scholarly journals Molecular recognition of organic ammonium ions in solution using synthetic receptors

2010 ◽  
Vol 6 ◽  
Author(s):  
Andreas Späth ◽  
Burkhard König
Keyword(s):  
Molecular Recognition ◽  
Hydrophobic Interactions ◽  
Covalent Bond ◽  
Ammonium Ion ◽  
Synthetic Receptors ◽  
Ammonium Ions ◽  
Wide Range ◽  
Covalent Bond Formation ◽  
Reversible Covalent ◽  
Ion Receptors

Ammonium ions are ubiquitous in chemistry and molecular biology. Considerable efforts have been undertaken to develop synthetic receptors for their selective molecular recognition. The type of host compounds for organic ammonium ion binding span a wide range from crown ethers to calixarenes to metal complexes. Typical intermolecular interactions are hydrogen bonds, electrostatic and cation–π interactions, hydrophobic interactions or reversible covalent bond formation. In this review we discuss the different classes of synthetic receptors for organic ammonium ion recognition and illustrate the scope and limitations of each class with selected examples from the recent literature. The molecular recognition of ammonium ions in amino acids is included and the enantioselective binding of chiral ammonium ions by synthetic receptors is also covered. In our conclusion we compare the strengths and weaknesses of the different types of ammonium ion receptors which may help to select the best approach for specific applications.

Dynamic Covalent Bond Constrained Ureas for Multimode Fluorescence Switching, Thermally Induced Emission, and Chemical Signaling Cascades

2021 ◽  
Author(s):  
Fazli Sattar ◽  
Zelin Feng ◽  
Hanxun Zou ◽  
Hebo Ye ◽  
Yi Zhang ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Covalent Bond ◽  
Signaling Cascades ◽  
Materials Chemistry ◽  
Chemical Signaling ◽  
Thermally Induced ◽  
Fluorescence Switching ◽  
Reversible Covalent ◽  
Molecular Recognition Features

Urea groups play an important role in organic, supramolecular, and materials chemistry owing to unique structural and molecular recognition features. Herein a strategy of reversible covalent bond constrained ureas was...

Infrared spectra of the ammonium ion in crystals. Part XII. Low-temperature transitions in ammonium dichromate, (NH4)2Cr2O7

1982 ◽  
Vol 60 (15) ◽  
pp. 1972-1977
Author(s):  
Gábor Keresztury ◽  
Osvald Knop ◽  
Michael Falk
Keyword(s):  
Hydrogen Bonding ◽  
Infrared Spectra ◽  
Room Temperature ◽  
Abundance Ratio ◽  
Ammonium Ion ◽  
Ammonium Ions ◽  
Hydrogen Bonding Interactions ◽  
Wide Range ◽  
Ammonium Dichromate ◽  
The Difference

Examination of the infrared spectra of the probe ions NH3D+ and NHD3+ in ammonium dichromate confirms the existence of the lowest (Ttr ~ 125 K) of the three transitions that are known, from nonspectroscopic evidence, to occur in this crystal below room temperature. Below Ttr the ammonium ions are of two types, in an abundance ratio of 1:1 and both of symmetry C1. Above Ttr the probe ion spectra are difficult to interpret in detail. The strength of the hydrogen-bonding interactions covers a wide range, as indicated by the difference between the highest and the lowest values of the isotopically isolated ND stretching frequencies at 10 K, 2392 and 2234 cm−1.

scholarly journals In Silico Docking Studies of Antimalarial Drug Hydroxychloroquine to SARS-CoV Proteins :An Emerging Pandemic Worldwide

2020 ◽  
Author(s):  
Priyanka H. Jokhakar ◽  
Rishee Kalaria ◽  
Hiren K. Patel
Keyword(s):  
Antimalarial Drug ◽  
Hydrophobic Interactions ◽  
Computational Study ◽  
Covalent Bond ◽  
Docking Studies ◽  
Protein Docking ◽  
Viral Attachment ◽  
Discovery Studio ◽  
In Silico Docking ◽  
Covalent Bond Formation

<p>This computational study comprises screening and prediction of interaction of selected antimalarial drug hydroxychloroquine with targeted two proteins of coronavirus. One is SARS enveloped E pantameric ion channel protein and another is SARS-CoV-2 main apoprotein protease. Both are vital for viral attachment and entry to the host cell for infection. After molecular protein docking with different confirmations, stable interacting complex of ligand and macromolecules were obtained. Interacting Lysine, Threonine and Tyrosine of E protein were found for participation of stable interaction with selected drug having docking affinity energy of -6.3kcal/mol. For apoprotein protease stable confirmation was screened out having bonding Threonine residue with same drug of energy -6.0 kcal/mol. Irreversible covalent bond formation and van der Waals interaction favours the selectivity and stability of both targeted proteins towards selected drug. Conventional as well as hydrophobic interactions are found in Ligplot and Discovery studio analysis also indicates stabilized confirmations between ligand and drug. Thus, this study delivers the putative mechanism of the drug interactions to target proteins hence comprising landmark for future investigation for antimalarial hydroxychloroquine as anti COVID 19 drug in this experimental time.</p>

scholarly journals In Silico Docking Studies of Antimalarial Drug Hydroxychloroquine to SARS-CoV Proteins :An Emerging Pandemic Worldwide

2020 ◽  
Author(s):  
Priyanka H. Jokhakar ◽  
Rishee Kalaria ◽  
Hiren K. Patel
Keyword(s):  
Antimalarial Drug ◽  
Hydrophobic Interactions ◽  
Computational Study ◽  
Covalent Bond ◽  
Docking Studies ◽  
Protein Docking ◽  
Viral Attachment ◽  
Discovery Studio ◽  
In Silico Docking ◽  
Covalent Bond Formation

<p>This computational study comprises screening and prediction of interaction of selected antimalarial drug hydroxychloroquine with targeted two proteins of coronavirus. One is SARS enveloped E pantameric ion channel protein and another is SARS-CoV-2 main apoprotein protease. Both are vital for viral attachment and entry to the host cell for infection. After molecular protein docking with different confirmations, stable interacting complex of ligand and macromolecules were obtained. Interacting Lysine, Threonine and Tyrosine of E protein were found for participation of stable interaction with selected drug having docking affinity energy of -6.3kcal/mol. For apoprotein protease stable confirmation was screened out having bonding Threonine residue with same drug of energy -6.0 kcal/mol. Irreversible covalent bond formation and van der Waals interaction favours the selectivity and stability of both targeted proteins towards selected drug. Conventional as well as hydrophobic interactions are found in Ligplot and Discovery studio analysis also indicates stabilized confirmations between ligand and drug. Thus, this study delivers the putative mechanism of the drug interactions to target proteins hence comprising landmark for future investigation for antimalarial hydroxychloroquine as anti COVID 19 drug in this experimental time.</p>

scholarly journals RNA-Peptide Conjugation through an Efficient Covalent Bond Formation

2020 ◽  
Vol 10 (24) ◽  
pp. 8920
Author(s):  
Shun Nakano ◽  
Taiki Seko ◽  
Zhengxiao Zhang ◽  
Takashi Morii
Keyword(s):  
Covalent Bond ◽  
Fluorescent Sensors ◽  
Reaction Yield ◽  
Cationic Peptide ◽  
Solution Ph ◽  
Wide Range ◽  
Peptide Conjugation ◽  
Rnp Complex ◽  
Covalent Bond Formation ◽  
Diagnostic Applications

Many methods for modification of an oligonucleotide with a peptide have been developed to apply for the therapeutic and diagnostic applications or for the assembly of nanostructure. We have developed a method for the construction of receptor-based fluorescent sensors and catalysts using the ribonucleopeptide (RNP) as a scaffold. Formation of a covalent linkage between the RNA and the peptide subunit of RNP improved its stability, thereby expanding the application of functional RNPs. A representative method was applied for the formation of Schiff base or dihydroxy-morpholino linkage between a dialdehyde group at the 3′-end of sugar-oxidized RNA and a hydrazide group introduced at the C-terminal of a peptide subunit through a flexible peptide linker. In this report, we investigated effects of the solution pH and contribution of the RNA and peptide subunits to the conjugation reaction by using RNA and peptide mutants. The reaction yield reached 90% at a wide range of solution pH with reaction within 3 h. The efficient reaction was mainly supported by the electrostatic interaction between the RNA subunit and the cationic peptide subunit of the RNP scaffold. Formation of the RNP complex was verified to efficiently promote the reaction for construction of the RNA-peptide conjugate.

scholarly journals Efficient targeted degradation via reversible and irreversible covalent PROTACs

2020 ◽  
Author(s):  
Ronen Gabizon ◽  
Amit Shraga ◽  
Paul Gehrtz ◽  
Ella Livnah ◽  
Yamit Shorer ◽  
...  
Keyword(s):  
Cell Activation ◽  
Covalent Bond ◽  
Lymphocytic Leukemia ◽  
B Cell Activation ◽  
Irreversible Binding ◽  
Relevant Model ◽  
Reversible Binding ◽  
Covalent Bond Formation ◽  
Reversible Covalent ◽  
Primary Chronic Lymphocytic Leukemia

<p>PROteolysis Targeting Chimeras (PROTACs) represent an exciting inhibitory modality with many advantages, including sub-stoichiometric degradation of targets. Their scope, though, is still limited to-date by the requirement for a sufficiently potent target binder. A solution that proved useful in tackling challenging targets is the use of electrophiles to allow irreversible binding to the target. However, such binding will negate the catalytic nature of PROTACs. Reversible covalent PROTACs potentially offer the best of both worlds. They possess the potency and selectivity associated with the formation of the covalent bond, while being able to dissociate and regenerate once the protein target is degraded. Using Bruton’s tyrosine kinase (BTK) as a clinically relevant model system, we show efficient covalent degradation by non-covalent, irreversible covalent and reversible covalent PROTACs, with <10 nM DC50’s and >85% degradation. Our data suggests that part of the degradation by our irreversible covalent PROTACs is driven by reversible binding prior to covalent bond formation, while the reversible covalent PROTACs drive degradation primarily by covalent engagement. The PROTACs showed enhanced inhibition of B cell activation compared to Ibrutinib, and exhibit potent degradation of BTK in patients-derived primary chronic lymphocytic leukemia cells. The most potent reversible covalent PROTAC, RC-3, exhibited enhanced selectivity towards BTK compared to non-covalent and irreversible covalent PROTACs. These compounds may pave the way for the design of covalent PROTACs for a wide variety of challenging targets.</p>

scholarly journals Efficient targeted degradation via reversible and irreversible covalent PROTACs

2020 ◽  
Author(s):  
Ronen Gabizon ◽  
Amit Shraga ◽  
Paul Gehrtz ◽  
Ella Livnah ◽  
Yamit Shorer ◽  
...  
Keyword(s):  
Cell Activation ◽  
Covalent Bond ◽  
Lymphocytic Leukemia ◽  
B Cell Activation ◽  
Irreversible Binding ◽  
Relevant Model ◽  
Reversible Binding ◽  
Covalent Bond Formation ◽  
Reversible Covalent ◽  
Primary Chronic Lymphocytic Leukemia

<p>PROteolysis Targeting Chimeras (PROTACs) represent an exciting inhibitory modality with many advantages, including sub-stoichiometric degradation of targets. Their scope, though, is still limited to-date by the requirement for a sufficiently potent target binder. A solution that proved useful in tackling challenging targets is the use of electrophiles to allow irreversible binding to the target. However, such binding will negate the catalytic nature of PROTACs. Reversible covalent PROTACs potentially offer the best of both worlds. They possess the potency and selectivity associated with the formation of the covalent bond, while being able to dissociate and regenerate once the protein target is degraded. Using Bruton’s tyrosine kinase (BTK) as a clinically relevant model system, we show efficient covalent degradation by non-covalent, irreversible covalent and reversible covalent PROTACs, with <10 nM DC50’s and >85% degradation. Our data suggests that part of the degradation by our irreversible covalent PROTACs is driven by reversible binding prior to covalent bond formation, while the reversible covalent PROTACs drive degradation primarily by covalent engagement. The PROTACs showed enhanced inhibition of B cell activation compared to Ibrutinib, and exhibit potent degradation of BTK in patients-derived primary chronic lymphocytic leukemia cells. The most potent reversible covalent PROTAC, RC-3, exhibited enhanced selectivity towards BTK compared to non-covalent and irreversible covalent PROTACs. These compounds may pave the way for the design of covalent PROTACs for a wide variety of challenging targets.</p>

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