Abstract
Drug development is one of the most significant processes in the pharmaceutical industry. Various computational methods have dramatically reduced the time and cost of drug discovery. In this review, we firstly discussed roles of multiscale biomolecular simulations in identifying drug binding sites on the target macromolecule and elucidating drug action mechanisms. Then, virtual screening methods (e.g., molecular docking, pharmacophore modeling, and QSAR) as well as structure- and ligand-based classical/de novo drug design were introduced and discussed. Last, we explored the development of machine learning methods and their applications in aforementioned computational methods to speed up the drug discovery process. Also, several application examples of combining various methods was discussed. A combination of different methods to jointly solve the tough problem at different scales and dimensions will be an inevitable trend in drug screening and design.
Highlights
With the rapid development of both computer hardware, software, and algorithms, drug screening and design have benefited much from various computational methods which greatly reduce the time and cost of drug development
Biomolecular simulations with multiscale models allow for investigations of both structural and thermodynamic features of target proteins on different levels [4], which are useful for identifying drug binding sites and elucidating drug action mechanisms
Different drug design methods and virtual screening will be very useful to design and find rational drug molecules based on the target macromolecule that interacts with the drug and speed up the whole drug discovery process
Summary
With the rapid development of both computer hardware, software, and algorithms, drug screening and design have benefited much from various computational methods which greatly reduce the time and cost of drug development. Bioinformatics can help reveal the key genes from a massive amount of genomic data [1,2] and provide possible target proteins for drug screening and design. Virtual screening searches chemical libraries to provide possible drug candidates based on drug binding sites on target proteins [5,6,7]. With greatly reduced amount of possible drug candidates, in-vitro cell experiments can further evaluate the efficacy of these molecules. In addition to virtual screening, de novo drug design methods [8], which generate synthesizable small molecules with high binding affinity, provide another type of computer-aided drug design direction.
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