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Stepwise development of structure-activity relationship of diverse PARP-1 inhibitors through comparative and validated in silico modeling techniques and molecular dynamics simulation.
J Biomol Struct Dyn. 2015; 33(8):1756-79.JB

Abstract

Inhibitors of poly (ADP-ribose) polymerase-1 (PARP-1) enzyme are useful for the treatment of various diseases including cancer. Comparative in silico studies were performed on different ligand-based (2D-QSAR, Kernel-based partial least square (KPLS) analysis, Pharmacophore Search Engine (PHASE) pharmacophore mapping), and structure-based (molecular docking, MM-GBSA analyses, Gaussian-based 3D-QSAR analyses on docked poses) modeling techniques to explore the structure-activity relationship of a diverse set of PARP-1 inhibitors. Two-dimensional (2D)-QSAR highlighted the importance of charge topological index (JGI7), fractional polar surface area (JursFPSA3), and connectivity index (CIC2) along with different molecular fragments. Favorable and unfavorable fingerprints were demonstrated in KPLS analysis, whereas important pharmacophore features (one acceptor, one donor, and two ring aromatic) along with favorable and unfavorable field effects were demonstrated in PHASE-based pharmacophore model. MM-GBSA analyses revealed significance of different polar, non-polar, and solvation energies. Docking-based alignment of ligands was used to perform Gaussian-based 3D-QSAR study that further demonstrated importance of different field effects. Overall, it was found that polar interactions (hydrogen bonding, bridged hydrogen bonding, and pi-cation) play major roles for higher activity. Steric groups increase the total contact surface area but it should have higher fractional polar surface area to adjust solvation energy. Structure-based pharmacophore mapping spotted the positive ionizable feature of ligands as the most important feature for discriminating highly active compounds from inactives. Molecular dynamics simulation, conducted on highly active ligands, described the dynamic behaviors of the protein complexes and supported the interpretations obtained from other modeling analyses. The current study may be useful for designing PARP-1 inhibitors.

Authors+Show Affiliations

a Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology , Jadavpur University , P.O. Box 17020, Kolkata 700032 , India.No affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

25350685

Citation

Halder, Amit K., et al. "Stepwise Development of Structure-activity Relationship of Diverse PARP-1 Inhibitors Through Comparative and Validated in Silico Modeling Techniques and Molecular Dynamics Simulation." Journal of Biomolecular Structure & Dynamics, vol. 33, no. 8, 2015, pp. 1756-79.
Halder AK, Saha A, Saha KD, et al. Stepwise development of structure-activity relationship of diverse PARP-1 inhibitors through comparative and validated in silico modeling techniques and molecular dynamics simulation. J Biomol Struct Dyn. 2015;33(8):1756-79.
Halder, A. K., Saha, A., Saha, K. D., & Jha, T. (2015). Stepwise development of structure-activity relationship of diverse PARP-1 inhibitors through comparative and validated in silico modeling techniques and molecular dynamics simulation. Journal of Biomolecular Structure & Dynamics, 33(8), 1756-79. https://doi.org/10.1080/07391102.2014.969772
Halder AK, et al. Stepwise Development of Structure-activity Relationship of Diverse PARP-1 Inhibitors Through Comparative and Validated in Silico Modeling Techniques and Molecular Dynamics Simulation. J Biomol Struct Dyn. 2015;33(8):1756-79. PubMed PMID: 25350685.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Stepwise development of structure-activity relationship of diverse PARP-1 inhibitors through comparative and validated in silico modeling techniques and molecular dynamics simulation. AU - Halder,Amit K, AU - Saha,Achintya, AU - Saha,Krishna Das, AU - Jha,Tarun, Y1 - 2014/10/28/ PY - 2014/10/29/entrez PY - 2014/10/29/pubmed PY - 2016/2/26/medline KW - KPLS KW - MM-GBSA KW - PARP-1 inhibitors KW - molecular dynamics KW - pharmacophore mapping SP - 1756 EP - 79 JF - Journal of biomolecular structure & dynamics JO - J Biomol Struct Dyn VL - 33 IS - 8 N2 - Inhibitors of poly (ADP-ribose) polymerase-1 (PARP-1) enzyme are useful for the treatment of various diseases including cancer. Comparative in silico studies were performed on different ligand-based (2D-QSAR, Kernel-based partial least square (KPLS) analysis, Pharmacophore Search Engine (PHASE) pharmacophore mapping), and structure-based (molecular docking, MM-GBSA analyses, Gaussian-based 3D-QSAR analyses on docked poses) modeling techniques to explore the structure-activity relationship of a diverse set of PARP-1 inhibitors. Two-dimensional (2D)-QSAR highlighted the importance of charge topological index (JGI7), fractional polar surface area (JursFPSA3), and connectivity index (CIC2) along with different molecular fragments. Favorable and unfavorable fingerprints were demonstrated in KPLS analysis, whereas important pharmacophore features (one acceptor, one donor, and two ring aromatic) along with favorable and unfavorable field effects were demonstrated in PHASE-based pharmacophore model. MM-GBSA analyses revealed significance of different polar, non-polar, and solvation energies. Docking-based alignment of ligands was used to perform Gaussian-based 3D-QSAR study that further demonstrated importance of different field effects. Overall, it was found that polar interactions (hydrogen bonding, bridged hydrogen bonding, and pi-cation) play major roles for higher activity. Steric groups increase the total contact surface area but it should have higher fractional polar surface area to adjust solvation energy. Structure-based pharmacophore mapping spotted the positive ionizable feature of ligands as the most important feature for discriminating highly active compounds from inactives. Molecular dynamics simulation, conducted on highly active ligands, described the dynamic behaviors of the protein complexes and supported the interpretations obtained from other modeling analyses. The current study may be useful for designing PARP-1 inhibitors. SN - 1538-0254 UR - https://www.unboundmedicine.com/medline/citation/25350685/Stepwise_development_of_structure_activity_relationship_of_diverse_PARP_1_inhibitors_through_comparative_and_validated_in_silico_modeling_techniques_and_molecular_dynamics_simulation_ DB - PRIME DP - Unbound Medicine ER -