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Chemical Libraries

Definition
Definition
Definition

A chemical library is a collection of stored chemicals that are used in high-throughput screening or industrial manufacturing. These libraries can consist of small molecules, natural products, peptides, or other types of compounds. The primary purpose of chemical libraries is to provide a diverse set of compounds that can be tested against biological targets to identify potential leads for drug development. Challenges include formatting and storage conditions. An alternative are virtual chemical libraries of enumerated compounds. Then, only the building blocks need to be stored.

Importance in Computational Drug Discovery:

  1. High-Throughput Screening: Chemical libraries are essential for high-throughput screening (HTS), where thousands of compounds are tested rapidly against a target to identify active compounds.
  2. Diversity: A diverse chemical library increases the chances of finding a hit, as it covers a wide range of chemical space.
  3. Lead Identification: Chemical libraries are used to identify lead compounds that can be further optimized into drug candidates.
  4. Virtual Screening: In computational drug discovery, chemical libraries can be screened virtually using molecular docking and other computational methods to prioritize compounds for biological testing.
  5. Structure-Activity Relationship (SAR) Studies: Libraries facilitate SAR studies by providing a range of structurally related compounds to understand the relationship between chemical structure and biological activity.
  6. Fragment-Based Drug Discovery: Fragment libraries, which consist of chemical fragments up to 17 heavy atoms, are used in fragment-based drug discovery to identify small binders that can be linked or grown into potent ligands.

Key Tools

  1. RDKit:
    • An open-source cheminformatics library that provides tools for managing and analyzing chemical libraries, including molecular fingerprints, substructure searching, and property prediction.
  2. Open Babel:
    • An open-source chemical toolbox designed to interconvert file formats and handle molecular data, useful for preparing and analyzing chemical libraries.
  3. Schrödinger Suite:
    • A comprehensive suite of tools for molecular modeling and drug discovery, including Glide for docking, Phase for pharmacophore modeling, and Maestro for visualization and analysis.
  4. DeepChem:
    • An open-source library that uses deep learning models for various cheminformatics tasks, including virtual screening and property prediction using chemical libraries.
  5. ChEMBL Database:
    • A database of bioactive molecules with drug-like properties, providing a rich source of chemical compounds for drug discovery research.
  6. DeepOrigin Tools:
    • Use Balto to search, filter, analyze, visualize, and virtually screen chemical libraries for desirable properties, drug-likeness, and target binding potential.

Literature

Chemical libraries in drug discovery

  • Publication Date: 1995-07-01
  • DOI: 10.1016/S0167-7799(00)88957-X
  • Summary: This early paper discusses the role of chemical libraries in drug discovery, emphasizing their importance in identifying potential drug candidates.

Design and Diversity Analysis of Chemical Libraries in Drug Discovery

  • Publication Date: 2023-07-05
  • DOI: 10.2174/1386207326666230705150110
  • Summary: Discusses the integration of computational tools and artificial intelligence in the design and diversity analysis of chemical libraries, highlighting their impact on drug discovery processes.

Future challenges with DNA-encoded chemical libraries in the drug discovery domain

  • Publication Date: 2019-05-21
  • DOI: 10.1080/17460441.2019.1614559
  • Summary: Reviews the use of DNA-encoded chemical libraries (DELs) in drug discovery, discussing technological components, challenges, and future directions.

Double-click enables synthesis of chemical libraries for drug discovery

  • Publication Date: 2019-10-01
  • DOI: 10.1038/d41586-019-02905-w
  • Summary: Highlights a streamlined synthesis method for chemical libraries using click chemistry, aimed at accelerating the development of new materials.

SICLOPPS cyclic peptide libraries in drug discovery

  • Publication Date: 2017-06-01
  • DOI: 10.1016/j.cbpa.2017.02.016
  • Summary: Details the use of SICLOPPS libraries for identifying cyclic peptide inhibitors, discussing their application in drug discovery.

Strategic Expansion and Management of Chemical Libraries for Drug Discovery

  • Publication Date: 2018-06-01
  • DOI: 10.1002/BKCS.11478
  • Summary: Discusses strategies for expanding and managing chemical libraries to enhance their utility in drug discovery.

MBC and ECBL libraries: outstanding tools for drug discovery

  • Publication Date: 2023-08-11
  • DOI: 10.3389/fphar.2023.1244317
  • Summary: Presents the updated versions of the MBC and ECBL libraries, highlighting their chemical diversity and potential for identifying new drug hits.

Fragment‐based drug discovery—the importance of high‐quality molecule libraries

  • Publication Date: 2022-06-24
  • DOI: 10.1002/1878-0261.13277
  • Summary: Reviews the design and optimization of fragment libraries, emphasizing their role in fragment-based drug discovery.

Methods for generating and screening libraries of genetically encoded cyclic peptides in drug discovery

  • Publication Date: 2020-01-17
  • DOI: 10.1038/s41570-019-0159-2
  • Summary: Details various platforms for generating and screening genetically encoded cyclic peptide libraries, discussing their advantages and applications in drug discovery.

Chemspace Atlas: Multiscale Chemography of Ultralarge Libraries for Drug Discovery

  • Publication Date: 2022-09-14
  • DOI: 10.1021/acs.jcim.2c00509
  • Summary: Introduces the ChemSpace Atlas, a tool for visualizing and analyzing large chemical libraries, supporting activity profiling and analogue search.