Open Access Open Access  Restricted Access Subscription or Fee Access

A Comprehensive Study on Protein-Protein Interaction in Drug Development: Future Prospective and Challenges

Pankaj Malhotra, Simran Rai, Deepika Yadav, Ankit .

Abstract


Protein-protein interactions (PPIs) play important roles in various cellular processes and have become a major area in drug development. Most of the studies which are related to Protein-protein interactions (PPIs) are correlated with different types of diseases including infectious diseases, Cancer and Neurodegenerative disorders. Therefore, targeting PPIs constitutes a therapeutic avenue for disease and an essential strategy for new drug development. In the last 10 years, PPI has been an emerging field of the study of drug intervention and it's the most difficult task for drug discovery. In recent years most PPI modulators have not only been developed but clinical trials have also been carried out on them for the investigations there potential to treat a particular disease, those that have been approved from an industrial point of view have been suggested by the experts that they have a broad future in drug discovery. In this study, we focus on summarizing recent advances in the field of PPI, including computational analysis, its types, detection methods, and the future perspectives for the design of type new drugs targeting PPIs in the future.

Keywords


Protein-protein interactions, computational analysis, detection methods, future design, drug development.

Full Text:

PDF

References


Skwarczynska M, Ottmann C. Protein-protein interactions as drug targets. Future medicinal chemistry, 2015, 7(16): 2195-2219.https://www.creative-proteomics.com/blog/index.php/brief-introduction-of-protein-protein-interaction-ppi/

White, A. W., Westwell, A. D. & Brahemi, G. Protein-protein interactions as targets for small-molecule therapeutics in cancer. Expert Rev. Mol. Med. 10, e8 (2008).

Llères D, Swift S, Lamond AI. Detecting protein-protein interactions in vivo with FRET using multiphoton fluorescence lifetime imaging microscopy (FLIM) Current Protocols in Cytometry.2007;12,Unit12.10.https://www.creative-proteomics.com/blog/index.php/brief-introduction-of-protein-protein-interaction-ppi/.

Nooren IM, Thornton JM. NEW EMBO MEMBER'S REVIEW: Diversity of protein–protein interactions, EMBO J, 2003, vol. 22 (pg. 3486-92). 5.V. Srinivasa Rao, K. Srinivas, G. N. Sujini and G. N. Sunand Kumar, Protein-Protein Interaction Detection: Methods and Analysis, Int J Proteomics. 2014: 147648.https://doi: 10.1155/2014/147648.

Arkin MR, Randal M, DeLano WL et al (2003) Binding of small molecules to an adaptive protein–protein interface. Proc Natl Acad Sci USA 100:1603–1608. https://doi.org/10.1073/pnas.252756299

Acuner Ozbabacan S E, Engin H B, Gursoy A, et al. Transient protein-protein interactions. Protein engineering, design and selection, 2011, 24(9): 635-648.

Rao V S, Srinivas K, Sujini G N, et al. Protein-protein interaction detection: methods and analysis[J]. International journal of proteomics, 2014, 2014.

Skwarczynska M, Ottmann C. Protein-protein interactions as drug targets. Future medicinal chemistry, 2015, 7(16): 2195-2219.

Snider, J.; Kotlyar, M.; Saraon, P.; Yao, Z.; Jurisica, I.; Stagljar, I. Fundamentals of protein interaction network mapping. Mol. Syst. Biol. 2015, 11, 848.

Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, Seraphin B. A generic protein purification method for protein complex characterization and proteome exploration. Nature Biotechnology. 1999;17(10):1030–1032.

Pitre S, Alamgir M, Green JR, Dumontier M, Dehne F, Golshani A. Computational methods for predicting protein-protein interactions. Advances in Biochemical Engineering/Biotechnology. 2008;110:247–267.

Rohila JS, Chen M, Cerny R, Fromm ME. Improved tandem affinity purification tag and methods for isolation of protein heterocomplexes from plants. Plant Journal. 2004;38(1):S172–S181.

MacBeath G, Schreiber SL. Printing proteins as microarrays for high-throughput function determination. Science. 2000;289(5485):1760–1763.

Gavin A-C, Bösche M, Krause R, et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 2002;415(6868):141–147.

Tong AHY, Evangelista M, Parsons AB, et al. Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science. 2001;294(5550):2364–2368.

Clackson T, Wells JA (1995) A hot spot of binding energy in a hormone-receptor interface. Science 267:383–386. https://doi.org/10.1126/science.7529940

Michnick SW, Ear PH, Landry C, Malleshaiah MK, Messier V. Protein-fragment complementation assays for large-scale analysis, functional dissection and dynamic studies of protein-protein interactions in living cells. Methods in Molecular Biology. 2011;756:395–425.

Casari G, Sander C, Valencia A. A method to predict Functional residue in proteins. Nat Struct Biol 1995;2:171-8

Uetz P, Glot L, Cagney G, et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature. 2000;403(6770):623–627.

Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proceedings of the National Academy of Sciences of the United States of America. 2001;98(8):4569–4574.

Zhang A. Protein Interaction Networks-Computational Analysis. New York, NY, USA: Cambridge University Press; 2009.

Zotenko, E.; Mestre, J.; O’Leary, D.P.; Przytycka, T.M. Why do hubs in the yeast protein interaction network tend to be essential: Reexamining the connection between the network topology and essentiality. PLoS Comput. Biol. 2008, 4, e1000140.

Pazos F, Valencia A. In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins. 2002;47(2):219–227. 25.https://genomemedicine.biomedcentral.com/articles/10.1186/gm441

Berman H, Henrick K, Nakamura H, Markley JL. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Research. 2007;35(1):D301–D303.

Hosur R, Xu J, Bienkowska J, Berger B. IWRAP: an interface threading approach with application to prediction of cancer-related protein-protein interactions. Journal of Molecular Biology. 2011;405(5):1295–1310.

Hosur R, Peng J, Vinayagam A, Stelzl U, et al. A computational framework for boosting confidence in high-throughput protein-protein interaction datasets. Genome Biology. 2012;13(8):p. R76.

Zhang QC, Petrey D, Deng L, et al. Structure-based prediction of protein-protein interaction on genome widescale Nature. 2012;490(7421): 556, 560.

Nguyen, T.P.; Ho, T.B. An integrative domain-based approach to predicting protein-protein interactions. J. Bioinform. Comput. Biol. 2008, 6, 1115–1132.

Wagner A. How the global structure of protein interaction networks evolves. Proceedings of the Royal Society B. 2003;270(1514):457–466.

Du L, Grigsby SM, Yao A et al (2018) Peptidomimetics for targeting protein–protein interactions between DOT1L and MLL oncofusion proteins AF9 and ENL. ACS Med Chem Lett 9:895–900. https://doi.org/10.1021/acsmedchemlett.8b00175

Feng Y, Wang Q, Wang T et al (2017) Drug target protein-protein interaction networks: a systematic perspective. Biomed Res Int 2017:1–13. https://doi.org/10.1155/2017/1289259

Haberman AB, “Advances in the discovery of protein-protein interaction modulators.” SCRIP Insights Informa 2012.

Tong AHY, Drees B, Nardelli G, et al. A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science. 2002;295(5553):321–324.

Modell AE, Blosser SL, Arora PS (2016) Systematic targeting of protein-protein interactions. Trends Pharmacol Sci 37:702–713. https://doi.org/10.1016/j.tips.2016.05.008

Landon M, Lancia DR, Yu J et al (2007) Identification of hot spots within druggable binding regions by computational solvent mapping of proteins. J Med Chem 50:1231–1240. https://doi.org/10.1021/jm061134b

Cox, A. D., Fesik, S. W., Kimmelman, A. C., Luo, J. & Der, C. J. Drugging the undruggable RAS: mission possible? Nat. Rev. Drug Discov. 13, 828–851 (2014).

Nooren IM, Thornton JM. NEW EMBO MEMBER'S REVIEW: Diversity of protein–protein interactions, EMBO J, 2003, vol. 22 (pg. 3486-92).


Refbacks

  • There are currently no refbacks.


Copyright (c) 2023 Research & Reviews: A Journal of Drug Design & Discovery