scholarly journals Natural Products Containing ‘Rare’ Organophosphorus Functional Groups

Molecules ◽  
2019 ◽  
Vol 24 (5) ◽  
pp. 866 ◽  
Author(s):  
Janusz Petkowski ◽  
William Bains ◽  
Sara Seager
Keyword(s):  
Amino Acids ◽  
Natural Products ◽  
Functional Groups ◽  
Functional Group ◽  
Organophosphorus Compounds ◽  
Living Cells ◽  
Unusual Amino Acids ◽  
Biological Source ◽  
Technological Limitations

Phosphorous-containing molecules are essential constituents of all living cells. While the phosphate functional group is very common in small molecule natural products, nucleic acids, and as chemical modification in protein and peptides, phosphorous can form P–N (phosphoramidate), P–S (phosphorothioate), and P–C (e.g., phosphonate and phosphinate) linkages. While rare, these moieties play critical roles in many processes and in all forms of life. In this review we thoroughly categorize P–N, P–S, and P–C natural organophosphorus compounds. Information on biological source, biological activity, and biosynthesis is included, if known. This review also summarizes the role of phosphorylation on unusual amino acids in proteins (N- and S-phosphorylation) and reviews the natural phosphorothioate (P–S) and phosphoramidate (P–N) modifications of DNA and nucleotides with an emphasis on their role in the metabolism of the cell. We challenge the commonly held notion that nonphosphate organophosphorus functional groups are an oddity of biochemistry, with no central role in the metabolism of the cell. We postulate that the extent of utilization of some phosphorus groups by life, especially those containing P–N bonds, is likely severely underestimated and has been largely overlooked, mainly due to the technological limitations in their detection and analysis.

scholarly journals Syntheses of Cyclomarins – Interesting Marine Natural Products with Distinct Mode of Action towards Malaria and Tuberculosis

Synthesis ◽  
2018 ◽  
Vol 51 (01) ◽  
pp. 107-121 ◽  
Author(s):  
Alexander Kiefer ◽  
Uli Kazmaier
Keyword(s):  
Amino Acids ◽  
Plasmodium Falciparum ◽  
Natural Products ◽  
Total Synthesis ◽  
Building Blocks ◽  
Distinct Mode ◽  
Unusual Amino Acids ◽  
Caseinolytic Protease ◽  
A Subunit ◽  
Cyclomarin A

The cyclomarins are cyclic heptapeptides from marine streptomycetes containing four rather unusual amino acids. Interestingly, the cyclomarins address two completely different targets: ClpC1, a subunit of the caseinolytic protease of Mycobacterium tuberculosis (MTB), as well as PfAp3Aase of Plasmodium falciparum. Therefore, the cyclomarins are interesting lead structures for the development of drugs targeting tuberculosis and malaria. As a result, several synthetic protocols towards the synthesis of these unusual building blocks as well as the natural products themselves have been developed, which will be discussed in this review.1 Introduction2 Synthesis of the Building Blocks3 Total Synthesis of Cyclomarin C by Yao and Co-workers4 Total Synthesis of Cyclomarin A and C by Barbie and Kazmaier5 Conclusion

scholarly journals Intramolecular bridges formed by photoswitchable click amino acids

2012 ◽  
Vol 8 ◽  
pp. 884-889 ◽  
Author(s):  
Christian Hoppmann ◽  
Ronald Kühne ◽  
Michael Beyermann
Keyword(s):  
Amino Acids ◽  
Functional Group ◽  
Click Reaction ◽  
Helical Structure ◽  
Thiol Group ◽  
Living Cells ◽  
Cysteine Residue ◽  
Side Chain ◽  
Model Peptide ◽  
Reducing Conditions

Photoswitchable click amino acids (PSCaa) are amino acids bearing a side chain consisting of a photoswitchable unit elongated with a functional group that allows for a specific click reaction, such as an alkene that can react with the thiol group of a cysteine residue. An intramolecular click reaction results in the formation of a photoswitchable bridge, which can be used for controlling conformational domains in peptides and proteins. The ability to control conformations as well as the efficiency of the intramolecular bridging depends on the length of the PSCaa side chain and the distance to the cysteine residue to be clicked with. On comparing i,i+4 and i,i+7 spacings of PSCaa and cysteine in a model peptide without a preferred conformation, it was seen that the thiol–ene click reaction takes place efficiently in both cases. Upon induction of an α-helical structure by the addition of trifluoroethanol, the thiol click reaction occurs preferentially with the i,i+4 spacing. Even in the presence of glutathione as an additional thiol the click reaction of the PSCaa occurs intramolecularly with the cysteine rather than with the glutathione, indicating that the click reaction may be used even under reducing conditions occurring in living cells.

scholarly journals Functional group and diversity analysis of BIOFACQUIM: A Mexican natural product database

F1000Research ◽  
2020 ◽  
Vol 8 ◽  
pp. 2071 ◽  
Author(s):  
Norberto Sánchez-Cruz ◽  
B. Angélica Pilón-Jiménez ◽  
José L. Medina-Franco
Keyword(s):  
Natural Products ◽  
Content Analysis ◽  
Natural Product ◽  
Functional Groups ◽  
Functional Group ◽  
Group Analysis ◽  
Global Diversity ◽  
Starting Point ◽  
Structural Content ◽  
Functional Group Analysis

Background: Natural product databases are important in drug discovery and other research areas. An analysis of its structural content, as well as functional group occurrence, provides a useful overview, as well as a means of comparison with related databases. BIOFACQUIM is an emerging database of natural products characterized and isolated in Mexico. Herein, we discuss the results of a first systematic functional group analysis and global diversity of an updated version of BIOFACQUIM. Methods: BIOFACQUIM was augmented through a literature search and data curation. A structural content analysis of the dataset was performed. This involved a functional group analysis with a novel algorithm to automatically identify all functional groups in a molecule and an assessment of the global diversity using consensus diversity plots. To this end, BIOFACQUIM was compared to two major and large databases: ChEMBL 25, and a herein assembled collection of natural products with 169,839 unique compounds. Results: The structural content analysis showed that 15.7% of compounds and 11.6% of scaffolds present in the current version of BIOFACQUIM have not been reported in the other large reference datasets. It also gave a diversity increase in terms of scaffolds and molecular fingerprints regarding the previous version of the dataset, as well as a higher similarity to the assembled collection of natural products than to ChEMBL 25, in terms of diversity and frequent functional groups. Conclusions: A total of 148 natural products were added to BIOFACQUIM, which meant a diversity increase in terms of scaffolds and fingerprints. Regardless of its relatively small size, there are a significant number of compounds and scaffolds that are not present in the reference datasets, showing that curated databases of natural products, such as BIOFACQUIM, can serve as a starting point to increase the biologically relevant chemical space.

scholarly journals Versatile synthesis of amino acid functionalized nucleosides via a domino carboxamidation reaction

2014 ◽  
Vol 10 ◽  
pp. 2566-2572 ◽  
Author(s):  
Vicky Gheerardijn ◽  
Jos Van den Begin ◽  
Annemieke Madder
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Nucleic Acid ◽  
Functional Groups ◽  
Functional Group ◽  
Binding Properties ◽  
Dna And Rna ◽  
Straightforward Method ◽  
Nucleic Acid Structures ◽  
Proof Of Principle

Functionalized oligonucleotides have recently gained increased attention for incorporation in modified nucleic acid structures both for the design of aptamers with enhanced binding properties as well as the construction of catalytic DNA and RNA. As a shortcut alternative to the incorporation of multiple modified residues, each bearing one extra functional group, we present here a straightforward method for direct linking of functionalized amino acids to the nucleoside base, thus equipping the nucleoside with two extra functionalities at once. As a proof of principle, we have introduced three amino acids with functional groups frequently used as key-intermediates in DNA- and RNAzymes via an efficient and straightforward domino carboxamidation reaction.

Role of functional groups in determining interactions in ternary aqueous solutions of enantiomeric α-amino acids: a calorimetric study at 298 K

1999 ◽  
Vol 1 (24) ◽  
pp. 5653-5657 ◽  
Author(s):  
Giuseppina Castronuovo ◽  
Vittorio Elia ◽  
Marcella Niccoli ◽  
Daniela Strollo ◽  
Filomena Velleca
Keyword(s):  
Amino Acids ◽  
Aqueous Solutions ◽  
Functional Groups ◽  
Calorimetric Study

Revealing the critical role of template functional group ordering in the template-directed crystallization of pyrazinamide

CrystEngComm ◽  
2019 ◽  
Vol 21 (42) ◽  
pp. 6382-6389 ◽  
Author(s):  
Keke Zhang ◽  
Shijie Xu ◽  
Junbo Gong ◽  
Weiwei Tang
Keyword(s):  
Functional Groups ◽  
Functional Group ◽  
Critical Role ◽  
Directed Crystallization ◽  
Specific Orientation

The nucleation of γ form pyrazinamide can be directed by the ordering and specific orientation of the template functional groups.

Intramolecular functional group differentiation as a strategy for the synthesis of bridged bicyclic β-amino acids

RSC Advances ◽  
2016 ◽  
Vol 6 (27) ◽  
pp. 22737-22748 ◽  
Author(s):  
Andriy V. Tymtsunik ◽  
Serhii O. Kokhan ◽  
Yevhen M. Ivon ◽  
Igor V. Komarov ◽  
Oleksandr O. Grygorenko
Keyword(s):  
Amino Acids ◽  
Functional Groups ◽  
Functional Group ◽  
Amino Group ◽  
Group Differentiation

Differentiation of identical electrophilic functional groups (carboxylates) by a strategically placed internal nucleophile (an amino group) in cyclic precursors was used as a key general approach to functionalized azabicyclic scaffolds.

scholarly journals Functional group and diversity analysis of BIOFACQUIM: A Mexican natural product database

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 2071 ◽  
Author(s):  
Norberto Sánchez-Cruz ◽  
B. Angélica Pilón-Jiménez ◽  
José L. Medina-Franco
Keyword(s):  
Natural Products ◽  
Content Analysis ◽  
Natural Product ◽  
Functional Groups ◽  
Functional Group ◽  
Chemical Space ◽  
Group Analysis ◽  
Global Diversity ◽  
Structural Content ◽  
Functional Group Analysis

Background: Natural product databases are important in drug discovery and other research areas. Their structural contents and functional group analysis are relevant to increase their knowledge in terms of chemical diversity and chemical space coverage. BIOFACQUIM is an emerging database of natural products characterized and isolated in Mexico. Herein, we discuss the results of a first systematic functional group analysis and global diversity of an updated version of BIOFACQUIM. Methods: BIOFACQUIM was augmented through a literature search and data curation. A structural content analysis of the dataset was done. This involved a functional group analysis with a novel algorithm to identify automatically all functional groups in a molecule and an assessment of the global diversity using consensus diversity plots. To this end, BIOFACQUIM was compared to two major and large databases: ChEMBL 25, and a herein assembled collection of natural products with 169,839 unique compounds. Results: The structural content analysis showed that 16.1% of compounds, 11.3% of scaffolds, and 6.3% of functional groups present in the current version of BIOFACQUIM have not been reported in the other large reference datasets. It also gave a diversity increase in terms of scaffolds and molecular fingerprints regarding the previous version of the dataset, as well as a higher similarity to the assembled collection of natural products than to ChEMBL 25, in terms of diversity and frequent functional groups. Conclusions: A total of 148 natural products were added to BIOFACQUIM, which meant a diversity increase in terms of scaffolds and fingerprints. Regardless of its relatively small size, there are a significant number of compounds, scaffolds, and functional groups that are not present in the reference datasets, showing that curated databases of natural products, such as BIOFACQUIM, can serve as a starting point to increase the biologically relevant chemical space.

Steel Industry Wastes Treatment in Buffer Ponds

1987 ◽  
Vol 19 (12) ◽  
pp. 363-364
Author(s):  
V. M. Bagnyuk
Keyword(s):  
Functional Groups ◽  
Steel Industry ◽  
Functional Group ◽  
Ecological Factors ◽  
The Self ◽  
Biogenic Elements ◽  
Limiting Factor ◽  
High Turbidity

The bioprocesses of steel industry wastes self-purification in buffer ponds have been studied. The representatives of 6-7 divisions of microalgae and many functional groups of bacteria have been found in the ponds. The important role of a new functional group, the “lytic” microorganisms, in the regulation of microecosystems and in bacterial self-purification has been established. It was found that the activity of self-purification bioprocesses in the buffer ponds studied depends on a variety of ecological factors. The main limiting factor has been shown to be the high turbidity of water, and its deficit of dissolved phosphates and oxygen. To accelerate the self-purification of steel industry wastes in buffer ponds the concentration of organic and mineral forms of the main biogenic elements (C,N,P) should be regulated. Water clarification and aeration were recommended and effectively used.

scholarly journals Complexations of Divalent Metallic Ions with Fulvic Acids

2018 ◽  
Vol 43 (1) ◽  
pp. 54
Author(s):  
Denise De Oliveira Vaz ◽  
Andreia Neves Fernandes ◽  
Bruno Szpoganicz
Keyword(s):  
Functional Groups ◽  
Functional Group ◽  
Fulvic Acids ◽  
Aquatic Environments ◽  
Metallic Ions ◽  
Divalent Ions ◽  
Proton Dissociation ◽  
Bivalent Ions ◽  
Suwannee River Fulvic Acid

In this work, the interactions of the functional groups of fulvic acids with copper, cadmium and zinc bivalent ions was investigated by potentiometry. The BEST7 software was employed to investigate the interactions of the functional groups. The software SPE and SPEPLOT were used to generate and to plot the species diagrams. It was used the Suwannee River fulvic acid (SRFA) of the IHSS (International Humic Substances Society) to illustrate the process. The values of the proton dissociation and complexation constants with the divalent ions for each functional group were calculated and their values were very close tothose previously published. The functional group present in the highest quantity in the complexes was cathecol, and it complexed with all the divalent ions, although to a greater extent with Cu(II). According to the results obtained by potentiometry, the reactivity series for the divalent ions and the SRFA is: Cu(II) >> Cd(II) > Zn(II). Thus, the method employed could be useful to estimate the role of fulvic acids in the transport of metals in the aquatic environments.

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