Modulation of Protein-Protein Interactions with Pre-Structured Peptides

Marijn Maas

doi:10.21996/r8dn-6c84

Modulation of Protein-Protein Interactions with Pre-Structured Peptides

Marijn Maas

Institut for Fysik, Kemi og Farmaci

Publikation: Afhandling › Ph.d.-afhandling

Abstract

Protein-protein interaktioner regulerer biokemiske processer forbundet med helbred ogsygdom, og er generelt betragtet at være kompliceret at designe lægemidler til grundet de storeog udefinerede natur af overfladerne på de deltagende proteiner. Udvikling af nye kemisketeknologier, som muliggør undersøgelsen heraf, vil åbne døren for det rationelle design afpotente og specifikke prober eller terapeutiske midler, der er rettet mod specifikke PPI-netværkinvolveret i nøgleprocesser i helbred og sygdom. Præstrukturerede peptider har appliceret sompotente redskaber til at undersøge eller inhibere proteinkompleksdannelse. Fokus for denneph.d.-afhandling er at opnå indsigt i vigtigheden af konformationel peptid fleksibilitet for atlette genkendelse af deres bindingspartnere gennem præ-strukturering af peptidrygraden.

I kapitel 3 havde vi til formål at udvikle lactam-baserede i,i+4 præstrukturerede hACE2- peptider rettet mod SARS CoV-2 Spike-proteinet. Inhibering af Spike-proteinet RBD-hACE2- kompleksdannelse blev observeret igennem in vitro-assays med præstruktureret hACE221- 55A36K-F40-peptid (IC59: 3,6 μM, Kd: 2,1 μM), hvilket indikerer at hACE2-peptider kunne danne grundlag for udvikling af COVID-19 terapeuter.

Kapitel 4 udforsker den katalytiske selektivitet af PAD2 og PAD4 overfor præstrukturerede histonhaler. Udvalgte histon-peptider, præstuktureret igennem i, i+3 hæftning blev effektivt citrullineret af PAD2 og blev ikke accepteret som substrater for histonmethyleller acetyltransferaser. i,i+3 hæftede peptider blev identificeret som kompetitive inhibitorer af PAD2 (IC = 4.0 μM) and PAD4 (IC50 = 8.1 μM).

I kapitel 5 rapporterer vi om den katalytiske specificitet af SETD3 overfor præstrukturerede i, i+3 hæftede β-actin peptider. Begrænsning af konformationsfleksibiliteten af β-actin resulterer i nedsat SETD3-katalyseret Nτ-His73-methylering. Desuden virkede ingen af de præstrukturerede β-actin peptider som kompetitive inhibitorer af SETD3. Disse resultater tyder på, at reduceret β-actin rygradsfleksibilitet forhindrer optimale protein-protein interaktioner mellem substratet og enzymet.

I kapitel 6 illustrerer termodynamisk analyse med ITC, at præstukturering af den Nterminale histon 3-hale, der bærer et trimethyllysinmærke, kan forbedre genkendelsen af
epigenetiske læsere BPTFPHD og JMJD2ATTD betydeligt gennem forbedrede entropikomponenter. I modsætning hertil er genkendelse af JARID1APHD3 svækket gennem ikke-favorable entalpiske og entropiske komponenter. Dette tyder på, at der er et niveau af selektivitet mellem læsere af H3K4me3 for peptider med forskellige niveauer af konformationel frihed.

Originalsprog	Engelsk
Bevilgende institution	Syddansk Universitet
Vejledere/rådgivere	Mecinovic, Jasmin, Hovedvejleder
Dato for forsvar	23. aug. 2022
Udgiver	Syddansk Universitet. Det Naturvidenskabelige Fakultet
DOI	https://doi.org/10.21996/r8dn-6c84
Status	Udgivet - 14. sep. 2022

Note vedr. afhandling

Afhandlingen kan læses på SDUs bibliotek.

Dokumenter og links

10.21996/r8dn-6c84

SDU link

Tjek adgangen til materialet i Syddansk Universitetsbiblioteks søgemaskine

6 Tidsskriftartikel

Amide-derived lysine analogues as substrates and inhibitors of histone lysine methyltransferases and acetyltransferases
Hintzen, J. C. J., Merx, J., Maas, M. N., Langens, S. G. H. A., White, P. B., Boltje, T. J. & Mecinović, J., 2022, I: Organic & Biomolecular Chemistry. 20, 1, s. 173-181
Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review
Importance of Ile71 in β-actin on histidine methyltransferase SETD3 catalysis
Bilgin, N., Moesgaard, L., Maas, M., Hintzen, J., Witecka, A., Drozak, J., Kongsted, J. & Mecinović, J., 28. feb. 2022, I: Organic & Biomolecular Chemistry. 20, 8, s. 1723-1730 8 s., 1723.
Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review
Probing lysine posttranslational modifications by unnatural amino acids
Maas, M. N., Hintzen, J. C. J. & Mecinović, J., 4. jul. 2022, I: Chemical Communications. 58, 52, s. 7216-7231
Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

Citationsformater

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abstract = "Protein-protein interactions regulate biochemical processes associated with health and diseaseand are generally considered {\textquoteleft}undruggable{\textquoteright} due to the large and undefined nature of the surfacesof the participating proteins. Development of new chemical technologies which allow for thestudy thereof would open the door towards the rational design of potent and specific probes ortherapeutics which target specific PPI networks involved with key processes involved in healthand disease. Pre-structured peptides have surfaced as potent tools to study or inhibit proteincomplex formation. The focus of this PhD dissertation is to gain insight into the importance ofpeptide conformational flexibility towards facilitating recognition by their binding partnersthrough pre-structuring of the peptide backbone. In chapter 3 we set out to develop lactam-based i,i + 4 pre-structured hACE2 peptides targeting the SARS-CoV-2 spike protein. Inhibition of the Spike protein RBD-hACE2 complex formation was observed through in vitro assays with pre-structured hACE221-55A36K-F40E peptide (IC50: 3.6 μM, Kd: 2.1 μM), suggesting that hACE2 peptides could form the basis for the development of anti-COVID-19 therapeutics. In chapter 4 we report on the catalytic specificity of SETD3 towards pre-structured i,i + 3 stapled β-actin peptides. Limiting the conformation flexibility of β-actin results in decreased SETD3-catalyzed Nτ-His73 methylation. Moreover, none of the pre-structured βactin peptides acted as competitive inhibitors of SETD3. These findings suggest that reduced β-actin backbone flexibility prevents optimal protein-protein interactions between the substrate and enzyme. Chapter 5 explores the catalytic selectivity of PAD2 and PAD4 towards pre-structured histone tails. Select histone peptides pre-structured through i,i+3 stapling were efficiently citrullinated by PAD2, and were not accepted as substrates for histone methyl- or acetyl transferases. i,i+3 stapled histone peptides were identified as competitive inhibitors of PAD2 (IC50 = 4.0 μM) and PAD4 (IC50 = 8.1 μM). In chapter 6, thermodynamic analysis with ITC illustrates that pre-structuring of the Nterminal histone 3 tail bearing a trimethyllysine mark can significantly improve recognition by epigenetic readers BPTFPHD and JMJD2ATTD through enhanced entropy components. In contrast, recognition by JARID1APHD3 is impaired through unfavorable enthalpic and entropic components. This suggests that there is a level of selectivity between readers of H3K4me3 for peptides with different levels of conformational freedom.",

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DO - 10.21996/r8dn-6c84

M3 - Ph.D. thesis

PB - Syddansk Universitet. Det Naturvidenskabelige Fakultet

ER -

Modulation of Protein-Protein Interactions with Pre-Structured Peptides

Abstract

Note vedr. afhandling

Dokumenter og links

SDU link

Fingeraftryk

Relaterede publikationer

Amide-derived lysine analogues as substrates and inhibitors of histone lysine methyltransferases and acetyltransferases

Importance of Ile71 in β-actin on histidine methyltransferase SETD3 catalysis

Probing lysine posttranslational modifications by unnatural amino acids

Citationsformater