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Investigation of activation mechanism and conformational stability of N -(4-chloro-3-trifluoromethyl-phenyl)-2-ethoxybenzamide and N -(4-chloro-3-trifluoromethyl-phenyl)-2-ethoxy-6-pentadecyl-benzamide in the: active site of p300 histone acetyl transferase enzyme by molecular dynamics and binding free energy studies.
- Source :
-
Journal of biomolecular structure & dynamics [J Biomol Struct Dyn] 2019 Sep; Vol. 37 (15), pp. 4006-4018. Date of Electronic Publication: 2019 Jan 13. - Publication Year :
- 2019
-
Abstract
- The CBP (CREB-binding protein) and p300 are related to transcriptional coactivator family and are involved in several post-translational modifications, in which the acetylation is an important factor because it commences the transcription process. Experimental studies report that CTPB ( N -(4-chloro-3-trifluoromethyl-phenyl)-2-ethoxy-6-pentadecyl-benzamide) and CTB ( N -(4-chloro-3-trifluoromethyl-phenyl)-2-ethoxybenzamide) are good activators of p300 HAT enzyme, but yet, the molecular mechanism of their activation is not explored. The present study pertains to determine the intermolecular interactions, stability and binding free energy of CTB and CTPB from the molecular docking, molecular dynamics (MD) simulation and binding free energy calculation. The docking studies of the molecules reveal that the docking score of CTPB (-15.64 kcal/mol) is higher than that of CTB (-12.30 kcal/mol); on the contrary, CTB forms a strong interaction with the key residues of catalytic site (Tyr1467 and Trp1436) compared with CTPB. The MD simulation shows the stability of both molecules in the active site of p300 and their interactions. Furthermore, both docking and MD simulation studies of CTB confirm that it forms expected key interactions and retain the interactions with the active site amino acid residues of p300 when compared with CTPB. For this reason, the CTB recruits more acetyl-CoA in the active site of p300 compared with CTPB; it leads to activate the acetylation process; hence, CTB may be a best activator than CTPB. The binding free energy value of CTPB (-24.79 ± 2.38 kcal/mol) is higher when compared with that of CTB (-12.14 ± 1.30 kcal/mol) molecule; perhaps, the interaction of pentadecyl chain of CTPB with p300, whereas in CTB, such a group is absent. Communicated by Ramaswamy H. Sarma.
- Subjects :
- Algorithms
Amino Acids
Binding Sites
Humans
Models, Theoretical
Molecular Conformation
Molecular Structure
Protein Binding
Structure-Activity Relationship
Benzamides chemistry
Catalytic Domain
Molecular Docking Simulation
Molecular Dynamics Simulation
Salicylamides chemistry
p300-CBP Transcription Factors chemistry
Subjects
Details
- Language :
- English
- ISSN :
- 1538-0254
- Volume :
- 37
- Issue :
- 15
- Database :
- MEDLINE
- Journal :
- Journal of biomolecular structure & dynamics
- Publication Type :
- Academic Journal
- Accession number :
- 30301423
- Full Text :
- https://doi.org/10.1080/07391102.2018.1533497