Article
Chemistry, Inorganic & Nuclear
Armando Berlanga-Vazquez, Radu A. Talmazan, Carlos A. Reyes-Mata, Edmundo G. Percastegui, Marcos Flores-Alamo, Maren Podewitz, Ivan Castillo
Summary: Functionalization of p-tert-butylcalix[8]arene with phenanthroline at the phenolic rim created two regioisomers, with substitution at positions 1 and 5 producing a known symmetric regioisomer and substitution at positions 1 and 4 producing a newly described symmetric regioisomer. The C-S coupling reaction using the newly synthesized regioisomer showed lower activity compared to the previously reported system, potentially due to a difference in the exposed catalytic center caused by a deformation in the regioisomer's structure. Detailed computational investigations confirmed the 1,4-connectivity and revealed the influence of the calix[8]arene macrocyclic morphology on accessible conformations.
EUROPEAN JOURNAL OF INORGANIC CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Dipanjan Mukherjee, Priya Singh, Soumendra Singh, Debanjona Singh Roy, Subhankar Singha, Uttam Pal, Jhimli Sengupta, Rami J. Obaid, Saleh A. Ahmed, Tanusri Saha Dasgupta, Ranjan Das, Samir Kumar Pal
Summary: The study investigates the molecular recognition and binding process between CD1 and HSA, revealing that different host vehicles can impact the rate of drug binding to the protein, thereby modulating the release rate of the drug mimic.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Chemistry, Medicinal
Masatake Sugita, Satoshi Sugiyama, Takuya Fujie, Yasushi Yoshikawa, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama
Summary: The study investigated the membrane permeation process of cyclic peptides across the lipid bilayer and found that crossing the center of the membrane is the main obstacle to membrane permeation, with barrier height correlated to electrostatic interactions. Peptides were observed to change orientation and conformation according to the surrounding environment to permeate the membrane.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Review
Biochemistry & Molecular Biology
Aranyak Mitra, Nandini Sarkar
Summary: All proteins have the ability to transform into amyloid fibrils under specific conditions. Disulfide bonds play a crucial role in modulating the propensity of protein aggregation. Intra-molecular disulfide bonds stabilize the native structure, while intermolecular disulfide bonds aid in the aggregation process. This review analyzes the effects of these bonds on the amyloid aggregation of proteins associated with amyloid disorders.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Jiayuan Miao, Marc L. Descoteaux, Yu-Shan Lin
Summary: Recent research has made significant progress in using machine learning models and molecular dynamics simulations to predict the complete structural ensembles of cyclic peptides. This method can provide molecular dynamics simulation-quality predictions for hundreds of thousands of sequences in less than 1 second.
Article
Biochemistry & Molecular Biology
Jigar Desai, Christopher Francis, Kenneth Longo, Andrew Hoss
Summary: In this study, a predictive model called Exon ByPASS was developed to assess the importance of exon inclusion based solely on protein amino acid sequence. The model was validated and shown to accurately predict exon skipping, making it a potential tool for therapeutic purposes.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Dongyao Li, Tian Qin, Xinlu Liu, Boyuan Zhang, Fangrui Zhong, Chunmiao Ma, Quan Gan
Summary: In this study, a twisted macrocycle was synthesized through the rearrangement of hydrogen bonding preference. Single-crystal X-ray structure and NMR spectroscopy demonstrated the ability of the macrocycle to transform between twisted and boxlike conformations. Additionally, it was found that flat aromatic guests could bind to the macrocycle in a 1:1 stoichiometry and could be released by the addition of base.
Article
Chemistry, Medicinal
Karen M. Corbett, Leigh Ford, Dallas B. Warren, Colin W. Pouton, David K. Chalmers
Summary: Cyclosporins are a class of peptides with wide pharmaceutical applications, some of which exhibit high membrane permeability not easily explained by structural metrics. Experimental studies have been conducted to understand the structure and permeability of cyclosporins, including their interaction with metal complexes. Models have been proposed to explain the conformation-dependent permeability of cyclosporins and similar compounds, with gaps in current knowledge identified for further exploration.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Spectroscopy
Hiroshi Abe, Hiroaki Kishimura, Mikio Uruichi
Summary: The crystal polymorphs of fluorinated ionic liquids (fILs) were studied at low temperature, showing a correlation between conformational flexibility and alkyl chain length.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2023)
Article
Multidisciplinary Sciences
Tushar Modi, Valeria A. Risso, Sergio Martinez-Rodriguez, Jose A. Gavira, Mubark D. Mebrat, Wade D. Van Horn, Jose M. Sanchez-Ruiz, S. Banu Ozkan
Summary: TEM-1 β-lactamase evolved from ancestral enzymes that degraded a variety of β-lactam antibiotics with moderate efficiency and degrades β-lactam antibiotics with a strong preference for penicillins. The authors developed a computational approach to rationally mold a protein flexibility profile based on a hinge-shift mechanism and successfully engineered a putative Precambrian β-lactamase that mimics the modern TEM-1 β-lactamase with only 21 amino acid replacements.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Suman Samantray, Olujide O. Olubiyi, Birgit Strodel
Summary: The research focuses on the biochemical importance of glycosaminoglycans (GAGs) and reveals the impact of sulfation on GAGs structure through molecular dynamics simulations, as well as the effects of increasing NaCl and KCl concentrations. The study findings suggest that sulfation at position 6 and binding of metal ions in the absence of chloride ions have significant effects on GAGs structure.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Physical
Yoshihiro Koyama, Seiya Shimono, Hiroaki Kishimura, Takahiro Takekiyo, Yukihiro Yoshimura, Hiroshi Abe, Kiyoto Matsuishi
Summary: The high-pressure crystal polymorph of a fluorinated ionic liquid was determined through X-ray diffraction and Raman spectroscopy, revealing irreversible changes in crystal structure upon compression and decompression. Conformational variance/invariance of the ions in the Raman spectra corresponded to the high-pressure crystal polymorph, indicating a switch in conformational variance at a specific pressure point leading to a change in crystal system. The high-pressure crystal polymorph was shown to be entirely different from the low-temperature crystal polymorph.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Biochemistry & Molecular Biology
Samuel G. Holmes, Balaji Nagarajan, Umesh R. Desai
Summary: This study discovered novel compact topologies of heparan sulfate (HS) that are influenced by the 3-O-sulfation of cis-idoA residues. The transition in HS topology is driven by rotations that reduce like-charge repulsion, release water molecules, and establish specific interactions. These findings reveal a dynamic sulfation code in natural HS that could be utilized for selective recognition of target proteins.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Chemistry, Medicinal
Dongjae Lee, Jieun Choi, Min June Yang, Chin-Ju Park, Jiwon Seo
Summary: This study investigates the influence of structural changes on chameleonic behavior and membrane permeability of the cyclosporin O (CsO) scaffold by controlling backbone and side chain modifications. The results show that beta-hydroxylation at specific positions enhances permeability, while the introduction of additional transannular H-bond slows down the permeation rate. These findings contribute to the discovery of potent macrocycles capable of targeting undruggable targets.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
George J. Saunders, Andrei K. Yudin
Summary: The passive membrane permeability of macrocycles can be greatly improved by incorporating heterocyclic grafts. However, the permeability does not scale linearly with the number of heterocycles, highlighting the subtleties of the conformation-property relationship in this class of molecules.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)