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Ligand Binding Sites

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

Ligand Binding and Linkage

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

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Related Experiment Video

Updated: Aug 23, 2025

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

Published on: May 29, 2021

Two Ligand-Binding Sites on SARS-CoV-2 Non-Structural Protein 1 Revealed by Fragment-Based X-ray Screening.

Shumeng Ma¹, Shymaa Damfo¹, Jiaqi Lou¹

¹School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK.

International Journal of Molecular Sciences

|October 27, 2022

Summary

Researchers identified potential antiviral drug targets by screening for compounds that bind to SARS-CoV-2 non-structural protein 1 (nsp1). This protein is crucial for viral replication and suppressing host immunity, making it a key target for new antiviral therapies.

Keywords:

COVID-19 SARS-CoV-2 cross-binding effects fragment-based X-ray screening ligands non-structural protein 1 structure-based drug design

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Last Updated: Aug 23, 2025

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

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Published on: May 29, 2021

Engineering Antiviral Agents via Surface Plasmon Resonance

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Published on: June 14, 2022

Nano-Differential Scanning Fluorimetry for Screening in Fragment-based Lead Discovery

Nano-Differential Scanning Fluorimetry for Screening in Fragment-based Lead Discovery

Published on: May 16, 2021

Area of Science:

Virology and Structural Biology
Drug Discovery and Development

Background:

Recurrent coronavirus (CoV) outbreaks, including the ongoing SARS-CoV-2 pandemic, necessitate novel antiviral strategies beyond vaccines.
Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) non-structural protein 1 (nsp1) is a critical virulence factor, essential for viral replication and immune evasion.

Purpose of the Study:

To identify and characterize fragment-based inhibitors targeting the SARS-CoV-2 nsp1 protein.
To provide a foundation for developing new antiviral drugs against SARS-CoV-2 by targeting nsp1.

Main Methods:

Fragment-based screening using X-ray crystallography to identify initial binding compounds against SARS-CoV-2 nsp1.
High-resolution (0.99 Å) structural determination of nsp1.
Orthogonal biophysical assays, including microscale thermophoresis and thermal shift assays, to assess binding affinities and compound stability.

Main Results:

Identification of multiple fragment hits binding to the N-terminal domain of SARS-CoV-2 nsp1.
Determination of two distinct ligand-binding pockets (deep and shallow) on nsp1.
These binding sites were found to be non-conserved across SARS, SARS-CoV-2, and MERS coronaviruses.

Conclusions:

The identified fragment hits represent promising starting points for developing potent nsp1-targeting antiviral inhibitors.
Structural insights into nsp1 binding sites facilitate further drug design and functional studies for novel coronavirus therapies.