Structure Based Multitargeted Molecular Docking Analysis of Selected 2.pptx

This power point presentation is the explanation of how molecular docking can be used to treat the disease Breast cancer. The natural compounds are used to docked and their binding affinity is compared with reference compounds.

1. Structure Based Multitargeted Molecular Docking Analysis of Selected Furanocoumarins against Breast Cancer Submitted By Sakshi goel

2. Breast cancer is the Type of Hormonal cancer because it contains glandular tissue which are highly sensitive to Hormonal changes in the body. Majorly two hormones create potential risk factors for the development of breast cancer that are Estrodiol and progesterone hormones . So its current chemotherapy is to target the Hormone receptors by the use of partial agonist / Antagonist. The Targeted receptors are: ER alpha (Estrogen receptors alpha) PR (Progesterone receptor) EGFR(Epidermal growth factor Receptor) mTOR (Mammalian target of rapamycin)

3. Coumarin As Drug Coumarins are phenolic compounds  . Coumarins are lactones with the basic structure of 1,2-benzopyron. most are oxygenated at C-7 position and have isoprenoid chains, attached to a carbon or oxygen or both. IUPAC NAME :chromen-2-one, CCDC Number:266081

4. Coumarins tend to show extensive therapeutic activities including photo chemotherapy, anti-neoplastic activity, anti-HIV, anti-coagulants, anti-bacterial, anti-inflammatory, CNS stimulants etc. The derivatives of coumarins are pyranocoumarins, furanocoumarins , coumarin sulfamates (coumates), etc. The furanocoumarins used for docking analysis in the current study. In this study Various Furanocoumarin compounds are available in Pubchem were docked and their binding affinities, RSMD values were evaluated. 23 Furabocoumurin compounds having anti- cancer property ( plant-derived compounds, disrupt DNA replication upon UV exposure, showing promise for anti-cancer therapies targeting malignant transformations . ). Among 23 Furanocoumarins screamed , 20 compounds exhibited docking energy value above – 6 Kcal/mol for breast cancer receptor.

5. Furanocoumarins with  hydroxyl Furanocoumarins  with methyoxy groups:

6. Methodology 1) The 3D structures of breast cancer receptors were obtained are ER alpha , PR , EGFR, and mTOR from PDB database. Receptors: - ER α: PDB ID 3ERT22 PR: PDB ID 4OAR23 EGFR: PDB ID 2J6M24 mTOR : PDB ID 4DRH25 2) Ligand Preparation: - Ligands: - Drawn using ChemDraw Ultra 10.0 (2D and 3D options) – Saved in mol2 format - Imported into Maestro 8.5 Schrodinger – Energy minimization, conformational analysis, and ligand preparation were performed using the Lig prep 2.2 application option . saved in SDF format. these molecules were imported into the docking library of FlexX 2.1.3 docking sofware and used for docking.

7. Maestro 8.5 Schrodinger Using Maestro, prepare a protein and ligand, as well as dock a ligand into a protein receptor using Schrödinger’s Glide. They will also analyze protein-ligand interactions from a Ligand Interaction Diagram . Prepare ligand and protein structures in Maestro. Analyze integral protein-ligand interactions within an active site using the Ligand Interaction Diagram

8. Maestro provides a suite of tools specifically designed for ligand preparation, including tools for structure optimization , protonation , tautomeric state determination, and generation of alternative conformations . These tools ensure that ligand structures are prepared in a physiologically relevant and chemically accurate manner, which is crucial for subsequent molecular docking and virtual screening studies . validate ligand structures before and after preparation. Maestro undergoes rigorous testing and validation to ensure accuracy and reproducibility , instilling confidence in the results obtained from ligand preparation studies.

9. In the Entry List, double click on files- right-click on 1FJS_prepared _dry Choose Split > Into Ligands, Water, Other Two new entries appear in the Entry List Only the ligand is displayed in the Workspace. Go to Tasks > Browse > LigPrep The LigPrep panel opens. In Leg prep For Use structures from, choose Workspace Under Stereoisomers- choose Determine chiralities from 3D structure . Change Job name to ligprep_1fjs 5 . 5. Click Run 6. Click Tree to open the Property Tree Different calculated properties can be toggled on and off Click the arrow next to each application to view more properties

10. Molecular Docking Molecular docking is a method which analyses the conformation and orientation (referred together as the “ pose ” ) of molecules into the binding site of a macromolecular target . Searching algorithms generate possible poses, which are ranked by scoring functions.   Molecular docking is a methodology applied to study molecular behavior on target proteins binding . It is a tool which is used extensively in drug discovery . The Top software used for best scores in docking are AutoDock , MOE-DOCK ( Molecular Operating Software), FLexX and GOLD (G enetic Optimization for Ligand Docking). ) respectively. For this study BioSolveIT FLexX (2.3.1) used to evaluate the anticancer activity of the concerned phytochemicals.

11. FlexX Software and How does it works It is very flexible and fast algorithm for small ligands docking in binding sites of receptors and enzymes. It is based on an incremental construction algorithm . FlexX also incorporates interactions between protein and ligand, ligand core placement , and complete ligand rebuilding

12. In FleXx Target Selection: ER α, PR, EGFR, mTOR Retrieve Crystal Structures and Ligands from PDB Prepare Binding Sites using Receptor Preparation Wizard active site of the target protein was defined around a radius of 6.50Å (radius : 6.50Å) Software Validation: Redock Co-crystallized Ligands Calculate RMSD Values Compare with Reference Compounds Evaluate Docking Scores and Generate 2D/3D Views Analyze Interactions and Binding Affinities of Furanocoumarins

13. Advantages Docking for non-experts: no more receptor preparation – simply dock ! Accurate binding mode prediction Dock gigantic libraries by using ultra-high-speed docking (< 1 s/ligand)- You can screen a library of ~1,000 compounds in less than an hour on a laptop with 8 cores. FlexX4 accurately predicts the geometry of the protein-ligand complex within a few seconds.

14. Reference Compound

15. Docking Result The top fve furanocoumarins that exhibited the highest binding affnity energies towards ER α, PR, EGFR and mTOR were XAN, BER, ANG, PSO and IMP.

16. Further evaluation of molecular properties of furanocoumarin using Molinspiration to fit into Lipinski Rule of Five , which is the key way to satisfy the rational drug design. 20 out of 23 were found to be no violations for the lipinski rule. Lipinski Rule of Five Not more than 5 hydrogen bond donors. Not more than 10 hydrogen bond acceptors. Partition cofficient not more than 5 (Log P). Total Polar surface area not more than 140. Molecular Weight less than 500g/mol.

17. miLogP : This column represents the predicted octanol-water partition coefficient (log P) of each phytochemical, which is a measure of its hydrophobicity . it generally falls within the range of -2 to 6. Higher values indicate higher hydrophobicity TPSA : Total Polar Surface Area (TPSA) indicates the molecular surface area that is polar and capable of hydrogen bonding . ranges from 0 to 200 square angstroms (Ų ). nAtoms : This column shows the number of atoms in each phytochemical molecule. MW : Molecular weight (MW) is the sum of the atomic weights of all atoms in a molecule . molecular weights usually range from around 100 to 700 Da. nON : Number of oxygen atoms. nOHNH : Number of nitrogen and oxygen atoms. nViolation : This column indicates the number of Lipinski's Rule of Five violations for each compound. nRotB : Number of rotatable bonds in the molecule . The number of rotatable bonds can range from 0 to the total number of single bonds in the molecule. Volume : Molecular volume of the compound . small drug-like molecules range from 50 to 500 ų.

18. . Molecular docking analysis of XAN. (a) Pose view of interaction of Xanthotoxol with receptors ER α, PR, EGFR and mTOR . (b) Overlay of XAN in active pockets of ER α, PR, EGFR and mTOR . XAN: Xanthotoxol , ER α: Estrogen receptor, PR: Progesterone receptor, EGFR: Epidermal growth factor receptor and mTOR : Mammalian target of Rapamycin .

19. . Molecular docking analysis of BER. (a) Pose view of interaction of BER with receptors ER α, PR, EGFR and mTOR . (b) Overlay of BER in active pockets of ER α, PR, EGFR and mTOR . BER: Bergapten , ER α: Estrogen receptor, PR: Progesterone receptor, EGFR: Epidermal growth factor receptor and mTOR : Mammalian target of Rapamycin .

20. Molecular docking analysis of PSO. (a) Pose view of interaction of PSO with receptors ER α, PR, EGFR and mTOR . (b) Overlay of PSO in active pockets of ER α, PR, EGFR and mTOR . PSO: Psoralen , ER α: Estrogen receptor, PR: Progesterone receptor, EGFR: Epidermal growth factor receptor and mTOR : Mammalian target of Rapamycin

21. Molecular docking analysis of ISO. (a) Pose view of interaction of ISO with receptors ER α, PR, EGFR and mTOR . (b) Overlay of ISO in active pockets of ER α, PR, EGFR and mTOR . IMP: Isoimperatorin , ER α: Estrogen receptor, PR: Progesterone receptor, EGFR: Epidermal growth factor receptor and mTOR : Mammalian target of Rapamycin .

22. Discussion and Conclusion Breast cancer is one of the biggest global dilemmas and its current therapy is to target the hormone receptors by the use of partial agonists/antagonists. Potent drugs for breast cancer treatment are Tamoxifen , Trastuzumab , Paclitaxel, etc. which show adverse efects and resistance in patients. The aim of the study has been on certain phytochemicals which has potent actions on ERα, PR, EGFR and mTOR inhibition. The current study is performed by the use of molecular docking as protein-ligand interactions play a vital role in drug design. The 3D structures of ERα, PR, EGFR and mTOR were obtained from the protein data bank and docked with 23 3D PubChem structures of furanocoumarin compounds using FlexX . Drug-likeness property was checked by applying the Lipinski’s rule of fve on the furanocoumarins to evaluate anti-breast cancer activity.