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Engineering protein fragments via evolutionary and protein-protein interaction algorithms: De novo design of peptide inhibitors for FOF1-ATP synthase
1
,
Luis Pablo Ávila-Barrientos
2
,
Enrique Hernández-García
2
,
*
3, 4
,
4, 5
,
*
6
Academic Editor: Humbert G. Díaz
Published:
30 December 2022
by MDPI
in MOL2NET'22, Conference on Molecular, Biomed., Comput. & Network Science and Engineering, 8th ed.
congress CHEMBIO.INFO-08: Cheminfo., Chemom., Comput. Chem. & Bioinfo., Congress München, GR-Cambridge, UK-Ch. Hill, USA, 2022.
Abstract:
Enzyme’s subunits interfaces have remarkable potential in drug design as both target and scaffold for their own inhibitors. We show an evolution-driven strategy for the de novo design of peptide inhibitors targeting interfaces of the E. coli’s FoF1-ATP synthase as a case study. The evolutionary algorithm ROSE is applied to generate diversity-oriented peptide libraries by engineering peptide fragments from ATP synthase interfaces. The resulting peptides are scored with PPI-Detect, a sequence-based predictor of protein-protein interactions. Two selected peptides were confirmed by in vitro inhibition and binding tests. The proposed methodology can be widely applied to design peptides targeting relevant interfaces of enzymatic complexes (https://doi.org/10.1002/1873-3468.13988).
Keywords: peptide drug design, protein interfaces; sequence evolution; peptide library; PPI-Detect; ROSE.
Comments on this paper
Andrea Ruiz-Escudero
2 January 2023
Dear authors thank you for your support to the conference.
Now we closed the publication phase and launched the post-publication phase of the conference.
REVIEWWWERS'08 Brainstorming Workshop is Now Open from 2023-Jan-01 to 2023-Jan-31.
MOL2NET Committee, Authors, and Validated Social Media Followers Worldwide ... are invited to Post Moderated Questions/Answers, Comments, about papers.
These are my Questions (Q) to you, please kindly post your public Answers (A) below to promote scientific discussion and training of conference readers :
Q1. What are the potential benefits and limitations of using endogenous peptide inhibitors of ATP synthase as treatments for diseases?
Q2. What are the potential implications of the successful design of these peptides for the development of treatments for diseases, and what are the next steps in this process?
Thank you for your kind support. Please make questions to other papers in different Mol2Net congresses
Commenting Steps: Login, Go to Papers List, Select Paper, Write Comment, Click Post Comment
Papers list: https://mol2net-08.sciforum.net/presentations/view
Workshop link: https://mol2net-08.sciforum.net/#reviewwwers
Now we closed the publication phase and launched the post-publication phase of the conference.
REVIEWWWERS'08 Brainstorming Workshop is Now Open from 2023-Jan-01 to 2023-Jan-31.
MOL2NET Committee, Authors, and Validated Social Media Followers Worldwide ... are invited to Post Moderated Questions/Answers, Comments, about papers.
These are my Questions (Q) to you, please kindly post your public Answers (A) below to promote scientific discussion and training of conference readers :
Q1. What are the potential benefits and limitations of using endogenous peptide inhibitors of ATP synthase as treatments for diseases?
Q2. What are the potential implications of the successful design of these peptides for the development of treatments for diseases, and what are the next steps in this process?
Thank you for your kind support. Please make questions to other papers in different Mol2Net congresses
Commenting Steps: Login, Go to Papers List, Select Paper, Write Comment, Click Post Comment
Papers list: https://mol2net-08.sciforum.net/presentations/view
Workshop link: https://mol2net-08.sciforum.net/#reviewwwers
Jeachul Jang
9 January 2023
Q1. What are the potential benefits and limitations of using endogenous peptide inhibitors of ATP synthase as treatments for diseases?
Author Answer: It is a new approach where fragments of the same enzyme involved on its own regulation are used to develop inhibitory peptides which are expected to show low toxicity for antibiotics development.
Q2. What are the potential implications of the successful design of these peptides for the development of treatments for diseases, and what are the next steps in this process?
Author Answer: The discovery of new inhibitory peptides of the ATP synthase has great potentialities for antibiotics development against multi-drug resistant strains of E. coli which are the responsible of many infectious diseases. Next steps will imply optimization process accompanied with further in vitro and in vivo tests.
Author Answer: It is a new approach where fragments of the same enzyme involved on its own regulation are used to develop inhibitory peptides which are expected to show low toxicity for antibiotics development.
Q2. What are the potential implications of the successful design of these peptides for the development of treatments for diseases, and what are the next steps in this process?
Author Answer: The discovery of new inhibitory peptides of the ATP synthase has great potentialities for antibiotics development against multi-drug resistant strains of E. coli which are the responsible of many infectious diseases. Next steps will imply optimization process accompanied with further in vitro and in vivo tests.
Jeachul Jang
9 January 2023
Q1. What are the potential benefits and limitations of using endogenous peptide inhibitors of ATP synthase as treatments for diseases?
Author Answer: It is a new approach where fragments of the same enzyme involved on its own regulation are used to develop inhibitory peptides which are expected to show low toxicity for antibiotics development.
Q2. What are the potential implications of the successful design of these peptides for the development of treatments for diseases, and what are the next steps in this process?
Author Answer: The discovery of new inhibitory peptides of the ATP synthase has great potentialities for antibiotics development against multi-drug resistant strains of E. coli which are the responsible of many infectious diseases. Next steps will imply optimization process accompanied with further in vitro and in vivo tests.
Author Answer: It is a new approach where fragments of the same enzyme involved on its own regulation are used to develop inhibitory peptides which are expected to show low toxicity for antibiotics development.
Q2. What are the potential implications of the successful design of these peptides for the development of treatments for diseases, and what are the next steps in this process?
Author Answer: The discovery of new inhibitory peptides of the ATP synthase has great potentialities for antibiotics development against multi-drug resistant strains of E. coli which are the responsible of many infectious diseases. Next steps will imply optimization process accompanied with further in vitro and in vivo tests.
