[Paper Review] Targeting Receptor Binding Domain and Cryptic Pocket of Spike glycoprotein from SARS-CoV-2 by biomolecular modeling

Kewin Otazu, Manuel Enrique Chenet Zuta+9 more|arXiv (Cornell University)|Jun 11, 2020

Computational Drug Discovery Methods4 citations

TL;DR

This study identifies two promising drug candidates—TCMDC-124223 and TCMDC-133766—through biomolecular modeling that target the Receptor Binding Domain (RBD) and a cryptic pocket in the N-Terminal Domain (NTD) of the SARS-CoV-2 Spike protein, respectively. The compounds show superior binding affinity compared to control drugs (hesperidin and emodin), suggesting potential for synergistic inhibition of viral entry by blocking ACE2 interaction and conformational changes necessary for membrane fusion.

ABSTRACT

SARS-CoV-2, the causative agent of the disease known as Covid-19, has so far reported around 3,435,000 cases of human infections, including more than 239,000 deaths in 187 countries, with no effective treatment currently available. For this reason, it is necessary to explore new approaches for the development of a drug capable of inhibiting the entry of the virus into the host cell. Therefore, this work includes the exploration of potential inhibitory compounds for the Spike protein of SARS-CoV-2 (PDB ID: 6VSB), which were obtained from The Patogen Box. Later, they were filtered through virtual screening and molecular docking techniques, thus obtaining a top of 1000 compounds, which were used against a binding site located in the Receptor Binding Domain (RBD) and a cryptic site located in the N-Terminal Domain (NTD), resulting in good pharmaceutical targets for the blocking the infection. From the top 1000, the best compound (TCMDC-124223) was selected for the binding site. It interacts with specific residues that intervene in the recognition and subsequent entry into the host cell, resulting in a more favorable binding free energy in comparison to the control compounds (Hesperidine and Emodine). In the same way, the compound TCMDC-133766 was selected for the cryptic site. These identified compounds are potential inhibitors that can be used for the development of new drugs that allow effective treatment for the disease.

Motivation & Objective

• To identify small molecules capable of inhibiting SARS-CoV-2 entry by targeting the Receptor Binding Domain (RBD) of the Spike glycoprotein.
• To explore a cryptic allosteric site in the N-Terminal Domain (NTD) of the Spike protein as a novel drug target.
• To evaluate the binding affinity and interaction mechanisms of identified compounds with key residues involved in ACE2 recognition.
• To compare the inhibitory potential of identified compounds with FDA-approved controls (hesperidin and emodin) using molecular docking.
• To provide a pharmacophore-informed basis for rational drug design targeting SARS-CoV-2 Spike protein.

Proposed method

• Virtual screening of 1,000 compounds from The Patris Box against the RBD and cryptic NTD sites of the SARS-CoV-2 Spike protein (PDB: 6VSB).
• Molecular docking simulations using AutoDock Vina to predict binding affinities and interaction modes with key residues in the RBD and cryptic site.
• Analysis of hydrogen bonding, hydrophobic, and polar interactions between ligands and critical residues (e.g., N487, Y489, K417, Y83 on ACE2) in the RBD-ACE2 interface.
• Evaluation of binding free energy (ΔG) for top compounds and comparison with control compounds (hesperidin and emodin).
• Identification of common functional groups (e.g., secondary amine, hydroxyl, carboxamine) in top hits for pharmacophore modeling and lead optimization.
• Use of established structural data from SARS-CoV-2 Spike-ACE2 complex (PDB: 6VSB) to guide target site selection and validation.

Experimental results

Research questions

• RQ1 Which small molecules from The Patris Box exhibit strong binding affinity to the Receptor Binding Domain (RBD) of the SARS-CoV-2 Spike protein?
• RQ2 Can a cryptic allosteric site in the N-Terminal Domain (NTD) of the Spike protein serve as a viable target for antiviral drug development?
• RQ3 How do the binding interactions of top compounds compare to those of control drugs (hesperidin and emodin) in terms of binding energy and residue-specific contacts?
• RQ4 What functional groups in the top compounds contribute to favorable binding and may inform future pharmacophore modeling?
• RQ5 Can dual targeting of the RBD and the cryptic NTD site lead to synergistic inhibition of viral entry?

Key findings

• TCMDC-124223 exhibited the strongest binding affinity to the RBD with a binding free energy of -10.25 kcal/mol, outperforming control compounds (hesperidin: -5.62 kcal/mol, emodin: -2.46 kcal/mol).
• TCMDC-124223 formed hydrogen bonds with key RBD residues N487 and Y489, and hydrophobic interactions with K417, which are critical for ACE2 recognition.
• TCMDC-133766 showed the highest affinity for the cryptic NTD site with a binding free energy of -10.66 kcal/mol, indicating strong potential for allosteric inhibition.
• Eight compounds formed hydrophobic interactions with Y489, and six formed hydrogen bonds with N487, suggesting interference with the ACE2-RBD interface.
• The top compounds share functional groups such as secondary amines, hydroxyls, and carboxamines, which are suitable for pharmacophore modeling and lead optimization.
• The study identifies a potential synergistic therapeutic strategy by co-targeting the RBD and the cryptic NTD site to block viral entry more effectively.