Natural Product Drug Discovery Research Articles

Paradigms and Success Stories of Natural Products in Drug Discovery Against Neurodegenerative Disorders (NDDs).

Neurodegenerative disorders (NDDs) are multifaceted complex disorders that have put a great health and economic burden around the globe nowadays. The multi-factorial nature of NDDs has presented a great challenge in drug discovery and continuous efforts are in progress in search of suitable therapeutic candidates. Nature has a great wealth of active principles in its lap that has cured the human population since ancient times. Natural products have revealed several benefits over conventional synthetic medications and scientists have shifted their vision towards exploring the therapeutic potentials of natural products in the past few years. The structural mimicking of natural compounds to endogenous ligands has presented them as a potential therapeutic candidate to prevent the development of NDDs. In the presented review, authors have summarized demographical facts about various NDDs including Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD) and various types of sclerosis in the brain. The significant findings of new active principles of natural origin along with their therapeutic potentials on NDDs have been included. Also, a description of clinical trials and patents on natural products has been enlisted in this compilation. Although natural products have shown promising success in drug discovery against NDDs, still their use is associated with several ethical issues which need to be solved in the upcoming time.

DNA G-quadruplexes as Targets for Natural Product Drug Discovery

DNA G-quadruplexes as Targets for Natural Product Drug Discovery

Unveiling the Potential of Ent-Kaurane Diterpenoids: Multifaceted Natural Products for Drug Discovery.

Natural products hold immense potential for drug discovery, yet many remain unexplored in vast libraries and databases. In an attempt to fill this gap and meet the growing demand for effective drugs, this study delves into the promising world of ent-kaurane diterpenoids, a class of natural products with huge therapeutic potential. With a dataset of 570 ent-kaurane diterpenoids obtained from the literature, we conducted an in silico analysis, evaluating their physicochemical, pharmacokinetic, and toxicological properties with a focus on their therapeutic implications. Notably, these natural compounds exhibit drug-like properties, aligning closely with those of FDA-approved drugs, indicating a high potential for drug development. The ranges of the physicochemical parameters were as follows: molecular weights-288.47 to 626.82 g/mol; number of heavy atoms-21 to 44; the number of hydrogen bond donors and acceptors-0 to 8 and 1 to 11, respectively; the number of rotatable bonds-0 to 11; fraction Csp3-0.65 to 1; and TPSA-20.23 to 189.53 Ų. Additionally, the majority of these molecules display favorable safety profiles, with only 0.70%, 1.40%, 0.70%, and 46.49% exhibiting mutagenic, tumorigenic, reproduction-enhancing, and irritant properties, respectively. Importantly, ent-kaurane diterpenoids exhibit promising biopharmaceutical properties. Their average lipophilicity is optimal for drug absorption, while over 99% are water-soluble, facilitating delivery. Further, 96.5% and 28.20% of these molecules exhibited intestinal and brain bioavailability, expanding their therapeutic reach. The predicted pharmacological activities of these compounds encompass a diverse range, including anticancer, immunosuppressant, chemoprotective, anti-hepatic, hepatoprotectant, anti-inflammation, antihyperthyroidism, and anti-hepatitis activities. This multi-targeted profile highlights ent-kaurane diterpenoids as highly promising candidates for further drug discovery endeavors.

Biosynthesis of Cytosporones in Leotiomycetous Filamentous Fungi.

Polyketides with the isochroman-3-one pharmacophore are rare among fungal natural products as their biosynthesis requires an unorthodox S-type aromatic ring cyclization. Genome mining uncovered a conserved gene cluster in select leotiomycetous fungi that encodes the biosynthesis of cytosporones, including isochroman-3-one congeners. Combinatorial biosynthesis in total biosynthetic and biocatalytic formats in Saccharomyces cerevisiae and in vitro reconstitution of key reactions with purified enzymes revealed how cytosporone structural and bioactivity diversity is generated. The S-type acyl dihydroxyphenylacetic acid (ADA) core of cytosporones is assembled by a collaborating polyketide synthase pair. Thioesterase domain-catalyzed transesterification releases ADA esters, some of which are known Nur77 modulators. Alternatively, hydrolytic release allows C6 hydroxylation by a flavin-dependent monooxygenase, yielding a trihydroxybenzene moiety. Reduction of the C9 carbonyl by a short chain dehydrogenase/reductase initiates isochroman-3-one formation, affording cytosporones with cytotoxic and antimicrobial activity. Enoyl di- or trihydroxyphenylacetic acids are generated as shunt products, while isocroman-3,4-diones are formed by autoxidation. The cytosporone pathway offers novel polyketide biosynthetic enzymes for combinatorial synthetic biology to advance the production of "unnatural" natural products for drug discovery.

New Polyene Macrolide Compounds from Mangrove-Derived Strain Streptomyces hiroshimensis GXIMD 06359: Isolation, Antifungal Activity, and Mechanism against Talaromyces marneffei.

Mangrove-derived actinomycetes represent a rich source of novel bioactive natural products in drug discovery. In this study, four new polyene macrolide antibiotics antifungalmycin B-E (1-4), along with seven known analogs (5-11), were isolated from the fermentation broth of the mangrove strain Streptomyces hiroshimensis GXIMD 06359. All compounds from this strain were purified using semi-preparative HPLC and Sephadex LH-20 gel filtration while following an antifungal activity-guided fractionation. Their structures were elucidated through spectroscopic techniques including UV, HR-ESI-MS, and NMR. These compounds exhibited broad-spectrum antifungal activity against Talaromyces marneffei with minimum inhibitory concentration (MIC) values being in the range of 2-128 μg/mL except compound 2. This is the first report of polyene derivatives produced by S. hiroshimensis as bioactive compounds against T. marneffei. In vitro studies showed that compound 1 exerted a significantly stronger antifungal activity against T. marneffei than other new compounds, and the antifungal mechanism of compound 1 may be related to the disrupted cell membrane, which causes mitochondrial dysfunction, resulting in leakage of intracellular biological components, and subsequently, cell death. Taken together, this study provides a basis for compound 1 preventing and controlling talaromycosis.

Structural, biochemical and bioinformatic analyses of nonribosomal peptide synthetase adenylation domains.

Covering: 1997 to July 2023The adenylation reaction has been a subject of scientific intrigue since it was first recognized as essential to many biological processes, including the homeostasis and pathogenicity of some bacteria and the activation of amino acids for protein synthesis in mammals. Several foundational studies on adenylation (A) domains have facilitated an improved understanding of their molecular structures and biochemical properties, in particular work on nonribosomal peptide synthetases (NRPSs). In NRPS pathways, A domains activate their respective acyl substrates for incorporation into a growing peptidyl chain, and many nonribosomal peptides are bioactive. From a natural product drug discovery perspective, improving existing bioinformatics platforms to predict unique NRPS products more accurately from genomic data is desirable. Here, we summarize characterization efforts of A domains primarily from NRPS pathways from July 1997 up to July 2023, covering protein structure elucidation, in vitro assay development, and in silico tools for improved predictions.

Source, Synthesis, and Biological Evaluation of Natural Occurring 2,2'-Bipyridines.

Molecules containing bipyridine scaffold are fascinating and versatile compounds in the field of natural product chemistry and drug discovery, and these molecules have possible therapeutic applications due to possession of potent biological activities such as antimicrobial, immunomodulatory, antitumor, and phytotoxic. Significant efforts have been devoted to isolating various 2,2' bipyridine compounds from natural sources, with antimicrobial, anti-cancer, and immunosuppressive properties. This review describes recent developments in isolation from different microbial origins, synthesis, and investigation of different kinds of biological activities of 2,2' bipyridines, with a particular emphasis on caerulomycins, collismycins, and related derivates thereof in detail.

Catalytic, dearomative 2,3-difluorination of indoles

Indolines, characterized by their diverse biological activities and structural significance, have garnered considerable attention in the realms of natural product synthesis and drug discovery. Concurrently, the incorporation of fluorine atoms into organic molecules has emerged as a powerful strategy to enhance their pharmacological properties. Herein, we report a robust and diastereoselective approach for the synthesis of 2,3-difluorinated indolines through the iodine(I/III)-catalyzed dearomatization of readily available indoles. The protocol operates under mild conditions, displaying excellent functional group tolerance and remarkable diastereoselectivity. By employing this developed protocol, vicinal-difluorinated analogues of indole-containing drugs can be efficiently accessed. Theoretical calculations have shed light on the underlying reaction mechanism, proposing the formation of a β-fluorine-substituted carbocation intermediate. It is postulated that the observed high diastereoselectivity can be attributed to the dipole-dipole interactions facilitated by the C–F bond. Crystallographic analysis has revealed the profound impact of fluorine atom introduction on the conformational preferences of the indoline core. Given the unique structural characteristics and pharmacological significance of 2,3-difluorinated indolines, we anticipate their widespread application in medicinal chemistry and drug discovery endeavors.

An Integrated Molecular Networking and Docking Approach to Characterize the Metabolome of Helichrysum splendidum and Its Pharmaceutical Potentials.

South Africa is rich in diverse medicinal plants, and it is reported to have over 35% of the global Helichrysum species, many of which are utilized in traditional medicine. Various phytochemical studies have offered valuable insights into the chemistry of Helichrysum plants, hinting at bioactive components that define the medicinal properties of the plant. However, there are still knowledge gaps regarding the size and diversity of the Helichrysum chemical space. As such, continuous efforts are needed to comprehensively characterize the phytochemistry of Helichrysum, which will subsequently contribute to the discovery and exploration of Helichrysum-derived natural products for drug discovery. Thus, reported herein is a computational metabolomics work to comprehensively characterize the metabolic landscape of the medicinal herb Helichrysum splendidum, which is less studied. Metabolites were methanol-extracted and analyzed on a liquid chromatography-tandem mass spectrometry (LC-MS/MS) system. Spectral data were mined using molecular networking (MN) strategies. The results revealed that the metabolic map of H. splendidum is chemically diverse, with chemical superclasses that include organic polymers, benzenoids, lipid and lipid-like molecules, alkaloids, and derivatives, phenylpropanoids and polyketides. These results point to a vastly rich chemistry with potential bioactivities, and the latter was demonstrated through computationally assessing the binding of selected metabolites with CDK-2 and CCNB1 anti-cancer targets. Molecular docking results showed that flavonoids (luteolin, dihydroquercetin, and isorhamnetin) and terpenoids (tiliroside and silybin) interact strongly with the CDK-2 and CCNB1 targets. Thus, this work suggests that these flavonoid and terpenoid compounds from H. splendidum are potentially anti-cancer agents through their ability to interact with these proteins involved in cancer pathways and progression. As such, these actionable insights are a necessary step for further exploration and translational studies for H. splendidum-derived compounds for drug discovery.

Natural product drug discovery and drug design: two approaches shaping new pharmaceutical development.

Natural product drug discovery and drug design: two approaches shaping new pharmaceutical development.

Artificial intelligence for natural product drug discovery.

Developments in computational omics technologies have provided new means to access the hidden diversity of natural products, unearthing new potential for drug discovery. In parallel, artificial intelligence approaches such as machine learning have led to exciting developments in the computational drug design field, facilitating biological activity prediction and de novo drug design for molecular targets of interest. Here, we describe current and future synergies between these developments to effectively identify drug candidates from the plethora of molecules produced by nature. We also discuss how to address key challenges in realizing the potential of these synergies, such as the need for high-quality datasets to train deep learning algorithms and appropriate strategies for algorithm validation.

Molecular Docking Study on Phytochemical Profiling of Trichosanthes Dioica (Pointed gourd) against Antitumor Evaluation as Cyclin Dependent Kinase -2(CDK2) inhibitors

Natural products in drug discovery have been extensively documented, including their subscription to the evolution of present drugs. Trichosanthes dioca, a group of family Cucurbitaceae, is an annual or perennial herb distributed in tropical Asia and Australia. Pointed gourd (Trichosanthes dioica Roxb.) is investigated by a common name of parwal and is cultivated predominantly as a vegetable. The remarkable medicinal properties are antihyperglycemic, antihyperlipidemic, antitumor, cytotoxic, arsenic poisoning, ameliorative, anti-inflammatory, antidiarrheal, and varieties of pharmacological activities of T. dioica. D.T. dioica root demonstrates remarkable cytotoxic and genotoxic properties thus suggesting the feasibility of its possible use as a natural antitumor agent. The 3D crystal structure of the protein 1KE9 (CYCLIN-DEPENDENT KINASE 2 (CDK2) was retrieved from Protein Data Bank (PDB) and protein binding sites of the compounds were identified. The 2D structure of Indian compounds of derivatives of glycosides and triterpenes was derived from the PubChem database. The present study analyzed the molecular docking studies on the protein which is responsible for anticancer with the compounds evolved from Trichosanthes dioca. The Docking was done by Schrodinger Maestro 12.4 software tool, compounds of colocynthin' derivatives of glycosides having better docking scores than the other compounds. So it has been concluded that derivatives of glycosides can be used as an anticancer drug.

The Library of Pseudoalteromonas


 Natural products (NPs) are compounds that are produced by living things, like bacteria. These compounds are encoded by what are known as biosynthetic gene clusters (BGCs). A BGC is a set of genes that when all expressed, work together to form a particular NP. NPs are of extreme importance as they are used for many different medical applications, particularly as antibiotics. Since bacteria must evolve quickly to compete against one another for resources, it makes sense to turn to these organisms to find a solution for bacterial infections. The problem is that pathogenic bacteria have been evolving methods to fight antibiotics faster than we have been able to discover new ones. There is a great need to improve the natural product drug discovery pipeline. One way to do this is to change the conditions microbes grow in to have them express previously silent BGCs. In order to do this effectively, it is beneficial to have a strong baseline for molecules produced under standard conditions. Pseudoalteromonas is a relatively underexplored genus of marine bacteria. Thus, my goal is to catalogue the natural products produced by Pseudoalteromonas under standard culture conditions using Mass Spectrometry analysis. The starting point for this so-called Library Project has involved identifying existing natural product databases. The databases that have been explored can be classified into four categories that are also reflective of the order in which they will be used. These categories for the databases are: databases for culturing information, databases to catalog known natural products, mass spectrometry (MS) analysis tool-based databases, and databases that will associate novel natural products with BGCs. Now that the appropriate databases have been identified, the next step is to begin culturing and extracting from these microbes, to then run and analyze mass spectrums of these extracts.

Structural diversification of natural substrates modified by the O-methyltransferase AurJ from Fusarium Graminearum

Aromatic polyketide and phenylpropanoid derivatives are a large class of natural products produced by bacteria, fungi, and plants. The O-methylation is a unique decoration that can increase structural diversity of aromatic compounds and improve their pharmacological properties, but the substrate specificity of O-methyltransferase hinders the discovery of more natural products with O-methylation through biosynthesis. Here, we reported that the O-methyltransferase AurJ from plant pathogenic fungus Fusarium graminearum could methylate a broad range of natural substrates of monocyclic, bicyclic, and tricyclic aromatic precursors, exhibiting excellent substrate tolerance. This finding will partly change our stereotype about the specificity of traditional methyltransferases, and urge us to mine more O-methyltransferases with good substrate tolerance and discover more methylated natural products for drug discovery and development through directed evolution and combinatorial biosynthesis.

Editorial on Special Issue “Natural Products for Drug Discovery and Development”

Natural products have always played a vital role in the search for novel drugs, and their exploration continues to captivate researchers in the field of drug discovery and development [...]

Lipidated variants of the antimicrobial peptide nisin produced via incorporation of methionine analogs for click chemistry show improved bioactivity

The increase in antibiotic resistance calls for accelerated molecular engineering strategies to diversify natural products for drug discovery. The incorporation of non-canonical amino acids (ncAAs) is an elegant strategy for this purpose, offering a diverse pool of building blocks to introduce desired properties into antimicrobial lanthipeptides. We here report an expression system using Lactococcus lactis as a host for non-canonical amino acid incorporation with high efficiency and yield. We show that incorporating the more hydrophobic analog ethionine (instead of methionine) into nisin improves its bioactivity against several Gram-positive strains we tested. New-to-nature variants were further created by click chemistry. By azidohomoalanine (Aha) incorporation and subsequent click chemistry, we obtained lipidated variants at different positions in nisin or in truncated nisin variants. Some of them show improved bioactivity and specificity against several pathogenic bacterial strains. These results highlight the ability of this methodology for lanthipeptide multi-site lipidation, to create new-to-nature antimicrobial products with diverse features, and extend the toolbox for (lanthi)peptide drug improvement and discovery.

Separation of similarly structured isoflavones by simultaneous competitive and selective adsorption on UiO-66 metal-organic framework

Natural products often contain a large number of structurally similar compounds, however, from which the isolation of monomer compounds is complex and time-consuming. In this study, for the first time, a Zr-based metal-organic framework (MOF), UiO-66, was used for the separation of three isoflavones (genistein (GEN), puerarin (PUE), and daidzein (DDZ)) with similar structures. UiO-66 was demonstrated to have a distinct high adsorption capacity (qe, 105.42 ± 2.36 mg/g) for GEN with high separation factors from PUE (α, 35.52 ± 1.22) and DDZ (α, 7.41 ± 0.76), dramatically increasing the purity of GEN from ∼33–92% after primary separation. According to SEM-EDS and XPS characterizations together with RDF analysis, GEN and PUE were adsorbed on the surface of UiO-66 at the same dominant Zr cluster site (O…Zr), while DDZ was bound onto the inferior site via weak hydrogen bonding (H…O), indicating the separation of GEN from PUE was in a competitive manner, while the separation from DDZ was selective. For these three drugs, their adsorption kinetics and adsorption isotherms conformed Pseudo-second-order kinetic model and Langmuir model, respectively, indicating that the monolayer adsorption of isoflavones on UiO-66 surface was the dominant mechanism. The thermodynamic study demonstrated that both adsorptions of GEN and PUE were spontaneous (ΔG0 < 0), whereas the DDZ adsorption is non-spontaneous (ΔG0 > 0). Compared to traditional separation techniques, this study provided a simple and efficient approach to isolate structurally similar compounds from natural products in drug discovery.

The Role of Aquatic Plants in Natural Products and Drug Discovery

Background: Phytochemicals and their derivatives/analogues represent over 50% of the current medicines worldwide in clinical use. Despite a significant contribution to the total bioactive natural plant products, aquatic plants are underestimated, and several species are extinct and in the endangered list. Objective: The aim of this review article is to draw the attention of common people and scientists toward a few important contributions of the aquatic plants to natural product chemistry and drug discovery by highlighting the chemical and pharmaceutical aspects of the same. Methods: The presented data were collected and selected from the literature obtained by an online search for the ethnomedicinal properties, biological activities and bioactive chemical constituents of aquatic plants using Google Scholar, PubMed and Scifinder chemical abstract service. Results: The selected literature data revealed that the extract and compounds isolated from several aquatic plants possess significant biological/pharmaceutical properties. For example, the α-asarone (24) and asiatic acid (33) isolated from Acorus calamus and Centella asiatica, respectively, exhibited significant neuroprotective effects in vitro and in vivo. The cripowellin A (59), cripowellin C (60), cripowellin B (61) and cripowellin D (62), isolated from Crinum erubescens, exhibited potent antiplasmodial and antiproliferative activities with half maximal inhibitory concentration (IC50) in nanomolar range (11-260 nM). Several other alkaloids from different Crinum species have also shown anticancer properties against different cancer cell lines with IC50 value &lt;5 μM. Alkaloids and resin glycosides, isolated from different Ipomoea species, have displayed significant psychotropic, psychotomimetic, anticancer, and antibacterial activities with IC50 value &lt;5 μM. Conclusion: The aquatic plants play a significant role in the discovery of bioactive natural products. Although several biological activities and bioactive compounds have been reported from these plants, further assessment and scientific validation of most of their traditional usages still need to be done. There are several other similar species that are underestimated and not much explored. Many aquatic plants, such as Ipomoea carnea Jacq., Juncus lomatophyllus Spreng., Commelina benghalensis Linn, Gunnera perpensa L., Scirpus maritimus L. and Mentha longifolia (L.) L., may be considered for further evaluation. In addition to these, one should not undermine the potential of Crinum macowanii for COVID-19 pathogenesis, as its chemical constituent lycorine has shown significant SARS-CoV-2 inhibitory potential (EC50, 0.3 μM; SI &gt;129). Furthermore, most rural communities are still using the wetland resources for their cultural, medicinal, economic, domestic, and agricultural needs. Hence, the conservation of aquatic plants and wetlands is an issue of great concern.

Modular and Computational Access to Innocuous Multistep Metal-Free Synthesis of 1,3,4-Oxadiazoles as Enzyme Inhibitors.

An array of 1,3,4-oxadiazole hybrids, 7a-s, structurally intriguing cores with potential in natural product synthesis and drug discovery, have been synthesized using innovative comparable conventional and microwave-assisted protocols. The synthesis was performed by the reaction of secondary amine-based acetamides, 6a-s, as the electrophile and piperidine-based oxadiazoles as the nucleophile, 3, under the metal-free reaction conditions. High yield in minimum time with highest purity was obtained by the microwave-irradiated method instead of the conventional one. The structural elucidations were made through infrared, 1H NMR, 13C NMR, and elemental analysis studies. The whole array of synthesized compounds, 7a-s, was evaluated for their potential against α-glucosidase and butyryl cholinesterase (BChE) enzymes. Natural bond orbital and structural optimizations were made by using the B3LYP method and the basis set of 6-311++G(d,p). Frontier molecular orbitals and molecular electrostatic potential were calculated at the same level of selected compounds as potential candidates against BChE and α-glucosidase enzymes utilizing the time-dependent density functional theory. Fifteen compounds out of 19 were observed to be active against α-glucosidase enzyme in comparison with acarbose as the reference standard and 7 against the BChE enzyme compared to eserine as the reference standard. The highest potential of compound 7j against BChE is well correlated by the higher binding interaction with target protein as -10.2, calculated by docking studies. The recruited compounds against both enzymes could be the best anti-enzymatic drugs and part of drugs discovery programs after further analysis.

Complete Genome Sequence of Streptomyces sp. HP-A2021, a Promising Bacterium for Natural Product Discovery.

Streptomyces are one of the most prolific sources of bioactive and structurally diverse secondary metabolites for natural product drug discovery. Genome sequencing and bioinformatics analysis revealed that the genomes of Streptomyces harbor a wealth of cryptic secondary metabolite biosynthetic gene clusters that could encode novel compounds. In this work, a genome mining approach was employed to investigate the biosynthetic potential of Streptomyces sp. HP-A2021, isolated from rhizosphere soil of Ginkgo biloba L. The complete genome of HP-A2021 was sequenced and contained the 9,607,552 base pair linear chromosome with a GC content of 71.07%. The annotation results revealed the presence of 8534 CDSs, 76 tRNA genes, and 18 rRNA genes in HP-A2021. The highest dDDH and ANI values based on genome sequences between HP-A2021 and the most closely related type strain, Streptomyces coeruleorubidus JCM 4359, were 64.2% and 92.41%, respectively. In total, 33 secondary metabolite biosynthetic gene clusters with an average length of 105,594bp were identified, including the putative thiotetroamide, alkylresorcinol, coelichelin, and geosmin. The antibacterial activity assay confirmed that the crude extracts of HP-A2021 showed potent antimicrobial activity against human pathogenic bacteria. Our study demonstrated that Streptomyces sp. HP-A2021 will propose a potential use in biotechnological and novel bioactive secondary metabolite biosynthetic applications.