Abstract
Coronavirus Disease 2019 (COVID−19) elicited by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS−CoV−2) is calling for novel targeted drugs. Since the viral entry into host cells depends on specific interactions between the receptor−binding domain (RBD) of the viral Spike protein and the membrane−bound monocarboxypeptidase angiotensin converting enzyme 2 (ACE2), the development of high affinity RBD binders to compete with human ACE2 represents a promising strategy for the design of therapeutics to prevent viral entry. Here, we report the discovery of such a binder and its improvement via a combination of computational and experimental approaches. The binder micasin, a known fungal defensin from the dermatophytic fungus Microsporum canis with antibacterial activity, can dock to the crevice formed by the receptor−binding motif (RBM) of RBD via an extensive shape complementarity interface (855.9 Å2 in area) with numerous hydrophobic and hydrogen−bonding interactions. Using microscale thermophoresis (MST) technique, we confirmed that micasin and its C−terminal γ−core derivative with multiple predicted interacting residues exhibited a low micromolar affinity to RBD. Expanding the interface area of micasin through a single point mutation to 970.5 Å2 accompanying an enhanced hydrogen bond network significantly improved its binding affinity by six−fold. Our work highlights the naturally occurring fungal defensins as an emerging resource that may be suitable for the development into antiviral agents for COVID−19.
Highlights
Severe acute respiratory syndrome corona virus 2 (SARS−CoV−2) is the pathogen of Coronavirus Disease 2019 (COVID−19), a recently emerged worldwide pandemic that is causing a global health crisis
The results showed that this peptide could dock on the receptor−binding domain (RBD) receptor−binding motif to form a stable complex via extensive shape complementarity
Micasin is a typical cysteine−stabilized α−helical and β−sheet (CSαβ)−type defensin of 38 residues with a structure that includes two distinct subdomains, namely, the N−terminal helix−associated region (HAR) comprising the α−helix and the N−terminal loop and the C−terminal γ−core region essentially comprising two antiparallel β−strands connected by a loop
Summary
Severe acute respiratory syndrome corona virus 2 (SARS−CoV−2) is the pathogen of Coronavirus Disease 2019 (COVID−19), a recently emerged worldwide pandemic that is causing a global health crisis. In addition to the Mpro , SARS−CoV−2 Spike protein is becoming an even more attractive target for exploiting targeted drugs. This trimeric protein protrudes from the double−layered lipid envelope of the SARS−CoV−2 virion and is responsible for viral entry into the host cell through the receptor−binding domain (RBD) to recognize and bind the membrane−bound monocarboxypeptidase angiotensin converting enzyme 2 (ACE2) [4]. Targeting the protein−protein interactions (PPIs) via competitively binding the RBD has been proved to be efficient in blocking the initial stage of virus entry.
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