Structural Diversity Of Natural Products Research Articles

NIMO: A Natural Product-Inspired Molecular Generative Model Based on Conditional Transformer.

Natural products (NPs) have diverse biological activity and significant medicinal value. The structural diversity of NPs is the mainstay of drug discovery. Expanding the chemical space of NPs is an urgent need. Inspired by the concept of fragment-assembled pseudo-natural products, we developed a computational tool called NIMO, which is based on the transformer neural network model. NIMO employs two tailor-made motif extraction methods to map a molecular graph into a semantic motif sequence. All these generated motif sequences are used to train our molecular generative models. Various NIMO models were trained under different task scenarios by recognizing syntactic patterns and structure-property relationships. We further explored the performance of NIMO in structure-guided, activity-oriented, and pocket-based molecule generation tasks. Our results show that NIMO had excellent performance for molecule generation from scratch and structure optimization from a scaffold.

The evolutionary origin of naturally occurring intermolecular Diels-Alderases from Morus alba

Biosynthetic enzymes evolutionarily gain novel functions, thereby expanding the structural diversity of natural products to the benefit of host organisms. Diels-Alderases (DAs), functionally unique enzymes catalysing [4 + 2] cycloaddition reactions, have received considerable research interest. However, their evolutionary mechanisms remain obscure. Here, we investigate the evolutionary origins of the intermolecular DAs in the biosynthesis of Moraceae plant-derived Diels-Alder-type secondary metabolites. Our findings suggest that these DAs have evolved from an ancestor functioning as a flavin adenine dinucleotide (FAD)-dependent oxidocyclase (OC), which catalyses the oxidative cyclisation reactions of isoprenoid-substituted phenolic compounds. Through crystal structure determination, computational calculations, and site-directed mutagenesis experiments, we identified several critical substitutions, including S348L, A357L, D389E and H418R that alter the substrate-binding mode and enable the OCs to gain intermolecular DA activity during evolution. This work provides mechanistic insights into the evolutionary rationale of DAs and paves the way for mining and engineering new DAs from other protein families.

Molecular Docking Analysis of Adhatoda vasica with Thromboxane A2 Receptor (TXA2R) (6IIU) and Antiviral Molecules for Possible Dengue Complications.

The present study is an in silico model of platelet amplification potential of Adhatoda vasica, which can be used to treat thrombocytopenia in dengue complications. Docking studies have proved to be an essential tool that facilitates the structural diversity of natural products to be harnessed in an organized manner. In the present study, vasicine containing natural anti-dengue potential was subjected to docking studies using Schrodinger glides software (ver.11.1). The docking study was carried out to find out the potential molecular targets for selected protein. The docking was carried out on different ligands, like vasicine, ramatroban, chloroquine, celgosivir, and standard eltrombopag downloaded from PubChem and retrieved to glide software and ligands prepared using lig prep wizard. Docking was performed using the ligand docking wizard of Glide-maestro 2018. The docking score of vasicine (-5.27) is nearly identical to the standard eltrombopag (-6.08), and both ligands bind with one hydrogen bond. The validation score of ramatroban is -12.39, binding with five hydrogen bonds, Celgosivir exhibited a docking score of -7.3 with three hydrogen bonds, and chloroquine displayed no hydrogen bond but had a docking score of -4.6. Vasicine was found to be the most suitable target of platelet amplification potential from Adhatoda vasica. However, the molecular docking results are preliminary, and it has been indicated that vasicine could be one of the potential ligands to treat the thrombocytopenia of dengue; experimental evaluation will be carried out in the near future.

Oxidosqualene cyclases in triterpenoids biosynthesis: a review

Triterpenoids are one of the most diverse compounds in plant metabolites, and they have a wide variety of physiological activities and are of important economic value. Oxidosqualene cyclases catalyze the cyclization of 2, 3-oxidosqualene to generate different types of sterols and plant triterpenoids, which is of great significance to the structural diversity of natural products. However, the mechanism of the diversified cyclization of 2, 3-oxidosqualene catalyzed by oxidosqualene cyclases remains unclear. This review summarized the research progress of oxidosqualene cyclases from the aspects of catalytic function, molecular evolutionary relationship between genes and proteins, protein structure, molecular simulation and molecular calculations, which may provide a reference for protein engineering and metabolic engineering of triterpene cyclase.

MOLECULAR DOCKING OF MACELIGNAN A POLYPHENOLIC DERIVATIVE ISOLATED FROM LEUCAS CEPHALOTES &LEUCAS ASPERA ON COLORECTAL CANCER RECEPTOR PROTEIN AND ITS ADMET PREDICTION.

The aim of the present study is to analyze the molecular aspects of the lignan macelignan, against colorectal cancer receptors, namely vascular endothelial growth factor 2(VEGF-2), cytochrome P450(CYP), caspase-3, BAX, BCl -2, CDK – 2 and epidermal growth factor receptor (EGFR). Macelignan identified as lignan, a polyphenolic phytocompound that has been successfully isolated from Leucas cephalotes & Leucas aspera is traditionally identified as a medicinal herb and several studies have shown that they exert antimicrobial, anticarcinogenic and antiaging property. The docking studies have proven to be an essential tool for opening up the structural diversity of natural products to be used in an orderly manner. Molecular docking was effectively done with Schrodinger Glide software version 2020-4. The binding affinity -1 was found to be in the range of -7.8 to -6.3 kcalmol . From the toxicity assessment, which was carried out with pkCSM online server, it was found that the macelignan had no show skin sensitization, hepatotoxicity and AMES toxicity and that the ADMET behavior was within the acceptable limits of the drug behavior.

Multiplexed Screening of Thousands of Natural Products for Protein-Ligand Binding in Native Mass Spectrometry.

The structural diversity of natural products offers unique opportunities for drug discovery, but challenges associated with their isolation and screening can hinder the identification of drug-like molecules from complex natural product extracts. Here we introduce a mass spectrometry-based approach that integrates untargeted metabolomics with multistage, high-resolution native mass spectrometry to rapidly identify natural products that bind to therapeutically relevant protein targets. By directly screening crude natural product extracts containing thousands of drug-like small molecules using a single, rapid measurement, we could identify novel natural product ligands of human drug targets without fractionation. This method should significantly increase the efficiency of target-based natural product drug discovery workflows.

Structure, function and application of serine carboxypeptidase-like acyltransferases from plants

Plant serine carboxypeptidase-like acyltransferases (SCPL-AT) have similar structural characteristics and high homology compared to the serine carboxypeptidase. They can transfer the acyl from acyl glucose esters to many natural products, participate in the acylation modification of plant secondary metabolites, enrich the structural diversity of natural products, and improve the physicochemical properties such as water solubility and stability of compounds. This review summarizes the structural characteristics, catalytic mechanism, functional characterization, and biocatalytic applications of SCPL-AT from plants. This will help to promote the functional characterization of these acyltransferase genes and the biosynthesis of useful plant secondary metabolites by synthetic biotechnology.

A Mini-Review on Molecular Docking Studies and Pharmacological Activities of Stevia rebaudiana

Stevia is a small perennial shrub belonging to the Astraceae family with approximately 240 species, which has been used as a natural sweetener. In addition to its sweetening property, it has medicinal values and other uses. Indigenous tribes of South America were using Stevia rebaudiana Bertoni for centuries for its medicinal value. Leaves of stevia produce diterpene glycosides (Stevioside and Rebaudiosides), non-nutritive, non-toxic, high-potency sweeteners. The traditional medicinal system is getting more and more appreciation nowadays, but the therapeutic targets for most of these medicines remain unclear, which slows down the novel drug discovery from these natural products. Computational molecular docking studies are effective tools, which are broadly utilized to identify therapeutic targets and interpret molecular aspects of the ligand-protein interactions during drug discovery. Thus, it also enables the extraordinary structural diversity of natural products to be harnessed in an effective manner. The aim of this article is to present a review on the molecular docking studies and pharmacological activities of steviol glycoside isolated from Stevia rebaudiana. In this article, the recently published papers about Stevia rebaudiana were reviewed, using scientific sites such as Mendeley, PubMed and Google Scholar.

Extensive expansion of the chemical diversity of fusidane-type antibiotics using a stochastic combinational strategy

Fusidane-type antibiotics, represented by helvolic acid, fusidic acid and cephalosporin P1, are fungi-derived antimicrobials with little cross-resistance to commonly used antibiotics. Generation of new fusidane-type derivatives is therefore of great value, but this is hindered by available approaches. Here, we developed a stochastic combinational strategy by random assembly of all the post-tailoring genes derived from helvolic acid, fusidic acid, and cephalosporin P1 biosynthetic pathways in a strain that produces their common intermediate. Among a total of 27 gene combinations, 24 combinations produce expected products and afford 58 fusidane-type analogues, of which 54 are new compounds. Moreover, random gene combination can induce unexpected activity of some post-tailoring enzymes, leading to a further increase in chemical diversity. These newly generated derivatives provide new insights into the structure‒activity relationship of fusidane-type antibiotics. The stochastic combinational strategy established in this study proves to be a powerful approach for expanding structural diversity of natural products.

Perylenequinones production induced by co-culturing Setophoma sp. and Penicillium brasilianum

Abstract Co-culture strategy can be applied to produce structural diversity of natural products. This approach also enables the understanding of the interaction mechanisms in microbial ecology. The present study aimed at the secondary metabolism diversification of the endophytic fungus Setophoma sp. by co-culturing it with Penicillium brasilianum and Talaromyces wortmannii, species also isolated as endophytes, and with Penicillium digitatum, a phytopathogenic fungus dangerous to Brazilian citriculture. The increase of perylenequinones (stemphyperylenol and derivatives) produced by Setophoma sp. strain was observed in the co-cultures in response to the endophytic P. brasilianum. The induced stemphyperylenol was isolated by combined chromatographic procedures and identified by spectroscopic techniques. Other perylenequinone derivatives were detected by UHPLC-DAD-HRMS based dereplication data analysis. Stemphyperylenol exhibited antifungal effects not only against P. brasilianum, but also against P. digitatum, the main postharvest pathogen of orange fruits, and Aspergillus fumigatus, an important human pathogenic fungus ubiquitous in soil. Preliminary insights concerning the mode of action of stemphyperylenol were determined by evaluating a collection of A. fumigatus mutants. Thus, stemphyperylenol may have the potential for agricultural applications, and it is also promising as a human antifungal compound. Moreover, the co-culture of an endophyte-endophyte system may represent a potential way to achieve the chemical diversity of bioactive molecules.

Acyltransferase that catalyses the condensation of polyketide and peptide moieties of goadvionin hybrid lipopeptides.

Fusions of fatty acids and peptides expand the structural diversity of natural products; however, polyketide/ribosomally synthesized and post-translationally modified peptides (PK/RiPPs) hybrid lipopeptides are relatively rare. Here we report a family of PK/RiPPs called goadvionins, which inhibit the growth of Gram-positive bacteria, and an acyltransferase, GdvG, which catalyses the condensation of the PK and RiPP moieties. Goadvionin comprises a trimethylammonio 32-carbon acyl chain and an eight-residue RiPP with an avionin structure. The positions of six hydroxyl groups and one double bond in the very-long acyl chain were determined by radical-induced dissociation tandem mass spectrometry, which collides radical ion species to generate C-C bond cleavage fragments. GdvG belongs to the Gcn5-related N-acetyltransferase superfamily. Unlike conventional acyltransferases, GdvG transfers a very long acyl chain that is tethered to an acyl carrier protein to the N-terminal amino group of the RiPP moiety. gdvG homologues flanked by PK/fatty acid and RiPP biosynthesis genes are widely distributed in microbial species, suggesting that acyltransferase-catalysed condensation of PKs and RiPPs is a general strategy in biosynthesis of similar lipopeptides.

Strepimidazoles A-G from the Plant Endophytic Streptomyces sp. PKU-EA00015 with Inhibitory Activities against a Plant Pathogenic Fungus.

Seven new 4-acyl-2-aminoimidazoles, designated strepimidazoles A-G (1-7), were discovered from the endophytic Streptomyces sp. PKU-EA00015 isolated from Salvia miltiorrhiza Bunge, whose dry root "Danshen" is one of the most widely used traditional Chinese medicines. The resonance signals of the 2-aminoimidazole moiety in 1-7 were absent in the NMR spectra due to tautomerization, and the structures of 1-7 were identified after preparation of their acetylation products 1a-7a, respectively. Compounds 1-7 represent a new family of 2-aminoimidazole-containing natural products, enriching the structural diversity of natural products from endophytic origin. Compounds 1-7 showed different degrees of inhibitory activities against the plant pathogenic fungus Verticillium dahliae V991, revealing structure-activity relationships on the acyl moieties. The plant pathogenic fungus V. dahliae has been confirmed to cause serious chlorosis of cultivated S. miltiorrhiza Bunge in China. This study opens the door for further investigation of mutualistic relationships between S. miltiorrhiza Bunge and their endophytic actinomycetes and for possible antifungal agent development for biological control of V. dahliae in the future.

Identification and Heterologous Expression of the Albucidin Gene Cluster from the Marine Strain Streptomyces Albus Subsp. Chlorinus NRRL B-24108.

Herbicides with new modes of action and safer toxicological and environmental profiles are needed to manage the evolution of weeds that are resistant to commercial herbicides. The unparalleled structural diversity of natural products makes these compounds a promising source for new herbicides. In 2009, a novel nucleoside phytotoxin, albucidin, with broad activity against grass and broadleaf weeds was isolated from a strain of Streptomyces albus subsp. chlorinus NRRL B-24108. Here, we report the identification and heterologous expression of the previously uncharacterized albucidin gene cluster. Through a series of gene inactivation experiments, a minimal set of albucidin biosynthetic genes was determined. Based on gene annotation and sequence homology, a model for albucidin biosynthesis was suggested. The presented results enable the construction of producer strains for a sustainable supply of albucidin for biological activity studies.

Increasing Structural Diversity of Natural Products by Michael Addition with ortho-Quinone Methide as the Acceptor.

The active form of clavatol, ortho-quinone methide, can be generated from hydroxyclavatol in an aqueous system and used as a highly reactive intermediate for coupling with diverse natural products under very mild conditions. These include flavonoids, hydroxynaphthalenes, coumarins, xanthones, anthraquinones, phloroglucinols, phenolic acids, indole derivatives, tyrosine analogues, and quinolines. The clavatol moiety was mainly attached via C-C bonds to the ortho- or para-positions of phenolic hydroxyl/amino groups and the C2-position of the indole ring.

Secondary metabolites, their structural diversity, bioactivity, and ecological functions: An overview

Abstract Natural products are also called secondary metabolites to distinguish them from the primary metabolites, i.e. those natural compounds like glucose, amino acids, etc. that are present in every living cell and are used and required in the essential life processes of cells. Natural products are classified according to their metabolic building blocks into alkaloids, fatty acids, polyketides, phenyl propanoids and aromatic polyketides, and terpenoids. The structural diversity of natural products is explored using the scaffold approach focusing on the characteristic carbon frameworks. Aside from discussing specific alkaloids that are either pharmacologically (e.g. boldine, berberine, galantamine, etc.) or historically (caffeine, atropine, lobeline, etc.) important alkaloids, a single chart is presented which shows the typical scaffolds of the most important subclasses of alkaloids. How certain classes of natural products are formed in nature from simple biochemical ‘building blocks’ are shown using graphical schemes. This has been done for a typical tetra-ketide (6-methylsalicylic acid) from acetyl coenzyme A, or in general to all the major subclasses of terpenes. An important aspect of understanding the structural diversity of natural products is to recognize how some compounds can be visualized as key intermediates for enzyme mediated transformation to several other related structures. This is seen in the case of how arachidonic acid can transform into prostaglandins, or geranyl diphosphate to various monoterpenes, or squalene epoxide to various pentacyclic triterpenes, or cholesterol transforming to sex hormones, bile acids and the cardioactive cardenolides and bufadienolides. These are presented in carefully designed schemes and charts that are appropriately placed in the relevant sections of the narrative texts. The ecological functions and pharmacological properties of natural products are also presented showing wherever possible how the chemical scaffolds have led to developing drugs as well as commercial products like sweeteners.

Sesquiterpenoids Produced by Combining Two Sesquiterpene Cyclases with Promiscuous Myxobacterial CYP260B1.

Sesquiterpenes represent a class of important terpenoids with high structural diversity and a wide range of applications. The cyclized core skeletons are generated by sesquiterpene cyclases, and the structural diversity is further increased by a series of modification steps. Cytochromes P450 (P450s) are a class of monooxygenases and one of the main contributors to the structural diversity of natural products. Some of these P450s show a broad substrate range and might be promising candidates for the implementation of cascade reactions. In this study, a combinatorial biosynthesis approach was utilized by the combination of a promiscuous myxobacterial P450 (CYP260B1) with two sesquiterpene cyclases (FgJ01056, FgJ09920) of filamentous fungi. Two oxygenated products, culmorin and culmorone, and a new compound, koraidiol, were successfully generated and characterized. This approach suggests the potential use of noncognate P450s to produce novel oxygenated terpenoids, or to generate a novel biosynthetic route for known terpenoids by a combinatorial biosynthesis strategy.

Anticancer potential of natural products: a review focusing on Sri Lankan plants.

In the pharmaceutical industry, the expected surge in production of new therapeutic entities promised by technological advances, such as high-throughput screening, synthetic libraries and advances in molecular biology and genomics, has not materialized. The unique structural diversity of natural products continues to provide opportunities to discover novel compounds. Secondary metabolites, active components of natural products such as marine organisms, microbial organisms and terrestrial plants, are particularly exciting untapped resources for exploration as medicines. Sri Lanka is home to around 3700 plant species, half of which are considered as medicinal plants. Seventy per cent of the Sri Lankan population relies on this plant-based traditional medicine system for treating various illnesses such as tumors. As such these medicinal plant sources should be used to conquer terminal diseases and for prevention of diseases. Sri Lankan researchers have found several plant species that possess cytotoxic activity. This review summarizes the current information regarding the Sri Lankan plant materials that possess anticancer properties.

Construction of a Meroterpenoid-Like Compounds Library Based on Diversity-Enhanced Extracts.

The structural diversity of natural products and their derivatives have long contributed to the development of new drugs. However, the difficulty in obtaining compounds bearing skeletally novel structures has recently led to a decline of pharmaceutical research into natural products. This paper reports the construction of a meroterpenoid-like library containing 25 compounds with diverse molecular scaffolds obtained from diversity-enhanced extracts. This method constitutes an approach for increasing the chemical diversity of natural-product-like compounds by combining natural product chemistry and diversity-oriented synthesis. Extensive pharmacological screening of the library revealed promising compounds for anti-osteoporotic and anti-lymphoma/leukemia drugs. This result indicates that the use of diversity-enhanced extracts is an effective methodology for producing chemical libraries for the purpose of drug discovery.

In Silico Molecular Docking Analysis of Natural Pyridoacridines as Anticancer Agents

Docking studies are proved to be an essential tool that facilitates the structural diversity of natural products to be harnessed in an organized manner. In this study, pyridoacridines containing natural anticancer pigments were subjected to docking studies using Glide (Schrodinger). Investigations were carried out to find out the potential molecular targets for these selected pigments. The docking was carried out on different cancer macromolecules involved in different cell cycle pathways, that is, CDK-2, CDK-6, Bcl-2, VEGFR-2, IGF-1R kinase, and G-Quadruplexes. CDK-6 was found to be the most suitable anticancer target for the pyridoacridines. In addition, effectiveness of the study was further evaluated by performing docking of known inhibitors against their respective selected macromolecules. However, the results are preliminary and experimental evaluation will be carried out in near future.

Research progress of plant BAHD acyltransferase family

Acylation conducted by acyltransferase is a ubiquitous process in structure modification of secondary metabolites. It plays an important role in the structural diversity of natural products and contributes significantly to their improved stabilities, increased solubilities, and enhanced bioavailabilities. BAHD acyltransferase family is a typical kind of acyltransferase original from plants, which involved in the biosynthesis of various bioactive acylated natural products. In order to provide references for future investigations of BAHD acyltransferase family, research progresses on basic properties, three-dimensional structures, catalytic mechanisms, enzymatic functional identifications and phylogenetic analyses of BAHD family from plants is summarized in this paper.