3 Chemical similarity methods for analyzing secondary metabolite structures

2021 ◽  
pp. 57-74
Author(s):  
Lena Y. E. Ekaney ◽  
Donatus B. Eni ◽  
Fidele Ntie-Kang
Planta Medica ◽  
2008 ◽  
Vol 74 (09) ◽  
Author(s):  
SA Van der Sar ◽  
KM Fisch ◽  
C Gurgui ◽  
TA Nguyen ◽  
J Piel ◽  
...  

2020 ◽  
Author(s):  
Cameron Hargreaves ◽  
Matthew Dyer ◽  
Michael Gaultois ◽  
Vitaliy Kurlin ◽  
Matthew J Rosseinsky

It is a core problem in any field to reliably tell how close two objects are to being the same, and once this relation has been established we can use this information to precisely quantify potential relationships, both analytically and with machine learning (ML). For inorganic solids, the chemical composition is a fundamental descriptor, which can be represented by assigning the ratio of each element in the material to a vector. These vectors are a convenient mathematical data structure for measuring similarity, but unfortunately, the standard metric (the Euclidean distance) gives little to no variance in the resultant distances between chemically dissimilar compositions. We present the Earth Mover’s Distance (EMD) for inorganic compositions, a well-defined metric which enables the measure of chemical similarity in an explainable fashion. We compute the EMD between two compositions from the ratio of each of the elements and the absolute distance between the elements on the modified Pettifor scale. This simple metric shows clear strength at distinguishing compounds and is efficient to compute in practice. The resultant distances have greater alignment with chemical understanding than the Euclidean distance, which is demonstrated on the binary compositions of the Inorganic Crystal Structure Database (ICSD). The EMD is a reliable numeric measure of chemical similarity that can be incorporated into automated workflows for a range of ML techniques. We have found that with no supervision the use of this metric gives a distinct partitioning of binary compounds into clear trends and families of chemical property, with future applications for nearest neighbor search queries in chemical database retrieval systems and supervised ML techniques.


2018 ◽  
Vol 1 (1) ◽  
Author(s):  
Hooi-Leng Ser ◽  
Wai-Fong Yin ◽  
Kok-Gan Chan ◽  
Nurul-Syakima Ab Mutalib ◽  
Learn-Han Lee

Novosphingobium malaysiense strain MUSC 273T is a recently identified Gram-negative, aerobic alpha-proteobacterium. The strain was isolated from intertidal soil with strong catalase activity. The genome sequence comprises 5,027,021 bp, with 50 tRNA and 3 rRNA genes. Further analysis identified presence of secondary metabolite gene clusters within genome of MUSC 273T. Knowledge of the genomic features of the strain may allow further biotechnological exploitation, particularly for production of secondary metabolites as well as production of industrially important enzymes


2019 ◽  
Vol 20 (5) ◽  
pp. 376-389 ◽  
Author(s):  
Sonali Mishra ◽  
Nupur Srivastava ◽  
Velusamy Sundaresan ◽  
Karuna Shanker

Background: Decalepis arayalpathra (J. Joseph and V. Chandras.) Venter is used primarily for nutrition besides its therapeutic values. Traditional preparations/formulations from its tuber are used as a vitalizer and blood purifier drink. The folklore medicinal uses cover inflammation, cough, wound healing, antipyretic, and digestive system management. A comprehensive review of the current understanding of the plant is required due to emerging concerns over its safety and efficacy. Objective: The systematic collection of the authentic information from different sources with the critical discussion is summarised in order to address various issues related to botanical identity, therapeutic medicine, nutritional usage, phytochemical, and pharmacological potentials of the D. arayalpathra. Current use of traditional systems of medicine can be used to expand future research opportunities. Materials and Methods: Available scripted information was collected manually, from peered review research papers and international databases viz. Science Direct, Google Scholar, SciFinder, Scopus, etc. The unpublished resources which were not available in database were collected through the classical books of ‘Ayurveda’ and ‘Siddha’ published in regional languages. The information from books, Ph.D. and MSc dissertations, conference papers and government reports were also collected. We thoroughly screened the scripted information of classical books, titles, abstracts, reports, and full-texts of the journals to establish the reliability of the content. Results: Tuber bearing vanilla like signature flavor is due to the presence of 2-hydroxy-4-methoxybenzaldehyde (HMB). Among five other species, Decalepis arayalpathra (DA) has come under the ‘critically endangered’ category, due to over-exploitation for traditional, therapeutic and cool drink use. The experimental studies proved that it possesses gastro-protective, anti-tumor, and antiinflammatory activities. Some efforts were also made to develop better therapeutics by logical modifications in 2-Hydroxy-4-methoxy-benzaldehyde, which is a major secondary metabolite of D. arayalpathra. ‘Amruthapala’ offers the enormous opportunity to develop herbal drink with health benefits like gastro-protective, anti-oxidant and anti-inflammatory actions. Results: The plant has the potential to generate the investigational new lead (IND) based on its major secondary metabolite i.e. 2-Hydroxy-4-methoxy-benzaldehyde. The present mini-review summarizes the current knowledge on Decalepis arayalpathra, covering its phytochemical diversity, biological potentials, strategies for its conservation, and intellectual property rights (IPR) status. Chemical Compounds: 2-hydroxy-4-methoxybenzaldehyde (Pubchem CID: 69600), α-amyrin acetate (Pubchem CID: 293754), Magnificol (Pubchem CID: 44575983), β-sitosterol (Pubchem CID: 222284), 3-hydroxy-p-anisaldehyde (Pubchem CID: 12127), Naringenin (Pubchem CID: 932), Kaempferol (Pubchem CID: 5280863), Aromadendrin (Pubchem CID: 122850), 3-methoxy-1,2-cyclopentanedione (Pubchem CID: 61209), p-anisaldehyde (Pubchem CID: 31244), Menthyl acetate (Pubchem CID: 27867), Benzaldehyde (Pubchem CID: 240), p-cymene (Pubchem CID: 7463), Salicylaldehyde (Pubchem CID: 6998), 10-epi-γ-eudesmol (Pubchem CID: 6430754), α -amyrin (Pubchem CID: 225688), 3-hydroxy-4-methoxy benzaldehyde (Pubchem CID: 12127).


2020 ◽  
Vol 16 (4) ◽  
pp. 473-485
Author(s):  
David Mary Rajathei ◽  
Subbiah Parthasarathy ◽  
Samuel Selvaraj

Background: Coronary heart disease generally occurs due to cholesterol accumulation in the walls of the heart arteries. Statins are the most widely used drugs which work by inhibiting the active site of 3-Hydroxy-3-methylglutaryl-CoA reductase (HMGCR) enzyme that is responsible for cholesterol synthesis. A series of atorvastatin analogs with HMGCR inhibition activity have been synthesized experimentally which would be expensive and time-consuming. Methods: In the present study, we employed both the QSAR model and chemical similarity search for identifying novel HMGCR inhibitors for heart-related diseases. To implement this, a 2D QSAR model was developed by correlating the structural properties to their biological activity of a series of atorvastatin analogs reported as HMGCR inhibitors. Then, the chemical similarity search of atorvastatin analogs was performed by using PubChem database search. Results and Discussion: The three-descriptor model of charge (GATS1p), connectivity (SCH-7) and distance (VE1_D) of the molecules is obtained for HMGCR inhibition with the statistical values of R2= 0.67, RMSEtr= 0.33, R2 ext= 0.64 and CCCext= 0.76. The 109 novel compounds were obtained by chemical similarity search and the inhibition activities of the compounds were predicted using QSAR model, which were close in the range of experimentally observed threshold. Conclusion: The present study suggests that the QSAR model and chemical similarity search could be used in combination for identification of novel compounds with activity by in silico with less computation and effort.


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