Inhibition of SARS-CoV-2 Entry into Host Cells Using Small Molecules

Abstract

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), a virus belonging to the Coronavirus family, is now known to cause Coronavirus Disease (Covid-19) which was first recognized in December 2019. Covid-19 leads to respiratory illnesses ranging from mild infections to pneumonia and lung failure. Strikingly, within a few months of its first report, Covid-19 has spread worldwide at an exceptionally high speed and it has caused enormous human casualties. As yet, there is no specific treatment for Covid-19. Designing inhibitory drugs that can interfere with the viral entry process constitutes one of the main preventative therapies that could combat SARS-CoV-2 infection at an early stage. In this review, we provide a brief introduction of the main features of coronaviruses, discuss the entering mechanism of SARS-CoV-2 into human host cells and review small molecules that inhibit SARS-CoV-2 entry into host cells. Specifically, we focus on small molecules, identified by experimental validation and/or computational prediction, that target the SARS-CoV-2 spike protein, human angiotensin converting enzyme 2 (ACE2) receptor and the different host cell proteases that activate viral fusion. Given the persistent rise in Covid-19 cases to date, efforts should be directed towards validating the therapeutic effectiveness of these identified small molecule inhibitors.

Keywords: Covid-19; SARS-CoV-2; angiotensin converting enzyme 2; inhibitors; small molecule; spike protein.

Figure 1

Basic structure of SARS-CoV-2 including its genome RNA and the four main structural proteins. The schematic is not drawn to scale. Enlargement has been employed to better depict the structures.

Figure 2

Entry mechanism of Sars-CoV-2 into human host cells. SARS-CoV-2 enters host cell by attaching its surface-anchored spike protein to the cell surface receptor ACE2. Such attachment activates various host cell proteases and causes them to cleave the spike protein at a site near the S1/S2 boundary. Cleavage of the spike protein, in turn, facilitates viral fusion and subsequent insertion of the viral genome into the host cell. Sites of inhibition by small molecules, namely the site of receptor binding, the site of host protein cleavage and the site of membrane fusion, are marked at each stage of viral entry. The schematic is not drawn to scale. Enlargement has been employed to better depict the viral entry mechanism.

Figure 3

SARS-CoV-2 spike protein. (A) The 3D structure of the SARS-CoV-2 trimeric spike protein colored by its monomers. (B) Magnified visualization of the secondary structure of the SARS-CoV-2 spike RBD where Beta sheets are labelled and colored in magenta, alpha helices are colored in cyan and loops are colored in pink. The RBM which directly interacts with ACE2 is colored in gray and its beta sheets are labelled. This figure was generated using PyMOL (Version 2) from the PDB: 6VSB for (A) and PDB: 6M0J for (B).

Figure 4

SARS CoV-2 spike RBD−ACE2 binding interface. (A) The resolved 3D crystal structure of the SARS CoV-2 spike RBD in contact with human ACE2 receptor (PDB: 6LZG). The ACE2 is colored in cyan and its interacting amino acids are colored in magenta while the RBD is colored in green and its interacting amino acids are colored in red. (B) Zoom-in (or enlarged) view of the ACE2 showing the residues that are involved in hydrogen binding with the RBD. (C) Zoom-in view of the RBD showing the residues that are involved in hydrogen binding with ACE2. The labelled amino acids of ACE2 and RBD in (B,C) refer to all the interacting residues that are reported in the four resolved RBD−ACE2 structures (PDBs 6VW1, 6M0J, 6M17 and 6LZG); PDB 6LZG was used as a representative only. Refer to Table 1 for the detailed description of hydrogen bonds formed by the highlighted residues. This figure was generated using PyMOL (Version 2).

Figure 5

Pairwise amino acid sequence alignment of the receptor binding domain (RBD) of SARS-CoV-1 (Uniprot ID: P59594) and SARS-CoV-2 (Uniprot ID: P0DTC2) performed using Clustal Omega [44]. The asterisk * denotes positions with a single, fully conserved residue. The colon: denotes positions with conservation of groups of strongly similar properties. The period denotes conservation of groups of weakly similar properties. The region labelled in red denotes the receptor binding motif (RBM). RBD of SARS-CoV-1 and SARS-CoV-2 share a 73% identity while their RBMs share only a 50% identity. The amino acid substitutions in the RBM of SARS-CoV-2 result in a greater number of residues interacting with the host cell surface receptor.