tetano
Editor, Senior Moderator
PLoS One
. 2023 Oct 24;18(10):e0293263.
doi: 10.1371/journal.pone.0293263. eCollection 2023. Computational design of novel nanobodies targeting the receptor binding domain of variants of concern of SARS-CoV-2
Phoomintara Longsompurana[SUP] 1 [/SUP], Thanyada Rungrotmongkol[SUP] 2 3 [/SUP], Nongluk Plongthongkum[SUP] 1 [/SUP], Kittikhun Wangkanont[SUP] 4 5 [/SUP], Peter Wolschann[SUP] 6 [/SUP], Rungtiva P Poo-Arporn[SUP] 1 [/SUP]
Affiliations
The COVID-19 pandemic has created an urgent need for effective therapeutic and diagnostic strategies to manage the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the emergence of numerous variants of concern (VOCs) has made it challenging to develop targeted therapies that are broadly specific in neutralizing the virus. In this study, we aimed to develop neutralizing nanobodies (Nbs) using computational techniques that can effectively neutralize the receptor-binding domain (RBD) of SARS-CoV-2 VOCs. We evaluated the performance of different protein-protein docking programs and identified HDOCK as the most suitable program for Nb/RBD docking with high accuracy. Using this approach, we designed 14 novel Nbs with high binding affinity to the VOC RBDs. The Nbs were engineered with mutated amino acids that interacted with key amino acids of the RBDs, resulting in higher binding affinity than human angiotensin-converting enzyme 2 (ACE2) and other viral RBDs or haemagglutinins (HAs). The successful development of these Nbs demonstrates the potential of molecular modeling as a low-cost and time-efficient method for engineering effective Nbs against SARS-CoV-2. The engineered Nbs have the potential to be employed in RBD-neutralizing assays, facilitating the identification of novel treatment, prevention, and diagnostic strategies against SARS-CoV-2.
. 2023 Oct 24;18(10):e0293263.
doi: 10.1371/journal.pone.0293263. eCollection 2023. Computational design of novel nanobodies targeting the receptor binding domain of variants of concern of SARS-CoV-2
Phoomintara Longsompurana[SUP] 1 [/SUP], Thanyada Rungrotmongkol[SUP] 2 3 [/SUP], Nongluk Plongthongkum[SUP] 1 [/SUP], Kittikhun Wangkanont[SUP] 4 5 [/SUP], Peter Wolschann[SUP] 6 [/SUP], Rungtiva P Poo-Arporn[SUP] 1 [/SUP]
Affiliations
- PMID: 37874836
- DOI: 10.1371/journal.pone.0293263
The COVID-19 pandemic has created an urgent need for effective therapeutic and diagnostic strategies to manage the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the emergence of numerous variants of concern (VOCs) has made it challenging to develop targeted therapies that are broadly specific in neutralizing the virus. In this study, we aimed to develop neutralizing nanobodies (Nbs) using computational techniques that can effectively neutralize the receptor-binding domain (RBD) of SARS-CoV-2 VOCs. We evaluated the performance of different protein-protein docking programs and identified HDOCK as the most suitable program for Nb/RBD docking with high accuracy. Using this approach, we designed 14 novel Nbs with high binding affinity to the VOC RBDs. The Nbs were engineered with mutated amino acids that interacted with key amino acids of the RBDs, resulting in higher binding affinity than human angiotensin-converting enzyme 2 (ACE2) and other viral RBDs or haemagglutinins (HAs). The successful development of these Nbs demonstrates the potential of molecular modeling as a low-cost and time-efficient method for engineering effective Nbs against SARS-CoV-2. The engineered Nbs have the potential to be employed in RBD-neutralizing assays, facilitating the identification of novel treatment, prevention, and diagnostic strategies against SARS-CoV-2.