Ligand Design for Nuclear Receptors

As an experienced expert in PROTAC technology, Creative Biolabs is committed to providing first-class ligand design services targeting various disease-related proteins.

Introduction to Nuclear Receptors

Nuclear receptors (NRs) are a class of ligand-dependent transcriptional regulatory proteins that belong to the nuclear receptor family or the steroid hormone receptor superfamily. They have homology in primary structure and gene structure. Nuclear receptors are composed of three types of receptors: a) steroid hormone receptors (SR), including glucocorticoid receptors (GR), mineralocorticoid receptors (MR), progesterone receptors (PR), androgen receptor (AR), estrogen receptors ( ER), and 1,25- (OH)2 vitamin D3 receptor; b) thyroxine receptor (TR); c) retinoic acid receptor (RAR).

As a transcriptional regulatory protein, a nuclear receptor, after binding to a corresponding ligand, interacts with a specific DNA sequence in the target gene to regulate the expression of a hormone-responsive element (HRE), resulting in a biological effect. Since nuclear receptors can regulate the expression of specific genes, when they are missing, reduced or structurally abnormal for various reasons, various diseases will be induced, namely nuclear receptor diseases. This type of disease is manifested in the resistance of target cells to the corresponding hormones.

Structure of Nuclear Receptors

The structure of the nuclear receptors is modular, including the N-terminal regulatory domain, DNA binding domain (DBD), hinge region, ligand binding domain (LBD), and C-terminal domain.

  • N-terminal regulatory domain contains ligand-independent activation function 1 (AF-1), which can strongly down-regulate gene expression in synergy with AF-2.
  • DBD is a highly conserved domain containing two zinc fingers, capable of binding to specific DNA sequences of hormone response elements (HRE).
  • LBD is highly conservative in structure. Its structure is an alpha-helical sandwich fold. Three anti-parallel alpha spirals form a "sandwich filling." One side is two alpha spirals and the other is three alpha spirals. The ligand-binding cavity is located inside the LBD, just below the three anti-parallel helices "sandwich fillings".
  • Along with DBD, LBD participates in the dimerization interface of the receptor, and in addition, it can bind coactivators and coinhibitors. Furthermore, the activation function 2 (AF-2) of LBD, which depends on the presence of a binding ligand, is controlled by the conformation of helix 12 (H12).
  • The function of the hinge region is to connect DBD with LBD, and influence intracellular transport and subcellular distribution through target peptide sequences.

Structure of nuclear receptors. Fig.1 Structure of nuclear receptors.

Ligand Design for Nuclear Receptors

In view of the role of NRs in physiological processes and since NRs naturally contain hydrophobic pockets that can bind small hydrophobic molecules (most effective drugs are small hydrophobic molecules), NRs are a very popular class of drug targets. Therefore, the determination of natural or synthetic ligands of NRs has attracted much attention from scientists.

Tree of life, nuclear receptors, and potential ligand precursors. Fig.2 Tree of life, nuclear receptors, and potential ligand precursors. (Frances, 2011)

Ligands bound to nuclear receptors are usually lipophilic substances, such as endogenous hormones, fatty acids, exogenous endocrine disruptors, antibiotics, and the like. Based on the structural characteristics of NRs and NRs ligands, a basic criterion when designing ligands for NRs is that compounds can bind to the ligand-binding pockets of NRs. In addition, it has been found empirically that some hydrophobic compounds can also bind to the surface of NRs. For drug development, reversible binding is often considered ideal. Based on the consideration of drugability, structural modification and modification of existing NR ligands is also an efficient strategy.

Services at Creative Biolabs

  • Ligand discovery and identification including small molecules, peptides, and antibodies
  • Modification and improvement of existing ligands
  • Studies on ligand drugability and pharmacokinetics
  • Custom production of ligands

Creative Biolabs has long-term devoted to the development of PROTAC. Our scientists are confident in offering the best and most suitable ligand design solution for our customers all over the world. If you are considering developing a novel PROTAC against the target of interest, please do not hesitate to contact us for more details.


  1. Frances, M. Sladek. What are Nuclear Receptor Ligands? Mol Cell Endocrinol. 2011, 334(1-2): 3-13.
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