scholarly journals An ATP-Dependent Ligase with Substrate Flexibility Involved in Assembly of the Peptidyl Nucleoside Antibiotic Polyoxin

2018 ◽  
Vol 84 (13) ◽  
Author(s):  
Rong Gong ◽  
Jianzhao Qi ◽  
Pan Wu ◽  
You-Sheng Cai ◽  
Hongmin Ma ◽  
...  
Keyword(s):  
Binding Sites ◽  
Catalytic Mechanism ◽  
Structural Features ◽  
Combinatorial Biosynthesis ◽  
Amide Bond ◽  
Pathway Engineering ◽  
Nucleoside Antibiotics ◽  
Amide Bond Formation ◽  
Acyl Phosphate ◽  
Dependent Mechanism

ABSTRACT Polyoxin (POL) is an unusual peptidyl nucleoside antibiotic, in which the peptidyl moiety and nucleoside skeleton are linked by an amide bond. However, their biosynthesis remains poorly understood. Here, we report the deciphering of PolG as an ATP-dependent ligase responsible for the assembly of POL. A polG mutant is capable of accumulating multiple intermediates, including the peptidyl moiety (carbamoylpolyoxamic acid [CPOAA]) and the nucleoside skeletons (POL-C and the previously overlooked thymine POL-C). We further demonstrate that PolG employs an ATP-dependent mechanism for amide bond formation and that the generation of the hybrid nucleoside antibiotic POL-N is also governed by PolG. Finally, we determined that the deduced ATP-binding sites are functionally essential for PolG and that they are highly conserved in a number of related ATP-dependent ligases. These insights have allowed us to propose a catalytic mechanism for the assembly of peptidyl nucleoside antibiotic via an acyl-phosphate intermediate and have opened the way for the combinatorial biosynthesis/pathway engineering of this group of nucleoside antibiotics. IMPORTANCE POL is well known for its remarkable antifungal bioactivities and unusual structural features. Actually, elucidation of the POL assembly logic not only provides the enzymatic basis for further biosynthetic understanding of related peptidyl nucleoside antibiotics but also contributes to the rational generation of more hybrid nucleoside antibiotics via synthetic biology strategy.

scholarly journals Biosynthesis of 2′-Chloropentostatin and 2′-Amino-2′-Deoxyadenosine Highlights a Single Gene Cluster Responsible for Two Independent Pathways in Actinomadura sp. Strain ATCC 39365

2017 ◽  
Vol 83 (10) ◽  
Author(s):  
Yaojie Gao ◽  
Gudan Xu ◽  
Pan Wu ◽  
Jin Liu ◽  
You-sheng Cai ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Single Gene ◽  
Combinatorial Biosynthesis ◽  
Pathway Engineering ◽  
Enzymatic Reactions ◽  
Strain Atcc ◽  
Nudix Hydrolase ◽  
Nucleoside Antibiotics ◽  
Chemical Structures ◽  
Hydrolysis Of

ABSTRACT 2′-Chloropentostatin (2′-Cl PTN, 2′-chloro-2′-deoxycoformycin) and 2′-amino-2′-deoxyadenosine (2′-amino dA) are two adenosine-derived nucleoside antibiotics coproduced by Actinomadura sp. strain ATCC 39365. 2′-Cl PTN is a potent adenosine deaminase (ADA) inhibitor featuring an intriguing 1,3-diazepine ring, as well as a chlorination at C-2′ of ribose, and 2′-amino dA is an adenosine analog showing bioactivity against RNA-type virus infection. However, the biosynthetic logic of them has remained poorly understood. Here, we report the identification of a single gene cluster (ada) essential for the biosynthesis of 2′-Cl PTN and 2′-amino dA. Further systematic genetic investigations suggest that 2′-Cl PTN and 2′-amino dA are biosynthesized by independent pathways. Moreover, we provide evidence that a predicted cation/H+ antiporter, AdaE, is involved in the chlorination step during 2′-Cl PTN biosynthesis. Notably, we demonstrate that 2′-amino dA biosynthesis is initiated by a Nudix hydrolase, AdaJ, catalyzing the hydrolysis of ATP. Finally, we reveal that the host ADA (designated ADA1), capable of converting adenosine/2′-amino dA to inosine/2′-amino dI, is not very sensitive to the powerful ADA inhibitor pentostatin. These findings provide a basis for the further rational pathway engineering of 2′-Cl PTN and 2′-amino dA production. IMPORTANCE 2′-Cl PTN/PTN and 2′-amino dA have captivated the great interests of scientists, owing to their unusual chemical structures and remarkable bioactivities. However, the precise logic for their biosynthesis has been elusive for decades. Actually, the identification and elucidation of their biosynthetic pathways not only enrich the biochemical repertoire of novel enzymatic reactions but may also lay solid foundations for the pathway engineering and combinatorial biosynthesis of this family of purine nucleoside antibiotics to generate novel hybrid analogs with improved features.

scholarly journals One-Step Biocatalytic Synthesis of Sustainable Surfactants Using Selective Amide Bond Formation

2021 ◽  
Author(s):  
Max Lubberink ◽  
Christian Schnepel ◽  
Christopher Baldwin ◽  
Nicholas Turner ◽  
Sabine Flitsch
Keyword(s):  
Fatty Acids ◽  
Carboxylic Acid ◽  
Enzymatic Synthesis ◽  
Bond Formation ◽  
Amide Bond ◽  
Esterification Reaction ◽  
Amide Bond Formation ◽  
Selective Strategy ◽  
One Step ◽  
Acyl Phosphate

N-alkanoyl-N-methylglucamides (MEGAs) are non-toxic surfactants widely used in pharmaceutical and biochemical applications and hence more sustainable syntheses towards these compounds are highly desired. Here we present an aqueous, enzymatic synthesis route towards MEGAs and analogues using carboxylic acid reductase (CAR), which has been engineered to catalyse amide bond formation (CAR-A). Compared to lipase catalysed reactions, this biocatalyst is capable of selective amide bond formation between amino-polyols and fatty acids without the competing esterification reaction being observed. The wide substrate scope of CAR-A catalysed amidation was exemplified by the synthesis of 16 amides including several commercially relevant targets. The ATP co-factor could be recycled from cheap polyphosphate using a kinase. This work establishes acyl-phosphate mediated chemistry as a selective strategy for biocatalytic amide bond formation in the presence of competing alcohol functionalities.

Diethylphosphoryl-OxymaB (DEPO-B) as a Solid Coupling Reagent for Amide Bond Formation

2018 ◽  
Vol 16 (1) ◽  
pp. 30-33
Author(s):  
Ashish Kumar ◽  
Yahya E. Jad ◽  
Ayman El-Faham ◽  
Beatriz G. de la Torre ◽  
Fernando Albericio
Keyword(s):  
Bond Formation ◽  
Hydrolytic Stability ◽  
Solid Material ◽  
Amide Bond ◽  
Amide Bond Formation ◽  
Coupling Reagent

A new phosphonium based coupling reagent DEPO-B has been synthesized from 5- (hydroxyimino)-1,3-dimethylpyrimidine-2,4,6 (1H,3H,5H)-trione (Oxyma B) and diethyl chlorophosphate in presence of base. It is a solid material and the hydrolytic stability and solubility was evaluated for confirming its capability for usage in automated peptide synthesizer.

A Review of Amide Bond Formation in Microwave Organic Synthesis

2014 ◽  
Vol 11 (4) ◽  
pp. 592-604 ◽  
Author(s):  
Natalia Lukasik ◽  
Ewa Wagner-Wysiecka
Keyword(s):  
Organic Synthesis ◽  
Bond Formation ◽  
Amide Bond ◽  
Amide Bond Formation

scholarly journals Structure-Acid Lability Relationship of N-alkylated α,α-dialkylglycine Obtained via a Ugi Multicomponent Reaction

Molecules ◽  
2021 ◽  
Vol 26 (1) ◽  
pp. 197
Author(s):  
Iván Ramos-Tomillero ◽  
Marisa K. Sánchez ◽  
Hortensia Rodríguez ◽  
Fernando Albericio
Keyword(s):  
Solid Phase Synthesis ◽  
Solid Phase ◽  
Structural Features ◽  
Amide Bond ◽  
Acidic Media ◽  
Phase Synthesis ◽  
Acyl Chains ◽  
Cyclic Compounds ◽  
Relationship Of ◽  
Fine Tune

Using the classical Ugi four-component reaction to fuse an amine, ketone, carboxylic acid, and isocyanide, here we prepared a short library of N-alkylated α,α-dialkylglycine derivatives. Due to the polyfunctionality of the dipeptidic scaffold, this highly steric hindered system shows an interesting acidolytic cleavage of the C-terminal amide. In this regard, we studied the structure-acid lability relationship of the C-terminal amide bond (cyclohexylamide) of N-alkylated α,α-dialkylglycine amides 1a–n in acidic media and, afterward, it was established that the most important structural features related to its cleavage. Then, it was demonstrated that electron-donating effects in the aromatic amines, flexible acyl chains (Gly) at the N-terminal and the introduction of cyclic compounds into dipeptide scaffolds, increased the rate of acidolysis. All these effects are related to the ease with which the oxazolonium ion intermediate forms and they promote the proximity of the central carbonyl group to the C-terminal amide, resulting in C-terminal amide cleavage. Consequently, these findings could be applied for the design of new protecting groups, handles for solid-phase synthesis, and linkers for conjugation, due to its easily modulable and the fact that it allows to fine tune its acid-lability.

A computational study on the mechanism of ynamide-mediated amide bond formation from carboxylic acids and amines

2017 ◽  
Vol 15 (30) ◽  
pp. 6367-6374 ◽  
Author(s):  
Song-Lin Zhang ◽  
Hai-Xing Wan ◽  
Zhu-Qin Deng
Keyword(s):  
Reaction Mechanism ◽  
Carboxylic Acids ◽  
Computational Study ◽  
Bond Formation ◽  
Amide Bond ◽  
Reactivity Pattern ◽  
Amide Bond Formation ◽  
Coupling Reagent ◽  
Catalytic Effects ◽  
Acid Substrate

A detailed computational study is presented on the reaction mechanism of ynamide-mediated condensation of carboxylic acids with amines to produce amides, which elucidates the reactivity pattern of the coupling reagent ynamide and discloses crucial bifunctional catalytic effects of the carboxylic acid substrate during aminolysis.

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