Abstract:G-protein-coupled receptors (GPCRs), among various cell surface proteins, are essential targets in the fields of basic science and drug discovery. The discovery and development of modulators for the receptors have provided deep insights into the mechanism of action of receptors and have led to a new therapeutic option for human diseases. Although various modulators against GPCRs have been developed to date, the identification of new modulators for GPCRs remains a challenge due to several technical problems and… Show more
“…Recent success with this approach has been achieved using covalent attachments such as AMG 510 for oncogenic G12C-KRas, but this strategy depends on the availability of a reactive cysteine and can result in off-target attachment . Other strategies have largely included using peptides, proteomimetics, − nucleic acid aptamers, and antibodies; each of these methods carry their own set of benefits and drawbacks, and successful drug design has been rare. , There is a clear need for a greater understanding of how electrostatic complementarity combines with structural details to create protein–protein interfaces and how small molecules could interrupt those interactions in desired ways. To design a small molecule with the orthosteric, noncovalent binding found in most traditional drugs, a significantly better understanding of the complicated networks of electrostatic interactions between all charges and partial charges at these interfaces is clearly needed.…”
Protein−protein interactions regulate many cellular processes, making them ideal drug candidates. Design of such drugs, however, is hindered by a lack of understanding of the factors that contribute to the interaction specificity. Specific protein−protein complexes possess both structural and electrostatic complementarity, and while structural complementarity of protein complexes has been extensively investigated, fundamental understanding of the complicated networks of electrostatic interactions at these interfaces is lacking, thus hindering the rational design of orthosterically binding small molecules. To better understand the electrostatic interactions at protein interfaces and how a small molecule could contribute to and fit within that environment, we used a model protein−drug−protein system, Arf1-BFA-ARNO4M, to investigate how small molecule brefeldin A (BFA) perturbs the Arf1-ARNO4M interface. By using nitrile probe labeled Arf1 sites and measuring vibrational Stark effects as well as temperature dependent infrared shifts, we measured changes in the electric field and hydrogen bonding at this interface upon BFA binding. At all five probe locations of Arf1, we found that the vibrational shifts resulting from BFA binding corroborate trends found in Poisson−Boltzmann calculations of surface potentials of Arf1-ARNO4M and Arf1-BFA-ARNO4M, where BFA contributes negative electrostatic potential to the protein interface. The data also corroborate previous hypotheses about the mechanism of interfacial binding and confirm that alternating patches of hydrophobic and polar interactions lead to BFA binding specificity. These findings demonstrate the impact of BFA on this protein−protein interface and have implications for the design of other interfacial drug candidates.
“…Recent success with this approach has been achieved using covalent attachments such as AMG 510 for oncogenic G12C-KRas, but this strategy depends on the availability of a reactive cysteine and can result in off-target attachment . Other strategies have largely included using peptides, proteomimetics, − nucleic acid aptamers, and antibodies; each of these methods carry their own set of benefits and drawbacks, and successful drug design has been rare. , There is a clear need for a greater understanding of how electrostatic complementarity combines with structural details to create protein–protein interfaces and how small molecules could interrupt those interactions in desired ways. To design a small molecule with the orthosteric, noncovalent binding found in most traditional drugs, a significantly better understanding of the complicated networks of electrostatic interactions between all charges and partial charges at these interfaces is clearly needed.…”
Protein−protein interactions regulate many cellular processes, making them ideal drug candidates. Design of such drugs, however, is hindered by a lack of understanding of the factors that contribute to the interaction specificity. Specific protein−protein complexes possess both structural and electrostatic complementarity, and while structural complementarity of protein complexes has been extensively investigated, fundamental understanding of the complicated networks of electrostatic interactions at these interfaces is lacking, thus hindering the rational design of orthosterically binding small molecules. To better understand the electrostatic interactions at protein interfaces and how a small molecule could contribute to and fit within that environment, we used a model protein−drug−protein system, Arf1-BFA-ARNO4M, to investigate how small molecule brefeldin A (BFA) perturbs the Arf1-ARNO4M interface. By using nitrile probe labeled Arf1 sites and measuring vibrational Stark effects as well as temperature dependent infrared shifts, we measured changes in the electric field and hydrogen bonding at this interface upon BFA binding. At all five probe locations of Arf1, we found that the vibrational shifts resulting from BFA binding corroborate trends found in Poisson−Boltzmann calculations of surface potentials of Arf1-ARNO4M and Arf1-BFA-ARNO4M, where BFA contributes negative electrostatic potential to the protein interface. The data also corroborate previous hypotheses about the mechanism of interfacial binding and confirm that alternating patches of hydrophobic and polar interactions lead to BFA binding specificity. These findings demonstrate the impact of BFA on this protein−protein interface and have implications for the design of other interfacial drug candidates.
RNA aptamers are nucleic acids that are obtained using the systematic evolution of ligands by exponential enrichment (SELEX) method. When using conventional selection methods to immobilise target proteins on matrix beads using protein tags, sequences are obtained that bind not only to the target proteins, but also to the protein tags and matrix beads. In this study, we performed SELEX using β-1,3-glucan recognition protein (GRP)-tags and curdlan beads to immobilise the AML1 Runt domain (RD) and analysed the enrichment of aptamers using high-throughput sequencing. Comparison of aptamer enrichment using the GRP-tag and His-tag suggested that aptamers were enriched using the GRP-tag as well as using the His-tag. Furthermore, surface plasmon resonance analysis revealed that the aptamer did not bind to the GRP-tag and that the conjugation of the GRP-tag to RD weakened the interaction between the aptamer and RD. The GRP-tag could have acted as a competitor to reduce weakly bound RNAs. Therefore, the affinity system of the GRP-tagged proteins and curdlan beads is suitable for obtaining specific aptamers using SELEX.
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