5HTP-aptamer

Apr 20, 2024 • Yuhang Luo, Linfei Li

Description

In 2017, Robert T Batey et al. developed a novel approach: when secondary and tertiary structural scaffolds derived from biologically active riboswitches and small nuclease enzymes are applied to the neurotransmitter precursor 5-hydroxytryptophan, this approach yields easily recognizable and characterizable aptamers that can be coupled to readout structural domains, leading to the design of nucleic acid sensing devices that function in vitro and in cellular environments. And 2 Å of a 5-hydroxytryptophan aptamer was obtained by crystal diffraction^[1].

SELEX

Robert T Batey et al. used RNA libraries constructed on the basis of three different riboswitch and ribozyme backbones that include the xpt-pbuX guanine riboswitch from Bacillus subtilis, the Vc2 cyclic di-guanosine riboswitch from Vibrio cholerae, and the Schistosoma mansoni's hammerhead ribozyme. After seven rounds of screening, and through these screening rounds, RNA aptamers were identified that were able to specifically bind 5-hydroxytryptamine (5HTP.) By this method, and in particular by using the GR backbone, it was possible to screen for at least three major families of RNA aptamers, designated 5GR-I, 5GR-II, and 5GR-III, respectively.They determined the consensus secondary structures of six major clusters from the two selections against 5HTP^[1].
Detailed information are accessible on SELEX page.

Structure

2D representation

Here we use ribodraw to complete the figure, through the 3D structure information ^[1].

5'-GGACACUGAUGAUCGCGUGGAUAUGGCACGCAUUGAAUUGUUGGACACCGUAAAUGUCCUAACACGUGUCC-3'

3D visualisation

Robert T Batey obtained the structure of the 5-hydroxytryptamine (5HTP) aptamer by X-ray crystallography, which was obtained after screening based on the in vitro selection of three-dimensional structurally important points (SELEX) method. This structure shows details of 5HTP binding to the RNA aptamer, including the 3D structure of the RNA and details of the interaction with 5HTP. The resolution of this structure is 2.0 Å. In the structure, 5HTP is localized in the three-dimensional junction structure of RNA, with which it hydrogen bonds and stacking interactions mainly through nucleotides in the J2/3 region. In addition, the recognition of 5HTP interacts with a specific T-loop in the RNA structure, which is essential for the high affinity and specific binding of 5HTP.The PDB ID of this structure is 5KPY^[1].
Additional available structures that have been solved and detailed information are accessible on Structures page.

Binding pocket

Left: Surface representation of the binding pocket of the aptamer generated from PDB ID: 5KPY by X-ray crystallography. 5-Hydroxytryptophan (5-HTP) (shown in sticks) is labeled in yellow. Right: The hydrogen bonds of binding sites of the aptamer bound with 5HTP^[1].

Ligand information

SELEX ligand

Robert T Batey et al. use isothermal titration calorimetry (ITC) to determine the binding affinity and specificity between 5-HTP and 5GR-II RNA Aptamers. This method accurately measures the amount of heat absorbed or released during the binding process to derive dissociation constants. The specificity of this RNA was quantified by elution with 5-Hydroxytryptophan (5HTP),L-tryptophan, Serotonin (5-HT)and α-methyl 5-hydroxy-L-tryptophan(Me-5HTP)^[1].

Structure ligand

5-hydroxytryptophan is a tryptophan derivative that is tryptophan substituted by a hydroxy group at position 5. It has a role as a human metabolite and a neurotransmitter.-----from pubchem

PubChem CID	Molecular Formula	MW	CAS	Solubility	Drugbank ID
144	C11H12N2O3	220.22 g/mol	56-69-9	12.5 mg/mL	DB02959

Similar compound

We screened the compounds with great similarity to 5-Hydroxytryptophan (5HTP) by using the ZINC database and showed some of the compounds' structure diagrams. For some CAS numbers not available, we will supplement them with Pubchem CID.

Zinc_id	Named	CAS	Pubchem CID	Structure
ZINC000000083315	Tryptophan	73-22-3	6305
ZINC000000057156	5-Fluorotryptophan	154-08-5	9577
ZINC000003651522	Hyrtioerectine C	NA	11506813
ZINC000006045354	5-Amino-DL-tryptophan	6383-69-3	4018454
ZINC000000391257	5-Methyl-DL-tryptophan	951-55-3	92852
ZINC000000057131	5-Bromo-DL-tryptophan	6548-09-0	96735
ZINC000002572392	2-amino-3-(5-chloro-1H-indol-3-yl)propanoic acid	154-07-4	596210
ZINC000000057157	5-Fluoro-d-tryptophan	97749-24-1	688358

References

[1] Recurrent RNA motifs as scaffolds for genetically encodable small-molecule biosensors.
Porter EB, Polaski JT, Morck MM, Batey RT
Nature chemical biology. 2017 Mar;13(3):295-301. (2017)