scholarly journals Polymyxins and quinazolines are LSD1/KDM1A inhibitors with unusual structural features

2016 ◽  
Vol 2 (9) ◽  
pp. e1601017 ◽  
Author(s):  
Valentina Speranzini ◽  
Dante Rotili ◽  
Giuseppe Ciossani ◽  
Simona Pilotto ◽  
Biagina Marrocco ◽  
...  
Keyword(s):  
Amino Acids ◽  
Active Center ◽  
Drug Target ◽  
Malignant Tumors ◽  
Structural Features ◽  
Charged Amino Acids ◽  
Chemistry Research ◽  
Histone Lysine ◽  
Lysine Specific Demethylase ◽  
Positively Charged

Because of its involvement in the progression of several malignant tumors, the histone lysine-specific demethylase 1 (LSD1) has become a prominent drug target in modern medicinal chemistry research. We report on the discovery of two classes of noncovalent inhibitors displaying unique structural features. The antibiotics polymyxins bind at the entrance of the substrate cleft, where their highly charged cyclic moiety interacts with a cluster of positively charged amino acids. The same site is occupied by quinazoline-based compounds, which were found to inhibit the enzyme through a most peculiar mode because they form a pile of five to seven molecules that obstruct access to the active center. These data significantly indicate unpredictable strategies for the development of epigenetic inhibitors.

scholarly journals The Superagonistic Activity of Bovine Thyroid-stimulating Hormone (TSH) and the Human TR1401 TSH Analog Is Determined by Specific Amino Acids in the Hinge Region of the Human TSH Receptor

2009 ◽  
Vol 284 (24) ◽  
pp. 16317-16324 ◽  
Author(s):  
Sandra Mueller ◽  
Gunnar Kleinau ◽  
Mariusz W. Szkudlinski ◽  
Holger Jaeschke ◽  
Gerd Krause ◽  
...  
Keyword(s):  
Amino Acids ◽  
Thyroid Stimulating Hormone ◽  
Hinge Region ◽  
Camp Production ◽  
Glycoprotein Hormone ◽  
Charged Amino Acids ◽  
Bovine Thyroid ◽  
Positively Charged ◽  
Bovine Tsh ◽  
Signaling Activity

Bovine TSH (bTSH) has a higher affinity to the human TSHR (hTSHR) and a higher signaling activity than human TSH (hTSH). The molecular reasons for these phenomena are unknown. Distinct negatively charged residues (Glu297, Glu303, and Asp382) in the hinge region of the hTSHR are known to be important for bTSH binding and signaling. To investigate the potential relevance of these positions for differences between bTSH and hTSH in the interaction to the hTSHR, we determined bTSH- and hTSH-mediated cAMP production of several substitutions at these three hinge residues. To examine specific variations of hTSH, we also investigated the superagonistic hTSH analog TR1401 (TR1401), whose sequence differs from hTSH by four additional positively charged amino acids that are also present in bTSH. To characterize possible interactions between the acidic hTSHR positions Glu297, Glu303, or Asp382 and the additional basic residues of TR1401, we investigated TR1401 binding and signaling properties. Our data reveal increased cAMP signaling of the hTSHR using TR1401 and bTSH compared with hTSH. Whereas Asp382 seems to be important for bTSH- and TR1401-mediated but not for hTSH-mediated signaling, the substitution E297K exhibits a decreased signaling for all three TSH variants. Interestingly, bTSH and TR1401 showed only a slightly different binding pattern. These observations imply that specific residues of the hinge region are mediators of the superagonistic activity of bTSH and TR1401 in contrast to hTSH. Moreover, the simultaneous localization of binding components in the glycoprotein hormone molecule and the receptor hinge region permits important reevaluation of interacting hormone receptor domains.

scholarly journals RNA-binding region of Macrobrachium rosenbergii nodavirus capsid protein

2014 ◽  
Vol 95 (9) ◽  
pp. 1919-1928 ◽  
Author(s):  
Zee Hong Goh ◽  
Nur Azmina Syakirin Mohd ◽  
Soon Guan Tan ◽  
Subha Bhassu ◽  
Wen Siang Tan
Keyword(s):  
Amino Acids ◽  
Capsid Protein ◽  
Rna Binding ◽  
Macrobrachium Rosenbergii ◽  
Freshwater Prawn ◽  
Internal Deletion ◽  
Binding Region ◽  
Rna Molecules ◽  
Charged Amino Acids ◽  
Positively Charged

White tail disease (WTD) kills prawn larvae and causes drastic losses to the freshwater prawn (Macrobrachium rosenbergii) industry. The main causative agent of WTD is Macrobrachium rosenbergii nodavirus (MrNV). The N-terminal end of the MrNV capsid protein is very rich in positively charged amino acids and is postulated to interact with RNA molecules. N-terminal and internal deletion mutagenesis revealed that the RNA-binding region is located at positions 20–29, where 80 % of amino acids are positively charged. Substitution of all these positively charged residues with alanine abolished the RNA binding. Mutants without the RNA-binding region still assembled into virus-like particles, suggesting that this region is not a part of the capsid assembly domain. This paper is, to the best of our knowledge, the first to report the specific RNA-binding region of MrNV capsid protein.

scholarly journals A Stretch of Positively Charged Amino Acids at the N Terminus ofHansenula polymorphaPex3p Is Involved in Incorporation of the Protein into the Peroxisomal Membrane

2000 ◽  
Vol 275 (14) ◽  
pp. 9986-9995 ◽  
Author(s):  
Richard J. S. Baerends ◽  
Klaas Nico Faber ◽  
Anita M. Kram ◽  
Jan A. K. W. Kiel ◽  
Ida J. van der Klei ◽  
...  
Keyword(s):  
Amino Acids ◽  
Peroxisomal Membrane ◽  
Charged Amino Acids ◽  
N Terminus ◽  
Positively Charged

Study of R-group positively charged amino acids' UV

2009 ◽  
Author(s):  
Teng fei Tian ◽  
Gui zhong Liu ◽  
Xian hui Meng ◽  
Xiao qian Tan ◽  
Yong liang Liu
Keyword(s):  
Amino Acids ◽  
Charged Amino Acids ◽  
Positively Charged

Tetraphenyl porphyrin films as selective detectors for amino acid molecules

2020 ◽  
Vol 24 (10) ◽  
pp. 1215-1223
Author(s):  
Jesús Miguel Rivera ◽  
Margarita Rivera
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Quartz Crystal Microbalance ◽  
Quartz Crystal ◽  
Binding Energies ◽  
Charged Amino Acids ◽  
Tetraphenyl Porphyrin ◽  
Pseudo Second Order ◽  
Selective Detectors ◽  
Positively Charged

The interaction of different amino acids and vacuum evaporated tetraphenyl porphyrin films was investigated by using kinetic isotherms, UV-vis spectroscopy, quartz crystal microbalance and density functional theory techniques. The adsorption process was analyzed by using pseudo-first-order and pseudo-second-order models. From these results, the adsorption order changed depending on the chemical characteristics of the porphyrin film, although most of the interactions were classified as pseudo-second-order at the films interface. From absorbance measurements, red shifts on the Soret peak positions were observed for all amino acids interacting with the metal free and the ZnTPP systems, while the position of the Soret peak barely change for the CuTPP surface, except for a slight bathocromic shift for arginine. On the other hand, the broadening of the Soret peak was more important for the ZnTPP and H2TPP surfaces, but the interaction with the CuTPP interfaces decreased the width of the peaks in all cases. In addition, a quartz crystal microbalance analysis was employed to investigate the film sensing performance during amino acid exposure. From these results, positively charged amino acids were more easily adsorbed on the films in contrast with the polar (serine) molecule. DFT calculations exhibited important deformations for H2TPP, the out-of-plane displacement of the Zn atom for ZnTPP, and hydrogen bond interactions with the CuTPP molecule. DFT also showed high binding energies for the positively charged amino acids but low binding energies for serine in agreement with experimental data. From these results, porphyrin films could be used as selective detectors for various L-amino acid molecules.

scholarly journals Structure-Activity Relationship of Synthetic Variants of the Milk-Derived Antimicrobial Peptide αs2-Casein f(183–207)

2013 ◽  
Vol 79 (17) ◽  
pp. 5179-5185 ◽  
Author(s):  
Avelino Alvarez-Ordóñez ◽  
Máire Begley ◽  
Tanya Clifford ◽  
Thérèse Deasy ◽  
Kiera Considine ◽  
...  
Keyword(s):  
Amino Acids ◽  
Biological Activity ◽  
Amino Acid ◽  
Antimicrobial Peptide ◽  
Peptide Sequence ◽  
Content Type ◽  
Charged Amino Acids ◽  
Food Borne ◽  
Relationship Of ◽  
Positively Charged

ABSTRACTTemplate-based studies on antimicrobial peptide (AMP) derivatives obtained through manipulation of the amino acid sequence are helpful to identify properties or residues that are important for biological activity. The present study sheds light on the importance of specific amino acids of the milk-derived αs2-casein f(183–207) peptide to its antibacterial activity against the food-borne pathogensListeria monocytogenesandCronobacter sakazakii. Trimming of the peptide revealed that residues at the C-terminal end of the peptide are important for activity. Removal of the last 5 amino acids at the C-terminal end and replacement of the Arg at position 23 of the peptide sequence by an Ala residue significantly decreased activity. These findings suggest that Arg23 is very important for optimal activity of the peptide. Substitution of the also positively charged Lys residues at positions 15 and 17 of the αs2-casein f(183–207) peptide also caused a significant reduction of the effectiveness againstC. sakazakii, which points toward the importance of the positive charge of the peptide for its biological activity. Indeed, simultaneous replacement of various positively charged amino acids was linked to a loss of bactericidal activity. On the other hand, replacement of Pro residues at positions 14 and 20 resulted in a significantly increased antibacterial potency, and hydrophobic end tagging of αs2-casein f(193–203) and αs2-casein f(197–207) peptides with multiple Trp or Phe residues significantly increased their potency againstL. monocytogenes. Finally, the effect of pH (4.5 to 7.4), temperature (4°C to 37°C), and addition of sodium and calcium salts (1% to 3%) on the activity of the 15-amino-acid αs2-casein f(193–207) peptide was also determined, and its biological activity was shown to be completely abolished in high-saline environments.

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