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Kubyshkin V, Rubini M. Proline Analogues. Chem Rev 2024; 124:8130-8232. [PMID: 38941181 DOI: 10.1021/acs.chemrev.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Within the canonical repertoire of the amino acid involved in protein biogenesis, proline plays a unique role as an amino acid presenting a modified backbone rather than a side-chain. Chemical structures that mimic proline but introduce changes into its specific molecular features are defined as proline analogues. This review article summarizes the existing chemical, physicochemical, and biochemical knowledge about this peculiar family of structures. We group proline analogues from the following compounds: substituted prolines, unsaturated and fused structures, ring size homologues, heterocyclic, e.g., pseudoproline, and bridged proline-resembling structures. We overview (1) the occurrence of proline analogues in nature and their chemical synthesis, (2) physicochemical properties including ring conformation and cis/trans amide isomerization, (3) use in commercial drugs such as nirmatrelvir recently approved against COVID-19, (4) peptide and protein synthesis involving proline analogues, (5) specific opportunities created in peptide engineering, and (6) cases of protein engineering with the analogues. The review aims to provide a summary to anyone interested in using proline analogues in systems ranging from specific biochemical setups to complex biological systems.
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Affiliation(s)
| | - Marina Rubini
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
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2
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Tsai CL, Chang JW, Cheng KY, Lan YJ, Hsu YC, Lin QD, Chen TY, Shih O, Lin CH, Chiang PH, Simenas M, Kalendra V, Chiang YW, Chen CH, Jeng US, Wang SK. Comprehensive characterization of polyproline tri-helix macrocyclic nanoscaffolds for predictive ligand positioning. NANOSCALE ADVANCES 2024; 6:947-959. [PMID: 38298598 PMCID: PMC10825903 DOI: 10.1039/d3na00945a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/25/2023] [Indexed: 02/02/2024]
Abstract
Multivalent ligands hold promise for enhancing avidity and selectivity to simultaneously target multimeric proteins, as well as potentially modulating receptor signaling in pharmaceutical applications. Essential for these manipulations are nanosized scaffolds that precisely control ligand display patterns, which can be achieved by using polyproline oligo-helix macrocyclic nanoscaffolds via selective binding to protein oligomers and cell surface receptors. This work focuses on synthesis and structural characterization of different-sized polyproline tri-helix macrocyclic (PP3M) scaffolds. Through combined analysis of circular dichroism (CD), small- and wide-angle X-ray scattering (SWAXS), electron spin resonance (ESR) spectroscopy, and molecular modeling, a non-coplanar tri-helix loop structure with partially crossover helix ends is elucidated. This structural model aligns well with scanning tunneling microscopy (STM) imaging. The present work enhances the precision of nanoscale organic synthesis, offering prospects for controlled ligand positioning on scaffolds. This advancement paves the way for further applications in nanomedicine through selective protein interaction, manipulation of cell surface receptor functions, and developments of more complex polyproline-based nanostructures.
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Affiliation(s)
- Chia-Lung Tsai
- Department of Chemistry, National Tsing Hua University Hsinchu 300044 Taiwan
| | - Je-Wei Chang
- National Synchrotron Radiation Research Center Hsinchu 300092 Taiwan
| | - Kum-Yi Cheng
- Department of Chemistry and Centre for Emerging Materials and Advanced Devices, National Taiwan University Taipei 106319 Taiwan
| | - Yu-Jing Lan
- Department of Chemistry, National Tsing Hua University Hsinchu 300044 Taiwan
| | - Yi-Cheng Hsu
- Department of Chemistry, National Tsing Hua University Hsinchu 300044 Taiwan
| | - Qun-Da Lin
- Department of Chemistry, National Tsing Hua University Hsinchu 300044 Taiwan
| | - Tzu-Yuan Chen
- Department of Chemistry, National Tsing Hua University Hsinchu 300044 Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center Hsinchu 300092 Taiwan
| | - Chih-Hsun Lin
- Department of Chemistry and Centre for Emerging Materials and Advanced Devices, National Taiwan University Taipei 106319 Taiwan
| | - Po-Hsun Chiang
- Department of Chemistry, National Tsing Hua University Hsinchu 300044 Taiwan
| | - Mantas Simenas
- Faculty of Physics, Vilnius University Sauletekio 3 LT-10257 Vilnius Lithuania
| | - Vidmantas Kalendra
- Faculty of Physics, Vilnius University Sauletekio 3 LT-10257 Vilnius Lithuania
| | - Yun-Wei Chiang
- Department of Chemistry, National Tsing Hua University Hsinchu 300044 Taiwan
| | - Chun-Hsien Chen
- Department of Chemistry and Centre for Emerging Materials and Advanced Devices, National Taiwan University Taipei 106319 Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center Hsinchu 300092 Taiwan
- Department of Chemical Engineering, National Tsing Hua University Hsinchu 300044 Taiwan
- College of Semiconductor Research, National Tsing Hua University Hsinchu 300044 Taiwan
| | - Sheng-Kai Wang
- Department of Chemistry, National Tsing Hua University Hsinchu 300044 Taiwan
- Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University Hsinchu 300044 Taiwan
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Li MC, Liu YJ, Hsu KC, Lin TH, Lin CW, Horng JC, Wang SK. Design and synthesis of fluorinated peptides for analysis of fluorous effects on the interconversion of polyproline helices. Bioorg Chem 2021; 119:105491. [PMID: 34838334 DOI: 10.1016/j.bioorg.2021.105491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 12/15/2022]
Abstract
The unique interaction between fluorine atoms has been exploited to alter protein structures and to develop synthetic and analytical applications. To expand such fluorous interaction for novel applications, polyproline peptides represent an excellent molecular nanoscaffold for controlling the presentation of perfluoroalkyl groups on their unique secondary structure. We develop approaches to synthesis fluorinated peptides to systematically investigate how the number, location and types of the fluorous groups on polyproline affect the conformation by monitoring the transition between the two major polyproline structures PPI and PPII. This work provides valuable information on how fluorous interaction affects the peptide structure and also benefits the design of functional fluorous molecules.
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Affiliation(s)
- Meng-Che Li
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Ying-Jie Liu
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Kuang-Cheng Hsu
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Tse-Hsueh Lin
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chih-Wei Lin
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Jia-Cherng Horng
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan; Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Sheng-Kai Wang
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan; Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan.
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Shurpik DN, Aleksandrova YI, Mostovaya OA, Nazmutdinova VA, Zelenikhin PV, Subakaeva EV, Mukhametzyanov TA, Cragg PJ, Stoikov II. Water-soluble pillar[5]arene sulfo-derivatives self-assemble into biocompatible nanosystems to stabilize therapeutic proteins. Bioorg Chem 2021; 117:105415. [PMID: 34673453 DOI: 10.1016/j.bioorg.2021.105415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/24/2021] [Accepted: 10/06/2021] [Indexed: 02/07/2023]
Abstract
Pillar[5]arenes containing sulfonate fragments have been shown to form supramolecular complexes with therapeutic proteins to facilitate targeted transport with an increased duration of action and enhanced bioavailability. Regioselective synthesis was used to obtain a water-soluble pillar[5]arene containing the fluorescent label FITC and nine sulfoethoxy fragments. The pillar[5]arene formed complexes with the therapeutic proteins binase, bleomycin, and lysozyme in a 1:2 ratio as demonstrated by UV-vis and fluorescence spectroscopy. The formation of stable spherical nanosized macrocycle/binase complexes with an average particle size of 200 nm was established by dynamic light scattering and transmission electron microscopy. Flow cytometry demonstrated the ability of macrocycle/binase complexes to penetrate into tumor cells where they exhibited significant cytotoxicity towards A549 cells at 10-5-10-6 M while maintaining the enzymatic activity of binase.
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Affiliation(s)
- Dmitriy N Shurpik
- Kazan Federal University, A.M. Butlerov Chemistry Institute, 420008 Kremlevskaya, 18, Kazan, Russian Federation.
| | - Yulia I Aleksandrova
- Kazan Federal University, A.M. Butlerov Chemistry Institute, 420008 Kremlevskaya, 18, Kazan, Russian Federation
| | - Olga A Mostovaya
- Kazan Federal University, A.M. Butlerov Chemistry Institute, 420008 Kremlevskaya, 18, Kazan, Russian Federation
| | - Viktoriya A Nazmutdinova
- Kazan Federal University, A.M. Butlerov Chemistry Institute, 420008 Kremlevskaya, 18, Kazan, Russian Federation
| | - Pavel V Zelenikhin
- Kazan Federal University, Institute of Fundamental Medicine and Biology, 420008 Kremlevskaya, 18, Kazan, Russian Federation
| | - Evgenia V Subakaeva
- Kazan Federal University, Institute of Fundamental Medicine and Biology, 420008 Kremlevskaya, 18, Kazan, Russian Federation
| | - Timur A Mukhametzyanov
- Kazan Federal University, A.M. Butlerov Chemistry Institute, 420008 Kremlevskaya, 18, Kazan, Russian Federation
| | - Peter J Cragg
- School of Applied Sciences, University of Brighton, Huxley Building, Moulsecoomb, Brighton, East Sussex BN2 4GJ, UK
| | - Ivan I Stoikov
- Kazan Federal University, A.M. Butlerov Chemistry Institute, 420008 Kremlevskaya, 18, Kazan, Russian Federation.
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Tsai CL, Wu SY, Hsu HK, Huang SB, Lin CH, Chan YT, Wang SK. Preparation and conformational analysis of polyproline tri-helix macrocycle nanoscaffolds of varied sizes. NANOSCALE 2021; 13:4592-4601. [PMID: 33605962 DOI: 10.1039/d0nr08184a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Ligand patterns at the nanoscale are essential in modulating biological recognition and signaling through binding to receptor oligomers. Biocompatible nanoscaffolds that allow precise control of multiple ligand presentation would be of great use in manipulating cellular processes and understanding membrane receptor biology. We have previously developed tri-helix and tetra-helix macrocycle scaffolds based on the Pro9 peptide helix to control ligand arrangements that can selectively target receptor oligomers. A better understanding of the structure of these macromolecules would significantly reduce the difficulty in designing matching ligand positions for target receptors. In this work, we expand the arsenal of ligand patterns by preparing polyproline tri-helix macrocycle scaffolds of different sizes. These synthetic nanoscaffolds composed of peptide helices ranging from Pro6 to Pro12 also allowed us to systematically investigate their properties. With a combination of circular dichroism spectroscopy and ion mobility spectrometry-mass spectrometry (IMS-MS), the measurement for varied sizes of these scaffolds indicated the connecting dihedral angle between both ends of the helix affects the strain in the cyclic scaffold. The experimental collision cross section obtained from IMS-MS favors a propeller model for the helix arrangements. The results not only contribute conformational insights for the polyproline tri-helix system, but also provide precious information for the future design and synthesis of cyclic nanostructures based on peptide helices.
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Affiliation(s)
- Chia-Lung Tsai
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Shao-Yong Wu
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Hung-Kai Hsu
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan.
| | - Sheng-Bo Huang
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Cin-Hao Lin
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Yi-Tsu Chan
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan. and Center for Emerging Materials and Advanced Devices, National Taiwan University, Taipei 10617, Taiwan
| | - Sheng-Kai Wang
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan. and Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan
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Pietrzyk-Brzezinska AJ, Bujacz A. H-type lectins - Structural characteristics and their applications in diagnostics, analytics and drug delivery. Int J Biol Macromol 2020; 152:735-747. [PMID: 32119947 DOI: 10.1016/j.ijbiomac.2020.02.320] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/27/2020] [Accepted: 02/27/2020] [Indexed: 12/15/2022]
Abstract
Lectins are ubiquitous carbohydrate-binding proteins that interact with sugar moieties in a highly specific manner. H-type lectins represent a new group of lectins that were identified in invertebrates. These lectins share structural homology and bind mainly to N-acetylgalactosamine (GalNAc). Recent structural studies on the H-type lectins provided a detailed description of the GalNAc-lectin interaction that is already exploited in a number of biomedical applications. Two members of the H-type lectin family, Helix pomatia agglutinin (HPA) and Helix aspersa agglutinin (HAA), have already been extensively used in many diagnostic tests due their ability to specifically recognize GalNAc. This ability is especially important because aberrant glycosylation patterns of proteins expressed by cancer cells contain GalNAc. In addition, H-type lectins were utilized in diagnostics of other non-cancer diseases and represent great potential as components of drug delivery systems. Here, we present an overview of the H-type lectins and their applications in diagnostics, analytics and drug delivery.
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Affiliation(s)
- Agnieszka J Pietrzyk-Brzezinska
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, Lodz 90-924, Poland.
| | - Anna Bujacz
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, Lodz 90-924, Poland
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Augustine R, Kalva N, Kim HA, Zhang Y, Kim I. pH-Responsive Polypeptide-Based Smart Nano-Carriers for Theranostic Applications. Molecules 2019; 24:E2961. [PMID: 31443287 PMCID: PMC6719039 DOI: 10.3390/molecules24162961] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/12/2019] [Accepted: 08/13/2019] [Indexed: 02/07/2023] Open
Abstract
Smart nano-carriers have attained great significance in the biomedical field due to their versatile and interesting designs with different functionalities. The initial stages of the development of nanocarriers mainly focused on the guest loading efficiency, biocompatibility of the host and the circulation time. Later the requirements of less side effects with more efficacy arose by attributing targetability and stimuli-responsive characteristics to nano-carriers along with their bio- compatibility. Researchers are utilizing many stimuli-responsive polymers for the better release of the guest molecules at the targeted sites. Among these, pH-triggered release achieves increasing importance because of the pH variation in different organ and cancer cells of acidic pH. This specific feature is utilized to release the guest molecules more precisely in the targeted site by designing polymers having specific functionality with the pH dependent morphology change characteristics. In this review, we mainly concert on the pH-responsive polypeptides and some interesting nano-carrier designs for the effective theranostic applications. Also, emphasis is made on pharmaceutical application of the different nano-carriers with respect to the organ, tissue and cellular level pH environment.
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Affiliation(s)
- Rimesh Augustine
- BK 21 PLUS Center for Advanced Chemical Technology, Department of Polymer Science and Engineering, Pusan National University, Geumjeong-gu, Busan 46241, Korea
| | - Nagendra Kalva
- BK 21 PLUS Center for Advanced Chemical Technology, Department of Polymer Science and Engineering, Pusan National University, Geumjeong-gu, Busan 46241, Korea
| | - Ho An Kim
- BK 21 PLUS Center for Advanced Chemical Technology, Department of Polymer Science and Engineering, Pusan National University, Geumjeong-gu, Busan 46241, Korea
| | - Yu Zhang
- BK 21 PLUS Center for Advanced Chemical Technology, Department of Polymer Science and Engineering, Pusan National University, Geumjeong-gu, Busan 46241, Korea
| | - Il Kim
- BK 21 PLUS Center for Advanced Chemical Technology, Department of Polymer Science and Engineering, Pusan National University, Geumjeong-gu, Busan 46241, Korea.
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Wen HC, Lin CH, Huang JS, Tsai CL, Chen TF, Wang SK. Selective targeting of DC-SIGN by controlling the oligomannose pattern on a polyproline tetra-helix macrocycle scaffold. Chem Commun (Camb) 2019; 55:9124-9127. [PMID: 31298664 DOI: 10.1039/c9cc03124c] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
DC-SIGN and langerin receptors both bind to oligomannose but lead to opposite effects upon encountering HIV. Because selective targeting of DC-SIGN can lead to anti-viral effects, we developed a glycoconjugate, which provides over 4800-fold selectivity for DC-SIGN over langerin, by controlling the oligomannose pattern on a polyproline tetra-helix macrocycle scaffold.
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Affiliation(s)
- Hsin-Chuan Wen
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan.
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