.6698mol/kg as compared to the established compound having LD50 value as 23.4955mol/kg. Moreover, the compound was found to be non-carcinogenic.Entities:
Keywords: IL-6; Idiopathic Arthritis; Molecular Docking; Virtual Screening
Year: 2019 PMID: 31435158 PMCID: PMC6677908 DOI: 10.6026/97320630015121
Source DB: PubMed Journal: Bioinformation ISSN: 0973-2063
List of Established inhibitors collected from various literature
| S. No. | Inhibitors | Pub ID | MW in gm/mol | HBD | HBA | Logp | Ref | |
| 1 | Cyclosporine A | 5284373 | 1202.635 | 5 | 12 | 7.5 |
[ | |
| 2 | Chloroxine | 2722 | 214.045 | 1 | 2 | 3.5 |
[ | |
| 3 | Salazosulfapyridine | 5359476 | 398.393 | 3 | 9 | 2.3 |
[ | |
| 4 | Methotrexate (MTX) | 126941 | 454.447 | 5 | 12 | -1.8 |
[ | |
| 5 | Aspirin | 2244 | 180.159 | 1 | 4 | 1.2 |
[ | |
| 6 | celecoxib (Celebrex) | 2662 | 381.373 | 1 | 7 | 3.4 |
[ | |
| 7 | Diclofenac | 3033 | 296.147 | 2 | 3 | 4.4 |
[ | |
| 8 | Diflunisal (Dolobid) | 3059 | 250.201 | 2 | 5 | 4.4 |
[ | |
| 9 | etodolac (Lodine) | 3308 | 287.359 | 2 | 3 | 2.8 |
[ | |
| 10 | ibuprofen (Motrin, Advil) | 3672 | 206.285 | 1 | 2 | 3.5 |
[ | |
| 11 | indomethacin (Indocin) | 3715 | 357.79 | 1 | 4 | 4.3 |
[ | |
| 12 | Ketoprofen | 3825 | 254.285 | 1 | 3 | 3.1 |
[ | |
| 13 | Ketorolac | 3826 | 255.273 | 1 | 3 | 1.9 |
[ | |
| 14 | nabumetone (Relafen) | 4409 | 228.291 | 0 | 2 | 3.1 |
[ | |
| 15 | Naproxen | 156391 | 230.263 | 1 | 3 | 3.3 |
[ | |
| 16 | oxaprozin (Daypro) | 4614 | 293.322 | 1 | 4 | 4.2 |
[ | |
| 17 | piroxicam (Feldene) | 54676228 | 331.346 | 2 | 6 | 3.1 |
[ | |
| 18 | Salsalate | 5161 | 258.229 | 2 | 5 | 3 |
[ | |
| 19 | sulindac (Clinoril) | 1548887 | 356.411 | 1 | 5 | 3.4 |
[ | |
| 20 | tolmetin (Tolectin) | 5509 | 257.289 | 1 | 3 | 2.8 |
[ |
Figure 1Protein 3D structure of IL-6 obtained from PDB (PDBID: 1N26) Visualization in Accelrys Discovery Studio
Docking results of Established Drugs
| LIGAND | FILE NAME | MOLDOCK SCORE | RERANK SCORE | H BOND |
| 126941 | [00]126941 | -165.255 | -105.677 | -10.8923 |
| 126941 | [03]126941 | -129.781 | -97.6819 | -2.7623 |
| 5161 | [01]5161 | -114.55 | -90.8458 | -6.49702 |
| 4614 | [02]4614 | -119.216 | -89.5275 | -1.02526 |
| 5161 | [02]5161 | -111.018 | -88.7829 | -3.65241 |
| 3715 | [00]3715 | -118.311 | -88.6118 | -5 |
| 4614 | [00]4614 | -123.091 | -87.9868 | -4.39387 |
| 2244 | [01]2244 | -98.6621 | -87.9747 | -4.68577 |
| 156391 | [00]156391 | -105.996 | -87.7415 | -4.97939 |
| 3308 | [00]3308 | -115.385 | -87.5747 | -5.3458 |
| 2662 | [00]2662 | -124.171 | -87.5568 | -1.91396 |
Virtual Screening results
| FILE NAME | MOLDOCK SCORE | RERANK SCORE | H BOND | MW |
| [00]122677576 | -191.912 | -140.262 | -5.94855 | 496.519 |
| [00]102026478 | -217.813 | -138.97 | -11.4481 | 841.781 |
| [00]132255100 | -181.506 | -135.599 | -5.68666 | 439.428 |
| [00]16218627 | -180.136 | -135.525 | -7.672 | 440.413 |
| [00]100968121 | -192.426 | -135.379 | -2.42808 | 610.661 |
| [00]128780 | -173.361 | -134.132 | -6.10786 | 458.403 |
| [00]10696709 | -178.155 | -133.094 | -2.54635 | 500.483 |
| [00]456144 | -192.12 | -132.787 | -9.20054 | 712.667 |
| [00]444319 | -178.728 | -131.774 | -7.70866 | 455.447 |
| [01]101755837 | -199.698 | -130.665 | -6.95592 | 711.682 |
Drug-drug comparison
| Established Drug: Methotrexate | Virtual Screened Drug (PubChem id: 122677576) | |||
| Energy overview:Descriptors | MolDock Score | Rerank Score | MolDock Score | Rerank Score |
| Total Energy | -173.204 | -111.978 | -195.561 | -143.154 |
| External Ligand interactions | -185.718 | -132.69 | -209.335 | -172.055 |
| Protein - Ligand interactions | -185.718 | -132.69 | -209.335 | -172.055 |
| Steric (by PLP) | -166.874 | -114.476 | -199.728 | -137.014 |
| Steric (by LJ12-6) | -3.29 | -27.433 | ||
| Hydrogen bonds | -18.843 | -14.924 | -9.606 | -7.608 |
| Hydrogen bonds (no directionality) | 0 | 0 | ||
| Electrostatic (short range) | 0 | 0 | 0 | 0 |
| Electrostatic (long range) | 0 | 0 | 0 | 0 |
| Cofactor – Ligand | 0 | 0 | 0 | 0 |
| Steric (by PLP) | 0 | 0 | ||
| Steric (by LJ12-6) | 0 | 0 | ||
| Hydrogen bonds | 0 | 0 | 0 | 0 |
| Electrostatic | 0 | 0 | 0 | 0 |
| Water - Ligand interactions | 0 | 0 | 0 | 0 |
| Internal Ligand interactions | 12.513 | 20.712 | 13.774 | 28.9 |
| Torsional strain | 6.417 | 6.019 | 14.433 | 13.538 |
| Torsional strain (sp2-sp2) | 1.133 | 1.451 | ||
| Hydrogen bonds | 0 | 0 | ||
| Steric (by PLP) | 11.605 | 1.996 | 7.111 | 1.223 |
| Steric (by LJ12-6) | 11.565 | 12.688 | ||
| Electrostatic | 0 | 0 | 0 | 0 |
| Soft Constraint Penalty | 0 | 0 | ||
| Search Space Penalty | 0 | 0 |
Figure 2The most effective compound (PubChem id: 122677576) binding with IL-6 obtained from the virtual screening studies shows Van der Waals Interaction
Figure 3The most effective compound (PubChem id: 122677576) binding with IL-6 obtained from the virtual screening studies shows Ligand-receptor Interaction
ADMET profile calculation of both best-docked compounds by AdmetSAR
| Virtual Screened Drug | Established Drug | |||
| Model Absorption | Result | Probability | Result | Probability |
| Blood-Brain Barrier | BBB- | 0.6563 | BBB- | 0.9467 |
| Human Intestinal Absorption | HIA+ | 0.9575 | HIA+ | 0.8261 |
| Caco-2 Permeability | Caco2- | 0.7248 | Caco2- | 0.7754 |
| P-glycoprotein Substrate | Substrate | 0.7871 | Substrate | 0.8172 |
| P-glycoprotein Inhibitor | Non-inhibitor | 0.6111 | Non-inhibitor | 0.7752 |
| Non-inhibitor | 0.7509 | Non-inhibitor | 0.9879 | |
| Renal Organic Cation Transporter | Non-inhibitor | 0.8994 | Non-inhibitor | 0.8886 |
| Distribution | ||||
| Subcellular localization | Mitochondria | 0.5355 | Mitochondria | 0.4349 |
| Metabolism | ||||
| CYP450 2C9 Substrate | Non-substrate | 0.8783 | Non-substrate | 0.85 |
| CYP450 2D6 Substrate | Non-substrate | 0.7845 | Non-substrate | 0.7968 |
| CYP450 3A4 Substrate | Substrate | 0.584 | Substrate | 0.5177 |
| CYP450 1A2 Inhibitor | Non-inhibitor | 0.7249 | Non-inhibitor | 0.9045 |
| CYP450 2C9 Inhibitor | Non-inhibitor | 0.7417 | Non-inhibitor | 0.907 |
| CYP450 2D6 Inhibitor | Non-inhibitor | 0.9051 | Non-inhibitor | 0.9231 |
| CYP450 2C19 Inhibitor | Non-inhibitor | 0.693 | Non-inhibitor | 0.9025 |
| CYP450 3A4 Inhibitor | Non-inhibitor | 0.6359 | Non-inhibitor | 0.8333 |
| CYP Inhibitory Promiscuity | Low CYP Inhibitory Promiscuity | 0.7285 | Low CYP Inhibitory Promiscuity | 0.9739 |
| Excretion | ||||
| Toxicity | ||||
| Human Ether-a-go-go-Related Gene Inhibition | Weak inhibitor | 0.989 | Weak inhibitor | 0.9564 |
| Non-inhibitor | 0.6529 | Non-inhibitor | 0.6958 | |
| AMES Toxicity | Non AMES toxic | 0.7703 | Non AMES toxic | 0.9132 |
| Carcinogens | Non-carcinogens | 0.9039 | Non-carcinogens | 0.9517 |
| Fish Toxicity | Low FHMT | 0.9896 | Low FHMT | 0.9534 |
| Tetrahymena Pyriformis Toxicity | High TPT | 0.9052 | High TPT | 0.7836 |
| Honey Bee Toxicity | Low HBT | 0.7618 | Low HBT | 0.8736 |
| Biodegradation | Not ready biodegradable | 0.989 | Not ready biodegradable | 0.9741 |
| Acute Oral Toxicity | III | 0.5639 | II | 0.731 |
| Carcinogenicity (Three-class) | Non-required | 0.6139 | Non-required | 0.6979 |
ADMET profile (Regression)
| Virtual Screened Drug: CID122677576 | Established Drug | |||
| Model Absorption | Value | Unit | Value | Unit |
| Aqueous solubility | -3.643 | LogS | -3.0651 | LogS |
| Caco-2 Permeability | 0.0081 | LogPapp,cm/s | -0.3591 | LogPapp,cm/s |
| Distribution | ||||
| Metabolism | ||||
| Excretion | ||||
| Toxicity | ||||
| Rat Acute Toxicity | 2.6698 | LD50,mol/kg | 3.4955 | LD50,mol/kg |
| Fish Toxicity | 1.6179 | pLC50,mg/L | 1.82 | pLC50,mg/L |
| Tetrahymena Pyriformis Toxicity | 0.3464 | pIGC50,ug/L | 0.2833 | pIGC50,ug/L |
Figure 4Comparative ADMET studies of BBB, HIA, AMES toxicity and LD50 of the Established Compounds against Virtual screened compounds
Comparative ADMET profile of the test ligands and the control
| Compounds | Blood-Brain Barrier (BBB+/BBB-) | Human Intestinal Absorption(HIA) | AMES toxicity | Carcinogenicity | LD50 in rat |
| CID 126941 (Methotrexate) | 0.9467 (BBB-) | 0.8261 (HIA+) | 0.9132 (Non AMES Toxic) | Non- carcinogenic | 3.4955 |
| CID 5161 (Salsalate) | 0.8946 (BBB+) | 0.9161 (HIA+) | 0.9731 (Non AMES Toxic) | Non- carcinogenic | 2.4607 |
| CID (122677576) | 0.6563 (BBB-) | 0.9575 (HIA+) | 0.7703 (Non AMES Toxic) | Non- carcinogenic | 2.6698 |
| CID (102026478) | 0.9467 (BBB-) | 0.8261 (HIA+) | 0.9132 (Non AMES Toxic) | Non- carcinogenic | 3.4955 |