Advances, opportunities, and challenges in methods for interrogating the structure activity relationships of natural products

Time span in literature: 1985-early 2024Natural products play a key role in drug discovery, both as a direct source of drugs and as a starting point for the development of synthetic compounds. Most natural products are not suitable to be used as drugs without further modification due to insufficient activity or poor pharmacokinetic properties. Choosing what modifications to make requires an understanding of the compound's structure-activity relationships. Use of structure-activity relationships is commonplace and essential in medicinal chemistry campaigns applied to human-designed synthetic compounds. Structure-activity relationships have also been used to improve the properties of natural products, but several challenges still limit these efforts. Here, we review methods for studying the structure-activity relationships of natural products and their limitations. Specifically, we will discuss how synthesis, including total synthesis, late-stage derivatization, chemoenzymatic synthetic pathways, and engineering and genome mining of biosynthetic pathways can be used to produce natural product analogs and discuss the challenges of each of these approaches. Finally, we will discuss computational methods including machine learning methods for analyzing the relationship between biosynthetic genes and product activity, computer aided drug design techniques, and interpretable artificial intelligence approaches towards elucidating structure-activity relationships from models trained to predict bioactivity from chemical structure. Our focus will be on these latter topics as their applications for natural products have not been extensively reviewed. We suggest that these methods are all complementary to each other, and that only collaborative efforts using a combination of these techniques will result in a full understanding of the structure-activity relationships of natural products.

Isobavachalcone, a natural sirtuin 2 inhibitor, exhibits anti-triple-negative breast cancer efficacy in vitro and in vivo

Triple-negative breast cancer (TNBC) is the most aggressive and lethal clinical subtype and lacks effective targeted therapies at present. Isobavachalcone (IBC), the main active component of Psoralea corylifolia L., has potential anticancer effects. Herein, we identified IBC as a natural sirtuin 2 (SIRT2) inhibitor and characterized the potential mechanisms underlying the inhibition of TNBC. Molecular dynamics analysis, enzyme activity assay, and cellular thermal shift assay were performed to evaluate the combination of IBC and SIRT2. The therapeutic effects, mechanism, and safety of IBC were analyzed in vitro and in vivo using cellular and xenograft models. IBC effectively inhibited SIRT2 enzyme activity with an IC50 value of 0.84 ± 0.22 μM by forming hydrogen bonds with VAL233 and ALA135 within its catalytic domain. In the cellular environment, IBC bound to and stabilized SIRT2, consequently inhibiting cellular proliferation and migration, and inducing apoptosis and cell cycle arrest by disrupting the SIRT2/α-tubulin interaction and inhibiting the downstream Snail/MMP and STAT3/c-Myc pathways. In the in vivo model, 30 mg/kg IBC markedly inhibited tumor growth by targeting the SIRT2/α-tubulin interaction. Furthermore, IBC exerted its effects by inducing apoptosis in tumor tissues and was well-tolerated. IBC alleviated TNBC by targeting SIRT2 and triggering the reactive oxygen species ROS/β-catenin/CDK2 axis. It is a promising natural lead compound for future development of SIRT2-targeting drugs.

Rhodium(I)-Catalyzed O-H Insertions on O-Protected α-Diazo-β-Hydroxyesters

The X-H insertion reaction constitutes a powerful tool to create diversity through the diazo decomposition of diazocarbonyl compounds. However, until now, X-H insertion on α-diazo-β-aryl-β-hydroxyester scaffolds, readily prepared by aldol-type addition, remained a challenge for the organic chemist. We report herein the first O-H insertions on O-protected α-diazo-β-aryl-β-hydroxyesters, providing straightforward access to a wide range of α,β-dioxygenated esters through modulation of the alcohol and of the aryl substituent. The key feature to achieving this transformation is the use of Rh(I) catalysts, which proved to be crucial to favor the targeted O-H insertion product over the competing 1,2-H and 1,2-Ar migration products. Overall, 32 O-H insertion products have been prepared, in moderate to good yields, with a diastereoisomeric ratio up to 7.5:1 in favor of the syn diastereoisomer.

Deciphering the quest in the divergent total synthesis of natural products

The divergent synthesis of natural products is rapidly developing towards achieving the goal of efficiency and economy in total synthesis. However, presently, the sustainable development of the synthesis of natural products does not permit the linear synthesis of a single target. In this case, divergent total synthesis is based on the identification of an advanced intermediate with structural features that can be mapped in more than two molecules. However, the identification of this intermediate and its scalable synthesis in enantiopure form are challenging. Herein, we present the details of the ingenious efforts by researchers in the last six years toward the divergent synthesis of two to as many as eight natural products initially via a single route, and then diverging from a common intermediate and further branching out toward several natural products. The planning and strategies adopted can serve as guidelines for the future development of efficient divergent routes aimed at achieving higher efficiency toward multiple targets, causing divergent synthesis to become an accepted common practice.

Combining visible-light induction and copper catalysis for chemo-selective nitrene transfer for late-stage amination of natural products

Nitrene transfer chemistry is an effective strategy for introducing C-N bonds, which are ubiquitous in pharmaceuticals, agrochemicals and diverse bioactive natural products. The development of chemical methodology that can functionalize unique sites within natural products through nitrene transfer remains a challenge in the field. Herein, we developed copper catalyzed chemoselective allylic C-H amination and catalyst-free visible-light induced aziridination of alkenes through nitrene transfer. In general, both reactions tolerate a wide range of functional groups and occur with predictable regioselectivity. Furthermore, combination of these two methods enable the intermolecular chemo-selective late-stage amination of biologically active natural products, leading to C-H amination or C=C aziridination products in a tunable way. A series of control experiments indicate two-step radical processes were involved in both reaction systems.

Late-Stage Diversification: A Motivating Force in Organic Synthesis

Interest in therapeutic discovery typically drives the preparation of natural product analogs, but these undertakings contribute significant advances for synthetic chemistry as well. The need for a highly efficient and scalable synthetic route to a complex molecular scaffold for diversification frequently inspires new methodological development or unique application of existing methods on structurally intricate systems. Additionally, synthetic planning with an aim toward late-stage diversification can provide access to otherwise unavailable compounds or facilitate preparation of complex molecules with diverse patterns of substitution around a shared carbon framework. For these reasons among others, programs dedicated to the diversification of natural product frameworks and other complex molecular scaffolds have been increasing in popularity, a trend likely to continue given their fruitfulness and breadth of impact. In this Perspective, we discuss our experience using late-stage diversification as a guiding principle for the synthesis of natural product analogs and reflect on the impact such efforts have on the future of complex molecule synthesis.

A look around the West Indies: The spices of life are secondary metabolites

Natural products possess a wide range of bioactivities with potential for therapeutic usage. While the distribution of these molecules can vary greatly there is some correlation that exists between the biodiversity of an environment and the uniqueness and concentration of natural products found in that region or area. The Caribbean and pan-Caribbean area is home to thousands of species of endemic fauna and flora providing huge potential for natural product discovery and by way, potential leads for drug development. This can especially be said for marine natural products as many of are rapidly diluted through diffusion once released and therefore are highly potent to achieve long reaching effects. This review seeks to highlight a small selection of marine natural products from the Caribbean region which possess antiproliferative, anti-inflammatory and antipathogenic properties while highlighting any synthetic efforts towards bioactive analogs.

Procedure-Economical, Enantioselective Total Syntheses of Polycyclic Natural Products and Analogues Containing a 3a-Hydroxyhexahydropyrrolo[2,3-b]indole-2-carboxylic Acid Residue

The 3a-hydroxyhexahydropyrrolo[2,3-b]indole-2-carboxylic acid (HPIC) residue and its aza-analogue are found in many bioactive natural products. In this account, short divergent total syntheses of several such natural products, diastereomers and analogues are described. It is demonstrated that by appropriate combination of different efficient tactics such as biomimetic/bio-inspired synthesis, chemo/regioselective reactions, umpolung of regioselectivity and/or reactivity, and tandem reactions, the enantioselective syntheses of polycyclic molecules such as (+)-asperlicin E and (–)-robustanoids A and B can be achieved in a protecting-group-free and redox-economical manner, in only three to four steps starting from l-tryptophan.

1 Introduction

2 Strategic Considerations

2.1 Occurrence of HO-HPIC and HO-aza-HPIC Residues in Natural Products

2.2 Biosyntheses of HO-HPIC and HO-aza-HPIC Residues

2.3 Chemical Syntheses of HO-HPIC and HO-aza-HPIC Residues

3 Procedure-Economical Syntheses of HO-HPIC-Containing Natural Products

3.1 Protecting-Group-Free Syntheses of Asperlicin E, Its Diastereomer, and an Analogue

3.2 Divergent Syntheses of (–)-Robustanoids A and B, a Diastereomer, and Analogues

4 Conclusion and Future Perspectives

LYW-6, a novel cryptotanshinone derived STAT3 targeting inhibitor, suppresses colorectal cancer growth and metastasis

The constitutive activation of signal transducer and activator of transcription 3(STAT3) is associated with aggressive development and metastasis in colorectal cancer (CRC), but STAT3-targeting drugs remain elusive in clinic. Here, structure-based strategy was used to remodel the natural compound cryptotanshinone into a more effective STAT3 inhibitor LYW-6. Using the Biolayer Interferometry assay, we observed that LYW-6 exhibited specific interactions with STAT3(KD = 6.6 ± 0.7 μM). Western blot analysis and electrophoretic mobility shift assays (EMSA) showed that LYW-6 inhibited the phosphorylation of STAT3 tyrosine 705 (Tyr-705) and had slight effects on STAT1 and STAT5 phosphorylation. Western blot analysis on the upstream kinases of STAT3 confirmed that the inhibitory mechanism on p-STAT3 was independent of upstream kinases. Further investigation demonstrated that LYW-6 downregulated the expression of downstream oncogenes to inhibit cell viability, cell cycle development, and potently increased cell apoptosis in human CRC cells. The invasion and metastasis linked signaling was also blocked by LYW-6 treatment. LYW-6 was found to reduce the metastasis foci in lung on tail-lung metastasis models. In addition, it was observed that LYW-6 markedly diminished STAT3 phosphorylation in tumor tissue and significantly inhibited tumor growth on xenograft models. Tumor development on chemically-induced colorectal cancer model also significantly inhibited by LYW-6 treatment. These findings provided adequate evidence that STAT3 inhibitor LYW-6 might be a potential candidate agent for CRC treatment.

Diastereoselective construction of the benzannulated spiroketal core of chaetoquadrins enabled by a regiodivergent cascade

A remarkable acid-mediated methodology for the regiodivergent construction of a biologically interesting tricyclic benzannulated-spiroketal skeleton with diastereomeric specificity was uncovered to efficiently access analogs of chaetoquadrins .

Biological Effects of a Simplified Synthetic Analogue of Ion-Channel-Forming Polytheonamide B on Plasma Membrane and Lysosomes

Polytheonamide B (1) is a linear 48-mer natural peptide with alternating d- and l-amino acid residues. Compound 1 forms conducting channels for monovalent ions and exhibits potent cytotoxicity against MCF-7 cells. Previously, we reported that nanomolar concentrations of 1 induce plasma membrane depolarization and lysosomal pH disruption, which triggers apoptosis. Here, we report the cellular localization and biological action of a simplified synthetic analogue of 1, polytheonamide mimic 3. Compared with 1, the toxicity of 3 against MCF-7 cells is 16 times weaker. Although its plasma membrane depolarization effect is only 3.6 times lower, more 3 (20-fold) is required to neutralize lysosomal pH. Thus, the effective concentrations for lysosomal neutralization and cytotoxicity by 3 are comparable. These results strongly suggest that the activity of 3 against the lysosomal membrane is more important for apoptotic cell death than its effects on the plasma membrane, and provide valuable information regarding the unique behavior of polytheonamide-based molecules.

Recent advances in catalytic asymmetric dihydroxylation of olefins

Asymmetric dihydroxylation of olefinic groups is an extremely important synthetic transformation which has been widely utilized to obtain optically pure pharmaceuticals and other fine chemical products. In recent years, catalyst systems for the asymmetric C=C dihydroxylations have attracted significant interest, the major research efforts being focused on designing environmentally benign catalyst systems. This mini-review summarizes recent progress in the field, surveying both novel, less toxic modifications of the classical osmium-based catalysts, and the highly efficient and enantioselective non-osmium catalyst systems.

The bibliography includes 50 references.

An improved method for the preparation of Ginsenoside Rg5 from ginseng fibrous root powder

Ginsenoside-Rg5, which is derived from high temperature-processed ginseng, exhibits beneficial health effects. In the present study, ginsenoside-Rg5 was directly and rapidly prepared through the extraction of ginseng fibrous root powder (GFRP) at atmospheric pressure. The results showed that the highest extraction yield (3.79%) was obtained under optimal conditions (extraction temperature of 85 °C, acid concentration of 0.06 mol/L, sample to solvent ratio of 1:55 g/mL and ethanol concentration of 95% after 4 h). The current method integrates the extraction of original saponins and the modification of the saponins to rare ginsenosides Rg5, which was more simpler operation, more milder preparation condition and more efficient.

Design and Synthesis of Anti-Cancer Chimera Molecules Based on Marine Natural Products

In this paper, the chemical conjugation of marine natural products with other bioactive molecules for developing an advanced anti-cancer agent is described. Structural complexity and the extraordinary biological features of marine natural products have led to tremendous research in isolation, structural elucidation, synthesis, and pharmacological evaluation. In addition, this basic scientific achievement has made it possible to hybridize two or more biologically important skeletons into a single compound. The hybridization strategy has been used to identify further opportunities to overcome certain limitations, such as structural complexity, scarcity problems, poor solubility, severe toxicity, and weak potency of marine natural products for advanced development in drug discovery. Further, well-designed marine chimera molecules can function as a platform for target discovery or degradation. In this review, the design, synthesis, and biological evaluation of recent marine chimera molecules are presented.

9-Borabicyclo[3.3.l]nonane-induced Friedel-Crafts benzylation of arenes with benzyl fluorides

Friedel-Crafts benzylation of arenes with benzyl fluorides using 9-borabicyclo[3.3.l]nonane (9-BBN) as a mediator has been developed. This provides a simple and cheap route to the activation of C-F bonds to synthesize 1,1-diarylmethanes in good to excellent yields (up to 98%) under mild conditions. Functional group tolerance and the mechanism are considered.

P450 Monooxygenases Enable Rapid Late-Stage Diversification of Natural Products via C-H Bond Activation

The biological potency of natural products has been exploited for decades. Their inherent structural complexity and natural diversity might hold the key to efficiently address the urgent need for the development of novel pharmaceuticals. At the same time, it is that very complexity, which impedes necessary chemical modifications such as structural diversification, to improve the effectiveness of the drug. For this purpose, Cytochrome P450 enzymes, which possess unique abilities to activate inert sp3-hybridised C-H bonds in a late-stage fashion, offer an attractive synthetic tool. In this review the potential of cytochrome P450 enzymes in chemoenzymatic lead diversification is illustrated discussing studies reporting late-stage functionalisations of natural products and other high-value compounds. These enzymes were proven to extend the synthetic toolbox significantly by adding to the flexibility and efficacy of synthetic strategies of natural product chemists, and scientists of other related disciplines.

Metal-free construction of contiguous quaternary stereocentres with a polycyclic framework

A series of contiguous all-carbon quaternary stereocentres with an arene-annulated polycyclic framework were constructed efficiently by a metal-free and atom economic acid-catalyzed method. The reactions could be performed by acid-catalyzed cationic cyclization and rearrangement under mild conditions. Moreover, the resulting polycyclic products showed highly twisted architectures with two perpendicular planes.

Synthesis and preliminary evaluation of the anti-cancer activity on A549 lung cancer cells of a series of unsaturated disulfides

We synthesized a series of small symmetrical unsaturated disulfides by a multi-step reaction starting from organic alcohols, and we performed a preliminary test to evaluate the effect of these compounds on the viability of A549 lung cancer cells. The garlic-derived natural compound diallyl disulfide, known for its anticancer activity, was used as the lead compound in this study. We synthesized five DADS analogues having different carbon chain lengths and different positions of the double bonds. Two analogues exhibited a promising antitumor activity in vitro, and the allylic double bond did not seem to be the main driving force.

A new efficient domino approach for the synthesis of coumarin-pyrazolines as antimicrobial agents targeting bacteriald-alanine-d-alanine ligase

The inhibition ofd-alanine-d-alanine ligase (Ddl) prevents bacterial growth, which makes this enzyme an attractive and viable target in the urgent search for novel effective antimicrobial drugs.

Facile construction of diverse polyheterocyclic scaffolds via gold-catalysed dearomative spirocyclization/1,6-addition cascade

A post-Ugi gold-catalysed chemo- and diastereo-selective cascade dearomative spirocyclization/1,6-addition sequence is disclosed for the facile synthesis of diverse fused polyheterocyclic scaffolds bearing indole, pyrrole, benzothiophene, furan or electron-rich arene cores.

Why Are the Majority of Active Compounds in the CNS Domain Natural Products? A Critical Analysis

Small-molecule natural products (NPs) have a long and successful track record of providing first-in-class drugs and pharmacophore (scaffolds) in all therapeutic areas, serving as a bridge between modern and traditional medicine. This trajectory has been remarkably successful in three key areas of modern therapeutics: cancers, infections, and CNS diseases. Beginning with the discovery of morphine 200 years ago, natural products have remained the primary source of new drugs/scaffolds for CNS diseases. In this perspective, we address the question: why are the majority of active compounds in the CNS domain natural products? Our analysis indicates that ∼84% approved drugs for CNS diseases are NPs or NP-inspired, and interestingly, 20 natural products provided more than 400 clinically approved CNS drugs. We have discussed unique physicochemical properties of NPs and NP-inspired vis-à-vis synthetic drugs, isoform selectivity, and evolutionary relationship, providing a rationale for increasing focus on natural product driven discovery for next-generation drugs for neurodegenerative diseases.

Dendrimers in combination with natural products and analogues as anti-cancer agents

For the first time, an overview of dendrimers in combination with natural products and analogues as anti-cancer agents is presented. This reflects the development of drug delivery systems, such as dendrimers, to tackle cancers. The most significant advantages of using dendrimers in nanomedicine are their high biocompatibility, good water solubility, and their entry - with or without encapsulated, complexed or conjugated drugs - through an endocytosis process. This strategy has accelerated over the years in order to develop nanosystems as nanocarriers, to decrease the intrinsic toxicity of anti-cancer agents, to decrease the drug side effects, to increase the efficacy of the treatment, and consequently to improve patient compliance.

A new transformation of coumarins via direct C–H bond activation utilizing an iron–organic framework as a recyclable catalyst

A new mixed-linker iron-based MOF VNU-20 [Fe₃(BTC)(NDC)₂·6.65H₂O] was solvothermally synthesized, and utilized as catalyst for the coupling transformation of coumarins with N,N-dimethylanilines.

Dendrimers in combination with natural products and analogues as anti-cancer agents

Overview of the use of dendrimers in combination with encapsulated and conjugated natural products and analogues as anti-cancer agents.

Dendrimers in combination with natural products and analogues as anti-cancer agents

Overview of the use of dendrimers in combination with encapsulated and conjugated natural products and analogues as anti-cancer agents.

Cross-dehydrogenative coupling of coumarins with Csp3–H bonds using an iron–organic framework as a productive heterogeneous catalyst

The iron–organic framework VNU-20 was utilized as an active heterogeneous catalyst for the cross-dehydrogenative coupling of coumarins with Csp³–H bonds in alkylbenzenes, cyclohexanes, ethers, and formamides.

Design and synthesis of a hybrid framework of indanone and chromane: total synthesis of a homoisoflavanoid, brazilane

A chemical backbone of tetracyclic homoisoflavanoid natural products such as brazilin inspired us to design a new chemical scaffold, 6a,11b-dihydroindeno[2,1-c]chromen-7(6H)-one, which is a hybrid structure of indanone and chromane. Pd-catalyzed Suzuki-Miyaura cross-coupling of 4-chloro-2H-chromene-3-carbaldehydes with (hetero)aryl boronic acids was employed as a means to introduce a wide variety of (hetero)aryl groups as the D ring and intramolecular Friedel-Crafts acylation was utilized to construct the C ring of this skeleton. Total synthesis of the natural product, brazilane, was also demonstrated via this new chemical framework.

A Gold-Catalyzed Domino Cyclization Enabling Rapid Construction of Diverse Polyheterocyclic Frameworks

We report herein an efficient gold(I)-catalyzed post-Ugi domino dearomatization/ipso-cyclization/Michael sequence that enables access to libraries of diverse (hetero)arene-annulated tricyclic heterocycles. This process affords novel complex polycyclic scaffolds in moderate to good yields from readily available acyclic precursors with excellent chemo-, regio-, and diastereoselectivity. The power of this strategy has been demonstrated by the rapid synthesis of 40 highly functionalized polyheterocycles bearing indole, pyrrole, (benzo)furan, (benzo)thiophene, pyrazole, and electron-rich arene groups in two operational steps.

The Difference a Single Atom Can Make: Synthesis and Design at the Chemistry-Biology Interface

A Perspective of work in our laboratory on the examination of biologically active compounds, especially natural products, is presented. In the context of individual programs and along with a summary of our work, selected cases are presented that illustrate the impact single atom changes can have on the biological properties of the compounds. The examples were chosen to highlight single heavy atom changes that improve activity, rather than those that involve informative alterations that reduce or abolish activity. The examples were also chosen to illustrate that the impact of such single-atom changes can originate from steric, electronic, conformational, or H-bonding effects, from changes in functional reactivity, from fundamental intermolecular interactions with a biological target, from introduction of a new or altered functionalization site, or from features as simple as improvements in stability or physical properties. Nearly all the examples highlighted represent not only unusual instances of productive deep-seated natural product modifications and were introduced through total synthesis but are also remarkable in that they are derived from only a single heavy atom change in the structure.