Ligand-Receptor Interactions and Drug Design

Aggeliki Syriopoulou; Ioannis Markopoulos; Andreas G Tzakos; Thomas Mavromoustakos

doi:10.1007/978-1-0716-1209-5_5

Ligand-Receptor Interactions and Drug Design

Methods Mol Biol. 2021:2266:89-104. doi: 10.1007/978-1-0716-1209-5_5.

Authors

Aggeliki Syriopoulou¹, Ioannis Markopoulos², Andreas G Tzakos^{3

4}, Thomas Mavromoustakos⁵

Affiliations

¹ Department of Chemistry, Laboratory of Organic Chemistry, National and Kapodistrian University of Athens, Athens, Greece.
² Department of Chemistry, Laboratory of Inorganic Chemistry, National and Kapodistrian University of Athens, Athens, Greece.
³ Department of Chemistry, Section of Organic Chemistry and Biochemistry, University of Ioannina, Ioannina, Greece.
⁴ University Research Center of Ioannina (URCI), Institute of Materials Science and Computing, Ioannina, Ioannina, Greece.
⁵ Department of Chemistry, Laboratory of Organic Chemistry, National and Kapodistrian University of Athens, Athens, Greece. tmavrom@chem.uoa.gr.

PMID: 33759122
DOI: 10.1007/978-1-0716-1209-5_5

Abstract

In silico rational drug design is one of the major pylons in the drug discovery process. Drugs usually act on specific targets such as proteins, DNA, and lipid bilayers. Thus, molecular docking is an essential part of the rational drug design process. Molecular docking uses specific algorithms and scoring functions to reveal the strength of the interaction of the ligand to its target. AutoDock is a molecular docking suite that offers a variety of algorithms to tackle specific problems. These algorithms include Monte Carlo Simulated Annealing (SA), a Genetic Algorithm (GA), and a hybrid local search GA, also known as the Lamarckian Genetic Algorithm (LGA). This chapter aims to acquaint the reader with the docking process using AutoDockTools (GUI of AutoDock). Furthermore, herein is described the docking process of calf thymus DNA with three metal complexes, as a potential metallo-therapeutics as also the docking process of the plant flavonoid quercetin to the antiapoptotic protein BcL-xL.

Keywords: AutoDock; DNA; Drug design; Metal complexes; Molecular docking; Protein.

MeSH terms

Algorithms
Computer Simulation
DNA / chemistry*
Drug Design
Drug Discovery / methods*
Ligands
Metals / chemistry*
Molecular Docking Simulation / methods*
Protein Binding
Proteins / chemistry*
Quercetin / chemistry
Software
bcl-X Protein / chemistry

Substances

Ligands
Metals
Proteins
bcl-X Protein
DNA
calf thymus DNA
Quercetin