1
|
Petkowski JJ, Seager MD, Bains W, Seager S. General instability of dipeptides in concentrated sulfuric acid as relevant for the Venus cloud habitability. Sci Rep 2024; 14:17083. [PMID: 39048621 PMCID: PMC11269616 DOI: 10.1038/s41598-024-67342-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 07/10/2024] [Indexed: 07/27/2024] Open
Abstract
Recent renewed interest in the possibility of life in the acidic clouds of Venus has led to new studies on organic chemistry in concentrated sulfuric acid. We have previously found that the majority of amino acids are stable in the range of Venus' cloud sulfuric acid concentrations (81% and 98% w/w, the rest being water). The natural next question is whether dipeptides, as precursors to larger peptides and proteins, could be stable in this environment. We investigated the reactivity of the peptide bond using 20 homodipeptides and find that the majority of them undergo solvolysis within a few weeks, at both sulfuric acid concentrations. Notably, a few exceptions exist. HH and GG dipeptides are stable in 98% w/w sulfuric acid for at least 4 months, while II, LL, VV, PP, RR and KK resist hydrolysis in 81% w/w sulfuric acid for at least 5 weeks. Moreover, the breakdown process of the dipeptides studied in 98% w/w concentrated sulfuric acid is different from the standard acid-catalyzed hydrolysis that releases monomeric amino acids. Despite a few exceptions at a single concentration, no homodipeptides have demonstrated stability across both acid concentrations studied. This indicates that any hypothetical life on Venus would likely require a functional substitute for the peptide bond that can maintain stability throughout the range of sulfuric acid concentrations present.
Collapse
Affiliation(s)
- Janusz J Petkowski
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
- Faculty of Environmental Engineering, Wroclaw University of Science and Technology, 50-370, Wroclaw, Poland.
- JJ Scientific, 02-792, Mazowieckie, Warsaw, Poland.
| | - Maxwell D Seager
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
- Nanoplanet Consulting, Concord, MA, 01742, USA
| | - William Bains
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- School of Physics and Astronomy, Cardiff University, 4 The Parade, Cardiff, CF24 3AA, UK
- Rufus Scientific, Melbourn, Herts, SG8 6ED, UK
| | - Sara Seager
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Nanoplanet Consulting, Concord, MA, 01742, USA
- Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| |
Collapse
|
2
|
Guerassimoff L, Ferrere M, Bossion A, Nicolas J. Stimuli-sensitive polymer prodrug nanocarriers by reversible-deactivation radical polymerization. Chem Soc Rev 2024; 53:6511-6567. [PMID: 38775004 PMCID: PMC11181997 DOI: 10.1039/d2cs01060g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Indexed: 06/18/2024]
Abstract
Polymer prodrugs are based on the covalent linkage of therapeutic molecules to a polymer structure which avoids the problems and limitations commonly encountered with traditional drug-loaded nanocarriers in which drugs are just physically entrapped (e.g., burst release, poor drug loadings). In the past few years, reversible-deactivation radical polymerization (RDRP) techniques have been extensively used to design tailor-made polymer prodrug nanocarriers. This synthesis strategy has received a lot of attention due to the possibility of fine tuning their structural parameters (e.g., polymer nature and macromolecular characteristics, linker nature, physico-chemical properties, functionalization, etc.), to achieve optimized drug delivery and therapeutic efficacy. In particular, adjusting the nature of the drug-polymer linker has enabled the easy synthesis of stimuli-responsive polymer prodrugs for efficient spatiotemporal drug release. In this context, this review article will give an overview of the different stimuli-sensitive polymer prodrug structures designed by RDRP techniques, with a strong focus on the synthesis strategies, the macromolecular architectures and in particular the drug-polymer linker, which governs the drug release kinetics and eventually the therapeutic effect. Their biological evaluations will also be discussed.
Collapse
Affiliation(s)
- Léa Guerassimoff
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 91400, Orsay, France.
| | - Marianne Ferrere
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 91400, Orsay, France.
| | - Amaury Bossion
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 91400, Orsay, France.
| | - Julien Nicolas
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 91400, Orsay, France.
| |
Collapse
|
3
|
Zheng F, Ju M, Lü Y, Hua Y, Yao W, Wu H, Zhao M, Han S, Wei Y, Liu R. Carp scales derived double cross-linking hydrogels achieve collagen peptides sustained-released for bone regeneration. Int J Biol Macromol 2024; 255:128276. [PMID: 37992919 DOI: 10.1016/j.ijbiomac.2023.128276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 11/24/2023]
Abstract
Collagen peptide exhibits a great activity in osteogenic differentiation and wound healing. However, uncontrolled collagen peptide release in bone defects leads to unsatisfactory bone regeneration. In this work, we prepared collagen peptide loaded calcium alginate hydrogel (SA-CP/Ca) derived from Asia carp scales by mixing sodium alginate solution, collagen peptides, calcium carbonate, covalent cross-linking agents N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride (EDC), and N-hydroxysuccinimide (NHS) in one pot. Physically and chemically double cross-linking realized higher crosslink density, smaller porosity and pore size, and higher energy storage modulus and loss modulus, achieving sustained release of collagen peptides. The release profile is fitted to Keppas-Sahlin model, to find SA-CP/Ca hydrogels are more inclined to release collagen peptides through expansion and degradation. The compatibility and osteogenic ability of SA-CP/Ca are demonstrated in vitro and in vivo.
Collapse
Affiliation(s)
- Fei Zheng
- Jiangsu Key Laboratory of Research and Development in Marine Bio-resource Pharmaceutics, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China; School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China; Animal-Derived Chinese Medicine and Functional Peptides International Collaboration Joint Laboratory, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
| | - Miaomiao Ju
- Jiangsu Key Laboratory of Research and Development in Marine Bio-resource Pharmaceutics, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China; School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China; Animal-Derived Chinese Medicine and Functional Peptides International Collaboration Joint Laboratory, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
| | - Yijun Lü
- Jiangsu Key Laboratory of Research and Development in Marine Bio-resource Pharmaceutics, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China; School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China; Animal-Derived Chinese Medicine and Functional Peptides International Collaboration Joint Laboratory, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
| | - Yongqing Hua
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China; School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
| | - Weifeng Yao
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
| | - Hao Wu
- Jiangsu Key Laboratory of Research and Development in Marine Bio-resource Pharmaceutics, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China; School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
| | - Ming Zhao
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China; School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China; Animal-Derived Chinese Medicine and Functional Peptides International Collaboration Joint Laboratory, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
| | - Shuying Han
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
| | - Yuanqing Wei
- Jiangsu Key Laboratory of Research and Development in Marine Bio-resource Pharmaceutics, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China; School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China; Animal-Derived Chinese Medicine and Functional Peptides International Collaboration Joint Laboratory, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Rui Liu
- Jiangsu Key Laboratory of Research and Development in Marine Bio-resource Pharmaceutics, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China; School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China; Animal-Derived Chinese Medicine and Functional Peptides International Collaboration Joint Laboratory, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| |
Collapse
|
4
|
Śmiłowicz D, Eisenberg S, LaForest R, Whetter J, Hariharan A, Bordenca J, Johnson CJ, Boros E. Metal-Mediated, Autolytic Amide Bond Cleavage: A Strategy for the Selective, Metal Complexation-Catalyzed, Controlled Release of Metallodrugs. J Am Chem Soc 2023; 145:16261-16270. [PMID: 37434328 PMCID: PMC10530410 DOI: 10.1021/jacs.3c05492] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Activation of metalloprodrugs or prodrug activation using transition metal catalysts represents emerging strategies for drug development; however, they are frequently hampered by poor spatiotemporal control and limited catalytic turnover. Here, we demonstrate that metal complex-mediated, autolytic release of active metallodrugs can be successfully employed to prepare clinical grade (radio-)pharmaceuticals. Optimization of the Lewis-acidic metal ion, chelate, amino acid linker, and biological targeting vector provides means to release peptide-based (radio-)metallopharmaceuticals in solution and from the solid phase using metal-mediated, autolytic amide bond cleavage (MMAAC). Our findings indicate that coordinative polarization of an amide bond by strong, trivalent Lewis acids such as Ga3+ and Sc3+ adjacent to serine results in the N, O acyl shift and hydrolysis of the corresponding ester without dissociation of the corresponding metal complex. Compound [68Ga]Ga-10, incorporating a cleavable and noncleavable functionalization, was used to demonstrate that only the amide bond-adjacent serine effectively triggered hydrolysis in solution and from the solid phase. The corresponding solid-phase released compound [68Ga]Ga-8 demonstrated superior in vivo performance in a mouse tumor model compared to [68Ga]Ga-8 produced using conventional, solution-phase radiolabeling. A second proof-of-concept system, [67Ga]Ga-17A (serine-linked) and [67Ga]Ga-17B (glycine-linked) binding to serum albumin via the incorporated ibuprofen moiety, was also synthesized. These constructs demonstrated that complete hydrolysis of the corresponding [68Ga]Ga-NOTA complex from [67Ga]Ga-17A can be achieved in naïve mice within 12 h, as traceable in urine and blood metabolites. The glycine-linked control [68Ga]Ga-17B remained intact. Conclusively, MMAAC provides an attractive tool for selective, thermal, and metal ion-mediated control of metallodrug activation compatible with biological conditions.
Collapse
Affiliation(s)
- Dariusz Śmiłowicz
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, New York 11794, United States
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Shawn Eisenberg
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, New York 11794, United States
| | - Rochelle LaForest
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, New York 11794, United States
| | - Jennifer Whetter
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, New York 11794, United States
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Annapoorani Hariharan
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, New York 11794, United States
| | - Jake Bordenca
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, New York 11794, United States
| | - Christopher J Johnson
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, New York 11794, United States
| | - Eszter Boros
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, New York 11794, United States
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| |
Collapse
|
5
|
Schaefer D, Cheng X. Recent Advances in Covalent Drug Discovery. Pharmaceuticals (Basel) 2023; 16:ph16050663. [PMID: 37242447 DOI: 10.3390/ph16050663] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/10/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
In spite of the increasing number of biologics license applications, the development of covalent inhibitors is still a growing field within drug discovery. The successful approval of some covalent protein kinase inhibitors, such as ibrutinib (BTK covalent inhibitor) and dacomitinib (EGFR covalent inhibitor), and the very recent discovery of covalent inhibitors for viral proteases, such as boceprevir, narlaprevir, and nirmatrelvir, represent a new milestone in covalent drug development. Generally, the formation of covalent bonds that target proteins can offer drugs diverse advantages in terms of target selectivity, drug resistance, and administration concentration. The most important factor for covalent inhibitors is the electrophile (warhead), which dictates selectivity, reactivity, and the type of protein binding (i.e., reversible or irreversible) and can be modified/optimized through rational designs. Furthermore, covalent inhibitors are becoming more and more common in proteolysis, targeting chimeras (PROTACs) for degrading proteins, including those that are currently considered to be 'undruggable'. The aim of this review is to highlight the current state of covalent inhibitor development, including a short historical overview and some examples of applications of PROTAC technologies and treatment of the SARS-CoV-2 virus.
Collapse
Affiliation(s)
- Daniel Schaefer
- Buchmann Institute for Molecular Life Sciences, Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 15. R. 3.652, 60438 Frankfurt am Main, Germany
- Pharmaceutical Chemistry, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Xinlai Cheng
- Buchmann Institute for Molecular Life Sciences, Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 15. R. 3.652, 60438 Frankfurt am Main, Germany
- Pharmaceutical Chemistry, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, 60596 Frankfurt am Main, Germany
| |
Collapse
|
6
|
Kuzhelev AA, Denysenkov V, Ahmad IM, Rogozhnikova OY, Trukhin DV, Bagryanskaya EG, Tormyshev VM, Sigurdsson ST, Prisner TF. Solid-Effect Dynamic Nuclear Polarization in Viscous Liquids at 9.4 T Using Narrow-Line Polarizing Agents. J Am Chem Soc 2023; 145:10268-10274. [PMID: 37104685 DOI: 10.1021/jacs.3c01358] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Dynamic nuclear polarization (DNP) is a hyperpolarization method that is widely used for increasing the sensitivity of nuclear magnetic resonance (NMR) experiments. DNP is efficient in solid-state and liquid-state NMR, but its implementation in the intermediate state, namely, viscous media, is still less explored. Here, we show that a 1H DNP enhancement of over 50 can be obtained in viscous liquids at a magnetic field of 9.4 T and a temperature of 315 K. This was accomplished by using narrow-line polarizing agents in glycerol, both the water-soluble α,γ-bisdiphenylen-β-phenylallyl (BDPA) and triarylmethyl radicals, and a microwave/RF double-resonance probehead. We observed DNP enhancements with a field profile indicative of the solid effect and investigated the influence of microwave power, temperature, and concentration on the 1H NMR results. To demonstrate potential applications of this new DNP approach for chemistry and biology, we show hyperpolarized 1H NMR spectra of tripeptides, triglycine, and glypromate, in glycerol-d8.
Collapse
Affiliation(s)
- Andrei A Kuzhelev
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max von Laue Straße 7, 60438 Frankfurt am Main, Germany
| | - Vasyl Denysenkov
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max von Laue Straße 7, 60438 Frankfurt am Main, Germany
| | - Iram M Ahmad
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107 Reykjavik, Iceland
| | - Olga Yu Rogozhnikova
- N. N. Vorozhtsov Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences (SB RAS), Acad. Lavrentiev Avenue 9, 630090 Novosibirsk, Russia
| | - Dmitry V Trukhin
- N. N. Vorozhtsov Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences (SB RAS), Acad. Lavrentiev Avenue 9, 630090 Novosibirsk, Russia
| | - Elena G Bagryanskaya
- N. N. Vorozhtsov Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences (SB RAS), Acad. Lavrentiev Avenue 9, 630090 Novosibirsk, Russia
| | - Victor M Tormyshev
- N. N. Vorozhtsov Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences (SB RAS), Acad. Lavrentiev Avenue 9, 630090 Novosibirsk, Russia
| | - Snorri Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107 Reykjavik, Iceland
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max von Laue Straße 7, 60438 Frankfurt am Main, Germany
| |
Collapse
|
7
|
Boigenzahn H, Yin J. Glycine to Oligoglycine via Sequential Trimetaphosphate Activation Steps in Drying Environments. ORIGINS LIFE EVOL B 2022; 52:249-261. [DOI: 10.1007/s11084-022-09634-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/03/2022] [Indexed: 12/14/2022]
|
8
|
Optimized aptamer functionalization for enhanced anticancer efficiency in vivo. Int J Pharm 2022; 628:122330. [DOI: 10.1016/j.ijpharm.2022.122330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/15/2022] [Accepted: 10/18/2022] [Indexed: 11/18/2022]
|
9
|
Conformational analysis and water dynamics: a molecular dynamics study on the survival of a β-lactoglobulin peptide in the archaeological record. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
10
|
Singh J, Whitaker D, Thoma B, Islam S, Foden CS, Aliev AE, Sheppard TD, Powner MW. Prebiotic Catalytic Peptide Ligation Yields Proteinogenic Peptides by Intramolecular Amide Catalyzed Hydrolysis Facilitating Regioselective Lysine Ligation in Neutral Water. J Am Chem Soc 2022; 144:10151-10155. [PMID: 35640067 PMCID: PMC9204760 DOI: 10.1021/jacs.2c03486] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
The prebiotic origin
of catalyst-controlled peptide synthesis is
fundamental to understanding the emergence of life. Building on our
recent discovery that thiols catalyze the ligation of amino acids,
amides, and peptides with amidonitriles in neutral water, we demonstrate
the outcome of ligation depends on pH and that high pKa primary thiols are the ideal catalysts. While the most
rapid thiol catalyzed peptide ligation occurs at pH 8.5–9,
the most selective peptide ligation, that tolerates all proteinogenic
side chains, occurs at pH 7. We have also identified the highly selective
mechanism by which the intermediate peptidyl amidines undergo hydrolysis
to α-peptides while demonstrating that the hydrolysis of amidines
with nonproteinogenic structures, such as β- and γ-peptides,
displays poor selectivity. Notably, this discovery enables the highly
α-selective protecting-group-free ligation of lysine peptides
at neutral pH while leaving the functional ε-amine side chain
intact.
Collapse
Affiliation(s)
- Jyoti Singh
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Daniel Whitaker
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Benjamin Thoma
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Saidul Islam
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom.,Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Callum S Foden
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Abil E Aliev
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Tom D Sheppard
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Matthew W Powner
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| |
Collapse
|
11
|
Chaijan M, Rodsamai T, Charoenlappanit S, Roytrakul S, Panya A, Phonsatta N, Cheong L, Panpipat W. Antioxidant activity and stability of endogenous peptides from farmed hybrid catfish (
Clarias macrocephalus
×
Clarias gariepinus
) muscle. Int J Food Sci Technol 2022. [DOI: 10.1111/ijfs.15474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Manat Chaijan
- Food Technology and Innovation Research Centre of Excellence School of Agricultural Technology and Food Industry Walailak University Thasala Nakhon Si Thammarat 80161 Thailand
| | - Tanutchaporn Rodsamai
- Food Technology and Innovation Research Centre of Excellence School of Agricultural Technology and Food Industry Walailak University Thasala Nakhon Si Thammarat 80161 Thailand
| | - Sawanya Charoenlappanit
- Functional Proteomics Technology Laboratory Functional Ingredients and Food Innovation Research Group National Centre for Genetic Engineering and Biotechnology (BIOTEC) 113 Thailand Science Park, Phaholyothin Rd, Khlong Nueng Khlong Luang Pathumthani 12120 Thailand
| | - Sittiruk Roytrakul
- Functional Proteomics Technology Laboratory Functional Ingredients and Food Innovation Research Group National Centre for Genetic Engineering and Biotechnology (BIOTEC) 113 Thailand Science Park, Phaholyothin Rd, Khlong Nueng Khlong Luang Pathumthani 12120 Thailand
| | - Atikorn Panya
- Food Biotechnology Research Team Functional Ingredients and Food Innovation Research Group National Centre for Genetic Engineering and Biotechnology (BIOTEC) 113 Thailand Science Park, Phaholyothin Rd, Khlong Nueng Khlong Luang Pathumthani 12120 Thailand
| | - Natthaporn Phonsatta
- Food Biotechnology Research Team Functional Ingredients and Food Innovation Research Group National Centre for Genetic Engineering and Biotechnology (BIOTEC) 113 Thailand Science Park, Phaholyothin Rd, Khlong Nueng Khlong Luang Pathumthani 12120 Thailand
| | - Ling‐Zhi Cheong
- Zhejiang‐Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition College of Food and Pharmaceutical Science Ningbo University Ningbo 315211 China
| | - Worawan Panpipat
- Food Technology and Innovation Research Centre of Excellence School of Agricultural Technology and Food Industry Walailak University Thasala Nakhon Si Thammarat 80161 Thailand
| |
Collapse
|
12
|
Characterization of Antioxidant Peptides from Thai Traditional Semi-Dried Fermented Catfish. FERMENTATION-BASEL 2021. [DOI: 10.3390/fermentation7040262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Herein, the antioxidant peptides from a Thai traditional semi-dried fermented farmed hybrid catfish (Clarias macrocephalus × Clarias gariepinus) catfish, Pla Duk Ra, were characterized. After extraction and deproteinization, Pla Duk Ra crude peptide extract (CPE) was fractioned using 2 connected Hitrap Sephadex-G25 columns, yielding two significant fractions, F1 with higher browning intensity (A420) and F2. CPE, F1, and F2 had different amino acid profiles, contents, and sequences evaluated by LC-MS/MS, which could be responsible for their antioxidant properties. F2 contained the highest numbers of hydrophobic amino acid (HBA) (47.45%) and aromatic amino acid (27.31%), followed by F1, and CPE. The peptides with 8–24 amino acid residues were detected in CPE and its fractions. In CPE, F1, and F2, there were 69, 68, and 85 peptides with varied HBA content, respectively. ARHSYGMLYCSCPPND (50% HBA), ALRKMGRK (37.5% HBA), and ANWMIPLM (87.5% HBA) were the most prevalent peptides found in CPE, F1, and F2. Overall, F2 was the most effective at inhibiting free radicals (DPPH● and ABTS●+) and reactive oxygen species (hydroxyl radical, singlet oxygen, and hydrogen peroxide), followed by F1 and CPE. The metal chelation of F1 was, however, superior to that of F2 and CPE. For the stability test, the effects of pH, heating temperature, and in vitro digestion on the DPPH● scavenging activity of F2 were investigated. The activity was boosted by lowering the pH and raising the heating temperature. In the gastrointestinal tract model system, however, roughly 50% of DPPH● scavenging activity reduced after digesting.
Collapse
|
13
|
Reinders LMH, Klassen MD, Teutenberg T, Jaeger M, Schmidt TC. Development of a multidimensional online method for the characterization and quantification of monoclonal antibodies using immobilized flow-through enzyme reactors. Anal Bioanal Chem 2021; 413:7119-7128. [PMID: 34628527 DOI: 10.1007/s00216-021-03683-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/14/2021] [Accepted: 09/20/2021] [Indexed: 01/06/2023]
Abstract
Complete characterization and quantification of monoclonal antibodies often rely on enzymatic digestion with trypsin. In order to accelerate and automate this frequently performed sample preparation step, immobilized enzyme reactors (IMER) compatible with standard HPLC systems were used. This allows an automated online approach in all analytical laboratories. We were able to demonstrate that the required digestion time for the model monoclonal antibody rituximab could be reduced to 20 min. Nevertheless, a previous denaturation of the protein is required, which also needs 20 min. Recoveries were determined at various concentrations and were 100% ± 1% at 100 ng on column, 96% ± 7% at 250 ng on column and 98% ± 2% at 450 ng on column. Despite these good recoveries, complete digestion was not achieved, resulting in a poorer limit of quantification. This is 50 ng on column under optimized IMER conditions, whereas an offline digest on the same system achieved 0.3 ng on column. Furthermore, our work revealed that TRIS buffers, when used with an IMER system, led to alteration of the peptides and induced modifications in the peptides. Therefore, the addition of TRIS should be avoided when working at elevated temperatures of about 60 °C. Nevertheless, our results have shown that the recovery is not significantly influenced whether TRIS is used or not (recovery: 96 ± 7% with TRIS vs. 100 ± 9% without TRIS).
Collapse
Affiliation(s)
- Lars M H Reinders
- Institut für Energie und Umwelttechnik e. V. (IUTA, Institute of Energy and Environmental Technology), Bliersheimer Str. 58-60, 47229, Duisburg, Germany.,Hochschule Niederrhein, University of Applied Science, Reinarzstr. 49, 47805, Krefeld, Germany.,Faculty of Chemistry, Instrumental Analytical Chemistry, University Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Martin D Klassen
- Institut für Energie und Umwelttechnik e. V. (IUTA, Institute of Energy and Environmental Technology), Bliersheimer Str. 58-60, 47229, Duisburg, Germany
| | - Thorsten Teutenberg
- Institut für Energie und Umwelttechnik e. V. (IUTA, Institute of Energy and Environmental Technology), Bliersheimer Str. 58-60, 47229, Duisburg, Germany.
| | - Martin Jaeger
- Hochschule Niederrhein, University of Applied Science, Reinarzstr. 49, 47805, Krefeld, Germany
| | - Torsten C Schmidt
- Faculty of Chemistry, Instrumental Analytical Chemistry, University Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| |
Collapse
|
14
|
Tanaka M, Hayashi M, Roach L, Kiriki Y, Kadonosono T, Nomoto T, Nishiyama N, Choi J, Critchley K, Evans SD, Okochi M. Synthesis of near-infrared absorbing triangular Au nanoplates using biomineralisation peptides. Acta Biomater 2021; 131:519-531. [PMID: 34144213 DOI: 10.1016/j.actbio.2021.06.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/24/2021] [Accepted: 06/01/2021] [Indexed: 12/27/2022]
Abstract
Triangular Au nanoplates (TrAuNPls) possessing strong plasmonic properties can be used as photothermal agents in cancer therapy. However, the controlled preparation of such morphologies typically requires harsh synthetic conditions. Biomolecules offer an alternative route to developing biocompatible synthetic protocols. In particular, peptides offer a novel route for inorganic synthesis under ambient conditions. Herein, using the previously isolated peptide, ASHQWAWKWE, for Au nanoparticle (AuNP) synthesis, the conditions for preparing TrAuNPls via a one-pot synthetic process of mixing HAuCl4 and peptides at room temperature were investigated to effectively obtain particles possessing near-infrared absorbance for non-invasive optical diagnosis and phototherapy. By adjusting the peptide concentration, the size and property of TrAuNPls were controlled under neutral pH conditions. The synthesised particles showed potential as photothermal therapeutic agents in vitro. In addition, peptide characterisation using B3 derivatives revealed the importance of the third amino acid histidine in morphological regulation and potential circular Au nanoplates (AuNPl) synthesis with ASEQWAWKWE and ASAQWAWKWE peptides. These findings provide not only an easy and green synthetic method for TrAuNPls and circular AuNPls, but also some insight to help elucidate the regulation of peptide-based nanoparticle synthesis for use in cancer therapy. STATEMENT OF SIGNIFICANCE: Biological molecules have received increasing attention as a vehicle to synthesise inorganic materials with specific properties under ambient conditions; particularly, short peptides have the potential to control the synthesis of nanoscale materials with tailored functions. Here, the application of a previously isolated peptide was assessed in synthesising Au nanoparticles containing decahedral and triangular nanoplates with near-infrared absorbance. The size and absorbance peaks of the triangular nanoplates observed were peptide concentration-dependent. In addition, these fine-tuned triangular nanoplates exhibited potential as a phototherapeutic agent. Moreover, the peptide derivatives indicated the possibility of synthesising circular nanoplates. These findings may offer insight into development of new techniques for synthesising functional nanoparticles having biological applications using non-toxic molecules under mild conditions stituted in the original B3 peptide is underlined.
Collapse
|
15
|
Bio-Crude Production Improvement during Hydrothermal Liquefaction of Biopulp by Simultaneous Application of Alkali Catalysts and Aqueous Phase Recirculation. ENERGIES 2021. [DOI: 10.3390/en14154492] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
This study focuses on the valorization of the organic fraction of municipal solid waste (biopulp) by hydrothermal liquefaction. Thereby, homogeneous alkali catalysts (KOH, NaOH, K2CO3, and Na2CO3) and a residual aqueous phase recirculation methodology were mutually employed to enhance the bio-crude yield and energy efficiency of a sub-critical hydrothermal conversion (350 °C, 15–20 Mpa, 15 min). Interestingly, single recirculation of the concentrated aqueous phase positively increased the bio-crude yield in all cases, while the higher heating value (HHV) of the bio-crudes slightly dropped. Compared to the non-catalytic experiment, K2CO3 and Na2CO3 effectively increased the bio-crude yield by 14 and 7.3%, respectively. However, KOH and NaOH showed a negative variation in the bio-crude yield. The highest bio-crude yield (37.5 wt.%) and energy recovery (ER) (59.4%) were achieved when K2CO3 and concentrated aqueous phase recirculation were simultaneously applied to the process. The inorganics distribution results obtained by ICP reveal the tendency of the alkali elements to settle into the aqueous phase, which, if recovered, can potentially boost the circularity of the HTL process. Therefore, wise selection of the alkali catalyst along with aqueous phase recirculation assists hydrothermal liquefaction in green biofuel production and environmentally friendly valorization of biopulp.
Collapse
|
16
|
Frenkel-Pinter M, Samanta M, Ashkenasy G, Leman LJ. Prebiotic Peptides: Molecular Hubs in the Origin of Life. Chem Rev 2020; 120:4707-4765. [PMID: 32101414 DOI: 10.1021/acs.chemrev.9b00664] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.
Collapse
Affiliation(s)
- Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mousumi Samanta
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Luke J Leman
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| |
Collapse
|