Small Peptides Synthesis and Characterization to Target the 3-Chymotrypsin-like Protease of SARS-CoV-2
Disciplines
Biochemistry | Medicinal-Pharmaceutical Chemistry
Abstract (300 words maximum)
According to CDC estimates, the United States has had the largest COVID-19 burden, with more than five million infections and 160,000 fatalities. The main protease, also known as 3-Chymotrypsin-like Protease (3CLpro) determines the virus's lifespan. The crucial step in virus replication in human cells is to cleave the polyprotein of the virus into its functional proteins. 3-Chymotrypsin-like Protease has three domains. The catalytic site, which is in a cleft between domains I and II, contains the histidine/cysteine catalytic dyad. The overall aim of this work is to synthesize and characterize small peptides to target the 3CLpro. In this work, we have selected small peptides including HIP 1121 [LLEYSL], HIP 80 [IISYEL], and HIP 29 [YSYEL] which acted as protease inhibitors for other virus. Initially these peptides were modelled by Pepfold and docked against the 3CLpro to obtain their binding affinity and interactions. Molecular modelling results showed that these peptides interact with the catalytic sites of the protease. Based on our computational findings, these peptides were synthesized using CEM Liberty Blue Microwave Peptide Synthesizer. After the peptide synthesized, the peptide was then cleaved using a cocktail TFA, H2O, and TIPS. The cleavage peptide was separated under vacuum and precipitated adding cold ether. This peptide was characterized by LC-MS. HIP 29 peptide was eluted in 3.10 mins. Two peaks, corresponding to the [M+H]+ and [M+2H]2+ charge states, respectively, were seen at 337.75 and 674.42 Da. The dimer-related peak was also discovered at 1347.25 Da. It took 3.16 minutes to elute the HIP 80 peptide. Two peaks were noticed at 369.17 and 737.42. Which correlates to [M+H]+and [M+2H]2+ change states, respectively. Similar peaks are also observed for HIP1121. In future, these peptides will be used to perform biological assay to determine the inhibition efficiency in vitro.
Academic department under which the project should be listed
CSM - Chemistry and Biochemistry
Primary Investigator (PI) Name
Mohammad A. Halim
Small Peptides Synthesis and Characterization to Target the 3-Chymotrypsin-like Protease of SARS-CoV-2
According to CDC estimates, the United States has had the largest COVID-19 burden, with more than five million infections and 160,000 fatalities. The main protease, also known as 3-Chymotrypsin-like Protease (3CLpro) determines the virus's lifespan. The crucial step in virus replication in human cells is to cleave the polyprotein of the virus into its functional proteins. 3-Chymotrypsin-like Protease has three domains. The catalytic site, which is in a cleft between domains I and II, contains the histidine/cysteine catalytic dyad. The overall aim of this work is to synthesize and characterize small peptides to target the 3CLpro. In this work, we have selected small peptides including HIP 1121 [LLEYSL], HIP 80 [IISYEL], and HIP 29 [YSYEL] which acted as protease inhibitors for other virus. Initially these peptides were modelled by Pepfold and docked against the 3CLpro to obtain their binding affinity and interactions. Molecular modelling results showed that these peptides interact with the catalytic sites of the protease. Based on our computational findings, these peptides were synthesized using CEM Liberty Blue Microwave Peptide Synthesizer. After the peptide synthesized, the peptide was then cleaved using a cocktail TFA, H2O, and TIPS. The cleavage peptide was separated under vacuum and precipitated adding cold ether. This peptide was characterized by LC-MS. HIP 29 peptide was eluted in 3.10 mins. Two peaks, corresponding to the [M+H]+ and [M+2H]2+ charge states, respectively, were seen at 337.75 and 674.42 Da. The dimer-related peak was also discovered at 1347.25 Da. It took 3.16 minutes to elute the HIP 80 peptide. Two peaks were noticed at 369.17 and 737.42. Which correlates to [M+H]+and [M+2H]2+ change states, respectively. Similar peaks are also observed for HIP1121. In future, these peptides will be used to perform biological assay to determine the inhibition efficiency in vitro.