scholarly journals A versatile strategy for the synthesis of sequence-defined peptoids with side-chain and backbone diversity via amino acid building blocks

2019 ◽  
Vol 10 (5) ◽  
pp. 1531-1538 ◽  
Author(s):  
Shixue Wang ◽  
Yue Tao ◽  
Jianqun Wang ◽  
Youhua Tao ◽  
Xianhong Wang

De novo design and synthesis of sequence-defined peptoids via amino acid building blocks is reported.

2021 ◽  
Author(s):  
Chris Papadopoulos ◽  
Isabelle Callebaut ◽  
Jean-Christophe Gelly ◽  
Isabelle Hatin ◽  
Olivier Namy ◽  
...  

The noncoding genome plays an important role in de novo gene birth and in the emergence of genetic novelty. Nevertheless, how noncoding sequences' properties could promote the birth of novel genes and shape the evolution and the structural diversity of proteins remains unclear. Therefore, by combining different bioinformatic approaches, we characterized the fold potential diversity of the amino acid sequences encoded by all intergenic ORFs (Open Reading Frames) of S. cerevisiae with the aim of (i) exploring whether the large structural diversity observed in proteomes is already present in noncoding sequences, and (ii) estimating the potential of the noncoding genome to produce novel protein bricks that can either give rise to novel genes or be integrated into pre-existing proteins, thus participating in protein structure diversity and evolution. We showed that amino acid sequences encoded by most yeast intergenic ORFs contain the elementary building blocks of protein structures. Moreover, they encompass the large structural diversity of canonical proteins with strikingly the majority predicted as foldable. Then, we investigated the early stages of de novo gene birth by identifying intergenic ORFs with a strong translation signal in ribosome profiling experiments and by reconstructing the ancestral sequences of 70 yeast de novo genes. This enabled us to highlight sequence and structural factors determining de novo gene emergence. Finally, we showed a strong correlation between the fold potential of de novo proteins and the one of their ancestral amino acid sequences, reflecting the relationship between the noncoding genome and the protein structure universe.


RSC Advances ◽  
2020 ◽  
Vol 10 (38) ◽  
pp. 22397-22416
Author(s):  
Zahraa S. Al-Taie ◽  
Simon R. Anetts ◽  
Jeppe Christensen ◽  
Simon J. Coles ◽  
Peter N. Horton ◽  
...  

Catalysts assemble! We present the design and synthesis of a large family of amino acid derived guanidine organic moieties as catalysts in the solution state and building blocks towards extended H-bonded architectures upon crystallisation.


2021 ◽  
Vol 22 (22) ◽  
pp. 12428
Author(s):  
Yang Ai ◽  
Ben Wang ◽  
Shuai Xiao ◽  
Sang Luo ◽  
Yefu Wang

Tryptophan metabolism plays a role in the occurrence and development of hepatocellular carcinoma cells. By degrading certain amino acids, tumor growth can be limited while maintaining the body’s normal nutritional requirements. Tryptophan side-chain oxidase (TSO) enzyme can degrade tryptophan, and its inhibitory effect on hepatocellular carcinoma cells is worthy of further study. To investigate the degradation effect on tryptophan, TSO was isolated and purified from qq Pseudomonas. The reaction products were identified with high performance liquid chromatography (HPLC) and high-performance liquid chromatography tandem mass spectrometry (HPLC-MS). De novo sequencing provided the complete amino acid sequence of TSO. The results of CCK-8, colony formation, transwell, and qPCR confirmed that TSO had inhibitory effects on the proliferation and migration of HCCLM3 (human hepatocarcinoma cell line) and HepG2 cells. The results of flow cytometry confirmed its apoptotic activity. In animal experiments, we found that the tumor-suppressive effect was better in the oncotherapy group than the intraperitoneal injection group. The results of immunohistochemistry also suggested that TSO could inhibit proliferation and promote apoptosis. In conclusion, a specific enzyme that can degrade tryptophan and inhibit the growth of hepatoma cells was authenticated, and its basic information was obtained by extraction/purification and amino acid sequencing.


Author(s):  
Gregg B. Fields ◽  
Janelle L Lauer-Fields

Peptides play key structural and functional roles in biochemistry, pharmacology, and neurobiology, and are important probes for research in enzymology, immunology, and molecular biology. The amino acid building blocks can be among the 20 genetically encoded L-residues, or else unusual ones, and the sequences can be linear, cyclic, or branched. It follows that rapid, efficient, and reliable methodology for the chemical synthesis of these molecules is of utmost interest. A number of synthetic peptides are significant commercial or pharmaceutical products, ranging from the sweet dipeptide L-Asp-L-Phe-OMe (aspartame) to clinically used hormones such as oxytocin, adrenocorticotropic hormone, calcitonin, and gonadotropin releasing hormone (GnRH) super-agonists. Synthesis can lead to potent and selective new drugs by judicious substitutions that change functional groups and/or conformations of the parent peptide. These include introduction of N- or C-alkyl substituents, unnatural or D-amino acids, side-chain modifications including sulfate or phosphate groups or carbohydrate moieties, and constraints such as disulfide bridges between half-cystines or side-chain lactams between Lys and Asp or Glu. Commercially important products that evolved from such studies include protease inhibitors, such as captopril and other angiotensin converting enzyme (ACE) inhibitors, peptidomimetic HIV protease inhibitors, and the somatostatin analog lanreotide. Most of the biologically or medicinally important peptides which are the targets for useful structure-function studies by chemical synthesis comprise under 50 amino acid residues, but occasionally a synthetic approach can lead to important conclusions about small proteins (full or domains) in the 100-200 residue size range. Methods for synthesizing peptides are divided conveniently into two categories: solution (classical) and solid-phase pep tide synthesis (SPPS). The classical methods have evolved since the beginning of the twentieth century, and they are described amply in several reviews and books (Wünsch, 1974; Finn and Hofmann, 1976; Bodanszky and Bodanszky, 1984; Goodman et al, 2001). The solid-phase alternative was conceived and elaborated by R. B. Merrifield beginning in 1959, and has also been covered comprehensively (Erickson and Merrifield, 1976; Birr, 1978; Barany and Merrifield, 1979; Stewart and Young, 1984; Merrifield, 1986; Barany et al., 1987, 1988; Kent, 1988; Atherton and Sheppard, 1989; Fields and Noble, 1990; Barany and Albericio, 1991; Fields et al., 1992; Gutte, 1995; Fields, 1997; Lloyd-Williams et al., 1997; Chan and White, 2000; Kates and Albericio, 2000).


Author(s):  
Matthias Breuning ◽  
Tobias Häuser ◽  
Christian Mehler ◽  
Christian Däschlein ◽  
Carsten Strohmann ◽  
...  

An enantioselective route to four tricyclic amino acids and N-tosylamides, composed of a central norbornane framework with a 2-endo,3-endo-annelated pyrrolidine ring and a 5-endo-C1 or -C2 side chain, has been developed. A key intermediate was the chiral, N-Boc-protected ketone (1R,2S,6S,7R)-4-azatricyclo[5.2.1.02,6]decan-8-one, available from inexpensive endo-carbic anhydride in five steps and 47% yield. The rigid scaffold makes these amino acid derivatives promising candidates for β-turn-inducing building blocks in peptidomimetics and for chiral auxiliaries in asymmetric organocatalysis.


2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Jinghua Yang ◽  
Zhangping Li ◽  
Jinmin Lian ◽  
Guoning Qi ◽  
Pibiao Shi ◽  
...  

AbstractWasabi, horseradish and mustard are popular pungent crops in which the characteristic bioactive hydrolysis of specialized glucosinolates (GSLs) occurs. Although the metabolic pathways of GSLs are well elucidated, how plants have evolved convergent mechanisms to accumulate identical GSL components remains largely unknown. In this study, we discovered that sinigrin is predominantly synthesized in wasabi, horseradish and mustard in Brassicaceae. We de novo assembled the transcriptomes of the three species, revealing the expression patterns of gene clusters associated with chain elongation, side chain modification and transport. Our analysis further revealed that several gene clusters were convergently selected during evolution, exhibiting convergent shifts in amino acid preferences in mustard, wasabi and horseradish. Collectively, our findings provide insights into how unrelated crop species evolve the capacity for sinigrin super-accumulation and thus promise a potent strategy for engineering metabolic pathways at multiple checkpoints to fortify bioactive compounds for condiment or pharmaceutical purposes.


2021 ◽  
Vol 7 (20) ◽  
pp. eabg1448
Author(s):  
Mingming Wang ◽  
Yang Song ◽  
Shuai Zhang ◽  
Xin Zhang ◽  
Xiaoli Cai ◽  
...  

Inspired by the formation of hierarchically structured natural biominerals (e.g., bone and tooth), various sequence-defined polymers have been synthesized and exploited for design and synthesis of functional hybrid materials. Here, we synthesized a series of organic-inorganic hybrid peptoids by using polyhedral oligomeric silsesquioxane (POSS) nanoclusters as side chains at a variety of backbone locations. We further demonstrated the use of these hybrid peptoids as sequence-defined building blocks to assemble a new class of programmable two-dimensional (2D) nanocrystals. They are highly stable and exhibit an enhanced mechanical property and electron scattering due to the incorporated POSS nanoclusters. By varying peptoid side-chain chemistry, we further demonstrated the precise displacement of a large variety of function groups within these 2D nanocrystals and developed a highly efficient aqueous light-harvesting system for live cell imaging. Because these 2D nanocrystals are biocompatible and highly programmable, we expect that they offer unique opportunities for applications.


2021 ◽  
Author(s):  
Chris Papadopoulos ◽  
Isabelle Callebaut ◽  
Jean-Christophe Gelly ◽  
Isabelle Hatin ◽  
Olivier Namy ◽  
...  

The noncoding genome plays an important role in de novo gene birth and in the emergence of genetic novelty. Nevertheless, how noncoding sequences’ properties could promote the birth of novel genes and shape the evolution and the structural diversity of proteins remains unclear. Therefore, by combining different bioinformatic approaches, we characterized the fold potential diversity of the amino acid sequences encoded by all intergenic open reading frames (ORFs) of S. cerevisiae with the aim of (1) exploring whether the structural states’ diversity of proteomes is already present in noncoding sequences, and (2) estimating the potential of the noncoding genome to produce novel protein bricks that could either give rise to novel genes or be integrated into pre-existing proteins, thus participating in protein structure diversity and evolution. We showed that amino acid sequences encoded by most yeast intergenic ORFs contain the elementary building blocks of protein structures. Moreover, they encompass the large structural state diversity of canonical proteins, with the majority predicted as foldable. Then, we investigated the early stages of de novo gene birth by reconstructing the ancestral sequences of 70 yeast de novo genes and characterized the sequence and structural properties of intergenic ORFs with a strong translation signal. This enabled us to highlight sequence and structural factors determining de novo gene emergence. Finally, we showed a strong correlation between the fold potential of de novo proteins and one of their ancestral amino acid sequences, reflecting the relationship between the noncoding genome and the protein structure universe.


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