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Special Issue "DNA-Encoded Chemical Libraries"

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Chemical Biology".

Deadline for manuscript submissions: 31 March 2019

Special Issue Editors

Guest Editor
Dr. Raphael Franzini

Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, USA
Website | E-Mail
Interests: DNA-encoded libraries; medicinal chemistry; chemical probes; bioorthogonal chemistry; oligonucleotides
Guest Editor
Dr. Christopher Arico-Muendel

GSK Discovery @ Cambridge, 200 Cambridge Park Drive, Cambridge, MA 02140, USA
Website | E-Mail
Interests: drug discovery; DNA-encoded library technologies; bioorganic chemistry; medicinal chemistry; aptamers

Special Issue Information

Dear Colleagues,

Libraries of compounds encoded by DNA-sequence tags are rapidly gaining interest as advanced tools for the discovery of small-molecule hit compounds. Encoding pools of combinatorial compounds with DNA barcodes makes it possible to generate libraries of unprecedented size, which can be rapidly interrogated for protein binders using a simple affinity-selection protocol that requires only a fraction of the resources associated with conventional hit discovery methods. Due to the unique benefits of encoded libraries, they are being routinely used in pharmaceutical discovery efforts and are also being explored as disruptive technologies in other areas of chemistry and chemical biology. The objective of this Special Issue is to provide an overview of the ongoing efforts aimed at advancing encoded library technology. Areas of special interest include but are not limited to the development of reactions on DNA, encoding procedures, screening protocols including microfluidic technologies, and algorithms for the analysis of sequencing data. Reports of new libraries and the discovery of new molecules from screening such libraries are another focus of this Special Issue, as are novel applications, especially if the outcomes advance our quantitative understanding of affinity selection. Contributions relating to all types of encoded libraries are welcome, including libraries on beads, peptide libraries, libraries with unnatural backbones, and libraries designed for purposes other than drug discovery.

Dr. Raphael Franzini
Dr. Christopher Arico-Muendel
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.


  • DNA-encoded libraries
  • diversity screening
  • affinity selection
  • ELT
  • chemical biology
  • chemical probes
  • microfluidics

Published Papers

This special issue is now open for submission, see below for planned papers.

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Type: Review
Title: The affinity selection of DNA encoded libraries
Author: Xiaojie Lu, Hui Sun and Kuai Letian
Affiliation: Chinese Academy of Science
Abstract: The rapidly evolving field of DNA-encoded library (DEL) technology has brought about revolutionary changes in the entire process of drug research and development. Successive reports have been published on different kinds of affinity selection strategies matched with targets of corresponding forms. Based on this, hit profiles of several proteins have been disclosed. This review addresses the applications of DEL with an emphasis on its use in the various forms of candidate targets in human disease therapy. The chemical scaffold diversity of the molecular structures of small molecules extended to the macroscale are an extension of the application of DEL in new areas, such as PPI. Phenotypic screening, which combines DEL with CRISPR, would be one such application of this thriving technology.

Title: Encoded library technologies to identify small- and medium-sized starting points for lead generation
Authors: Christoph Dumelin; Johannes Ottl; Jonas Schaefer; Lukas Leder
Affiliation: Novartis Pharma AG, Basel, Switzerland
Email: christoph.dumelin@novartis.com
Abstract: The scope of targets investigated in pharmaceutical research is increasingly moving into uncharted territory. Encoded library technologies enable the rapid exploration of large chemical space for the identification of ligands for such targets. These ligands enable drug discovery projects both by the generation of tools for target validation, structural elucidation and assay development as well as by identifying starting points for medicinal chemistry. In the review, we will discuss how DNA-encoded small molecules libraries (DEL) as well as encoded peptide libraries can facilitate the drug discovery process.

Title: Finding Aptamers: Recent Development of Affinity-Based Selection from DNA Libraries for Binding Molecular Targets
Authors: Yan Li and Jae-Seung Lee
Affiliation: Department of Materials Science and Engineering, Korea University, Seoungbuk‐gu, Seoul, Korea
Email: jslee79@korea.ac.kr
Abstract: The functionality of DNA as a biological recognition element has been an important asset to chemists and materials scientists to date. Despite the history of DNA research in biology over a century, however, encoding DNA sequences for the chemical recognition of small molecules and metal ions has begun only in early 90s. DNA aptamers are single-stranded DNA sequences that are engineered to bind to a specific molecular target. The selection of an aptamer for a specific molecular target typically involves the preparation of a large library of random DNA sequences and the amplification after repeated screening.  Researchers further improved the affinity-based selection of aptamers by taking advantage of chemical modification of nucleobases and DNA backbones for enhanced biological stability and increased binding affinity. In this Review, we would like to introduce the recent development of affinity-based aptamer selection methods from large DNA libraries and to evaluate their advantages and disadvantages from critical viewpoints. The fundamentals of nucleic acid chemistry, as well as the diagnostic and therapeutic applications of the developed aptamers will be also briefly discussed in a separate subsection.

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