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.

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 The effect of NaOH addition on the characteristics of tilapia skin collagen

2021 ◽  
Vol 924 (1) ◽  
pp. 012089
Author(s):  
Nurhayati ◽  
R Kusumawati ◽  
Suryanti
Keyword(s):  
Surface Morphology ◽  
Functional Groups ◽  
Morphological Analysis ◽  
Functional Group ◽  
Group Analysis ◽  
Extraction Process ◽  
Fiber Structure ◽  
Skin Collagen ◽  
Fish Collagen ◽  
Functional Group Analysis

Abstract Research on fish collagen is now growing rapidly as the use of collagen in industry increases. Collagen extraction begins with the removal of non-collagen proteins using bases to maximize the extraction process. This research aims to determine the effect of differences in NaOH concentrations on the characteristics of tilapia skin collagen. NaOH in collagen extraction serves to remove alkaline soluble proteins to optimize the collagen extraction process. The bases used were NaOH with the concentration of 0.5, 1.0, and 1.5%. The extraction was carried out using the acid method. Using SEM, observation parameters for crude collagen from the tilapia skin include collagen yield, functional group analysis, lightness, and surface morphology. The results of functional groups analysis showed that the collagen obtained in all treatments had typical collagen characteristics, i.e., amide A, amide B, amide I, amide II, and amide III. The non-collagen deproteination treatment with 0.5% NaOH could produce better collagen than the 1.0 and 1.5% concentrations, as indicated by the highest yield (20.42%) and lightness (93.22). Morphological analysis showed that the collagen extracted has an irregular branched fiber structure.

scholarly journals The Effect of Addition of Avocado Fruit Seeds On Bioplastic Biodegradation

2020 ◽  
Vol 3 ◽  
pp. 137-145
Author(s):  
Viki Fathurohman ◽  
Darmawan Alisaputra ◽  
Endaruji Sedyadi
Keyword(s):  
Weight Loss ◽  
Functional Groups ◽  
Functional Group ◽  
Group Analysis ◽  
Base Material ◽  
Avocado Fruit ◽  
Soil Media ◽  
Functional Group Analysis ◽  
Avocado Starch

Bioplastics can be made with chitosan as a base material with a sorbitol plasticizer and avocado-based seed starch. This study tries to discuss the comparison of avocado seeds to bioplastic biodegradability required based on weight loss in soil media. This research was carried out in empathic, namely making avocado starch, making bioplastics, analyzing bioplastic functional groups, and testing biodegradation of bioplastics in soil media. Variations used are avocado seeds used are 0; 0.1; 0.3; 0.5; 0.7; and 1.4 grams. Bioplastic functional group analysis was performed using FTIR. Bioplastic biodegradability in soil media. Bioplastics are 76% degraded within 12 days in the soil. This shows that bioplastics can be biodegradable.

scholarly journals Chemical Elicitors Induce Rare Bioactive Secondary Metabolites in Deep-Sea Bacteria under Laboratory Conditions

Metabolites ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 107
Author(s):  
Rafael de Felício ◽  
Patricia Ballone ◽  
Cristina Freitas Bazzano ◽  
Luiz F. G. Alves ◽  
Renata Sigrist ◽  
...  
Keyword(s):  
Natural Products ◽  
Secondary Metabolites ◽  
Natural Product ◽  
Deep Sea ◽  
Chemical Space ◽  
Bacterial Genome ◽  
Vast Number ◽  
Bacterial Metabolites ◽  
Laboratory Conditions ◽  
Deep Sea Bacteria

Bacterial genome sequencing has revealed a vast number of novel biosynthetic gene clusters (BGC) with potential to produce bioactive natural products. However, the biosynthesis of secondary metabolites by bacteria is often silenced under laboratory conditions, limiting the controlled expression of natural products. Here we describe an integrated methodology for the construction and screening of an elicited and pre-fractionated library of marine bacteria. In this pilot study, chemical elicitors were evaluated to mimic the natural environment and to induce the expression of cryptic BGCs in deep-sea bacteria. By integrating high-resolution untargeted metabolomics with cheminformatics analyses, it was possible to visualize, mine, identify and map the chemical and biological space of the elicited bacterial metabolites. The results show that elicited bacterial metabolites correspond to ~45% of the compounds produced under laboratory conditions. In addition, the elicited chemical space is novel (~70% of the elicited compounds) or concentrated in the chemical space of drugs. Fractionation of the crude extracts further evidenced minor compounds (~90% of the collection) and the detection of biological activity. This pilot work pinpoints strategies for constructing and evaluating chemically diverse bacterial natural product libraries towards the identification of novel bacterial metabolites in natural product-based drug discovery pipelines.

scholarly journals MeFSAT: a curated natural product database specific to secondary metabolites of medicinal fungi

RSC Advances ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 2596-2607
Author(s):  
R. P. Vivek-Ananth ◽  
Ajaya Kumar Sahoo ◽  
Kavyaa Kumaravel ◽  
Karthikeyan Mohanraj ◽  
Areejit Samal
Keyword(s):  
Natural Products ◽  
Secondary Metabolites ◽  
Natural Product ◽  
Chemical Space ◽  
Therapeutic Uses ◽  
Medicinal Fungi ◽  
Fungal Natural Products

First dedicated manually curated resource on secondary metabolites and therapeutic uses of medicinal fungi. Cheminformatics based analysis of the chemical space of fungal natural products.

scholarly journals Natural product fragment combination to performance-diverse pseudo-natural products

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Michael Grigalunas ◽  
Annina Burhop ◽  
Sarah Zinken ◽  
Axel Pahl ◽  
José-Manuel Gally ◽  
...  
Keyword(s):  
Natural Products ◽  
Product Design ◽  
Natural Product ◽  
Chemical Space ◽  
Biological Evaluation ◽  
Product Structure ◽  
Biologically Relevant ◽  
Biologically Relevant Chemical Space

AbstractNatural product structure and fragment-based compound development inspire pseudo-natural product design through different combinations of a given natural product fragment set to compound classes expected to be chemically and biologically diverse. We describe the synthetic combination of the fragment-sized natural products quinine, quinidine, sinomenine, and griseofulvin with chromanone or indole-containing fragments to provide a 244-member pseudo-natural product collection. Cheminformatic analyses reveal that the resulting eight pseudo-natural product classes are chemically diverse and share both drug- and natural product-like properties. Unbiased biological evaluation by cell painting demonstrates that bioactivity of pseudo-natural products, guiding natural products, and fragments differ and that combination of different fragments dominates establishment of unique bioactivity. Identification of phenotypic fragment dominance enables design of compound classes with correctly predicted bioactivity. The results demonstrate that fusion of natural product fragments in different combinations and arrangements can provide chemically and biologically diverse pseudo-natural product classes for wider exploration of biologically relevant chemical space.

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