Toward the ideal synthesis and molecular function through synthesis-informed design

Enhanced Catalytic Activity of Binuclear Oxidovanadium(IV) Bisbenzimidazole Linked Porphyrin Dimer for the Generation of Biologically Active 3,4-Dihydropyrimidinones and Their Corresponding Thiones

Binuclear vanadyl(IV) porphyrin (V2BP), where two vanadium(IV) porphyrin macrocycles are linked through benzimidazole units at the β-positions, has been prepared and characterized with various techniques, such as UV-vis, Fourier transform-infrared, electron paramagnetic resonance, cyclic voltammetry, density functional transform calculations, and mass spectrometry. V2BP exhibits a red shift (Δλmax = 10 nm) in the Soret band as compared with unsubstituted parent vanadyl(IV) meso-tetraphenylporphyrin (VP). The synthesized binuclear vanadyl(IV) porphyrin (V2BP) has further been studied as a catalyst to explore a single-pot multicomponent Biginelli reaction producing biologically active 3,4-dihydropyrimidin-2-(1H)-one (DHPM)-based biomolecules and the corresponding thiones under solvent-free conditions and its catalytic activity has been compared with vanadyl(IV) meso-tetraphenylporphyrin (VP). Several reaction conditions, such as the amount of catalyst, time, solvent, and temperature, have been optimized to obtain the maximum yield of DHPMs or thiones. The synthesized β-functionalized V2BP porphyrin dimer manifests much higher conversion (84-95% yield) of DHPMs or the corresponding thiones under the optimized reaction conditions with high TON (4454-5037) and TOF (1113-1259 h-1) values for the one-pot multicomponent Biginelli reaction as compared to the literature. The catalyst exhibited excellent recyclability up to 10 cycles.

Nickel(II)-Catalyzed Formal [3+2] Cycloadditions between Indoles and Donor-Acceptor Cyclopropanes

This article describes the development of a nickel-catalyzed regio- and diastereoselective formal [3+2] cycloaddition between N-substituted indoles and donor-acceptor cyclopropanes to synthesize cyclopenta[b]indoles. Optimized reaction conditions provide the desired nitrogen-containing cycloadducts in up to 93% yield and dr 8.6:1 with complete regioselectivity. The substrate scope showed high tolerance to various substituted indoles and cyclopropanes, resulting in the synthesis of six new cyclopenta[b]indoles and the isolation of five derivatives previously reported in the literature. In addition, a mechanistic proposal for the reaction was studied through online reaction monitoring by ESI-MS, allowing for the identification of the reactive intermediates in the Ni(II) catalyzed process. X-ray crystallography confirmed the structure and relative endo stereochemistry of the products. This method enables the fast and efficient construction of fused indolines from readily accessible starting materials.

Construction of Octahydro-4H-cyclopenta[b]pyridin-6-one Skeletons using Pot, Atom, and Step Economy (PASE) Synthesis

Cascade aza-Piancatelli reaction and [3+3]/[4+2] cycloaddition reactions are carried out using the ideality principles of pot, atom, and step economy (PASE) synthesis. The reaction resulted in generation of octahydro-4H-cyclopenta[b]pyridin-6-one scaffolds. Moreover, octahydro-5,7a-epoxycyclopenta[cd]isoindol-4-one frameworks of gracilamine alkaloid and a novel decahydro-1H-dicyclopenta[cd,hi]isoindol-6-one were also realized in good yields with excellent regio- and diastereo-selectivities.

An efficient and eco-compatible multicomponent synthesis of 2,4,5-trisubstituted imidazole derivatives using modified-silica-coated cobalt ferrite nanoparticles with tungstic acid

The aim of this study has been to offer a method for the synthesis of 2,4,5-trisubstituted imidazole derivatives based on green chemistry principles. Therefore, a one-pot multicomponent cyclocondensation reaction through aldehyde interaction with ammonium acetate and 1,2-diketone under solvent-free conditions was utilized as an eco-effective synthetic route using CoFe₂O₄@SiO₂@(-CH₂)₃OWO₃H NPs as the catalyst. The stabilized tungstic acid on 3-chloropropyl-anchored SiO₂-coated CoFe₂O₄ magnetic nanoparticles was designed, prepared, and applied as a recyclable heterogeneous acid catalyst to attain high product yield in a short reaction time. The nanocatalyst structure was confirmed using FT-IR, Raman, XRD, FE-SEM, EDX, VSM, and TGA techniques, and the organic product structures were examined by melting point, FT-IR and ¹H NMR analyses.

Computational Approaches to Enzyme Inhibition by Marine Natural Products in the Search for New Drugs

The exploration of biologically relevant chemical space for the discovery of small bioactive molecules present in marine organisms has led not only to important advances in certain therapeutic areas, but also to a better understanding of many life processes. The still largely untapped reservoir of countless metabolites that play biological roles in marine invertebrates and microorganisms opens new avenues and poses new challenges for research. Computational technologies provide the means to (i) organize chemical and biological information in easily searchable and hyperlinked databases and knowledgebases; (ii) carry out cheminformatic analyses on natural products; (iii) mine microbial genomes for known and cryptic biosynthetic pathways; (iv) explore global networks that connect active compounds to their targets (often including enzymes); (v) solve structures of ligands, targets, and their respective complexes using X-ray crystallography and NMR techniques, thus enabling virtual screening and structure-based drug design; and (vi) build molecular models to simulate ligand binding and understand mechanisms of action in atomic detail. Marine natural products are viewed today not only as potential drugs, but also as an invaluable source of chemical inspiration for the development of novel chemotypes to be used in chemical biology and medicinal chemistry research.

A bioinspired, one-step total synthesis of peshawaraquinone

A concise synthesis of a stereochemically complex meroterpenoid, peshawaraquinone, via the unsymmetrical dimerization of its achiral precursor, dehydro-α-lapachone, is reported. Enabled by reversible oxa-6π-electrocyclizations of 2H-pyran intermediates, the base-catalyzed dimerization sets up an intramolecular (3 + 2) cycloaddition, with the formation of six stereocenters during the cascade. Combining the generation and in situ dimerization of dehydro-α-lapachone allows a one-step total synthesis of peshawaraquinone from lawsone and prenal.

Polymer-Supported Dioxidovanadium(V) Complex-Based Heterogeneous Catalyst for Multicomponent Biginelli Reaction Producing Biologically Active 3,4-Dihydropyrimidin-2-(1H)-ones

Dioxidovanadium(V) complex [VVO2(sal-aebmz)] (1) (where Hsal-aebmz = Schiff base derived from the condensation of salicylaldehyde and 2-aminoethylbenzimidazole) has been immobilized on chloromethylated polystyrene (PS-Cl) cross-linked with divinylbenzene to obtain [VVO2(sal-aebmz)]@PS (2), a heterogeneous complex. Both complexes, after characterization, have been used as catalysts to explore a single pot multicomponent (benzaldehyde or its derivatives, urea and ethyl acetoacetate) Biginelli reaction producing biologically active 3,4-dihydropyrimidin-2-(1H)-one (DHPM)-based biomolecules under solvent-free conditions in the presence of H2O2 as a green oxidant. Various reaction conditions such as amounts of catalyst and oxidant, temperature, time, and solvent have been optimized to obtain the maximum yield of DHPMs. The polymer-immobilized complex has been found to show excellent catalytic activity, giving ca. 95% yield of DHPMs under the optimized reaction conditions selectively. Oxidant plays an important role in enhancing the yield of DHPMs.

Constitutionally Selective Dynamic Covalent Nanoparticle Assembly

The future of materials chemistry will be defined by our ability to precisely arrange components that have considerably larger dimensions and more complex compositions than conventional molecular or macromolecular building blocks. However, exerting structural and constitutional control in the assembly of nanoscale entities presents a considerable challenge. Dynamic covalent nanoparticles are emerging as an attractive category of reaction-enabled solution-processable nanosized building block through which the rational principles of molecular synthetic chemistry can be extended into the nanoscale. From a mixture of two hydrazone-based dynamic covalent nanoparticles with complementary reactivity, specific molecular instructions trigger selective assembly of intimately mixed heteromaterial (Au–Pd) aggregates or materials highly enriched in either one of the two core materials. In much the same way as complementary reactivity is exploited in synthetic molecular chemistry, chemospecific nanoparticle-bound reactions dictate building block connectivity; meanwhile, kinetic regioselectivity on the nanoscale regulates the detailed composition of the materials produced. Selectivity, and hence aggregate composition, is sensitive to several system parameters. By characterizing the nanoparticle-bound reactions in isolation, kinetic models of the multiscale assembly network can be constructed. Despite ignoring heterogeneous physical processes such as aggregation and precipitation, these simple kinetic models successfully link the underlying molecular events with the nanoscale assembly outcome, guiding rational optimization to maximize selectivity for each of the three assembly pathways. With such predictive construction strategies, we can anticipate that reaction-enabled nanoparticles can become fully incorporated in the lexicon of synthetic chemistry, ultimately establishing a synthetic science that manipulates molecular and nanoscale components with equal proficiency.

Complexity reduction and opportunities in the design, integration and intensification of biocatalytic processes for metabolite synthesis

The biosynthesis of metabolites from available starting materials is becoming an ever important area due to the increasing demands within the life science research area. Access to metabolites is making essential contributions to analytical, diagnostic, therapeutic and different industrial applications. These molecules can be synthesized by the enzymes of biological systems under sustainable process conditions. The facile synthetic access to the metabolite and metabolite-like molecular space is of fundamental importance. The increasing knowledge within molecular biology, enzyme discovery and production together with their biochemical and structural properties offers excellent opportunities for using modular cell-free biocatalytic systems. This reduces the complexity of synthesizing metabolites using biological whole-cell approaches or by classical chemical synthesis. A systems biocatalysis approach can provide a wealth of optimized enzymes for the biosynthesis of already identified and new metabolite molecules.

Harnessing Natural Products by a Pharmacophore-Oriented Semisynthesis Approach for the Discovery of Potential Anti-SARS-CoV-2 Agents

Natural products possessing unique scaffolds may have antiviral activity but their complex structures hinder facile synthesis. A pharmacophore‐oriented semisynthesis approach was applied to (−)‐maoelactone A (1) and oridonin (2) for the discovery of anti‐SARS‐CoV‐2 agents. The Wolff rearrangement/lactonization cascade (WRLC) reaction was developed to construct the unprecedented maoelactone‐type scaffold during semisynthesis of 1. Further mechanistic study suggested a concerted mechanism for Wolff rearrangement and a water‐assisted stepwise process for lactonization. The WRLC reaction then enabled the creation of a novel family by assembly of the maoelactone‐type scaffold and the pharmacophore of 2, whereby one derivative inhibited SARS‐CoV‐2 replication in HPA EpiC cells with a low EC₅₀ value (19±1 nM) and a high TI value (>1000), both values better than those of remdesivir.

An Iterative Phosphate Tether Mediated Approach for the Synthesis of Complex Polyol Subunits

A pot-economical approach to advanced polyol subunits is reported. The key reactions involved are iterative use of a phosphate tether-mediated one-pot sequential RCM/CM/H₂ with subsequent utilization of either a regio-/diasteroselective cuprate addition or a Pd-catalyzed reductive allylic transposition. This method highlights the asymmetric synthesis of 12 complex polyol subunits in 4-6 one-pot sequential operations with a total of 12-14 reactions, of which 4-5 are catalytic, with minimal workup and purification procedures.

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.

Microwave-Assisted Electrostatically Enhanced Phenol-Catalyzed Synthesis of Oxazolidinones

An electrostatically enhanced phenol is utilized as a straightforward, sustainable, and potent one-component organocatalyst for the atom-economic transformation of epoxides to oxazolidinones under microwave irradiation. Integrating a positively charged center into phenols over a modular one-step preparation gives rise to a bifunctional system with improved acidity and activity, competent in rapid assembly of epoxides and isocyanates under microwave irradiation in a short reaction time (20-60 min). A careful assessment of the efficacy of various positively charged phenols and anilines and the impact of several factors, such as catalyst loading, temperature, and the kind of nucleophile, on catalytic reactivity were examined. Under neat conditions, this one-component catalytic platform was exploited to prepare more than 40 examples of oxazolidinones from a variety of aryl- and alkyl-substituted epoxides and isocyanates within minutes, where up to 96% yield and high degree of selectivity were attained. DFT calculations to achieve reaction barriers for different catalytic routes were conducted to provide mechanistic understanding and corroborated the experimental findings in which concurrent epoxide ring-opening and isocyanate incorporation were proposed.

Five Step Total Synthesis of Lythranidine

A concise synthesis of the alkaloid lythranidine is reported. The strategy exploits the target's local C₂ symmetry by adopting a two directional synthetic approach, first in an acyclic environment, then in a cyclic system and finally in a bridged macrocyclic domain. The latter phase of the synthesis, which installs all four stereocenters, involves a thermodynamically controlled, twofold intermolecular/transannular aza-Michael addition and a twofold hydride reduction. The synthesis is one third of the length of the most step-economic previous approach, providing access to gram quantities of the natural product. The broad-spectrum nature of the synthesis is demonstrated through the preparation of three diastereomeric analogues of the natural product.

Small rings in the bigger picture: ring expansion of three- and four-membered rings to access larger all-carbon cyclic systems

The release of the inherent ring strain of cyclobutane and cyclopropane derivatives allows a rapid build-up of molecular complexity. This review highlights the state-of-the-art of the ring expansions of three- and four-membered cycles and is organised by types of reactions with emphasis on the reaction mechanisms. Selected examples are discussed to illustrate the synthetic potential of this elegant synthetic tool.

Sulfamate-tethered aza-Wacker approach towards analogs of Bactobolin A

Here, we describe an approach towards analogs of the potent antibiotic Bactobolin A. Sulfamate-tethered aza-Wacker cyclization reactions furnish key synthons, which we envision can be elaborated into analogs of Bactobolin A. Docking studies show that the C4 epimer of Bactobolin A and the C4/C6 diastereomer interact with different residues of the 23S rRNA (bacterial ribosome 50S subunit) than the natural product, suggesting that these molecules could be valuable tool compounds for fundamental studies of the bacterial translational machinery.

Rapid synthetic approaches to libraries of diversified 1,2-dihydrochromeno[2,3-c]pyrrole-3,9-diones and 3-(2-hydroxyphenyl)-4,5-dihydropyrrolo[3,4-c]pyrazol-6(1H)-ones

An efficient and practical synthetic procedure for libraries of diversified 1,2-dihydrochromeno[2,3-c]pyrrole-3,9-diones using a multicomponent process is presented. A convenient synthetic procedure for obtaining functionalized 3-(2-hydroxyphenyl)-4,5-dihydropyrrolo[3,4-c]pyrazol-6(1H)-ones via ring-opening strategy has also been developed. This protocol was found to be compatible with a wide range of substituents and paves the way for the practical synthesis of title compounds with a broad range of substituents under mild condition. The products can be easily isolated by crystallization without the use of chromatography.

(Z)-Selective Hydrosilylation and Hydroboration of Terminal Alkynes Enabled by Ruthenium Complexes with an N-Heterocyclic Carbene Ligand

Metal-catalyzed trans-1,2-hydrosilylations and hydroborations of terminal alkynes that generate synthetically valuable (Z)-alkenylsilanes and (Z)-alkenylboranes remain challenging due to the (E)-selective nature of the reactions and the formation of the thermodynamically unfavorable (Z)-isomer. The development of new, efficient catalytic systems for the (Z)-selective hydrosilylation and hydroboration of terminal alkynes is thus highly desirable from a fundamental perspective as it would deepen our understanding of the metal-catalyzed (Z)-selective hydrosilylation and hydroboration of terminal alkynes. This personal account describes our research for developing a ruthenium complex that can efficiently catalyze the hydrosilylation and hydroboration of terminal alkynes, and for exploring the factors controlling (Z)-selectivity of the reactions. Our effort into the activation of B-protected boronic acids, R-B(dan) (dan=naphthalene-1,8-diaminato), that was believed not to participate in Suzuki-Miyaura cross-coupling, is also discussed.

Leveraging Marine Natural Products as a Platform to Tackle Bacterial Resistance and Persistence

Antimicrobial resistance to existing antibiotics represents one of the greatest threats to human health and is growing at an alarming rate. To further complicate treatment of bacterial infections, many chronic infections are the result of bacterial biofilms that are tolerant to treatment with antibiotics because of the presence of metabolically dormant persister cell populations. Together these threats are creating an increasing burden on the healthcare system, and a "preantibiotic" age is on the horizon if significant action is not taken by the scientific and medical communities. While the golden era of antibiotic discovery (1940s-1960s) produced most of the antibiotic classes in clinical use today, followed by several decades of limited development, there has been a resurgence in antibiotic drug discovery in recent years fueled by the academic and biotech sectors. Historically, great success has been achieved by developing next-generation variants of existing classes of antibiotics, but there remains a dire need for the identification of novel scaffolds and/or antimicrobial targets to drive future efforts to overcome resistance and tolerance. In this regard, there has been no more valuable source for the identification of antibiotics than natural products, with 69-77% of approved antibiotics either being such compounds or being derived from them.Our group has developed a program centered on the chemical synthesis and chemical microbiology of marine natural products with unusual structures and promising levels of activity against multidrug-resistant (MDR) bacterial pathogens. As we are motivated by preparing and studying the biological effects of these molecules, we are not initially pursuing a biological question but instead are allowing the observed phenotypes and activities to guide the ultimate project direction. In this Account, our recent efforts on the synoxazolidinone, lipoxazolidinone, and batzelladine natural products will be discussed and placed in the context of the field's greatest challenges and opportunities. Specifically, the synoxazolidinone family of 4-oxazolidinone-containing natural products has led to the development of several chemical methods to prepare antimicrobial scaffolds and has revealed compounds with potent activity as adjuvants to treat bacterial biofilms. Bearing the same 4-oxazolidinone core, the lipoxazolidinones have proven to be potent single-agent antibiotics. Finally, our synthetic efforts toward the batzelladines revealed analogues with activity against a number of MDR pathogens, highlighted by non-natural stereochemical isomers with superior activity and simplified synthetic access. Taken together, these studies provide several distinct platforms for the development of novel therapeutics that can add to our arsenal of scaffolds for preclinical development and can provide insight into the biochemical processes and pathways that can be targeted by small molecules in the fight against antimicrobial-resistant and -tolerant infections. We hope that this work will serve as inspiration for increased efforts by the scientific community to leverage synthetic chemistry and chemical microbiology toward novel antibiotics that can combat the growing crisis of MDR and tolerant bacterial infections.

Gram-Scale, Seven-Step Total Synthesis of (-)-Colchicine

Herein we report a streamlined, gram-scale total synthesis of (-)-colchicine that takes only 7 easy steps, with an overall yield of 27-36%. To warrant the synthetic efficiency and practicality of (-)-colchicine, we tactically utilized a modified version of a powerful Ir-catalyzed amidation reported by Carreira to install the key chiral C-7 acetamido group, Suzuki and biomimetic phenol oxidative coupling, and Banwell-inspired cyclopropane ring cleavage to construct (-)-colchicine precisely and rapidly. Remarkably, a described strategy also can shorten the synthesis of allocolchicinoid to 4 steps.

Synthesis and biological evaluation of the new ring system benzo[f]pyrimido[1,2-d][1,2,3]triazolo[1,5-a][1,4]diazepine and its cycloalkane and cycloalkene condensed analogues

Derivatives of the new ring system benzo[f]pyrimido[1,2-d][1,2,3]triazolo[1,5-a][1,4]diazepinone and its cycloalkane and cycloalkene condensed analogues have been conveniently synthesized through a three-step reaction sequence. An atom-economical, one-pot, three-step cascade process engaging five reactive centers (amide, amine, carbonyl, azide, and alkyne) has been performed for the synthesis of alicyclic derivatives of quinazolinotriazolobenzodiazepine using cyclohexane, cyclohexene, and norbornene β-amino amides. The stereochemistry and relative configurations of the synthesized compounds were determined by 1D and 2D NMR spectroscopy and X-ray crystallography. The reaction was also performed using enantiomeric starting materials leading to enantiomeric quinazolinotriazolobenzodiazepine with an ee of 95%. The synthesis of 9H-benzo[f]pyrimido[1,2-d][1,2,3]triazolo[1,5-a][1,4]diazepinone, a new heterocyclic system, was achieved in a good yield using a retro Diels-Alder (RDA) procedure. Some compounds were tested for antiproliferative activities against five human cancer cell lines of gynecological.

The Future of Retrosynthesis and Synthetic Planning: Algorithmic, Humanistic or the Interplay?

The practice of deploying and teaching retrosynthesis is on the cusp of considerable change, which in turn forces practitioners and educators to contemplate whether this impending change will advance or erode the efficiency and elegance of organic synthesis in the future. A short treatise is presented herein that covers the concept of retrosynthesis, along with exemplified methods and theories, and an attempt to comprehend the impact of artificial intelligence in an era when freely and commercially available retrosynthetic and forward synthesis planning programs are increasingly prevalent. Will the computer ever compete with human retrosynthetic design and the art of organic synthesis?

Green strategies for transition metal-catalyzed C–H activation in molecular syntheses

Sustainable strategies for the activation of inert C–H bonds towards improved resource-economy.

Advances in polycyclization cascades in natural product synthesis

Cascade reactions are among the most powerful means to achieve the construction of multiple ring systems in a single step. This tutorial review describes recent advances in the use of polycyclization cascades in natural product synthesis.

Access to molecular complexity. Multicomponent reactions involving five or more components

The evaluation of the significance of a chemical transformation addresses many factors, including such important characteristics as the number of chemical bonds formed in one step, the reaction time, labour intensity, the cost of reactants and catalysts and so on. The amount of waste produced in the reaction has also gained increasing importance in recent years. Multicomponent reactions (MCRs) occupy a special place as a synthetic tool in modern organic chemistry. These reactions allow the synthesis of target products with complex structures, minimizing labour costs. This review summarizes the literature on multicomponent reactions involving five or more components. The data in the review are classified according to the number of reactants participating in the reaction and the types of reactions. It is worth noting that in some cases, these transformations can be a part of a domino process, making this classification difficult, if not impossible. The structural diversity of the reaction products greatly increases with increasing number of components involved in the MCR, which becomes virtually unlimited when using combinations of MCRs. This review highlights the main trends of past decades in the field of MCRs. The last two decades have witnessed an explosive growth in the number of publications in this area of chemistry.

The bibliography includes 309 references.

Bridging the gap between natural product synthesis and drug discovery

Covering: 1986 to 2020Natural products are an enduring source of chemical information useful for probing biologically relevant chemical space. Toward gathering further structure-activity relationship (SAR) information for a particular natural product, synthetic chemists traditionally proceeded first by a total synthesis effort followed by the synthesis of simplified derivatives. While this approach has proven fruitful, it often does not incorporate hypotheses regarding structural features necessary for bioactivity at the synthetic planning stage, but rather focuses on the rapid assembly of the targeted natural product; a goal that often supersedes the opportunity to gather SAR information en route to the natural product. Furthermore, access to simplified variants of a natural product possessing only the proposed essential structural features necessary for bioactivity, typically at lower oxidation states overall, is sometimes non-trivial from the original established synthetic route. In recent years, several synthetic design strategies were described to streamline the process of finding bioactive molecules in concert with fathering further SAR studies for targeted natural products. This review article will briefly discuss traditional retrosynthetic strategies and contrast them to selected examples of recent synthetic strategies for the investigation of biologically relevant chemical space revealed by natural products. These strategies include: diversity-oriented synthesis (DOS), biology-oriented synthesis (BIOS), diverted-total synthesis (DTS), analogue-oriented synthesis (AOS), two-phase synthesis, function-oriented synthesis (FOS), and computed affinity/dynamically ordered retrosynthesis (CANDOR). Finally, a description of pharmacophore-directed retrosynthesis (PDR) developed in our laboratory and initial applications will be presented that was initially inspired by a retrospective analysis of our synthetic route to pateamine A completed in 1998.