Structure-Based Virtual Screening（SBVS）

Structure-based virtual screening (SBVS), also known as target-based virtual screening, is a widely popular method for finding novel and potent compounds that can interact with a target. These methods involve explicit molecular docking of each ligand to the target's affinity site. In addition, it generates a predicted binding mode for each database compound. In addition, it measures the quality of the fit of the compound at the target binding site. This information is then used to pick ligands from those that do not adhere strongly to the target protein. With the gradual deepening of ocular proteomics research, especially as more and more target proteins 3D structures related to the pathogenesis of ocular diseases are determined and become available. Compared to ligand-based techniques, structure-based approaches are gaining in importance, and the results tend to be more reliable and accurate. This lays the foundation for the screening of protein targets based on ocular diseases. This method has become an valuable tool to assist rapid and cost-effective ophthalmic drug discovery and lead optimization.

Fig.1. Structure-Based Virtual Screening work-flow. (Lionta E, et al., 2014)

Service Overview

Once a drug target has been identified for your research field of ocular disease, a question that urgently needs to be answered is: How do small molecule compounds bind to and change their biological activity? Based on computer technology and computational chemistry software, Ace Therapeutics provides a complete set of perfect structure-based virtual screening solutions for the development of ophthalmic small molecule compounds for global customers, including ocular disease small molecule database preparation, receptor structure preparation, and iterative screening by various means. Then to ADMET property evaluation, compound diversity analysis, and finally manual selection of potential active compounds for the next step of biological activity testing.

Main Technology Overview

• Target Identification for Different Ocular Diseases

Target selection is the first stage of structure-based virtual screening activities and is critical to a successful drug development process. Ace Therapeutics' talented scientists will modify the multiple preferred targets (proteins, polysaccharides, lipids, and nucleic acids) identified during the target identification and validation phase to obtain a single most plausible target based on your eye disease area of interest for follow-up studies. The structure of this target was obtained by our scientists using mainstream structural biology techniques such as X-ray crystallography, cryo-electron microscopy (cryo-EM), nuclear magnetic resonance spectroscopy, and molecular modeling.

• Ocular Disease Fragment Compound and Small Molecule Compound Library Preparation

In addition to the mainstream small molecule compound databases ZINC, Specs, Enamine, ChEMBL, BindingDB, etc., Ace Therapeutics scientists design and synthesize compound libraries containing small molecule fragments of various drugs and small molecule compound libraries for eye diseases. An ideal small molecule compound for ocular diseases should have a certain affinity for the active site of the target, such as a target protein or a target enzyme.

• Molecular Docking

Once the target protein and eye disease compound database is selected, a variety of methods can be applied to virtual screening. Ace Therapeutics provides multiple strategies such as pharmacophore, molecular docking, and QSAR to iteratively screen the compound library. Molecular docking is used to estimate the binding affinity of the protein-ligand complex by predicting the optimal interaction between the ligand and the target protein to form a complex, and using scoring functions, including but not limited to molecular docking and affinity scoring.

• Post-Processing Stage

Ace Therapeutics scientists conduct druggability analysis and toxicity assessment of the compounds that have completed the preliminary screening, and early screen out compounds that may lead to R&D failure. On this basis, further modify and optimize the final potential active compounds with balanced properties to obtain clinical research drug candidates.

Advantages of Ocular Diseases Small Molecule Compounds Structure-Based Virtual Screening

• Rich experience in structural analysis of protein targets for eye diseases and protein-ligand molecular docking.
• State-of-the-art computing equipment and advanced software programs/tools are available at every stage of the SBVS program.
• Broad, diverse, proprietary and targeted virtual compound library for ocular diseases.
• Flexible handling of molecular docking, molecular dynamics simulations, free energy calculations, affinity predictions, and so on.

Ace Therapeutics provides efficient ocular diseases small molecule compounds structure-based screening services with fast and accurate molecular docking and scoring procedures. In addition, Ace Therapeutics also provides fragment-based de novo ligand design and receptor-directed pharmacophore screening services for ophthalmic small molecule drug development. If you are interested in our services or need more detailed information, please feel free to contact us. Our experienced scientists are ready to help you!

References

1. Lionta E, Spyrou G, Vassilatis DK, et al. Structure-based virtual screening for drug discovery: principles, applications and recent advances. Current Topics in Medicinal Chemistry. 2014;14(16):1923-1938.
2. Aghamollaei H, Parvin S, Shahriary A. Review of proteomics approach to eye diseases affecting the anterior segment. J Proteomics. 2020 Aug 15;225:103881.

• Virtual Screening Services for Small Molecule Ophthalmic Drug Development
• Fragment-Based Virtual Screening Services for Small Molecule Ophthalmic Drug Development
• Phenotype-Based Virtual Screening Services for Small Molecule Ophthalmic Drug Development
• Structure-Based Screening Services for Small Molecule Ophthalmic Drug Development
• High Throughput Screening Services for Small Molecule Ophthalmic Drug Development
• Computer-Aided Screening Services for Small Molecule Ophthalmic Drug Development
• Ocular Diseases Small Molecules Compound Library

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