APPLICATION OF COMPUTATIONAL STRATEGIES FOR OPTIMIZATION OF ASPARGINYL t-RNA SYNTHETASE DOCKING STUDY OF QUINOXALINES

Rahul Ingle
2017 World Journal of Pharmaceutical Research  
The potential use of asparginyl t-RNA synthetase inhibitors as antifilarial agents for the treatment of filariasis. In our present work we have synthesized series of diphenyl quinoxalines derivatives. Molecular docking studies of these compounds were undertaken to evaluate the binding affinities of the compounds with enzyme asparginyl t-RNA synthetase (PDB: 2kqr). The current result shows fine correlation in enzyme inhibitory activity with docked ligand. stable conformer get selected and docked
more » ... selected and docked with ligands. For docking purpose download the PDB file from online (PDB: 2kqr) and purify proteins by removal of binded ligand, removal of water molecule and addition of hydrogen atom and make it ready for docking. Second step was drawn ligand in Chembiodraw 2D structures and get converted into 3D form. (.mol) Later on minimized the energy of selected molecules and optimized molecules for stability. Energy minimization was done by semi empirical method by MMFF (Merck Molecular Force Field) [5] and molecules became ready for docking purpose. Later on Grip study was done. www.wjpr.net Vol 6, Issue 10, 2017. 855 Rahul et al. World Journal of Pharmaceutical Research Target preparation The 3D structure of 2kqr was retrieved from the Protein Data Bank (www.rcsb.org). Finally, the 3D structures of protein 2kqr were imported into the workspace of V-Life MDS suit with the removal of all water molecules having more than 5Å specific distance. The standard V-Life algorithm was employed for rendering the missing charges, protonation states and assigning of polar hydrogen to the receptor. www.wjpr.net Vol 6, Issue 10, 2017. 857 Rahul et al. World Journal of Pharmaceutical Research Docking studies on Autodock 4.0 The force field appraise binding in two stepladders. The ligand and protein start off in an liberated conformation. In the first step, the intramolecular energetic are approximate for the evolution from these unbound states to the conformation of the ligand and protein in the spring state. The second step then evaluates the intermolecular energetics of uniting the ligand and protein in their bound conformation. The force field includes six pair-wise evaluations (V) and an approximation of the conformational entropy lost upon binding (ΔSconf): ΔG = (Vbound L-L +V unbound L-L)+(Vbound P -P +V unbound P-P)+(Vbound P-L +Vunbound P-L +ΔSconf) Where, L refers to the "ligand" and P refers to the "protein" in a ligand-protein docking calculation. Every of the pair-wise energetic terms includes evaluations for dispersion/repulsion, hydrogen bonding, electrostatics, and desolvation. The weighting constants we have been optimized to calibrate the empirical free energy based on a set of experimentally determined binding constants. The first term is a typical 6/12 potential for dispersion/repulsion interactions. The parameters are based on the Amber force field. The second term is a directional H-bond term based on a 10/12 potential. The parameters C and D are assigned to give a maximal well intensity of 5 kcal/mol at 1.9Å for hydrogen bonds with oxygen and nitrogen, and a well depth of 1 kcal/mol at 2.5Å for hydrogen bonds with sulfur. The function E(t) provides directionality based on the angle t from ideal H-bonding geometry. The third term is a screened Coulomb potential for electrostatics. The final term is a desolvation potential based on the volume of atoms (V) that surround a given atom and shelter it from solvent, weighted by a solvation parameter (S) and an exponential term with distance-weighting factor σ=3.5Å. For a detailed presentation of these functions. Prediction of ADME descriptors and toxicity The major reason for the failure of most of the drug candidates during clinical trial are poor ADME and high toxicity profile. Thus an important aspect of drug discovery is to evaluate critical physiochemical as well as toxicity profile in initial stages of drug discovery. Hence, to select a potential drug candidate, all hypothetical ligands were screened on the basis of ADME and toxicity filter using preadmet from PreMetabo software and was also employed to filter non-toxic hits on the basis of carcinogenicity and mutagenicity ( rat model) of the hypothetical designed ligands. input. Output showed a number of principal descriptors and www.wjpr.net Vol 6, Issue 10, 2017. 858 Rahul et al. World Journal of Pharmaceutical Research ADME properties as shown in Table 3 Lipinski rule of five was applied on the ligands and hits which were having more than one violation were rejected. Various other physicochemical properties were also calculated, represented by different descriptors such as molecular weight (MW), number of rotatable bonds (NRB), lipophilicity parameter [log P(o/w)], number of hydrogen bond acceptors (HBA), number of hydrogen bond donors (HBD), total polar surface area (TPSA), solubility (log s), solvent-accessible surface area (SASA), skin permeability (log Kp), binding to human serum albumin (log Khsa), bloodbrain partition coefficient (logBB), apparent MDCK cell permeability (affyPMDCK), apparent Caco-2 cell permeability (affyPCaco), percentage human oral absorption. Ideal ranges of various descriptors calculated with the reference to 95% of are presented in Table 3 . RESULTS AND DISCUSSION Pharmacophore and synthesis of test series The substituted sulfonamido quinoxalines were synthesized [8] [9] [10] [11] [12] [13] [14] using 2, 3diphenylquinoxaline-6-sulfonylchloride as an important intermediate which was synthesized by reported method in which was achieved by treating of 2, 3-diphenyl quinoxaline was refluxed with excess chlorosulfonic acid [15] on water bath for 5 hrs. The resultant mixture was poured into water to give sulfonylchloride derivative. Various different organic amines were treated at different reaction conditions to give the series of 6-sulfonamido derivatives of 2, 3diphenylquinoxaline. Now, docked the synthesized molecules on parasite Brugia malayi asparginyl t-RNA synthetase enzyme [16] which we got downloaded from protein data bank (PDB) site (PDB: 2kqr). Here use of V-Life MDS 4.5 Software to explore the binding mode of ligands. All ligands exhibited negative docking scores and analyzed for various types of interactions like hydrophobic bonding, aromatic bonding, hydrogen bonding and Vanderwaal's interactions. [17-21] Docked selected synthesized quinoxaline molecules with parasite Brugia malayi asparginyl t-RNA synthetase ligase enzyme. The results obtained from activity were in excellent correlation with docking outcomes of title compounds. Molecular docking was carried out to study the interaction of quinoxaline derivatives with Brugia malayi parasite. The most active compound of dataset was found to have dock score -66.609758 for R6 compound. In case of www.wjpr.net Vol 6, Issue 10, 2017. 859 Rahul et al. World Journal of Pharmaceutical Research parasitic enzyme compound R6 shows most promising dock score (Table 2) and binding interactions and affinity towards receptor. www.wjpr.net Vol 6, Issue 10, 2017. 860 Rahul et al. World Journal of Pharmaceutical Research Figure 1: The crystal structure of asparginyl t-RNA synthetase in complex with a R6 (pdb: 2kqr). There is an intramolecular VDW interaction (length = 3.528Å) between the oxygen atom O of ASP12A 183C residue and the oxygen atom O of ASP12A residue in 2kqr protein. Figure 2: Confirmation and amino acid interactions. www.wjpr.net Vol 6, Issue 10, 2017. 861 Rahul et al. World Journal of Pharmaceutical Research a) Conformation for R7 compound (R_7 C_75 P_29) b) Conformation for R7 compound (R7 C_71 P_30). c) Conformation for R7 compound (R7 C_45 P_4) d) Conformation for R7 compound (R7 C_92 P_21). e) Conformation for R4 compound (R4 C_63 P_28) f) Conformation for parent compound (Lead C_94 LP_3). g) Conformation for parent compound (Lead C_38 P_13) h) Conformation for parent compound (Lead 13_LP_4) i) Conformation for parent compound (Lead C_15 LP_2). Figure 3: Superimposition of R6_3D from the X-Ray crystal structure from the docking result. Figure 4: Model of interaction of R6_3D and asparginyl t-RNA synthetase. www.wjpr.net Vol 6, Issue 10, 2017. 862 Rahul et al. World Journal of Pharmaceutical Research CONCLUSION Docking of quinoxaline derivatives with Brugia malayi enzyme out of which derivative R6 gives best docking score as it good in vitro antifilarial study also. On the basis of dock score it was concluded that compound having good asparginyl t-RNA synthetase receptor binding capacity. ADME-T was performed successfully. Reported results revealed that almost all 44 analogues of the series, having a good binding affinity and exhibited strong hydrogen bond interactions with the receptor. Final screening was based on the ADME-T filter. The results indicated that Autodock algorithms were valid, as docking the native ligand to binding site of asparginyl t-RNA synthetase showed a RSMD value less than 4 A 3.3. The docking result revealed sulfonamido quinoxalines exhibited good binding interaction to catalytic site of parasite asparginyl t-RNA synthetase. Finally best hits were found on the basis of molecular docking and ADME-T studies. These most promising analogues can be explored further in designing of drugs against Brugia malayi also provide a way to synthesize the optimized lead compounds in the laboratory.
doi:10.20959/wjpr201710-9383 fatcat:555hd3wrwbecdiesnkzvv6bmn4