Article
Chemistry, Analytical
Mika Ishigaki, Atsushi Ito, Risa Hara, Shun-ichi Miyazaki, Kodai Murayama, Keisuke Yoshikiyo, Tatsuyuki Yamamoto, Yukihiro Ozaki
Summary: This study successfully developed a method of monitoring the increasing number of amide bonds with the elongation of peptide chain length using NIR spectroscopy. By evaluating the dehydration occurring between amino acids and constructing a calibration model with a high determination coefficient, the study provided valuable insights for analyzing amide bonds in the NIR spectra of proteins, polyamino acids, polypeptides, and polyamides.
ANALYTICAL CHEMISTRY
(2021)
Review
Chemistry, Multidisciplinary
Antonella lenia Alfano, Heiko Lange, Margherita Brindisi
Summary: The formation of amide bonds is essential in organic and synthetic medicinal chemistry. In recent years, the application of flow chemistry in amide bond formation has shown significant advantages and potential for development. This review summarizes and compares various methods and discusses future needs and prospects for sustainable synthesis.
Review
Biochemistry & Molecular Biology
Alexandre G. de Brevern
Summary: The β-turn is a significant secondary protein structure, but there is still confusion over its assignment and overlap with other structures, as well as the difficulty of software in assigning it.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Organic
Maria A. S. Yokomichi, Hanyeny R. L. Silva, Lorenza E. V. N. Brandao, Eduardo F. Vicente, Joao M. Batista Jr
Summary: This study presents the first VCD stereochemical investigation of orbitides, demonstrating the technique's ability to provide accurate structural characterization of these bioactive cyclic peptides. By combining IR/VCD experiments and DFT calculations, the researchers were able to determine the solution-state conformational behavior of a seven-residue orbitide and its linear precursor. VCD results revealed the prevalence of certain structural motifs and the existence of previously unidentified conformations. The conformational discriminatory power of VCD for both linear and cyclic peptides in different solvent systems may lead to more precise structure-activity relationship results.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Sungjoon Huh, George J. Saunders, Andrei K. Yudin
Summary: This study repurposes the rarely used Cornforth rearrangement to achieve single-atom ring contraction in cyclic peptide backbones. By investigating the kinetics and conformational analysis, it provides a new method for site-selective transformations.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Zhixing Zhao, Miaomiao Zhang, Bailing Tang, Peimin Weng, Yueyang Zhang, Xiaosheng Yan, Zhao Li, Yun-Bao Jiang
Summary: The design and synthesis of cyclic azapeptide as a transporter for fluoride transportation has been reported. Compared to acyclic control compounds, the cyclic receptor exhibits more stable beta-turn structures and a confined cavity for binding anions.
FRONTIERS IN CHEMISTRY
(2021)
Review
Chemistry, Applied
Hisashi Masui, Shinichiro Fuse
Summary: Peptides have gained increasing importance as drugs and drug candidates. Microflow synthesis, with an inner tube diameter of <=1 mm, offers advantages such as precise control of reaction time and temperature, as well as easy scale-up. The combination of microflow technology, automated synthesis, and online monitoring has improved synthetic efficiency and provided reliable data for machine learning models.
ORGANIC PROCESS RESEARCH & DEVELOPMENT
(2022)
Article
Chemistry, Multidisciplinary
Uttam Ghosh, Moumita Basu, Sudip Pal, Sanjeev Meena, Dipak Datta, Ravi Sankar Ampapathi, Tapas K. Kundu, Gajendra Singh, Tushar Kanti Chakraborty
Summary: The synthesized cyclic tetrapeptides may serve as potential HDAC inhibitors with novel structural features; cell-based experiments indicate that some cyclic tetrapeptides with hydroxamic acid side chain exhibit an induction of histone acetylation.
Article
Multidisciplinary Sciences
Pritha Ghosh, Nishant Raj, Hitesh Verma, Monika Patel, Sohini Chakraborti, Bhavesh Khatri, Chandrashekar M. Doreswamy, S. R. Anandakumar, Srinivas Seekallu, M. B. Dinesh, Gajanan Jadhav, Prem Narayan Yadav, Jayanta Chatterjee
Summary: Solvent shielding of the amide hydrogen bond donor has been used to increase the membrane permeability of macrocyclic peptides, and this can also be achieved by masking the amide hydrogen bond acceptor. Thioamide substitution reduces the desolvation penalty and enhances the membrane permeability of the macrocycle. Thioamidation also improves the bioavailability and duration of action of the macrocyclic peptide.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Uttam Ghosh, Vikash Kumar, Gajendra Singh, Tushar Kanti Chakraborty
Summary: In order to find more effective and safer anticoagulants, researchers used in silico structure-based design to discover new peptide-based thrombin inhibitors. The study demonstrated that tetrahydrofuran amino acid (TAA) based cyclic tetrapeptides (CTPs) can inhibit thrombin protein by interacting with Asp189 residue. This research synthesized and analyzed the conformation of TAA containing cyclic tetrapeptides, and studied their docking with thrombin protein using molecular docking.
Article
Chemistry, Multidisciplinary
Xiaona Li, Cristina Di Carluccio, He Miao, Lvfeng Zhang, Jintao Shang, Antonio Molinaro, Peng Xu, Alba Silipo, Biao Yu, You Yang
Summary: We report a promoter-controlled cycloglycosylation approach for the synthesis of cyclic α-(1→6)-linked mannosides up to a length of 32 units. The method relies on the role of a gold(I) complex in the proper preorganization of the ultra-large cyclic transition state. NMR experiments and a computational study revealed that the cyclic 2-mer, 4-mer, 8-mer, 16-mer, and 32-mer mannosides adopted different conformational states and shapes.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Thomas W. Harmon, W. Seth Horne
Summary: The study focuses on strategies to stabilize non-hairpin beta-turns by evaluating the effects of backbone alteration on the folded structure and stability of a helix-loop-helix protein. It found that conventional hairpin turn mimetics are often detrimental to folding stability and hydrophobic core packing, while reinforcing alternate turn types can improve stability and structural mimicry.
Article
Biochemistry & Molecular Biology
Neha V. Kalmankar, Bhuvaneshwari Rajendrakumar Gehi, Ramanathan Sowdhamini
Summary: Cyclotides extracted from Clitoria ternatea can inhibit the aggregation of beta-amyloid peptides, reduce oxidative stress, and weaken inter-strand hydrogen bonds of A beta peptides, thereby opening up their beta-sheet conformation. This study provides novel structural insights on the interaction between cyclotides and A beta fibrils and describes their potential in anti-amyloid aggregation.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Yan Xue, Gustav Nestor
Summary: This study identifies the NH protons of the amide cis forms of alpha- and beta-GlcNAc for the first time using NMR spectroscopy. The conformation of GlcNAc was analyzed by measuring J-couplings using protein NMR experiments. This approach shows promise for the detailed conformational analysis of GlcNAc in larger biomolecules.
Review
Pharmacology & Pharmacy
Vera D'Aloisio, Paolo Dognini, Gillian A. Hutcheon, Christopher R. Coxon
Summary: By 2020, over 100 approved peptides for therapeutic or diagnostic purposes had been developed, but the lack of a comprehensive free database poses a challenge for designing future peptide drug candidates. Unlike small-molecule drugs, there is no general set of guidelines for designing successful peptide-based drugs currently available.
DRUG DISCOVERY TODAY
(2021)
