Alanine-based Temporin L Peptide Analogs to Inhibit Viral Replication in SARS-CoV-2
Disciplines
Biochemistry | Medicinal-Pharmaceutical Chemistry
Abstract (300 words maximum)
Throughout the past several years, Covid-19 has taken a heavy toll on people’s health. Although small molecule drugs and vaccines have made an impact to improve patients’ immunity and have served preventative measures, relatively new peptide therapeutics is gaining popularity. Small molecule drugs often lack having specific target functions, cause unwanted complications, and drug resistance. However, peptide therapeutics are gaining in popularity due to their impeccable specificity, high potency, and fast approval process. The goal of this research project is to develop effect and potent analogs of Temporin L (TL) peptide to block the catalytic sites including Cys145 and His41 of the main protease of SARS-CoV-2. Utilizing computer aided design, 12 analogs were modelled incorporating alanine sequentially in the 12 positions of TL peptide. All analogs underwent molecular docking using HDOCK program to evaluate the binding energies against the main protease. The best three analogs (analog 3, 4, and 9) were evaluated by molecular dynamic modeling using YASARA software. The results were analyzed that reveal the radius of gyration, RMSD, solvent accessible surface area, and RMSF for each of the three analogs to compare their effectiveness. The best analog 3 was synthesized using the solid phase synthesis protocol using a rink-amide resin. Once the peptide synthesis is completed, the resin was removed by adding a high percentage of trifluoracetic acid (TFA). Subsequently, peptide solution was filtered and TFA was removed by blowing nitrogen and precipitated by adding iced-cold diether ether. Through a freeze-drying process, the peptide powder was created. Mass spectrometry was employed to confirm the mass of the synthesized peptides which showed two intense peaks at m/z 542.67 and 813.50 corresponding to [M+3H]3+ and [M+2H]2+, charge states, respectively. The inhibiting efficiency of this analog will be tested using FRET and LCMS based protease assays.
Academic department under which the project should be listed
CSM - Chemistry and Biochemistry
Primary Investigator (PI) Name
Mohammad Halim
Alanine-based Temporin L Peptide Analogs to Inhibit Viral Replication in SARS-CoV-2
Throughout the past several years, Covid-19 has taken a heavy toll on people’s health. Although small molecule drugs and vaccines have made an impact to improve patients’ immunity and have served preventative measures, relatively new peptide therapeutics is gaining popularity. Small molecule drugs often lack having specific target functions, cause unwanted complications, and drug resistance. However, peptide therapeutics are gaining in popularity due to their impeccable specificity, high potency, and fast approval process. The goal of this research project is to develop effect and potent analogs of Temporin L (TL) peptide to block the catalytic sites including Cys145 and His41 of the main protease of SARS-CoV-2. Utilizing computer aided design, 12 analogs were modelled incorporating alanine sequentially in the 12 positions of TL peptide. All analogs underwent molecular docking using HDOCK program to evaluate the binding energies against the main protease. The best three analogs (analog 3, 4, and 9) were evaluated by molecular dynamic modeling using YASARA software. The results were analyzed that reveal the radius of gyration, RMSD, solvent accessible surface area, and RMSF for each of the three analogs to compare their effectiveness. The best analog 3 was synthesized using the solid phase synthesis protocol using a rink-amide resin. Once the peptide synthesis is completed, the resin was removed by adding a high percentage of trifluoracetic acid (TFA). Subsequently, peptide solution was filtered and TFA was removed by blowing nitrogen and precipitated by adding iced-cold diether ether. Through a freeze-drying process, the peptide powder was created. Mass spectrometry was employed to confirm the mass of the synthesized peptides which showed two intense peaks at m/z 542.67 and 813.50 corresponding to [M+3H]3+ and [M+2H]2+, charge states, respectively. The inhibiting efficiency of this analog will be tested using FRET and LCMS based protease assays.