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Updated: Jul 15, 2026

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Current CMC challenges in oligonucleotide API development: from IND to NDA.

Daoqian Chen1, Xiaobing Zhang2, Songgen Xu3

  • 1Chemical Pharmaceutical Research Center, Changchun GeneScience Pharmaceutical Co., Ltd, Shanghai, 200120, P.R. China. chendaoqian0203@gmail.com.

Medicinal Chemistry Research : an International Journal for Rapid Communications on Design and Mechanisms of Action of Biologically Active Agents
|July 14, 2026
PubMed
Summary

Oligonucleotide therapeutics face unique Chemistry, Manufacturing, and Controls (CMC) challenges distinct from small molecules. This perspective details API CMC development hurdles from Investigational New Drug (IND) to New Drug Application (NDA).

Keywords:
APICMCINDManufacturingNDAOligonucleotideRegulation

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Area of Science:

  • Pharmaceutical Sciences
  • Drug Development
  • Regulatory Science

Background:

  • Oligonucleotide therapeutics represent a significant advancement in pharmaceutical innovation, expanding beyond rare diseases to oncology and chronic conditions.
  • Over 26 oligonucleotide drugs are approved, with hundreds more in clinical trials, highlighting their growing importance.
  • Despite their success, oligonucleotide therapeutics present unique Chemistry, Manufacturing, and Controls (CMC) challenges distinct from traditional small molecules.

Purpose of the Study:

  • To provide a comprehensive overview of the technical and regulatory hurdles in Active Pharmaceutical Ingredient (API) CMC development for oligonucleotide therapeutics.
  • To emphasize stage-appropriate CMC requirements throughout the drug development lifecycle, from Investigational New Drug (IND) to New Drug Application (NDA).
  • To address the challenges posed by the lack of harmonized International Council for Harmonisation (ICH) guidelines for oligonucleotides.

Main Methods:

  • Discussion of synthesis strategies, including conjugation with delivery systems.
  • Analysis of critical quality attributes and analytical method development for oligonucleotide APIs.
  • Exploration of regulatory pathways and considerations for oligonucleotide drug development.

Main Results:

  • Oligonucleotide CMC development requires specialized approaches for synthesis, purification, and characterization.
  • Navigating regulatory requirements involves addressing a 'grey area' between New Molecular Entities (NMEs) and biologics.
  • Stage-appropriate CMC strategies are crucial for successful progression from early-stage development to market approval.

Conclusions:

  • Addressing the unique CMC challenges of oligonucleotide therapeutics is essential for efficient drug development.
  • Clearer regulatory guidance and harmonized standards would benefit the field.
  • Successful navigation of technical and regulatory hurdles is key to realizing the full potential of oligonucleotide-based medicines.