Molecular Recognition of Azelaic Acid and Related Molecules with DNA Polymerase I Investigated by Molecular Modeling Calculations

  • Jakaria Shawon
  • Akib Mahmud Khan
  • Adhip Rahman
  • Mohammad Mazharol Hoque
  • Mohammad Abdul Kader Khan
  • Mohammed G. Sarwar
  • Mohammad A. Halim
Original Research Article

Abstract

Molecular recognition has central role on the development of rational drug design. Binding affinity and interactions are two key components which aid to understand the molecular recognition in drug-receptor complex and crucial for structure-based drug design in medicinal chemistry. Herein, we report the binding affinity and the nonbonding interactions of azelaic acid and related compounds with the receptor DNA polymerase I (2KFN). Quantum mechanical calculation was employed to optimize the modified drugs using B3LYP/6-31G(d,p) level of theory. Charge distribution, dipole moment and thermodynamic properties such as electronic energy, enthalpy and free energy of these optimized drugs are also explored to evaluate how modifications impact the drug properties. Molecular docking calculation was performed to evaluate the binding affinity and nonbonding interactions between designed molecules and the receptor protein. We notice that all modified drugs are thermodynamically more stable and some of them are more chemically reactive than the unmodified drug. Promise in enhancing hydrogen bonds is found in case of fluorine-directed modifications as well as in the addition of trifluoroacetyl group. Fluorine participates in forming fluorine bonds and also stimulates alkyl, pi-alkyl interactions in some drugs. Designed drugs revealed increased binding affinity toward 2KFN. A1, A2 and A3 showed binding affinities of −8.7, −8.6 and −7.9 kcal/mol, respectively against 2KFN compared to the binding affinity −6.7 kcal/mol of the parent drug. Significant interactions observed between the drugs and Thr358 and Asp355 residues of 2KFN. Moreover, designed drugs demonstrated improved pharmacokinetic properties. This study disclosed that 9-octadecenoic acid and drugs containing trifluoroacetyl and trifluoromethyl groups are the best 2KFN inhibitors. Overall, these results can be useful for the design of new potential candidates against DNA polymerase I.

Keywords

Rational drug design Azelaic acid Acne DNA polymerase I Density functional theory Nonbonding interactions Molecular docking 

Abbreviations

AzA

Azelaic acid

DFT

Density functional theory

ADMET

Absorption, distribution, metabolism, excretion, toxicity

QM

Quantum mechanics

CASTp

Computed Atlas of Surface Topography of proteins

SDF

Structure Data File

SMILES

Simplified molecular-input line-entry system

HOMO

Highest occupied molecular orbital

LUMO

Lowest unoccupied molecular orbital

hERG

Human ether-a-go-go-related gene

BBB

Blood brain barrier

Notes

Acknowledgments

We are grateful to our donors who supported to build a computational platform in Bangladesh http://grc-bd.org/donate/.

Author’s Contribution

MAH, MGS and MAKK conceived the idea. MAH, MGS, MAKK and MMH designed the drugs. JS performed the quantum calculations. JS, AMK and AR performed the molecular docking, ADME calculations, data collection and draft writing. All authors read and approved the manuscript.

Funding

This research does not receive any external funding.

Compliance with ethical standards

Conflict of interest

Authors declare that there are no competing interests regarding the publication of this paper.

Supplementary material

12539_2016_186_MOESM1_ESM.docx (481 kb)
Supplementary material 1 (DOCX 480 kb)

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Copyright information

© International Association of Scientists in the Interdisciplinary Areas and Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Jakaria Shawon
    • 1
    • 2
  • Akib Mahmud Khan
    • 1
    • 2
  • Adhip Rahman
    • 1
  • Mohammad Mazharol Hoque
    • 1
  • Mohammad Abdul Kader Khan
    • 3
  • Mohammed G. Sarwar
    • 4
  • Mohammad A. Halim
    • 1
    • 5
  1. 1.Division of Computer-Aided Drug Design, BICCBGreen Research CentreDhakaBangladesh
  2. 2.Department of Biochemistry and Molecular BiologyUniversity of DhakaDhakaBangladesh
  3. 3.Department of General StudiesJubail University CollegeJubail Industrial CitySaudi Arabia
  4. 4.Fakultät für Chemie und Biochemie, Organische Chemie IRuhr-Universität BochumBochumGermany
  5. 5.Institut Lumière Matière, Université Lyon 1 – CNRSUniversité de LyonVilleurbanne CedexFrance

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