Pseudoprolines as stereoelectronically tunable proline isosteres

Khan, R. Kashif M.; Meanwell, Nicholas A.; Hager, Harry H.

doi:10.1016/j.bmcl.2022.128983

Cited by 4 publications

(2 citation statements)

References 121 publications

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“…At present, the pseudoproline thiaproline, 1,3‐thiazolidine‐4‐carboxylic acid (Thp) (Figure 1 ), has been seldom incorporated into proteins (Budisa et al, 1998 ; Fang et al, 2019 ), in spite of its intriguing features. Thp displays beneficial pharmaceutical properties due its anti‐aging, anti‐cancer, and anti‐inflammatory activities and it is a promising tool for drug design (Ham et al, 2020 ; Khan et al, 2022 ; Liu et al, 2020 ). Moreover, Thp has proved to be a substrate for human prolyl 4‐hydroxylase (Gorres et al, 2008 ), and it was suggested that it could be exploited to design collagen‐related biomaterials (Hsu & Horng, 2023 ).…”

Section: Introductionmentioning

confidence: 99%

4‐Thiaproline accelerates the slow folding phase of proteins containing cis prolines in the native state by two orders of magnitude

Loughlin,

Zinovjev,

Napolitano

et al. 2024

Protein Science

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The cis/trans isomerization of peptidyl‐prolyl peptide bonds is often the bottleneck of the refolding reaction for proteins containing cis proline residues in the native state. Proline (Pro) analogues, especially C4‐substituted fluoroprolines, have been widely used in protein engineering to enhance the thermodynamic stability of peptides and proteins and to investigate folding kinetics. 4‐thiaproline (Thp) has been shown to bias the ring pucker of Pro, to increase the cis population percentage of model peptides in comparison to Pro, and to diminish the activation energy barrier for the cis/trans isomerization reaction. Despite its intriguing properties, Thp has been seldom incorporated into proteins. Moreover, the impact of Thp on the folding kinetics of globular proteins has never been reported. In this study, we show that upon incorporation of Thp at cisPro76 into the thioredoxin variant Trx1P the half‐life of the refolding reaction decreased from ~2 hours to ~35 seconds. A dramatic acceleration of the refolding rate could be observed also for the protein pseudo wild‐type barstar upon replacement of cisPro48 with Thp. Quantum chemical calculations suggested that the replacement of the CγH2 group by a sulfur atom in the pyrrolidine ring, might lower the barrier for cis/trans rotation due to a weakened peptide bond. The protein variants retained their thermodynamic stability upon incorporation of Thp, while the catalytic and enzymatic activities of the modified Trx1P remained unchanged. Our results show that the Pro isostere Thp might accelerate the rate of the slow refolding reaction for proteins containing cis proline residues in the native state, independent from the local structural environment.This article is protected by copyright. All rights reserved.

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Section: Introductionmentioning

confidence: 99%

4‐Thiaproline accelerates the slow folding phase of proteins containing cis prolines in the native state by two orders of magnitude

Loughlin,

Zinovjev,

Napolitano

et al. 2024

Protein Science

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“…Thp displays beneficial pharmaceutical properties due its anti-aging, anti-cancer, and anti-inflammatory activities and it is a promising tool for drug design. [29][30][31] Moreover, Thp has proved to be a substrate for human prolyl 4-hydroxylase, 32 and it was suggested that it could be exploited to design collagen-related biomaterials. 33 Although the thiazolidine ring in Thp displays a slightly different geometry in comparison to the pyrrolidine ring of Pro due to the larger size of the sulfur atom, Thp can be considered isosteric to Pro.…”

Section: Introductionmentioning

confidence: 99%

4-Thiaproline accelerates the slow folding phase of proteins containingcisprolines in the native state by two orders of magnitude

Loughlin

Zinovjev

Napolitano

et al. 2023

Preprint

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The cis/trans isomerization of peptidyl-prolyl peptide bonds is often the bottleneck of the refolding reaction for proteins containing cis proline residues in the native state. Proline (Pro) analogues, especially C4-substituted fluoroprolines, have been widely used in protein engineering to enhance the thermodynamic stability of peptides and proteins and to investigate folding kinetics. 4-thiaproline (Thp) has been shown to bias the ring pucker of Pro, to increase the cis population percentage of model peptides in comparison to Pro, and to diminish the activation energy barrier for the cis/trans isomerization reaction. Despite its intriguing properties, Thp has been seldom incorporated into proteins. Moreover, the impact of Thp on the folding kinetics of globular proteins has never been reported. In this study, we show that upon incorporation of Thp at cisPro76 into the thioredoxin variant Trx1P the half-life of the refolding reaction decreased from ~2 hours to ~35 seconds. A dramatic acceleration of the refolding rate could be observed also for the protein pseudo wild-type barstar upon replacement of cisPro48 with Thp. Quantum chemical calculations revealed that the replacement of the CγH2 group by a sulfur atom in the pyrrolidine ring, lowers the barrier for cis/trans rotation due to a weakened peptide bond. The protein variants retained their thermodynamic stability upon incorporation of Thp, while the catalytic and enzymatic activities of the modified Trx1P remained unchanged. Our results show that the Pro isostere Thp might eliminate the bottleneck of the refolding reaction of proteins containing cis proline residues in the native state, independent from the local structural environment.

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Proline Analogues in Drug Design: Current Trends and Future Prospects

Kubyshkin,

Mykhailiuk

2024

J. Med. Chem.

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Proline analogues are versatile chemical building blocks that enable modular construction of small-molecule drugs and pharmaceutical peptides. Over the past 15 years, the FDA has approved over 15 drugs containing proline analogues in their structures, five in the last three years alone (daridorexant, trofinetide, nirmatrelvir, rezafungin, danicopan). This perspective offers an analysis of the most common types of proline analogues currently trending in drug design. We focus on examples of fluoroprolines, α-methylproline, bicyclic proline analogues, and aminoprolines, while also highlighting proline analogues that remain underrepresented. We supplement our analysis with physicochemical information regarding the specific molecular properties of these moieties. Additionally, we discuss several intriguing cases where nonproline residues were replaced with proline analogues as a strategy to eliminate unwanted hydrogen bond donor sites. In conclusion, we present some suggestions for the future exploration of this promising class of molecular entities in drug discovery. ■ SIGNIFICANCEOver 15 drug structures approved in the past 15 years contain proline analogues. The cyclic nature of these analogues provides conformationally restricted 3D scaffolds, enhancing the activity and bioavailability of bioactive molecules and peptides. In this work, we analyze the most prominent proline analogues in current drug discovery, with a focus on fluoroprolines, αmethylproline, aminoprolines, and bicyclic analogues. Additionally, we provide detailed physicochemical data and creative suggestions to guide future research efforts.

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Pseudoprolines as stereoelectronically tunable proline isosteres

Cited by 4 publications

References 121 publications

4‐Thiaproline accelerates the slow folding phase of proteins containing cis prolines in the native state by two orders of magnitude

4‐Thiaproline accelerates the slow folding phase of proteins containing cis prolines in the native state by two orders of magnitude

4-Thiaproline accelerates the slow folding phase of proteins containingcisprolines in the native state by two orders of magnitude

Proline Analogues in Drug Design: Current Trends and Future Prospects

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