Rational Design of Hyper-glycosylated Human Chorionic Gonadotropin Analogs (A Bioinformatics Approach)

Abstract

Background: Protein pharmaceuticals routinely display a series of intrinsic physicochemical instability problems during their production and administration that can unfavorably affect their therapeutic effectiveness. Glycoengineering is one of the most desirable techniques to improve the attributes of therapeutic proteins. One aspect of glycoengineering is the rational manipulation of the peptide backbone to introduce new N-glycosylation consensus sequences (Asn-X-Ser/Thr, where X is any amino acid except proline). Methods: In this work, the amino acid sequence of human chorionic gonadotropin (hCG) was analyzed to identify the suitable positions in order to create new N-glycosylation sites. This survey led to the detection of 46 potential N-glycosylation sites. The N-glycosylation probability of the all potential positions was measured with the NetNGlyc 1.0 server. After theoretical reviews and the removal of unsuitable positions, the five acceptable ones were selected for more analyses. Then, three-dimensional (3D) structures of the selected analogs were generated and evaluated by SPDBV software. The molecular stability and flexibility profile of five designed analogs were examined using molecular dynamics (MD) simulations. Results: Finally, three analogs with one additional N-glycosylation site (V68T, V79N and R67N) were proposed as the qualified analogs that could be glycosylated at the new sites. Conclusion: According to the results of this study, further experimental investigations could be guided on the three analogs. Therefore, our computational strategy can be a valuable method due to the reduction in the number of the expensive, tiresome and time-consuming experimental studies of hCG analogs.

In silico designing of a novel epitope-based candidate vaccine against Streptococcus pneumoniae with introduction of a new domain of PepO as adjuvant

“…The MD simulation analysis was performed for 50 ns to compute the docked complex's stability using the GROMACS program [ 75 ] with GROMOS96 54A7 force field [ 76 ]. The MD run was performed in about two days for each selected complex, using the described conditions in our prior works [ 77 , 78 ]. Briefly, the target complexes were placed within a proper cubic box, solvated applying the TIP3P water type, and neutralized by adding sufficient Na + /Cl ions.…”

A new candidate epitope-based vaccine against PspA PhtD of Streptococcus pneumoniae: a computational experimental approach

“…Bioinformatics techniques could help scientists in different biological areas ( Shafaghi et al., 2019 ; Nabizadeh et al, 2020 ; Bahadori et al., 2021 ), especially for anticipation of potential immunoprotective epitopes to develop vaccine candidates ( Tapia et al., 2016 ; Fereshteh et al., 2022 ). In fact, the tools of immunoinformatics provide benefits in comparison with traditional vaccinology methods such as lower costs and faster outcomes ( Afshari et al., 2023a ).…”