peptide design
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2022 ◽  
Vol 13 (1) ◽  
Author(s):  
Cheng-Yu Tsai ◽  
Emmanuel Oluwatobi Salawu ◽  
Hongchun Li ◽  
Guan-Yu Lin ◽  
Ting-Yu Kuo ◽  
...  

AbstractThe systematic design of functional peptides has technological and therapeutic applications. However, there is a need for pattern-based search engines that help locate desired functional motifs in primary sequences regardless of their evolutionary conservation. Existing databases such as The Protein Secondary Structure database (PSS) no longer serves the community, while the Dictionary of Protein Secondary Structure (DSSP) annotates the secondary structures when tertiary structures of proteins are provided. Here, we extract 1.7 million helices from the PDB and compile them into a database (Therapeutic Peptide Design database; TP-DB) that allows queries of compounded patterns to facilitate the identification of sequence motifs of helical structures. We show how TP-DB helps us identify a known purification-tag-specific antibody that can be repurposed into a diagnostic kit for Helicobacter pylori. We also show how the database can be used to design a new antimicrobial peptide that shows better Candida albicans clearance and lower hemolysis than its template homologs. Finally, we demonstrate how TP-DB can suggest point mutations in helical peptide blockers to prevent a targeted tumorigenic protein-protein interaction. TP-DB is made available at http://dyn.life.nthu.edu.tw/design/.


Author(s):  
Seyed Amir Hossein Mohammadzadeh Hosseini Moghri ◽  
Ghanbar Mahmoodi Chalbatani ◽  
Mojtaba Ranjbar ◽  
Catarina Raposo ◽  
Arefeh Abbasian

2021 ◽  
Author(s):  
Pralhad Namdev Joshi ◽  
Evgeniy Mervinetsky ◽  
Ohad Solomon ◽  
Yu-Ju Chen ◽  
Shlomo Yitzchaik ◽  
...  

Kinases are important cancer biomarkers and are conventionally detected based on their catalytic activity. Kinases regulate cellular activities by phosphorylation of motif-specific multiple substrate proteins, resulting in a lack of selectivity of activity-based kinase biosensors. We present an alternative approach of sensing kinases based on the interactions of their allosteric docking sites with a specific partner protein. The new approach was demonstrated for the ERK2 kinase and its substrate ELK-1. A peptide derived from ELK-1 was bound to a gold electrode and ERK2 sensing was performed by electrochemical impedance spectroscopy. The sensors showed a high level of target selectivity for ERK2 when compared with p38gamma kinase and BSA. ERK2 was detected in its cellular concentration range, 0.2-8.0 microM. Using the flexibility of peptide design, our method is generic for developing sensitive and substrate-specific biosensors and other disease-related enzymes based on their interactions.


2021 ◽  
Author(s):  
Nairiti J. Sinha ◽  
Matthew G. Langenstein ◽  
Darrin J. Pochan ◽  
Christopher J. Kloxin ◽  
Jeffery G. Saven

2021 ◽  
Vol 22 (17) ◽  
pp. 9106
Author(s):  
Nikola Štambuk ◽  
Paško Konjevoda ◽  
Josip Pavan

Antisense peptide technology (APT) is based on a useful heuristic algorithm for rational peptide design. It was deduced from empirical observations that peptides consisting of complementary (sense and antisense) amino acids interact with higher probability and affinity than the randomly selected ones. This phenomenon is closely related to the structure of the standard genetic code table, and at the same time, is unrelated to the direction of its codon sequence translation. The concept of complementary peptide interaction is discussed, and its possible applications to diagnostic tests and bioengineering research are summarized. Problems and difficulties that may arise using APT are discussed, and possible solutions are proposed. The methodology was tested on the example of SARS-CoV-2. It is shown that the CABS-dock server accurately predicts the binding of antisense peptides to the SARS-CoV-2 receptor binding domain without requiring predefinition of the binding site. It is concluded that the benefits of APT outweigh the costs of random peptide screening and could lead to considerable savings in time and resources, especially if combined with other computational and immunochemical methods.


2021 ◽  
Vol 8 ◽  
Author(s):  
Zahra Sadat Hashemi ◽  
Mahboubeh Zarei ◽  
Mohsen Karami Fath ◽  
Mahmoud Ganji ◽  
Mahboube Shahrabi Farahani ◽  
...  

Large contact surfaces of protein–protein interactions (PPIs) remain to be an ongoing issue in the discovery and design of small molecule modulators. Peptides are intrinsically capable of exploring larger surfaces, stable, and bioavailable, and therefore bear a high therapeutic value in the treatment of various diseases, including cancer, infectious diseases, and neurodegenerative diseases. Given these promising properties, a long way has been covered in the field of targeting PPIs via peptide design strategies. In silico tools have recently become an inevitable approach for the design and optimization of these interfering peptides. Various algorithms have been developed to scrutinize the PPI interfaces. Moreover, different databases and software tools have been created to predict the peptide structures and their interactions with target protein complexes. High-throughput screening of large peptide libraries against PPIs; “hotspot” identification; structure-based and off-structure approaches of peptide design; 3D peptide modeling; peptide optimization strategies like cyclization; and peptide binding energy evaluation are among the capabilities of in silico tools. In the present study, the most recent advances in the field of in silico approaches for the design of interfering peptides against PPIs will be reviewed. The future perspective of the field and its advantages and limitations will also be pinpointed.


Author(s):  
Partha Hazra ◽  
Suma Sreenivas ◽  
Krishnamurthy Venkatesan ◽  
Mukesh B. Patale ◽  
Amarnath Chatterjee ◽  
...  

Author(s):  
Jessica A. Cross ◽  
Magda S. Chegkazi ◽  
Roberto A. Steiner ◽  
Derek N. Woolfson ◽  
Mark P. Dodding

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