scholarly journals Tailoring Tryptophan Synthase TrpB for Selective Quaternary Carbon Bond Formation

2019 ◽  
Author(s):  
Markus Dick ◽  
Nicholas S. Sarai ◽  
Michael W. Martynowycz ◽  
Tamir Gonen ◽  
Frances H. Arnold
Keyword(s):  
Condensation Reaction ◽  
Bond Formation ◽  
Tryptophan Synthase ◽  
Indole Derivatives ◽  
Quaternary Carbon ◽  
Noncanonical Amino Acids ◽  
Carbon Bond ◽  
E Coli ◽  
Tertiary Carbon ◽  
Quaternary Stereocenters

<div><div><div><p>We previously engineered the tryptophan synthase beta-subunit (TrpB), which catalyzes the condensation reaction between L-serine and indole to form L-tryptophan, to synthesize a range of modified tryptophans from serine and indole derivatives. In this study, we used directed evolution to engineer TrpB to accept 3-substituted oxindoles and form C–C bonds leading to new quaternary stereocenters. At first, the TrpBs that could use 3-substituted oxindoles preferentially formed N–C bonds by attacking the oxindole N<sub>1 </sub>atom. We found, however, that protecting the nitrogen encouraged evolution towards C-alkylation, which persisted even when this protection was removed. After seven rounds of evolution leading to a 400-fold improvement in activity, variant <i>Pf</i><sub>quat</sub> efficiently alkylates 3-substituted oxindoles to selectively form new stereocenters at the γ-position of the amino acid products. The configuration of the new γ-stereocenter of one of the products was determined from the crystal structure obtained by microcrystal electron diffraction (MicroED). Substrates structurally related to 3-methyloxindole such as lactones and ketones can also be used by the enzyme for quaternary carbon bond formation, where the biocatalyst exhibits excellent regioselectivity for the tertiary carbon atom. Highly thermostable and expressed at > 500 mg/L <i>E. coli</i> culture, TrpB <i>Pf</i><sub>quat </sub>provides an efficient and environmentally-friendly platform for the preparation of noncanonical amino acids bearing quaternary carbons.</p></div></div></div>

scholarly journals Tailoring Tryptophan Synthase TrpB for Selective Quaternary Carbon Bond Formation

2019 ◽  
Author(s):  
Markus Dick ◽  
Nicholas S. Sarai ◽  
Michael W. Martynowycz ◽  
Tamir Gonen ◽  
Frances H. Arnold
Keyword(s):  
Condensation Reaction ◽  
Bond Formation ◽  
Tryptophan Synthase ◽  
Indole Derivatives ◽  
Quaternary Carbon ◽  
Noncanonical Amino Acids ◽  
Carbon Bond ◽  
E Coli ◽  
Tertiary Carbon ◽  
Quaternary Stereocenters

<div><div><div><p>We previously engineered the tryptophan synthase beta-subunit (TrpB), which catalyzes the condensation reaction between L-serine and indole to form L-tryptophan, to synthesize a range of modified tryptophans from serine and indole derivatives. In this study, we used directed evolution to engineer TrpB to accept 3-substituted oxindoles and form C–C bonds leading to new quaternary stereocenters. At first, the TrpBs that could use 3-substituted oxindoles preferentially formed N–C bonds by attacking the oxindole N<sub>1 </sub>atom. We found, however, that protecting the nitrogen encouraged evolution towards C-alkylation, which persisted even when this protection was removed. After seven rounds of evolution leading to a 400-fold improvement in activity, variant <i>Pf</i><sub>quat</sub> efficiently alkylates 3-substituted oxindoles to selectively form new stereocenters at the γ-position of the amino acid products. The configuration of the new γ-stereocenter of one of the products was determined from the crystal structure obtained by microcrystal electron diffraction (MicroED). Substrates structurally related to 3-methyloxindole such as lactones and ketones can also be used by the enzyme for quaternary carbon bond formation, where the biocatalyst exhibits excellent regioselectivity for the tertiary carbon atom. Highly thermostable and expressed at > 500 mg/L <i>E. coli</i> culture, TrpB <i>Pf</i><sub>quat </sub>provides an efficient and environmentally-friendly platform for the preparation of noncanonical amino acids bearing quaternary carbons.</p></div></div></div>

scholarly journals Tailoring Tryptophan Synthase TrpB for Selective Quaternary Carbon Bond Formation

2019 ◽  
Vol 141 (50) ◽  
pp. 19817-19822 ◽  
Author(s):  
Markus Dick ◽  
Nicholas S. Sarai ◽  
Michael W. Martynowycz ◽  
Tamir Gonen ◽  
Frances H. Arnold
Keyword(s):  
Bond Formation ◽  
Tryptophan Synthase ◽  
Quaternary Carbon ◽  
Carbon Bond

scholarly journals Pentanidium-Catalyzed Direct Assembly of Vicinal All-Carbon Quaternary Stereocenters through C(sp3)-C(sp3) Bond Formation

2021 ◽  
Author(s):  
Choon-Hong Tan ◽  
Xu Ban ◽  
Yifan Fan ◽  
Tuan-Khoa Kha ◽  
Richmond Lee ◽  
...  
Keyword(s):  
Bond Formation ◽  
Direct Assembly ◽  
Tertiary Carbon ◽  
Asymmetric Coupling ◽  
Catalytic Asymmetric ◽  
Quaternary Stereocenters ◽  
Straightforward Approach

Abstract The stereoselective construction of vicinal all-carbon quaternary stereocenters has long been a formidable synthetic challenge. Direct asymmetric coupling of a tertiary carbon nucleophile with a tertiary carbon electrophile is the most straightforward approach but it is sterically and energetically disfavored. Herein, we described a catalytic asymmetric substitution, where racemic tertiary bromides directly couple with racemic secondary or tertiary carbanion, creating a series of congested carbon (sp3)-carbon(sp3) bonds, including isolated all-carbon quaternary stereocenters, vicinal tertiary/all-carbon quaternary stereocenters and vicinal all-carbon quaternary stereocenters. This double stereoconvergent process, using pentanidium as catalyst, affords substituted products in good enantioselectivities and diastereoselectivities.

scholarly journals Crystal structure of cytoplasmic acetoacetyl-CoA thiolase fromSaccharomyces cerevisiae

2018 ◽  
Vol 74 (1) ◽  
pp. 6-13 ◽  
Author(s):  
Pengfei Zhou ◽  
Zhongliang Zhu ◽  
Muhammad Hidayatullah Khan ◽  
Peiyi Zheng ◽  
Maikun Teng ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Mevalonate Pathway ◽  
Condensation Reaction ◽  
Bond Formation ◽  
Binding Pocket ◽  
Binding Mode ◽  
Carbon Bond ◽  
Carbon Carbon Bond ◽  
Binding Cavity ◽  
Comparative Binding

Thiolases are vital enzymes which participate in both degradative and biosynthetic pathways. Biosynthetic thiolases catalyze carbon–carbon bond formation by a Claisen condensation reaction. The cytoplasmic acetoacetyl-CoA thiolase fromSaccharomyces cerevisiae, ERG10, catalyses carbon–carbon bond formation in the mevalonate pathway. The structure of aS. cerevisiaebiosynthetic thiolase has not previously been reported. Here, crystal structures of apo ERG10 and its Cys91Ala variant were solved at resolutions of 2.2 and 1.95 Å, respectively. The structure determined shows that ERG10 shares the characteristic thiolase superfamily fold, with a similar active-site architecture to those of type II thiolases and a similar binding pocket, apart from Ala159 at the entrance to the pantetheine-binding cavity, which appears to be a determinant of the poor binding ability of the substrate. Moreover, comparative binding-pocket analysis of moleculeBin the asymmetric unit of the apo structure with that of the CoA-bound complex of human mitochondrial acetoacetyl-CoA thiolase indicates the canonical binding mode of CoA. Furthermore, the steric hindrance revealed in a structural comparison of moleculeAwith the CoA-bound form raise the possibility of conformational changes that are associated with substrate binding.

Carbon Dioxide-Mediated C(sp2)–H Arylation of Primary and Secondary Benzylamines

2018 ◽  
Author(s):  
Mohit Kapoor ◽  
Pratibha Chand-Thakuri ◽  
Michael Young
Keyword(s):  
Carbon Dioxide ◽  
Transition Metal ◽  
Bond Activation ◽  
Bond Formation ◽  
Carbon Bond ◽  
Chelate Effect ◽  
Free Amine ◽  
Carbon Carbon Bond ◽  
New Strategy ◽  
Metal Catalyzed

Carbon-carbon bond formation by transition metal-catalyzed C–H activation has become an important strategy to fabricate new bonds in a rapid fashion. Despite the pharmacological importance of <i>ortho</i>-arylbenzylamines, however, effective <i>ortho</i>-C–C bond formation from C–H bond activation of free primary and secondary benzylamines using Pd<sup>II</sup> remains an outstanding challenge. Presented herein is a new strategy for constructing <i>ortho</i>-arylated primary and secondary benzylamines mediated by carbon dioxide (CO<sub>2</sub>). The use of CO<sub>2</sub> is critical to allowing this transformation to proceed under milder conditions than previously reported, and that are necessary to furnish free amine products that can be directly used or elaborated without the need for deprotection. In cases where diarylation is possible, a chelate effect is demonstrated to facilitate selective monoarylation.

Design of Arylsulfonylhydrazones as Potential FabH Inhibitors: Synthesis, Antimicrobial Evaluation and Molecular Docking

2019 ◽  
Vol 15 ◽  
Author(s):  
Thais Batista Fernandes ◽  
Natanael Dante Segretti ◽  
Felipe Rebello Lourenço ◽  
Thalita Marcílio Cândido ◽  
André Rolim Baby ◽  
...  
Keyword(s):  
Antioxidant Activity ◽  
Molecular Docking ◽  
Antimicrobial Agents ◽  
Acyl Carrier Protein ◽  
Condensation Reaction ◽  
Lung Fibroblast ◽  
Fibroblast Cells ◽  
Human Lung Fibroblast ◽  
Persistent Problem ◽  
E Coli

Background: Antimicrobial resistance is a persistent problem about infections treatment and carries needing for develop new antimicrobial agents. Inhibiting of bacterial β-ketoacyl acyl carrier protein synthase III (FabH), which catalyzes the condensation reaction between a CoA-attached acetyl group and an ACP-attached malonyl group in bacteria is an interesting strategy to find new antibacterial agents. Objective: The aim of this work was to design and synthesize arylsulfonylhydrazones potentially FabH inhibitors and evaluate their antimicrobial activity. Methods: MIC50 of sulfonylhydrazones against E. coli and S. aureus was determined. Antioxidant activity was evaluated by DPPH (1-1’-diphenyl-2-picrylhydrazyl) assay and cytotoxicity against LL24 lung fibroblast cells was verified by MTT method. Principal component analysis (PCA) was performed in order to suggest a structure-activity relationship. Molecular docking allowed to propose sulfonylhydrazones interactions with FabH. Results: The most active compound showed activity against S. aureus and E. coli, with MIC50 = 0.21 and 0.44 µM, respectively. PCA studies correlated better activity to lipophilicity and molecular docking indicated that sulfonylhydrazone moiety is important to hydrogen-bond with FabH while methylcatechol ring performs π-π stacking interaction. The DPPH assay revealed that some sulfonylhydrazones derived from the methylcatechol series had antioxidant activity. None of the evaluated compounds was cytotoxic to human lung fibroblast cells, suggesting that the compounds might be considered safe at the tested concentration. Conclusion: Arylsufonylhydrazones is a promising scaffold to be explored for design of new antimicrobial agents.

Mixed ligand-metal Complexes of 2-(butan-2-ylidene) hydrazinecarbothioamide- Synthesis, Characterization, Computer Aided Drug Character Evaluation and in vitro Biological Activity Assessment

2019 ◽  
Vol 15 ◽  
Author(s):  
Tahmeena Khan ◽  
Rumana Ahmad ◽  
Iqbal Azad ◽  
Saman Raza ◽  
Seema Joshi ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Metal Complexes ◽  
Condensation Reaction ◽  
Dose Range ◽  
Biological Significance ◽  
Mixed Ligand ◽  
Binding Energies ◽  
Mixed Ligand Complexes ◽  
E Coli ◽  
Topo Ii

Background: Mixed ligand-metal complexes are efficient chelating agents because of flexible donor ability. Mixed ligand complexes containing hetero atoms sulphur, nitrogen and oxygen have been probed for their biological significance. Objective: Nine mixed ligand-metal complexes of 2-(butan-2-ylidene) hydrazinecarbothioamide (2-butanone thiosemicarbazone) and pyridine, bipyridine or 2-picoline as co-ligands were synthesized with Cu, Fe and Zn. The complexes were tested against MDA-MB231 (MDA) and A549 cell lines. Antibacterial activity was tested against S. aureus and E. coli. The drug character of the complexes was evaluated on several parameters viz. physicochemical properties, bioactivity scores, toxicity assessment and absorption, distribution, metabolism, excretion and toxicity (ADMET) profile assessment using various automated softwares. Molecular docking of the complexes was also performed with two target proteins. Method and Results: The mixed ligand-metal complexes were synthesized by condensation reaction for 4-5 h. The characterization was done by elemental analysis, 1H-NMR, FT-IR, molar conductance and UV spectroscopies. Molecular docking was performed against ribonucleotide reductase (RR) and topoisomerase II (topo II). [Cu(C5H11N3S)(py)2(CH3COO)2], [Zn(C5H11N3S)(bpy)(SO4)] and [Zn(C5H11N3S)(2-pic)2(SO4)] displayed the lowest binding energies with respect to RR. Against topo II [Cu(C5H11N3S)(py)2(CH3COO)2], [Cu(C5H11N3S)(bpy)(CH3COO)2] and [Zn(C5H11N3S)(2-pic)2(SO4)] had the lowest energies. The druglikness assessment was done using Leadlikeness and Lipinski’s rules. Against topo II [Cu(C5H11N3S)(py)2(CH3COO)2], [Cu(C5H11N3S)(bpy)(CH3COO)2] and [Zn(C5H11N3S)(2-pic)2(SO4)] had the lowest energies. Not more than two violations were obtained in case of each filtering rule showing drug like character of the mixed ligand complexes. Several of the complexes exhibited positive bioactivity scores and almost all the complexes were predicted to be safe with no hazardous effects. All the complexes were predicted to have no mutagenic character as shown by the Ames test [Zn(C5H11N3S)(py)2(SO4)] showed potential activity against MDA. [Co(C5H11N3S(bpy)(Cl)2] was also active against MDA. [Cu(C5H11N3S)(2-pic)2(CH3COO)2] also showed 27.6% cell viability at 100 µM against MDA. Against A549 [Co(C5H11N3S)(py)2(Cl)2], [Cu(C5H11N3S)(py)2(CH3COO)2] and [Co(C5H11N3S(bpy)(Cl)2] were active. [Co(C5H11N3S)(bpy)(Cl)2] and [Cu(C5H11N3S)(2-pic)2(CH3COO)2] were active against S. aureus. [Co(C5H11N3S)(2-pic)2(Cl)2] and [Zn(C5H11N3S)(2-pic)2(SO4)] were active at lower concentrations against S.aureus. Against E. coli, [Zn(C5H11N3S)(2-pic)2(SO4)] showed activity at 18-20mg dose range.

Modern Organic Synthesis in the Laboratory

2008 ◽  
Author(s):  
Jie Jack Li ◽  
Chris Limberakis ◽  
Derek A. Pflum
Keyword(s):  
Organic Chemistry ◽  
Graduate Students ◽  
Organic Synthesis ◽  
Functional Group ◽  
Bond Formation ◽  
Reaction Conditions ◽  
Carbon Bond ◽  
Oxidation Reduction ◽  
Carbon Carbon Bond ◽  
Daunting Task

Searching for reaction in organic synthesis has been made much easier in the current age of computer databases. However, the dilemma now is which procedure one selects among the ocean of choices. Especially for novices in the laboratory, it becomes a daunting task to decide what reaction conditions to experiment with first in order to have the best chance of success. This collection intends to serve as an "older and wiser lab-mate" one could have by compiling many of the most commonly used experimental procedures in organic synthesis. With chapters that cover such topics as functional group manipulations, oxidation, reduction, and carbon-carbon bond formation, Modern Organic Synthesis in the Laboratory will be useful for both graduate students and professors in organic chemistry and medicinal chemists in the pharmaceutical and agrochemical industries.

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