scholarly journals Menthyl esterification allows chiral resolution for the synthesis of artificial glutamate analogs

2021 ◽  
Vol 17 ◽  
pp. 540-550
Author(s):  
Kenji Morokuma ◽  
Shuntaro Tsukamoto ◽  
Kyosuke Mori ◽  
Kei Miyako ◽  
Ryuichi Sakai ◽  
...  
Keyword(s):  
Carboxylic Acid ◽  
Glutamate Receptor ◽  
Chiral Resolution ◽  
Ionotropic Glutamate Receptor ◽  
X Ray ◽  
X Ray Crystallography ◽  
Configurational Analysis ◽  
In Vivo Assay ◽  
Enantiospecific Synthesis

Herein, we report the enantiospecific synthesis of two artificial glutamate analogs designed based on IKM-159, an antagonist selective to the AMPA-type ionotropic glutamate receptor. The synthesis features the chiral resolution of the carboxylic acid intermediate by the esterification with ʟ-menthol, followed by a configurational analysis by NMR, conformational calculation, and X-ray crystallography. A mice in vivo assay showed that (2R)-MC-27, with a six-membered oxacycle, is neuroactive, whereas the (2S)-counterpart is inactive. It was also found that TKM-38, with an eight-membered azacycle, is neuronally inactive, showing that the activity is controlled by the ring C.

scholarly journals Menthyl esterification allows chiral resolution for synthesis of artificial glutamate analogs

2020 ◽  
Author(s):  
Kenji Morokuma ◽  
Shuntaro Tsukamoto ◽  
Kei Miyako ◽  
Ryuichi Sakai ◽  
Raku Irie ◽  
...  
Keyword(s):  
Carboxylic Acid ◽  
Glutamate Receptor ◽  
Chiral Resolution ◽  
Ionotropic Glutamate Receptor ◽  
X Ray ◽  
X Ray Crystallography ◽  
Configurational Analysis ◽  
In Vivo Assay ◽  
Enantiospecific Synthesis

Herein we report enantiospecific synthesis of two artificial glutamate analogs designed based on IKM–159, an antagonist selective to AMPA-type ionotropic glutamate receptor. The synthesis features chiral resolution of the carboxylic acid intermediate by esterification with L–menthol, followed by configurational analysis by NMR, conformational calculation, and X–ray crystallography. Mice in vivo assay showed that (2R)–MC–27 with six-membered oxacycle is neuroactive, whereas the (2S)–counterpart is inactive. It was also found that the TKM–38 with eight-membered azacycle is neuronally inactive to suggest the possibility that the analog with a smaller five-membered azacycle may act as a potent agent.

Tele-Substitution Reactions in the Synthesis of a Promising Class of Antimalarials

2020 ◽  
Author(s):  
Marat Korsik ◽  
Edwin Tse ◽  
David Smith ◽  
William Lewis ◽  
Peter J. Rutledge ◽  
...  
Keyword(s):  
Heterocyclic Ring ◽  
Ring System ◽  
Substitution Reactions ◽  
Laboratory Notebook ◽  
Polar Solvents ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Core ◽  
Nmr Data

<p></p><p>We have discovered and studied a <i>tele</i>substitution reaction in a biologically important heterocyclic ring system. Conditions that favour the <i>tele</i>-substitution pathway were identified: the use of increased equivalents of the nucleophile or decreased equivalents of base, or the use of softer nucleophiles, less polar solvents and larger halogens on the electrophile. Using results from X-ray crystallography and isotope labelling experiments a mechanism for this unusual transformation is proposed. We focused on this triazolopyrazine as it is the core structure of the <i>in vivo </i>active anti-plasmodium compounds of Series 4 of the Open Source Malaria consortium.</p> <p> </p> <p>Archive of the electronic laboratory notebook with the description of all conducted experiments and raw NMR data could be accessed via following link <a href="https://ses.library.usyd.edu.au/handle/2123/21890">https://ses.library.usyd.edu.au/handle/2123/21890</a> . For navigation between entries of laboratory notebook please use file "Strings for compounds in the article.pdf" that works as a reference between article codes and notebook codes, also this file contain SMILES for these compounds. </p><br><p></p>

scholarly journals Discovery of a New Class of Ionotropic Glutamate Receptor Antagonists by the Rational Design of (2S,3R)-3-(3-Carboxyphenyl)-pyrrolidine-2-carboxylic Acid

2010 ◽  
Vol 2 (2) ◽  
pp. 107-114 ◽  
Author(s):  
Ann M. Larsen ◽  
Raminta Venskutonytė ◽  
Elena Antón Valadés ◽  
Birgitte Nielsen ◽  
Darryl S. Pickering ◽  
...  
Keyword(s):  
Carboxylic Acid ◽  
Glutamate Receptor ◽  
Rational Design ◽  
Ionotropic Glutamate Receptor ◽  
Receptor Antagonists ◽  
New Class ◽  
Glutamate Receptor Antagonists

scholarly journals The C-terminal tail of the bacterial translocation ATPase SecA modulates its activity

2018 ◽  
Author(s):  
Mohammed Jamshad ◽  
Timothy J. Knowles ◽  
Scott A. White ◽  
Douglas G. Ward ◽  
Fiyaz Mohammed ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Metal Binding ◽  
Cytoplasmic Membrane ◽  
Protein Recognition ◽  
X Ray ◽  
Ribosome Binding ◽  
X Ray Crystallography ◽  
Substrate Protein ◽  
Metal Binding Domain

AbstractIn bacteria, the translocation of a subset of proteins across the cytoplasmic membrane by the Sec machinery requires SecA. Although SecA can recognise nascent polypeptides, the mechanism of cotranslational substrate protein recognition is not known. Here, we investigated the role of the C-terminal tail (CTT) of SecA, which consists of a flexible linker (FLD) and a small metal-binding domain (MBD), in its interaction with nascent polypeptides. Phylogenetic analysis and ribosome binding experiments indicated that the MBD interacts with 70S ribosomes. Disruption of the entire CTT or the MBD alone had opposing effects on ribosome binding, substrate-protein binding, ATPase activity and in vivo function. Autophotocrosslinking, mass spectrometry, x-ray crystallography and small-angle x-ray scattering experiments provided insight into the CTT-mediated conformational changes in SecA. Finally, photocrosslinking experiments indicated that binding of SecA to substrate protein affected its interaction with the ribosome. Taken together, our results suggest a mechanism for substrate protein recognition.Impact StatementSecA is an evolutionarily conserved ATPase that is required for the translocation of a subset of proteins across the cytoplasmic membrane in bacteria. We investigated how SecA recognises its substrate proteins at the ribosome as they are still being synthesised (i.e. cotranslationally).

scholarly journals Spc110 N-Terminal Domains Act Independently to Mediate Stable γ-Tubulin Small Complex Binding and γ-Tubulin Ring Complex Assembly

2018 ◽  
Author(s):  
Andrew Lyon ◽  
Alex Zelter ◽  
Shruthi Viswanath ◽  
Alison Maxwell ◽  
Richard Johnson ◽  
...  
Keyword(s):  
Structural Model ◽  
Coiled Coil ◽  
The Other ◽  
Assembly Process ◽  
X Ray ◽  
X Ray Crystallography ◽  
Small Complex ◽  
Ring Complex ◽  
Biochemical Analyses

AbstractMicrotubule (MT) nucleation in vivo is regulated by the γ-tubulin ring complex (γTuRC), an approximately 2-megadalton complex conserved from yeast to humans. In Saccharomyces cerevisiae, γTuRC assembly is a key point of regulation over the MT cytoskeleton. Budding yeast γTuRC is composed of seven γ-tubulin small complex (γTuSC) subassemblies which associate helically to form a template from which microtubules grow. This assembly process requires higher-order oligomers of the coiled-coil protein Spc110 to bind multiple γTuSCs, thereby stabilizing the otherwise low-affinity interface between γTuSCs. While Spc110 oligomerization is critical, its N-terminal domain (NTD) also plays a role that is poorly understood both functionally and structurally. In this work, we sought a mechanistic understanding of Spc110 NTD using a combination of structural and biochemical analyses. Through crosslinking-mass spectrometry (XL-MS), we determined that a segment of Spc110 coiled-coil is a major point of contact with γTuSC. We determined the structure of this coiled-coil segment by X-ray crystallography and used it in combination with our XL-MS dataset to generate an integrative structural model of the γTuSC-Spc110 complex. This structural model, in combination with biochemical analyses of Spc110 heterodimers lacking one NTD, suggests that the two NTDs within an Spc110 dimer act independently, one stabilizing association between Spc110 and γTuSC and the other stabilizing the interface between adjacent γTuSCs.

scholarly journals Identification and Mutagenesis of the Adeno-Associated Virus 5 Sialic Acid Binding Region

2014 ◽  
Vol 89 (3) ◽  
pp. 1660-1672 ◽  
Author(s):  
Sandra Afione ◽  
Michael A. DiMattia ◽  
Sujata Halder ◽  
Giovanni Di Pasquale ◽  
Mavis Agbandje-McKenna ◽  
...  
Keyword(s):  
Sialic Acid ◽  
Wild Type Virus ◽  
Fold Axis ◽  
Cell Tropism ◽  
Type Virus ◽  
Wild Type ◽  
X Ray ◽  
X Ray Crystallography ◽  
Sialic Acid Binding

ABSTRACTAs a genus, the dependoviruses use a diverse group of cell surface carbohydrates for attachment and entry. Despite the fact that a majority of adeno-associated viruses (AAVs) utilize sialic acid (SIA) for binding and transduction, this virus-carbohydrate interaction is poorly understood. Utilizing X-ray crystallography, two SIA binding regions were mapped for AAV5. The first site mapped to the depression in the center of the 3-fold axis of symmetry, while the second site was located under the βHI loop close to the 5-fold axis. Mutagenesis of amino acids 569 and 585 or 587 within the 3-fold depression resulted in elimination or alteration in SIA-dependent transduction, respectively. This change in SIA binding was confirmed using glycan microarrays. Mutagenesis of the second site identified a role in transduction that was SIA independent. Further studies of the mutants at the 3-fold site demonstrated a change in transduction activity and cell tropismin vivoas well as resistance to neutralization by a polyclonal antibody raised against the wild-type virus.IMPORTANCEDespite the fact that a majority of AAVs utilize sialic acid for binding and transduction, this virus-carbohydrate interaction is poorly understood. Utilizing X-ray crystallography, the sialic acid binding regions of AAV5 were identified and studied using a variety of approaches. Mutagenesis of this region resulted in elimination or alteration in sialic acid-dependent transduction in cell lines. This change in sialic acid glycan binding was confirmed using glycan arrays. Further study also demonstrated a change in transduction and activity and cell tropismin vivoas well as resistance to neutralization by antibodies raised against the wild-type virus.

scholarly journals An endogenous dAMP ligand in Bacillus subtilis class Ib RNR promotes assembly of a noncanonical dimer for regulation by dATP

2018 ◽  
Vol 115 (20) ◽  
pp. E4594-E4603 ◽  
Author(s):  
Mackenzie J. Parker ◽  
Ailiena O. Maggiolo ◽  
William C. Thomas ◽  
Albert Kim ◽  
Steve P. Meisburger ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Quaternary Structure ◽  
Dependent Manner ◽  
Α Subunit ◽  
X Ray ◽  
X Ray Crystallography ◽  
X Ray Scattering ◽  
Dna Replication And Repair ◽  
Class Ib

The high fidelity of DNA replication and repair is attributable, in part, to the allosteric regulation of ribonucleotide reductases (RNRs) that maintains proper deoxynucleotide pool sizes and ratios in vivo. In class Ia RNRs, ATP (stimulatory) and dATP (inhibitory) regulate activity by binding to the ATP-cone domain at the N terminus of the large α subunit and altering the enzyme’s quaternary structure. Class Ib RNRs, in contrast, have a partial cone domain and have generally been found to be insensitive to dATP inhibition. An exception is the Bacillus subtilis Ib RNR, which we recently reported to be inhibited by physiological concentrations of dATP. Here, we demonstrate that the α subunit of this RNR contains tightly bound deoxyadenosine 5′-monophosphate (dAMP) in its N-terminal domain and that dATP inhibition of CDP reduction is enhanced by its presence. X-ray crystallography reveals a previously unobserved (noncanonical) α2 dimer with its entire interface composed of the partial N-terminal cone domains, each binding a dAMP molecule. Using small-angle X-ray scattering (SAXS), we show that this noncanonical α2 dimer is the predominant form of the dAMP-bound α in solution and further show that addition of dATP leads to the formation of larger oligomers. Based on this information, we propose a model to describe the mechanism by which the noncanonical α2 inhibits the activity of the B. subtilis Ib RNR in a dATP- and dAMP-dependent manner.

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