27 June 2023

Diversity Compound Libraries for early drug discovery

MCE provides 90,000+ bioactive molecules and 200+ compound libraries.

Drug discovery is a time and resource consuming process, which includes initial target identification and validation, biological assay development, hit identification and validation, hit to lead optimization, lead to candidate optimization, and preclinical trials to select a candidate molecule for clinical development [ref. 1]. In the step of hit identification, screening techniques, such as high throughput screening (HTS) and virtual screening (VS), are employed to identify hit molecules that are able to interact with the fully validated target or have high activity in cell-based assays (Figure 1) [ref. 1]. The screening attrition rate in the current drug discovery protocols suggests that one marketable drug emerges from approximately one million screened compounds. A high-quality diversity compound library is the key to a successful hit identification campaign, it helps to save time and reduce cost by maximizing the number of initial hits while reducing the amount of false positives [ref. 2].

Figure 1. Overview of drug discovery screening assays [ref. 1].

Because of the complex nature of biological targets, screening a library with high level of functional and structural diversities increases the chance of identifying hit compounds with the desired properties [ref. 3]. Recent advances in combinatorial chemistry and diversity-oriented synthesis (DOS) allow the construction of small-molecule libraries containing structurally diverse scaffolds, and various bioactive compounds against undruggable targets were identified from unbiased phenotypic screens using these libraries [ref. 4]. MedChemExpress offers a large collection of commercially available compound libraries with high structural and functional diversities. Our customers have used these libraries and discovered many hit compounds in their research. For example, Charbord., et al. [ref. 5] identified a SIK inhibitor through in vivo screen that induces β cell proliferation. Zhang., et al. [ref. 6] found SARS-CoV-2 main and papain-like protease inhibitors through high-throughput screening. To meet the increasing demands for diversity compound libraries, MedChemExpress recently launched two unique scaffold collections (Table 1) with high skeletal diversity, high functional group diversity, and broad chemical space coverage.

Product nameSizeDescription
50K Diversity Library50,000 compoundsRepresentative diversity set and an ideal starting library for phenotypic and target-based HTS.
5K Scaffold Library5,000 compoundsAn exceptionally diverse library. Each compound represents one unique scaffold.
Table 1. The diversity libraries in MedChem Express.

MCE provides 90,000+ bioactive molecules and 200+ compound libraries.


  1. Hughes JP, Rees S, Kalindjian SB, Philpott KL. Principles of early drug discovery. Br J Pharmacol. 2011;162(6):1239-1249.
  2. Carnero A. High throughput screening in drug discovery. Clin Transl Oncol. 2006;8(7):482-490.
  3. Galloway WRJD, Isidro-Llobet A, Spring DR. Diversity-oriented synthesis as a tool for the discovery of novel biologically active small molecules. Nat Commun. 2010;1:80.
  4. Kim T, Ha MW, Kim J. Recent advances in divergent synthetic strategies for indole-based natural product libraries. Molecules. 2022;27(7):2171.
  5. Charbord J, Ren L, Sharma RB, et al. In vivo screen identifies a SIK inhibitor that induces β cell proliferation through a transient UPR. Nat Metab. 2021;3(5):682-700.
  6. Zang Y, Su M, Wang Q, et al. High-throughput screening of SARS-CoV-2 main and papain-like protease inhibitors. Protein Cell. 2023;14(1):17-27.

Diversity Compound Libraries for early drug discovery

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