Abstract
A semi-exhaustive approach and a heuristic search algorithm use a fragment-based drug design (FBDD) strategy for designing new inhibitors in an in silico process. A deconstruction reconstruction process uses a set of known Hsp90 ligands for generating new ones. The deconstruction process consists of cutting off a known ligand in fragments. The reconstruction process consists of coupling fragments to develop a new set of ligands. For evaluating the approaches, we compare the binding energy of the new ligands with the known ligands.
Highlights
Rational drug design remains a challenging problem for computational methods developed in bioinformatics and medicinal chemistry
We evaluate the binding energy (BE) for each ligand
It shows the number of known ligands (KL), the best binding energy obtained from KL, the number of fragments generated, the number of new ligands (NL), the best binding energy from NL, and the total computational time for each group
Summary
Rational drug design remains a challenging problem for computational methods developed in bioinformatics and medicinal chemistry. The first one consists of the exploration of an ample conformational space representing various potential binding modes, and the second one of obtaining an accurate prediction of the interaction energy associated with each of the predicted binding conformations [5] In this context, the molecular docking programs perform these tasks through a cyclical process, in which specific scoring functions evaluate the ligand conformation. From the point of view of searching for active compounds on one or more therapeutic targets using compound libraries, virtual screening (VS) based on molecular docking is an efficient method to recover new successful compounds in drug discovery. The two approaches use a fragment-based drug design (FBDD) strategy for designing new ligands.
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