Supplementary Information: Table S1. Potential energy and essential dynamics (ED) analysis of the MD simulations of the Bcl-2 complexes under study.
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1 Supplementary Information: Table S1. Potential energy and essential dynamics (ED) analysis of the MD simulations of the Bcl-2 complexes under study. Bcl2 and complex Potential energy (kj/mol) ED 2D projection (nm 2 ) Unbounded physiological form Venetoclax bounded physiological form Unbounded chimeric form Venetoclax bounded chimeric form
2 Table S2. List of Bcl-2 nssp with deleterious phenotype prediction. The nssp localization in Bcl-2 sequence is described and the correspondent predicted stabilities presented. SP ID Substitution Bcl-2 domain Stability prediction rs G8E BH4 Decrease rs D34Y Disordered Increase rs A43T Disordered Decrease rs H94P Decrease rs L97P Decrease rs F104S BH3 Decrease rs S105F Inconclusive rs S105P Decrease rs R129C Disordered Decrease rs G203S Disordered Decrease rs R207W Disordered Decrease rs G233D Disordered Decrease Table S3. Summary of results obtained from Protein sequence analysis (Residue positions are given in parenthesis, Blue color indicates residues influences the PTM process) Parameters Bcl2_WT Bcl2_A43T Bcl2_H94P Bcl2_L97P Bcl2_R129C Bcl2_G8E Bcl2_S105P Bcl2_S105F Bcl2_F104S Bcl2_R207W Bcl2_D34Y Bcl2_G233D Bcl2_G203S Physiochemical Properties Molecular Wt (Da) Theoretical pi egatively charged residues Positively charged residues Instability index Aliphatic index GRAVY Putative Post-translational modification sites C-Mannosylation Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent -Glycosylation Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent -Glycosylation (50,51,56,62, 69,70,74,87) (43,50,51,56,62, 69,70,74,87) (50,51,56,62,6 9,70,74,87) (50,51,56,62, 69,70,74,87) (50,51,56,62,69, 70,74,87) (50,51,56,62,69, 70,74,87) (50,51,56,62,69, 70,74,87) (50,51,56,62,69, 70,74,87) (50,51,56,62,69, 70,74,87) (50,51,56,62,69,70, 74,87) (50,51,56,62,69, 70,74,87) (50,51,56,62,69, 70,74,87) (50,51,56,62,69,70, 74,87) C-Glycosylation Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent GPI modification Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent -Myristoylation Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent S-Farnesylation S-Geranylgeranylation Prenylation Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent Acetylation Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent Phosphorylation (S/T/Y) (24,70,87,167,56,74,96,132, 28,180) (24,70,87,167,4 3,56,74,96,132, 28,180) (24,70,87,167, 56,74,96,132, 28,180) (24,70,87,167,56,74,96,132, 28,180) (24,70,87,167,5 6,74,96,132,28, 180) (7,9,24,70,87,16 7,56,74,96,132, 28,180) (24,70,87,167,5 6,74,96,132,28, 180) (24,70,87,167,5 6,74,96,132,28, 180) (24,70,87,104,1 05,167,56,74,96,132,28,180) (24,70,87,167,56,74,96,132,28,180) (24,34,70,87,16 7,56,74,96,132, 28,180) (24,70,87,167,5 6,74,96,132,28, 180) Tyrosine Sulfation Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent Absent (24,70,87,167,56,74,96,132,28,180,203)
3 Sumoylation
4 Table S4. Time averaged structural properties obtained from MD simulation for Wild-Type (WT) of Bcl-2 and its variants SP ID Substitution RMSD (nm) RMSF(nm) Radius of Gyration(nm) Intra-molecular hydrogen bonds Trace of the diagonalized covariance matrix (nm 2 ) Inter-molecular hydrogen bonds Hydrophobic area (nm 2 ) Hydrophilic area (nm 2 ) Domain Distances (nm) BH1-BH2 BH1-BH3 BH1-BH4 BH2-BH3 BH2-BH4 BH3-BH4 Bcl2_WT rs Bcl2_H94P rs Bcl2_L97P rs Bcl2_A43T rs Bcl2_R129C rs Bcl2_G8E rs Bcl2_S105P rs Bcl2_S105F rs Bcl2_F104S rs Bcl2_R207W rs Bcl2_D34Y rs Bcl2_G233D rs Bcl2_G203S
5 Table S5. List of putative and known inhibitors (Taxol) for FLD of Physiological Bcl-2 form. The putative inhibitors were identified from HTVS and docking analysis against Zinc Data base (Ranked according to CDRUG P-Value). Zinc Accession o Structure Ligand interaction Diagram ZIC H
6 ZIC F H F F
7 ZIC S H
8 ZIC H H
9 ZIC
10 Taxol (ZIC ) H H H H
11 Table S6. Specific input parameters for MD simulations of each Bcl-2 nssp studied. SP ID Substitution SPC water molecules (#) System net charge (e) Wild-Type rs G8E rs D34Y rs A43T rs H94P rs L97P rs F104S rs S105F rs S105P rs R129C rs G203S rs R207W rs G233D Ion replacement (# a + )
12 Figure S1. Molecular dynamics simulation results of Physiological Bcl2 form - Unbounded with Venetoclax bounded (a) Root Mean Square Deviation (Black: Apo & Red: complex), (b) Radius of Gyration (Black: Apo & Red: complex), (c) Potential energy (Black: Apo & Red: complex), (d) Principal component analysis (Black: Apo & Red: complex), (e) Solvent Accessible Surface Area for unbounded and (e) Solvent Accessible Surface Area for bounded forms
13 Figure S2. Molecular dynamics simulation results of Chimeric Bcl2 form - Unbounded with Venetoclax bounded (a) Root Mean Square Deviation (Black: Apo & Red: complex), (b) Radius of Gyration (Black: Apo & Red: complex), (c) Potential energy (Black: Apo & Red: complex), (d) Principal component analysis (Black: Apo & Red: complex), (e) Solvent Accessible Surface Area for unbounded and (e) Solvent Accessible Surface Area for bounded forms
14 Figure S3. Molecular dynamics simulation results of Physiological Bcl-2 form:venetoclax (Black) with Chimeric Bcl-2 form:venetoclax (Red) (a) Root Mean Square Deviation, (b) Radius of Gyration, (c) Intermolecular hydrogen bonds, (d) Potential energy, (e) Principal component analysis, (f) Solvent Accessible Surface Area for Physiological Bcl-2 form:venetoclax (g) Solvent Accessible Surface Area for Chimeric Bcl2 form:venetoclax
15 Figure S4. Surface representation of the residue occupancy probability of venetoclax towards (a) Chimeric and (b) Physiological Bcl-2 forms. The residues close to the ligand at less than 3 Å are represented in red, while the non-interacting residues are in gray. Representation was prepared by using PyML (PyML Molecular Graphics System, Version 1.8 Schrödinger, LLC).
16 Figure S5. Structural alignment of Bcl-2 (PDB ID: 1GJH) with Bcl-XL (PDB ID: 2LPC). Chain 1 is Bcl-2 and chain 2 is Bcl-XL. Residues are color-coded by similarity match. Figure S6. Structural alignment of Bcl-2 (PDB ID: 1GJH) with Bcl-W (PDB ID: 1MK3). Chain 1 is Bcl-2 and chain 2 is Bcl-W. Residues are color-coded by similarity match
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