Merging Ligand-Based and Structure-Based Methods in Drug Discovery: An Overview of Combined Virtual Screening Approaches
Abstract
:1. Introduction
2. LB and SB Strategies in VS
3. Sequential LB and SB Methods
4. Parallel LB and SB Approaches
5. Hybrid Approaches
5.1. Interaction-Based Methods
5.2. Similarity-Docking Strategies
5.2.1. Predicting the Pose of Ligands
5.2.2. Similarity-Guided Score Scheme
6. Exploiting Chemical Libraries and Biological Data
7. Conclusions
Author Contributions
Funding
Conflicts of Interest
References
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Algorithm | Description | Case Studies |
---|---|---|
ADDITION algorithms | Adds together the ranks from the different VS methods rank lists. Standard statistical measures, weighted or not, are used (i.e., sum, average, and median or max. value) to combine rank positions. | [66,67,103,116] |
PARETO ranking | Ranks a compound based on how many other compounds are better in all screening methods. Ties could be broken using the sum rank, as example. | [103] |
PARALLEL selection | Compounds are alternatively selected among the top-ranked compounds obtained from each screening method until the desired number of compounds is reached. | [81,103] |
Model | Methods | Description |
---|---|---|
Interaction fingerprint-based | SIFt [132] | Fingerprint encoding seven predefined types of target–ligand interactions. |
PLIP [133] | A web service for the detection and visualization of seven protein–ligand interaction types considering a 3D space. | |
FLIP [134] | For each residue, 7 different interactions are represented in 10 bits. | |
PADIF [135] | Fingerprints with the inclusion of information relative to the strength of interactions and unfavorable ones. | |
Pharmacophore-based | LigandScout [125] | Pharmacophores derived from six types of nonbonded protein-ligand interactions and volume constraints. |
FLAP [126] | Four-point pharmacophore fingerprints with a shape component. | |
IChem [136] | Converts the protein–ligand interaction pattern in fingerprints and graphs. | |
TIFP [137] | Encodes a string of unique triplets (two interacting atoms and an interaction pseudo-atom). |
Database | Type | No. Cpds |
---|---|---|
AstraZeneca with Enamine BBs | Proprietary | 1017 |
Boehr.-Ing. BICLAIM | Proprietary | 5 × 1011 |
CH/PMUNK | Public | >95 × 106 |
eMolecules Plus | Commercial | 5.9 × 108 |
Enamine Real | Commercial | >300 × 106 |
EVOspace | Proprietary | 1.6 × 1016 |
GDB-17 | Public | ~166 × 109 |
Lilly LPC | Proprietary | 2 × 1011 |
MASSIV | Proprietary | 1020 |
SAVI | Public | ~283 × 106 |
PGVL | Proprietary | 3 × 1012 |
PubChem | Public | 9.6 × 106 |
SCUBIDOO | Public | ~21 × 106 |
Sigma Aldrich | Commercial | 1.4 × 107 |
ZINC15 | Commercial | 2 × 106 |
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Vázquez, J.; López, M.; Gibert, E.; Herrero, E.; Luque, F.J. Merging Ligand-Based and Structure-Based Methods in Drug Discovery: An Overview of Combined Virtual Screening Approaches. Molecules 2020, 25, 4723. https://doi.org/10.3390/molecules25204723
Vázquez J, López M, Gibert E, Herrero E, Luque FJ. Merging Ligand-Based and Structure-Based Methods in Drug Discovery: An Overview of Combined Virtual Screening Approaches. Molecules. 2020; 25(20):4723. https://doi.org/10.3390/molecules25204723
Chicago/Turabian StyleVázquez, Javier, Manel López, Enric Gibert, Enric Herrero, and F. Javier Luque. 2020. "Merging Ligand-Based and Structure-Based Methods in Drug Discovery: An Overview of Combined Virtual Screening Approaches" Molecules 25, no. 20: 4723. https://doi.org/10.3390/molecules25204723