Fragment-based lead discovery is a new lead discovery approach in which much lower molecular weight (100-300Da) compounds are screened relative to HTS campaigns. The ALL Chemistry fragment library contains a large number of fragments with MW ≤ 300 and ClogP ≤ 3.0, readily available in stock for fragment-based drug discovery projects.
Introduction of Fragment Library
Fragment-based drug discovery (FBDD) has emerged in the past decade as an alternative approach to traditional lead identification via high-throughput screening (HTS). FBDD firstly screens the library of low molecular weight compounds (fragments) for the target protein of interest to identify "Hits". Then, through different strategies, the identified "Hits" were gradually optimized into drug-like molecules. Although FBDD can't replace High-Throughput Screening, HTS) in drug discovery, it still has some attractive advantages, such as saving experimental costs, providing diversified Hits, and showing various ways of drug development. The primary rationale for fragment-based screening is that the identified hits give access to a broader chemical space while screening a limited number of compounds. FBDD gives a better chance for the final lead compound to have standard drug-likeness parameters. Moreover, the likelihood of identifying a compound that is a perfect match for the intended target’s binding site is too slight to rely on because a multitude of interactions between the ligand and amino acid residues in the active site are often involved.
On the other hand, there are simpler molecules (fragments) with fewer unavoidable interactions and, thus, a much better possibility of orienting within the binding site favorably. Universal fragment library: Fragment-based screening and drug discovery (FBDD) has been proved to be an effective method to find new drugs. The emerging compounds are obtained by active screening of fragment compound library, and then the lead compounds are obtained by structural optimization. Characteristic fragment library: By combining and extending the screened active fragment molecules, new molecules can be obtained, and candidate drugs with higher activity can be obtained. In addition, the fragment compounds have the characteristics of small molecular weight, high solubility and so on, which makes it easier to optimize the structure and has better drug potential.
Fig.1 Fragment-Based Drug Design
(https://pubs.acs.org/doi/10.1021/acs.jmedchem.2c01004)
Classification of Fragment Library
Fragment Library can be classified into the following categories: Cysteine Targeted Covalent Fragment Library, F-Fragments Library, General Fragment Library, and 3D Diverse Fragment Library.
--Cysteine Targeted Covalent Fragment Library: Cysteine Targeted Covalent Fragment Library refers to a collection of small molecular fragments that are designed to selectively bind and react with cysteine residues in proteins. Cysteine is an amino acid with a thiol group, which can form covalent bonds with certain reactive fragments. At present, cysteine is the most common covalent amino acid residue in many covalent drugs, and various warheads that can react with cysteine are being developed, providing a key building block structure for the development of covalent drugs.
--F-Fragments Library: 19F-NMR has been proved to be a detection mode for studying protein structure and response in fragment-based drug discovery (FBDD). 19F is very similar in nuclear concentration detection, and its chemical principle and ligand-binding F(f)- fragment can be used for 19F-NMR detection after binding with target protein, which can be used as an effective 19F-NMR tool for drug discovery based on fragment. The F-Fragments Library provides a diverse set of fluorinated fragments that can be used in fragment-based drug discovery approaches. By screening this library, researchers can identify fragments that bind to specific target proteins, serving as starting points for further optimization and development of potential drug candidates.
--General Fragment Library: Fragment Library refers to a collection of small molecular fragments that are used in fragment-based drug discovery. Fragments are small, low molecular weight compounds that represent the minimal binding unit of a larger drug molecule. They typically have simple structures and low affinity for the target protein. By screening a Fragment Library, researchers can identify fragments that bind to the target protein, providing valuable starting points for the development of high-affinity drug candidates. FBDD is also the most attractive in academic circles. In particular, FBDD can deal with some novel and difficult-to-drug targets, which usually have no effective matching compounds in the existing library of highly selective screening compounds.
--3D Diverse Fragment Library: 3D Diverse Fragment Library is a collection of small molecular fragments that cover a broad range of chemical space in three-dimensional (3D) structure. This library is designed to provide a diverse set of fragments that can explore various protein binding sites and interact with different target proteins. As a powerful method to discover new drugs, fragment drug discovery (FBDD) has become the focus of pharmaceutical industry and academia.
Fragment Library Service at ALL Chemistry
Fragment-based drug discovery (FBDD) has become increasingly important in pre-clinical pharmaceutical research as an alternative approach towards the generation of hits and starting points, especially for previously intractable biological targets. ALL Chemistry has designed Fragment Libraries, including a selection of unique fragment subsets: Drug-Fragment Library, High Solubility Fragment Library, and Featured Fragment Library. All the fragment libraries are highly customizable on request. One can cherry-pick compounds, select quantities, format (dry/solid or DMSO solution), and compound concentration to meet any specific requirements.
We offer comprehensive support in developing your hit compounds. Naturally such programs are realised most efficiently when biological actives originate from our screening collection. However, even if the hit compounds are from the collections of other vendors lead identification and optimization projects can proceed most productively in our hands. Sometimes for this we only need to synthesize first examples of the given chemical series and validate synthesis route. A number of focused fragment libraries were designed to perfectly meet needs of our clients. We collaborate with the leading experts in FBDD field on design and supply of top fragment libraries.
Alternatively, you can send us your research target and we will customize the feasible screening library. Please contact us for more information.
Advantages of Our Services
-- Selection & design by Rule-of-Three criteria, and aimed at a broad portfolio of targets.
-- Chemically expandable and attractive to medicinal chemists
-- Guarantee integrity with small molecules covering a wide range of pharmacological targets and research areas.
-- Safety and Effective: all compounds are confirmed by literature, patent reports and clinical research.
-- Trust your results with selective, biologically active compounds that have proven pharmacological activity.
-- Stringent Quality Control: LC/MS and NMR reports, and ensure reproducibility with quality-controlled compounds.
-- Majority of compounds are singletons, and low overlap with commercial fragment libraries.
Project Workflow
Evaluation → Experiment Design → Formal Quotation → Custom Fragment Library Service → Results → Delivery
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