Natural Product-like Molecules Research Articles

Screening, Growing, and Validation by Catalog: Using Synthetic Intermediates from Natural Product Libraries to Discover Fragments for an Aspartic Protease Through Crystallography

Fragment screening directly on protein crystals has been applied using AnalytiCon’s collection of intermediates that have been utilized to generate libraries of larger synthetic natural product-like molecules. The fragments with well-balanced physicochemical properties show an impressively high hit rate for a screen using the aspartic protease endothiapepsin. The subsequent validation and expansion of the discovered fragment hits benefits from AnalytiCon’s comprehensive library design. Since the screened fragments are intermediates that share a common core with larger and closely related analogs with modulated substitution patterns, they allow for the retrieval of off-the-shelf follow-up compounds, which enable the development of design strategies for fragment optimization. A promising bicyclic core scaffold found in several fragment hits could be validated by selecting a set of enlarged follow-up compounds. Due to unexpected changes in binding mode and no significant improvement in ligand efficiency, this series was quickly deemed unsuitable and therefore discontinued. The structures of follow-up compounds of two other fragments helped to evaluate a putative fusion of two overlapping fragment hits. A design concept on how to fuse the two fragments could be proposed and helps to plan a suitable substitution pattern and promising central bridging element.

Unified Strategy Enables the Collective Syntheses of Structurally Diverse Indole Alkaloids.

Natural products and their analogues are significant sources of therapeutic lead compounds. However, synthetic strategies for generating large collections of these molecules remain a significant challenge. The most difficult step in their synthesis is the design of a common intermediate that can be easily transformed into natural products belonging to different families. This study demonstrates the evolution of synthetic tactics designed to assemble the functionalized piperidines present in indole alkaloids from a common intermediate. More importantly, we also report a previously unknown Ir- and Er-catalyzed dehydrogenative spirocyclization reaction that enables direct access to spirocyclic oxindole alkaloids. As a practical application, the asymmetric total syntheses of 29 natural alkaloids belonging to different families were accomplished by following a uniform synthetic route. The proposed methodology extends the capability of the iridium-catalyzed dehydrogenative coupling reaction to the realm of indole-alkaloid synthesis and provides new opportunities for the efficient preparation of natural product-like molecules.

Harnessing alcohols as sustainable reagents for late-stage functionalisation: synthesis of drugs and bio-inspired compounds.

Alcohol is ubiquitous with unparalleled structural diversity and thus has wide applications as a native functional group in organic synthesis. It is highly prevalent among biomolecules and offers promising opportunities for the development of chemical libraries. Over the last decade, alcohol has been extensively used as an environmentally friendly chemical for numerous organic transformations. In this review, we collectively discuss the utilisation of alcohol from 2015 to 2023 in various organic transformations and their application toward intermediates of drugs, drug derivatives and natural product-like molecules. Notable features discussed are as follows: (i) sustainable approaches for C-X alkylation (X = C, N, or O) including O-phosphorylation of alcohols, (ii) newer strategies using methanol as a methylating reagent, (iii) allylation of alkenes and alkynes including allylic trifluoromethylations, (iv) alkenylation of N-heterocycles, ketones, sulfones, and ylides towards the synthesis of drug-like molecules, (v) cyclisation and annulation to pharmaceutically active molecules, and (vi) coupling of alcohols with aryl halides or triflates, aryl cyanide and olefins to access drug-like molecules. We summarise the synthesis of over 100 drugs via several approaches, where alcohol was used as one of the potential coupling partners. Additionally, a library of molecules consisting over 60 fatty acids or steroid motifs is documented for late-stage functionalisation including the challenges and opportunities for harnessing alcohols as renewable resources.

67 million natural product-like compound database generated via molecular language processing

Natural products are a rich resource of bioactive compounds for valuable applications across multiple fields such as food, agriculture, and medicine. For natural product discovery, high throughput in silico screening offers a cost-effective alternative to traditional resource-heavy assay-guided exploration of structurally novel chemical space. In this data descriptor, we report a characterized database of 67,064,204 natural product-like molecules generated using a recurrent neural network trained on known natural products, demonstrating a significant 165-fold expansion in library size over the approximately 400,000 known natural products. This study highlights the potential of using deep generative models to explore novel natural product chemical space for high throughput in silico discovery.

Enzymatic cascade reactions for the efficient synthesis of natural products

Enzymatic cascade reactions are powerful technologies to develop environmentally friendly and cost-effective synthetic processes to manufacture natural products and other valuable molecules. The application of Single-Enzyme-Catalyzed Cascade reactions (SECC) greatly improves the efficiency of synthesis. This digest focuses on the recent inspiring examples of the application of cascade reactions catalyzed by a single enzyme in synthesizing natural products and natural product-like molecules, with particular emphasis on the unique advantages of these strategies.

Synthesis of natural product hybrids by the Ugi reaction in complex media containing plant extracts

Plant extracts are rich in a wide variety of molecules with diverse biological activities. Chemical engineering of plant extracts has provided a straightforward and simultaneous synthetic route for artificial molecules derived from plant products. This study achieved the synthesis of 13 natural product-like molecules by the Ugi multicomponent reaction using plant extracts as substrates. In particular, the engineering of a mixture of plant extracts demonstrated a unique synthetic route to a series of natural product hybrids, whereby otherwise unencountered naturally occurring molecules of different origins were chemically hybridized in complex media. Even though these reactions took place in complex media containing plant extracts, the well-designed process achieved a good conversion efficiency (~ 60%), chemoselectivity, and reproducibility. Additionally, some of the Ugi adducts exhibited promising inhibitory activity toward protease.

Screening of Natural Product and Natural Product like Molecules against SARS–CoV–2 Main Protease Using Molecular Modeling Methods


 Objective: To determine possible MPro enzyme inhibitors by using structure-based virtual screening methods, in the ZINC Biogenic Data Set containing natural products and natural product-like molecules.
 Materials and Methods: QVina, an AutoDockVina derivative, was used in virtual screening operations, GROMACS in molecular dynamics studies and SwissAdme server in ADME (Absorption, Distribution, Metabolism, and Excretion) calculations. KNIME (Konstanz Information Miner) and ChemAxon software were used for filtering data and creating three-dimensional structures of the molecules.
 Results: Seven out of totally screened 51535 natural products or natural products like molecules were identified as possible candidate to be used as SARS–CoV–2 Main Protease (MPro) enzyme inhibitors based on the results obtained from structure based virtual screening and ADME models.
 Conclusion: Among the seven potent molecules, two of them (ZINC000604382012 and ZINC000514288074) were selected as candidate molecules for further studies according to the results obtained from g_mmpbsa simulations and synthetic accessibility models. In addition, a workflow has been established to identify novel or potent Mpro enzyme inhibitors.

New Strategies in the Efficient Total Syntheses of Polycyclic Natural Products.

Polycyclic natural products are an inexhaustible source of medicinal agents, and their complex molecular architecture renders challenging synthetic targets where innovative and effective approaches for their rapid construction are urgently required. The total synthesis of polycyclic natural products has witnessed exponential progression along with the emergence of new synthetic strategies and concepts, such as sequential C-H functionalizations, radical-based transformations, and functional group pairing strategies. Our group exerts continued interest in the construction of bioactive and structurally complex natural products as well as evaluation of the mode of action of these molecules. In this Account, we will showcase how these new synthetic strategies are employed and guide our total synthesis endeavors.During the last two decades, a series of remarkable advances in C-H functionalization have led to the emergence of many new approaches to directly functionalize C-H bonds into useful functional groups. These selective transformations have provided a great opportunity for the step- and atom-economical construction of key fragments in complex molecule synthesis. We recently furnished the total syntheses for polycyclic natural products: incarviatone A, chrysomycin A, polycarcin V, and gilvocarcin V by employing a multiple C-H bond functionalization strategy. The polysubstituted benzene or naphthalene skeleton was constructed through sequential and site-selective C-H functionalizations from readily available simple starting materials, which reduced the number of steps and streamlined synthesis.Recently, we have also completed the total syntheses for a number of skeletally diverse tetracyclic Isodon diterpenoids inspired by their biogenesis and radical-based retrosynthetic disconnections. Radical transformations are strategically and tactically utilized in our syntheses, and radical-based reactions, including organo-SOMO catalysis, Birch reduction, regioselective 1,6-dienyne reductive cyclization, visible-light-mediated Schenck ene reaction, and photoradical-mediated late-stage skeletal rearrangement, play significant roles in our synthetic endeavors. Protecting-group-free and scalable syntheses are also built into our work to achieve the "ideal" synthesis. Furthermore, our synthetic work reveals that late-stage skeletal rearrangement through a photo radical process is possible in a biological setting in complement with nature's carbocation chemistry in complex natural product biosynthesis.Lycopodium alkaloids are a large family of structurally unique polycyclic natural products with impressive biological activities. Owing to their fascinating polycyclic architectures and diverse biological activities, these alkaloids have continued to serve as targets as well as inspirations for the synthetic community for decades. To access these bioactive natural products or natural product-like molecules for biological exploration and drug discovery, we applied a novel functional group pairing strategy to furnish the total syntheses for several Lycopodium alkaloids and obtained numerous skeletally diverse compounds with structural complexity comparable to natural products.

A synthesis strategy for tetracyclic terpenoids leads to agonists of ER\u03b2

Natural product and natural product-like molecules continue to be important for the development of pharmaceutical agents, as molecules in this class play a vital role in the pipeline for new therapeutics. Among these, tetracyclic terpenoids are privileged, with >100 being FDA-approved drugs. Despite this significant pharmaceutical success, there remain considerable limitations to broad medicinal exploitation of the class due to lingering scientific challenges associated with compound availability. Here, we report a concise asymmetric route to forging natural and unnatural (enantiomeric) C19 and C20 tetracyclic terpenoid skeletons suitable to drive medicinal exploration. While efforts have been focused on establishing the chemical science, early investigations reveal that the emerging chemical technology can deliver compositions of matter that are potent and selective agonists of the estrogen receptor beta, and that are selectively cytotoxic in two different glioblastoma cell lines (U251 and U87).

Synthesis of indole terpenoid mimics through a functionality-tolerated Eu(fod)3 -catalyzed conjugate addition.

The chemical synthesis of indole terpenoids of structural and biological interests has attracted remarkable attention. Here we report an Eu(fod)3 -catalyzed indole conjugate addition reaction, which tolerates various acid-sensitive functional groups. A collection of indole terpenoid mimics have been prepared from natural product-derived α,β-unsaturated enones on the basis of this reaction. The further conversion of the indole adducts into more complex natural product-like molecules has also been demonstrated.

Diversity-oriented synthesis of Lycopodium alkaloids inspired by the hidden functional group pairing pattern.

Natural products continue to provide a rich source of inspiration for both chemists and biologists. The efficient synthesis of bioactive natural products or natural product-like molecules has offered tremendous opportunities for complex biological processes exploration and drug discovery. However, because natural products usually contain numerous stereogenic centres and polycyclic ring systems, significant synthetic challenges remain. Here we employ the build/couple/pair strategy that is frequently used in diversity-oriented synthesis to obtain skeletally diverse compounds with complexities comparable to natural products. Inspired by the functional group pairing patterns hidden in Lycopodium alkaloids, we efficiently and in parallel construct four natural products, (+)-Serratezomine A, (-)-Serratinine, (+)-8α-Hydroxyfawcettimine and (-)-Lycoposerramine-U, as well as six different unnatural scaffolds, following the advanced build/couple/pair algorithm. This newly developed strategy is expected to be applied to the efficient synthesis of other complex natural products possessing functional group pairing patterns as well as skeletally diverse natural product-like molecules.

Biosynthonics: Charting the Future Role of Biocatalysis and Metabolic Engineering in Drug Discovery

Ironic as it sounds, the pharmaceutical industry is ailing. Despite doubling their R&D expenditures over the past decade, innovator drug companies have struggled to increase their annual drug approval rates. Worse still, candidate attrition rates and development times actually rose during this period. It now costs well in excess of a billion dollars and takes over a decade to discover and develop a new drug. A variety of prognostications have been made regarding the future course that the pharmaceutical industry might take, but none has been as controversial as the suggestion that small-molecule drugs could disappear by 2030. Rest assured that these claims could not be further from the truth. Herein, I outline how biocatalysis and metabolic engineering could drive the next wave of innovation in small-molecule drug discovery. The recent past has witnessed staggering developments in analytical chemistry, genome sequencing and assembly, flow chemistry, chemi- and bioinformatics, metabolic engineering and synthetic chemistry, as well as exponential improvements in the raw computing power that is available for drug research; integrating these parallel innovations into a single platform could translate a vastly higher number of small-molecule drugs to the bedside. I term this integrated approach as “biosynthonics”. Many of its individual elements are already in use drug discovery and development, albeit in a scattered manner, and despite the substantial progress that has occurred in each individual domain, a lot still remains to be achieved if biosynthonics is to become a broad platform for generating focused libraries of natural product-like molecules. It is hoped that this article spurs debate and future collaborations toward achieving these goals, which, if successful, would undoubtedly improve small-molecule R&D productivity.

High-Content, High-Throughput Screening for the Identification of Cytotoxic Compounds Based on Cell Morphology and Cell Proliferation Markers

Toxicity is a major cause of failure in drug discovery and development, and whilst robust toxicological testing occurs, efficiency could be improved if compounds with cytotoxic characteristics were identified during primary compound screening. The use of high-content imaging in primary screening is becoming more widespread, and by utilising phenotypic approaches it should be possible to incorporate cytotoxicity counter-screens into primary screens. Here we present a novel phenotypic assay that can be used as a counter-screen to identify compounds with adverse cellular effects. This assay has been developed using U2OS cells, the PerkinElmer Operetta high-content/high-throughput imaging system and Columbus image analysis software. In Columbus, algorithms were devised to identify changes in nuclear morphology, cell shape and proliferation using DAPI, TOTO-3 and phosphohistone H3 staining, respectively. The algorithms were developed and tested on cells treated with doxorubicin, taxol and nocodazole. The assay was then used to screen a novel, chemical library, rich in natural product-like molecules of over 300 compounds, 13.6% of which were identified as having adverse cellular effects. This assay provides a relatively cheap and rapid approach for identifying compounds with adverse cellular effects during screening assays, potentially reducing compound rejection due to toxicity in subsequent in vitro and in vivo assays.

Discovery of a Phosphine-Mediated Cycloisomerization of Alkynyl Hemiketals: Access to Spiroketals and Dihydropyrazoles via Tandem Reactions

Reported here are details on the discovery of a phosphine-catalyzed isomerization of hemiketals and subsequent reactions of the cyclic keto enol ether products. The new cycloisomerization complements a previously reported amine-catalyzed process that gave oxepinones from the same hemiketal starting materials. In the absence of functionality (R(2)) on the cyclic keto enol ether, a rapid and facile dimerization occurs, giving spiroketal products. When the enone is substituted (i.e., R(2) = Ph), the cyclic keto enol ether is sufficiently stable so that it can be isolated; it can then be further reacted in the same pot to provide the corresponding dihydropyrazoles. Both the spiroketal and dihydropyrazole products arise by a tandem reaction that begins with the novel cycloisomerization. The method allows for the rapid introduction of complexity in the products from relatively simple starting materials. It should find application in the synthesis of natural product-like molecules.

Strategies for Total and Diversity‐Oriented Synthesis of Natural Product(‐like) Macrocycles

AbstractFor Abstract see ChemInform Abstract in Full Text.

Hydrocarbon Oxidation vs C−C Bond-Forming Approaches for Efficient Syntheses of Oxygenated Molecules

[Reaction: see text] A hydrocarbon oxidation approach has been applied to the construction of several linear (E)-allylic alcohols that have served as intermediates in the synthesis of natural products and natural product-like molecules. In the original syntheses, these intermediates were constructed using a standard Wittig-type olefination approach. We report here that routes to these same intermediates designed around a hydrocarbon oxidation approach are more efficient both in the total number of functional group manipulations (FGMs) and overall steps, as well as in the overall yield.

Diversity oriented synthesis and branching reaction pathway to generate natural product-like compounds.

Combinatorial chemistry can be used to synthesize diversified molecules on a large scale. As with all large-scale experiments, this process requires a major investment in equipment, consumables and time. Therefore, careful design is critical. As the complexity of the libraries to be generated increases, additional considerations become important. What are the issues that should be considered when planning combinatorial chemistry projects? Which features in the design strategy are critical to consider ensuring that all of the potential products will be synthesized? How are the reactants selected to optimize product synthesis and yield? Over the last several years, through an experimental process, we have successfully developed and optimized our synthetic strategy. Our approach incorporates a number of critical components into a tightly controlled process that generates molecules with maximal structural complexity. This complexity emanates from carbon-carbon bond formation, which is extremely stable and it is reminiscent of complex natural product molecules. Our studies have illustrated that transition metal catalysts are powerful reagents that can be used to drive the synthesis of diverse small molecules from less complex starting materials. In this review, we will describe some of our recent efforts to synthesize natural product-like molecules and their derivative structures to successfully create libraries of complex molecules for drug discovery applications. Our diversity-oriented synthesis methods incorporate transition metal catalysts, as a versatile tool for creating carbon-carbon bonds and structural complexity, and the branched reaction pathway, as a method for incorporating diversity into the molecular scaffolds. We will review our combinatorial chemistry program, focusing on the decisions that we made for (1) the scaffold selection; (2) the design of a diversity oriented approach for library synthesis; (3) the incorporation of the branched reaction pathway to generate natural product-like molecules from the same starting material; and (4) the process steps that we selected for chemistry development and library generation.

Combinatorial synthesis of natural product-like molecules using a first-generation spiroketal scaffold.

Recently, significant attention has been focused on the synthesis small-molecule libraries based on natural product or natural product-like structures. In this paper, we report our initial studies on the use of the 1,7-dioxaspiro[5,5]undecane (spiroketal) moiety as a rigid-core template for elaboration using parallel synthesis techniques. The synthesis of a spiroketal scaffold that is reminiscent of the spiroketal subunits found in the spiroketal macrolide antibiotics will be described. Elaboration of three independently addressable functional groups on the scaffold using solution-phase parallel synthesis techniques led to the preparation of a small library of natural product-like compounds. These studies pave the way for evaluation of highly functionalized spiroketals in phenotypic assays and as prospective antagonists of protein-protein interactions.

Optimization study of Sonogashira cross-coupling reaction on high-loading macrobeads using a silyl linker

Two types of Sonogashira reactions were systematically evaluated on silyl linker based high-loading polystyrene macrobeads, this study paves the way for their future application in the combinatorial syntheses of some natural product-like molecules.

Small molecule-dependent genetic selection in stochastic nanodroplets as a means of detecting protein-ligand interactions on a large scale.

Understanding the cellular role of a protein often requires a means of altering its function, most commonly by mutating the gene encoding the protein. Alternatively, protein function can be altered directly using a small molecule that binds to the protein, but no general method exists for the systematic discovery of small molecule ligands. Split-pool synthesis provides a means of synthesizing vast numbers of small molecules. Synthetic chemists will soon be able to synthesize natural product-like substances by this method, so compatible screening methods that detect the activity of minute quantities of molecules among many inactive ones will be in demand. We describe two advances towards achieving the above goals. First, a technique is described that uses a simple spray gun to create 5000-8000 droplets randomly, each having a volume of 50-200 nanoliters. The individual 'nanodroplets' contain a controlled number of cells and many also contain individual synthesis beads. As small molecules can be photochemically released from the beads in a time-dependent manner, the concentration of ligands that the cells are exposed to can be controlled. The spatial segregation of nanodroplets prevents the mixing of compounds from other beads so the effects of each molecule can be assayed individually. Second, a small molecule-dependent genetic selection involving engineered budding yeast cells was used to detect intracellular protein-ligand interactions in nanodroplets. The technique described here should facilitate the discovery of new cell-permeable ligands, especially when combined with a positive selection assay that detects intracellular binding of small molecules to proteins. Using 'anchored combinatorial libraries', it may be possible to screen entire libraries of natural product-like molecules against the entire collection of proteins encoded within cDNA libraries in a single experiment.