Computer-aided rational drug design encompasses the identification of potential biological targets for drug candidates followed by an intensive search ensues to find a drug-like small molecules that can modulate the function of the identified macromolecule resulting in a therapeutic effect. This approach becomes possible due to the availability of information about the three-dimensional chemical structures of ligands and biomolecules. Thus, to be efficient, computer-aided drug design (CADD) techniques including both ligand- and structure-based, must be accurate with the structural data manipulation as the knowledge of macromolecules and ligands structures as well as unbound and receptor-bound conformations is the precondition of the vital importance for the application of 3D computational molecular modeling approaches.
The aim of the current work was to analyze, systematize and summarize the recent literature data discussing conformational ensembles of small organic molecules, the main approaches and techniques applied for their generation and the conformational sampling of drug-like molecules significance in modern computer-aided drug design.
Three-dimensional spatial arrangements of atoms that organic molecules can adopt are known as conformations, their diversity is ensured by rotational bonds, changes in bond lengths, bond angles and torsions, interconversion between different conformations can be achieved by rotations about formally single bonds. Thus, a set of stable spatial geometric structures of a molecule with the constant connectivity matrix constitutes the set of its conformations. In their turn, conformational ensembles are represented by the sets of equilibrium conformations existing under certain thermodynamic conditions in defined environmental medium. Consequently, thorough conformational analysis is critically important in many areas of research, such as drug discovery, protein engineering, and the design of catalysts.
Conformer generation leading to exploring and sampling the low energy conformational space of drug-like molecules continues to be a relevant task focusing on ligands structure pre-organization with the aim to minimize energetic penalties associated with undesired flexibility, sub-optimal arrangement of functional groups interacting with the protein binding site or unwanted internal stabilization.
Drug-like molecules can adopt a great number of conformations depending on the amount of rotatable bonds, angels and torsions flexibility and the rigidity properties of their rings and cycles. It was shown that even the solid-state ligands bounded to corresponding biotargets can possess conformational diversity. Structural data drawn from the Protein Data Bank (PDB) revealed that the same ligand precented in at least two different protein−ligand structures may be found in multiple conformations which differed significantly (RMSD > 2 Å) [1]. This means that a small molecule must adopt the bioactive conformation that is the conformation which can be recognized by the receptor and produce the biological response. Bioactive conformations construction for flexible small organic molecules is challenging and complex problem in modern drug design reasoned by the large number of degrees of freedom even for relatively small ligands.