Bioactivity-guided navigation of chemical space

Functionality and Health-Promoting Properties of Polysaccharide and Plant-Derived Substances from Mesona chinensis

Mesona chinensis, in Thai called Chao Kuay and in Chinese Hsian-tsao, belongs to the Lamiaceae family. This herbal plant grows widely in Southern China, Taiwan (China), Malaysia, the Philippines, Indonesia, Vietnam, and Thailand. The Mesona plant is used to make functional products such as drinks and soft textured sweet treats, and also traditional medicine, to treat heat stroke, high blood pressure, heart attack, high blood sugar, hepatic diseases, colon diseases, inflammatory conditions, and to alleviate myalgia. The proximate composition of M. chinensis is a mixture of protein, fat, fiber, ash, and minerals. The main biological compounds in M. chinensis extracts are polysaccharides, terpenoids, flavonoids, and polyphenols, with wide-ranging pharmacological properties including antioxidant, antidiabetic, antilipidemic, carcinoma-inhibitory, renal-protective, antihypertensive, DNA damage-protective, and anti-inflammatory effects. This review investigated the proximate composition, polysaccharide type, and pharmacological properties of M. chinensis extracts. Phytochemical properties enhance the actions of the gut microbiota and improve health benefits. This review assessed the functional and medicinal activities of M. chinensis extracts. Future studies should further elucidate the in vitro/in vivo mechanisms of this plant extract and its impact on gut health.

6-Endo-dig versus 5-exo-dig: Exploring Radical Cyclization Preference with First-, Second-, and Third-row Linkers using High-level Quantum Chemical Methods

As an expansion upon Baldwin rules, the cyclization reactions of hex-5-yn-1-yl radical systems with different first-, second-, and third-row linkers are explored at the CCSD(T) level via means of the SMD(benzene)-G4(MP2) thermochemical protocol. Unlike C, O, and N linkers, systems with B, Si, P, S, Ge, As, and Se linkers are shown to favor 6-endo-dig cyclization. This offers fundamental insights into the rational synthetic design of cyclic compounds. A thorough analysis of stereoelectronic effects, cyclization barriers, and intrinsic barriers illustrates that structural changes alter the cyclization preference by mainly impacting 5-exo-dig reaction barriers. Based on the high-level computational modeling, we proceed to develop a new tool for cyclization preference prediction from the correlation between cyclization barriers and radical structural parameters (e. g., linker bond length and bond angle). A strong correlation is found between the radical attack trajectory angle and the reaction barrier heights, i. e., cyclization preference. Finally, the influence of stereoelectronic effects on the two radical cyclization pathways is further investigated in stereoisomers of hypervalent silicon system, which provides novel insight into cyclization control.

Modeling the expansion of virtual screening libraries

Recently, 'tangible' virtual libraries have made billions of molecules readily available. Prioritizing these molecules for synthesis and testing demands computational approaches, such as docking. Their success may depend on library diversity, their similarity to bio-like molecules and how receptor fit and artifacts change with library size. We compared a library of 3 million 'in-stock' molecules with billion-plus tangible libraries. The bias toward bio-like molecules in the tangible library decreases 19,000-fold versus those 'in-stock'. Similarly, thousands of high-ranking molecules, including experimental actives, from five ultra-large-library docking campaigns are also dissimilar to bio-like molecules. Meanwhile, better-fitting molecules are found as the library grows, with the score improving log-linearly with library size. Finally, as library size increases, so too do rare molecules that rank artifactually well. Although the nature of these artifacts changes from target to target, the expectation of their occurrence does not, and simple strategies can minimize their impact.

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.

Switchable synthesis of natural-product-like lawsones and indenopyrazoles through regioselective ring-expansion of indantrione

Lawsones and indenopyrazoles are the prevalent structural motifs and building blocks in pharmaceuticals and bioactive molecules, but their synthesis has always remained challenging as no comprehensive protocol has been outlined to date. Herein, a metal-free, ring-expansion reaction of indantrione with diazomethanes, generated in situ from the N-tosylhydrazones, has been developed for the synthesis of lawsone and indenopyrazole derivatives in acetonitrile and alcohol solvents, respectively. It provides these valuable lawsone and pyrazole skeletons in good yields and high levels of diastereoselectivity from simple and readily available starting materials. DFT calculations were used to explore the mechanism in different solutions. The synthetic application example also showed the prospects of this method for the preparation of valuable compounds.

Access to Cyclic N-Trifluoromethyl Ureas through Photocatalytic Activation of Carbamoyl Azides

We report the mild activation of carbamoyl azides to the corresponding nitrenes using a blue light/[Ir]-catalyzed strategy, which enables stereospecific access to N-trifluoromethyl imidazolidinones and benzimidazolones. These novel structural motifs proved to be highly robust, allowing their downstream diversification. On the basis of our combined computational and experimental studies, we propose that an electron rebound with the excited metal catalyst is undergone, involving a reduction-triggered nitrogen loss, followed by oxidation to the corresponding carbamoyl nitrene and subsequent C-H insertion.

Ring opening and skeletal reconstruction of 3-vinyl benzofuranone-chromone synthons: catalyst-free access to skeletally-diverse 2-pyridone and optically active imidazoline derivatives

Herein is reported the first example of ring opening and skeletal reconstruction of 3-vinyl benzofuranone-chromones 1 as versatile synthons, which can react with ammonia or primary aliphatic amines as binucleophiles, for the eco-friendly and atom-economical synthesis of diverse and functionalized 2-pyridones 3 with potential biological activity in good to excellent yields (77-93%). When using optically active 1,2-diphenylethylenediamine 2 as the binucleophile, the in situ generated 2-pyridone intermediates are successfully transformed to novel optically active functionalized imidazoline derivatives 4 with high efficiency (up to 87% yield). In particular, this is the first report on the catalyst-free intramolecular cyclization occurring between an amide and a primary aliphatic amine for the construction of imidazoline molecules.

Chemical Evolution of Natural Product Structure

Natural products are the result of Nature’s exploration of biologically relevant chemical space through evolution and an invaluable source of bioactive small molecules for chemical biology and medicinal chemistry. Novel concepts for the discovery of new bioactive compound classes based on natural product structure may enable exploration of wider biologically relevant chemical space. The pseudo-natural product concept merges the relevance of natural product structure with efficient exploration of chemical space by means of fragment-based compound development to inspire the discovery of new bioactive chemical matter through de novo combination of natural product fragments in unprecedented arrangements. The novel scaffolds retain the biological relevance of natural products but are not obtainable through known biosynthetic pathways which can lead to new chemotypes that may have unexpected or unprecedented bioactivities. Herein, we cover the workflow of pseudo-natural product design and development, highlight recent examples, and discuss a cheminformatic analysis in which a significant portion of biologically active synthetic compounds were found to be pseudo-natural products. We compare the concept to natural evolution and discuss pseudo-natural products as the human-made equivalent, i.e. the chemical evolution of natural product structure.

Natural product drug discovery in the artificial intelligence era

Natural products (NPs) are primarily recognized as privileged structures to interact with protein drug targets. Their unique characteristics and structural diversity continue to marvel scientists for developing NP-inspired medicines, even though the pharmaceutical industry has largely given up. High-performance computer hardware, extensive storage, accessible software and affordable online education have democratized the use of artificial intelligence (AI) in many sectors and research areas. The last decades have introduced natural language processing and machine learning algorithms, two subfields of AI, to tackle NP drug discovery challenges and open up opportunities. In this article, we review and discuss the rational applications of AI approaches developed to assist in discovering bioactive NPs and capturing the molecular "patterns" of these privileged structures for combinatorial design or target selectivity.

Combination of high-throughput microfluidics and FACS technologies to leverage the numbers game in natural product discovery

High-throughput platforms facilitating screening campaigns of environmental samples are needed to discover new products of natural origin counteracting the spreading of antimicrobial resistances constantly threatening human and agricultural health. We applied a combination of droplet microfluidics and fluorescence-activated cell sorting (FACS)-based technologies to access and assess a microbial environmental sample. The cultivation performance of our microfluidics workflow was evaluated in respect to the utilized cultivation media by Illumina amplicon sequencing of a pool of millions of droplets, respectively. This enabled the rational selection of a growth medium supporting the isolation of microbial diversity from soil (five phyla affiliated to 57 genera) including a member of the acidobacterial subgroup 1 (genus Edaphobacter). In a second phase, the entire diversity covered by 1071 cultures was used for an arrayed bioprospecting campaign, resulting in > 6000 extracts tested against human pathogens and agricultural pests. After redundancy curation by using a combinatorial chemical and genomic fingerprinting approach, we assigned the causative agents present in the extracts. Utilizing UHPLC-QTOF-MS/MS-guided fractionation and microplate-based screening assays in combination with molecular networking the production of bioactive ionophorous macrotetrolides, phospholipids, the cyclic lipopetides massetolides E, F, H and serratamolide A and many derivatives thereof was shown.

A general synthesis of azetidines by copper-catalysed photoinduced anti-Baldwin radical cyclization of ynamides

A general anti-Baldwin radical 4-exo-dig cyclization from nitrogen-substituted alkynes is reported. Upon reaction with a heteroleptic copper complex in the presence of an amine and under visible light irradiation, a range of ynamides were shown to smoothly cyclize to the corresponding azetidines, useful building blocks in natural product synthesis and medicinal chemistry, with full control of the regioselectivity of the cyclization resulting from a unique and underrated radical 4-exo-dig pathway.

The construction of four-membered rings via a 4-exo-dig cyclization was originally theorized to be unfavourable and only recently shown in sparse examples. Here the authors present a photochemical, radical 4-exo-dig cyclization of ynamides to form azetidines, promoted by copper photoredox catalysis.

3-Vinyl oxindole-chromone synthon as a skeletal reconstruction reactant for the synthesis of 2-hydroxy benzoyl pyridones

The first example of 3-vinyl oxindole-chromones in the ring opening and recyclization reaction.

The Role of Natural Products as Sources of Therapeutic Agents for Innovative Drug Discovery

Emerging threats to human health require a concerted effort in search of both preventive and treatment strategies, placing natural products at the center of efforts to obtain new therapies and reduce disease spread and associated mortality. The therapeutic value of compounds found in plants has been known for ages, resulting in their utilization in homes and in clinics for the treatment of many ailments ranging from common headache to serious conditions such as wounds. Despite the advancement observed in the world, plant based medicines are still being used to treat many pathological conditions or are used as alternatives to modern medicines. In most cases, these natural products or plant-based medicines are used in an un-purified state as extracts. A lot of research is underway to identify and purify the active compounds responsible for the healing process. Some of the current drugs used in clinics have their origins as natural products or came from plant extracts. In addition, several synthetic analogues are natural product-based or plant-based. With the emergence of novel infectious agents such as the SARS-CoV-2 in addition to already burdensome diseases such as diabetes, cancer, tuberculosis and HIV/AIDS, there is need to come up with new drugs that can cure these conditions. Natural products offer an opportunity to discover new compounds that can be converted into drugs given their chemical structure diversity. Advances in analytical processes make drug discovery a multi-dimensional process involving computational designing and testing and eventual laboratory screening of potential drug candidates. Lead compounds will then be evaluated for safety, pharmacokinetics and efficacy. New technologies including Artificial Intelligence, better organ and tissue models such as organoids allow virtual screening, automation and high-throughput screening to be part of drug discovery. The use of bioinformatics and computation means that drug discovery can be a fast and efficient process and enable the use of natural products structures to obtain novel drugs. The removal of potential bottlenecks resulting in minimal false positive leads in drug development has enabled an efficient system of drug discovery. This review describes the biosynthesis and screening of natural products during drug discovery as well as methods used in studying natural products.

New Diterpenoids from Mesona procumbens with Antiproliferative Activities Modulate Cell Cycle Arrest and Apoptosis in Human Leukemia Cancer Cells

Mesona procumbens is a popular material used in foods and herbal medicines in Asia for clearing heat and resolving toxins. However, phytochemical research on this plant is very rare. In this study, eleven new diterpenoids, mesonols A-K (1–11), comprising seven ent-kauranes, three ent-atisanes, and one sarcopetalane, were isolated from its methanolic extract. Structural elucidation of compounds 1–11 was performed by spectroscopic methods, especially 2D NMR, HRESIMS, and X-ray crystallographic analysis. All isolates were assessed for their antiproliferative activity, and compounds 1–4 showed potential antiproliferative activities against A549, Hep-3B, PC-3, HT29, and U937 cancer cells, with IC₅₀ values ranging from 1.97 to 19.86 µM. The most active compounds, 1 and 2, were selected for further investigation of their effects on cell cycle progression, apoptosis, and ROS generation in U937 human leukemia cancer cells. Interestingly, it was found that compounds 1 and 2 induced antiproliferative effects in U937 cells through different mechanisms. Compound 1 caused cell cycle arrest at the G2/M phase and subsequent cell death in a dose- and time-dependent manner. However, 2-mediated antiproliferation of U937 cells triggered ROS-mediated mitochondrial-dependent apoptosis. These results provide insight into the molecular mechanism involved in the antiproliferative activities of compounds 1 and 2 in U937 cells. Altogether, the study showed that new diterpenoid compounds 1 and 2 from M. procumbens are potent and promising anticancer agents.

Natural spirocyclic alkaloids and polyphenols as multi target dementia leads

The U rhynchophylla, U tomentosa, Isatis indigotica Fortune, Voacanga Africana, herbal constituents, fungal extracts from Aspergillus duricaulis culture media, include spirooxindoles, polyphenols or bridged spirocyclic alkaloids. Their constituents exhibit specific and synergistic multiple neuroprotective properties including inhibiting of Aβ fibril induced cytotoxicity, NMDA receptor inhibition in mice models of Alzheimer's disease (AD). The pioneering research from Woodward to Waldmann has advanced the synthesis of spirocyclic alkaloids. Furthermore, the elucidation of the genetic analysis, biochemical pathways that links strictosidine to the alkaloids akuammicine, stemmadenine, tabersonine, catharanthine, will now enable the biotechnological generation, also stimulate synthesis of related bridged spirocyclic alkaloids for medicinal investigations. From the value of spirocyclic structures as multi target dementia leads, we hypothesise that simpler Lipinski-like natural/synthetic alkaloid analogues may likewise be discovered that provide neurocognitive enhancing activities against dementia and AD.

Beyond Pseudo-natural Products: Sequential Ugi/Pictet-Spengler Reactions Leading to Steroidal Pyrazinoisoquinolines That Trigger Caspase-Independent Death in HepG2 Cells

In this work, we describe how stereochemically complex polycyclic compounds can be generated by applying a synthetic sequence comprising an intramolecular Ugi reaction followed by a Pictet-Spengler cyclization on steroid-derived scaffolds. The resulting compounds, which combine a fragment derived from a natural product and a scaffold not found in nature. are both structurally distinct and globally similar to natural products at the same time, and interrogate an alternative region of the chemical space. One of the new compounds showed significant antiproliferative activity on HepG2 cells through a caspase-independent cell-death mechanism, an appealing feature when new antitumor compounds are searched.

Chromone–indanedione reactant: a bifunctional 3C synthon for diastereoselective construction of skeleton-diversified bispiro-[chromanocyclopentane-oxindole-indanedione]

A new type of bifunctional 3C synthon, a chromone–indanedione precursor, was employed for diastereoselective Michael/Michael cycloaddition with methyleneindolinones to generate a series of potentially bioactive bispiro-[chromanocyclopentane-oxindole-indanedione] frameworks with skeletal diversity in a single operation.

A sequential Ugi–Smiles/transition-metal-free endo-dig Conia–ene cyclization: the selective synthesis of saccharin substituted 2,5-dihydropyrroles

A convenient, transition-metal-free access to a series of unprecedented saccharin substituted 2,5-dihydropyrroles is reported.

Drug design targeting active posttranslational modification protein isoforms

Modern drug design aims to discover novel lead compounds with attractable chemical profiles to enable further exploration of the intersection of chemical space and biological space. Identification of small molecules with good ligand efficiency, high activity, and selectivity is crucial toward developing effective and safe drugs. However, the intersection is one of the most challenging tasks in the pharmaceutical industry, as chemical space is almost infinity and continuous, whereas the biological space is very limited and discrete. This bottleneck potentially limits the discovery of molecules with desirable properties for lead optimization. Herein, we present a new direction leveraging posttranslational modification (PTM) protein isoforms target space to inspire drug design termed as "Post-translational Modification Inspired Drug Design (PTMI-DD)." PTMI-DD aims to extend the intersections of chemical space and biological space. We further rationalized and highlighted the importance of PTM protein isoforms and their roles in various diseases and biological functions. We then laid out a few directions to elaborate the PTMI-DD in drug design including discovering covalent binding inhibitors mimicking PTMs, targeting PTM protein isoforms with distinctive binding sites from that of wild-type counterpart, targeting protein-protein interactions involving PTMs, and hijacking protein degeneration by ubiquitination for PTM protein isoforms. These directions will lead to a significant expansion of the biological space and/or increase the tractability of compounds, primarily due to precisely targeting PTM protein isoforms or complexes which are highly relevant to biological functions. Importantly, this new avenue will further enrich the personalized treatment opportunity through precision medicine targeting PTM isoforms.

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.

Construction of a meroterpenoid-like compound collection by precursor-assisted biosynthesis

Natural products (NPs) and their derivatives play a pivotal role in drug discovery due to their complexity and diversity. The strategies to rapidly generate NP-like compounds offer unique opportunities to access bioactive compounds. Here we present a new approach, precursor-assisted biosynthesis (PAB), for the creation of NP-like compounds by combination of artificial supplementation of common precursors and divergent post-modifications of precursor-deficient fungi. This method was applied to construct a meroterpenoid-like compound collection containing 43 compounds with diverse molecular scaffolds. Extensive bioactive screening of the collection revealed novel STING (stimulator of interferon genes) inhibitors, cytotoxic and antifungal compounds. This result indicates that PAB is an effective methodology for producing compound collections for the purpose of drug discovery.

Isolation and synthesis of cryptosanguinolentine (isocryptolepine), a naturally-occurring bioactive indoloquinoline alkaloid

Cryptosanguinolentine (isocryptolepine) is one of the minor naturally-occurring monomeric indoloquinoline alkaloids, isolated from the West African climbing shrub Cryptolepis sanguinolenta. The natural product displays such a simple and unique skeleton, which chemists became interested in well before it was found in Nature. Because of its structure and biological activity, the natural product has been targeted for synthesis on numerous occasions, employing a wide range of different strategies. Hence, discussed here are aspects related to the isolation of isocryptolepine, as well as the various approaches toward its total synthesis.

Diversity-oriented synthesis of 17-spirosteroids

A diversity-oriented synthesis (DOS) approach has been used to functionalize 17-ethynyl-17-hydroxysteroids through a one-pot procedure involving a ring-closing enyne metathesis (RCEYM) and a Diels–Alder reaction on the resulting diene, under microwave irradiations. Taking advantage of the propargyl alcohol moiety present on commercially available steroids, this classical strategy was applied to mestranol and lynestrenol, giving a collection of new complex 17-spirosteroids.

Deep SAR matrix: SAR matrix expansion for advanced analog design using deep learning architectures

Aim: Enhancing the structure–activity relationship matrix (SARM) methodology through integration of deep learning and expansion of chemical space coverage. Background: Analog design is of critical importance for medicinal chemistry. The SARM approach, which combines systematic structural organization of compound series with analog design, is put into scientific context. Methodology: The new DeepSARM concept is introduced. The architecture of SARM-integrated deep generative models is detailed and the workflow for advanced analog design and matrix expansion described. Exemplary application: The DeepSARM approach is applied to design analogs of kinase inhibitors taking kinome-wide chemical space into account. Future perspective: Practical applications of DeepSARM will be a major focal point. Different applications are discussed. New computational features will be added to prioritize virtual candidate compounds.

Bioactive supra decorated thiazolidine-4-carboxylic acid derivatives attenuate cellular oxidative stress by enhancing catalase activity

Bioactive (2S,4R)-3-(tert-butoxycarbonyl)-2-(2-hydroxyphenyl)thiazolidine-4-carboxylic acid molecules restructure enzymes through complexation, allowing enhancing their activity to protect cells from oxidative stress.

Water-triggered union of multi-component reactions towards the synthesis of a 4H-chromene hybrid scaffold

An unprecedented union of multi-component reactions to construct pyrazole- and pyranopyrazole-adorned 4H-chromene from simple reactants in water at ambient temperature is reported. This innovative tactic has integrated two distinct four-component reactions (4CRs) that occur transiently to form four new heterocycles via ten covalent bonds in a single step.

A union of multi-component reactions to construct pyrazole- and pyranopyrazole-adorned 4H-chromene from simple reactants in water at RT is reported. 2 distinct four-component reactions occur transiently to form 4 new heterocycles via 10 covalent bonds in a single step.

A transition metal-free approach towards the regioselective synthesis of β-carboline tethered pyrroles and 2,3-dihydro-1H-pyrroles

A transition metal-free one-pot sequential approach has been unfolded for the synthesis of β-carboline tethered pyrroles and 2,3-dihydro-1H-pyrroles by using highly diverse 1-formyl-9H-β-carbolines as a template.

Efficient identification of novel anti-glioma lead compounds by machine learning models

Glioblastoma multiforme (GBM) is the most devastating and widespread primary central nervous system tumor. Pharmacological treatment of this malignance is limited by the selective permeability of the blood-brain barrier (BBB) and relies on a single drug, temozolomide (TMZ), thus making the discovery of new compounds challenging and urgent. Therefore, aiming to discover new anti-glioma drugs, we developed robust machine learning models for predicting anti-glioma activity and BBB penetration ability of new compounds. Using these models, we prioritized 41 compounds from our in-house library of compounds, for further in vitro testing against three glioma cell lines and astrocytes. Subsequently, the most potent and selective compounds were resynthesized and tested in vivo using an orthotopic glioma model. This approach revealed two lead candidates, 4m and 4n, which efficiently decreased malignant glioma development in mice, probably by inhibiting thioredoxin reductase activity, as shown by our enzymological assays. Moreover, these two compounds did not promote body weight reduction, death of animals, or altered hematological and toxicological markers, making then good candidates for lead optimization as anti-glioma drug candidates.

Making endo-cyclizations favorable again: a conceptually new synthetic approach to benzotriazoles via azide group directed lithiation/cyclization of 2-azidoaryl bromides

Although benzotriazoles are important and ubiquitous, currently there is only one conceptual approach to their synthesis: bridging the two ortho-amino groups with an electrophilic nitrogen atom. Herein, we disclose a new practical alternative - the endo-cyclization of 2-azidoaryl lithiums obtained in situ from 2-azido-aryl bromides. The scope of the reaction is illustrated using twenty-four examples with a variety of alkyl, alkoxy, perfluoroalkyl, and halogen substituents. We found that the directing effect of the azide group allows selective metal-halogen exchange in aryl azides containing several bromine atoms. Furthermore, (2-bromophenyl)diazomethane undergoes similar cyclization to give an indazole. Thus, cyclizations of aryl lithiums containing an ortho-X = Y = Z group emerge as a new general approach for the synthesis of aromatic heterocycles. DFT computations suggested that the observed endo-selectivity applies to the anionic cyclizations of other functionalities that undergo "1,1-additions" (i.e., azides, diazo compounds, and isonitriles). In contrast, cyclizations with the heteroatomic functionalities that follow the "1,2-addition" pattern (cyanates, thiocyanates, isocyanates, isothiocyanates, and nitriles) prefer the exo-cyclization path. Hence, such reactions expand the current understanding of stereoelectronic factors in anionic cyclizations.

Thermal-mediated [1,3]-hydrogen transfer as the key step: access to oxindole-chromone hybrid collection with structural diversity

Inspired by the chemistry and biology of chromone and oxindole derivatives, herein we report the first example of thermal-mediated [1,3]-hydrogen transfer as the key step for the efficient synthesis of oxindole-chromone hybrid collections 2, which avoids additional catalyst and solvent conditions. All the oxindole-chromones 2 are smoothly obtained in >99% yields in all cases, avoiding column chromatography purification. In particular, the products 2 can act as potential synthons for further elaboration in structural diversity, which might be valuable in organic and medicinal chemistry.

Structural simplification: an efficient strategy in lead optimization

The trend toward designing large hydrophobic molecules for lead optimization is often associated with poor drug-likeness and high attrition rates in drug discovery and development. Structural simplification is a powerful strategy for improving the efficiency and success rate of drug design by avoiding "molecular obesity". The structural simplification of large or complex lead compounds by truncating unnecessary groups can not only improve their synthetic accessibility but also improve their pharmacokinetic profiles, reduce side effects and so on. This review will summarize the application of structural simplification in lead optimization. Numerous case studies, particularly those involving successful examples leading to marketed drugs or drug-like candidates, will be introduced and analyzed to illustrate the design strategies and guidelines for structural simplification.

Method for Systematic Analogue Search Using the Mega SAR Matrix Database

Analogue searching is a typical requirement in hit expansion, hit-to-lead, and lead optimization projects. A new computational methodology is introduced to search for existing and virtual analogues of active compounds. The approach is based upon the SAR matrix (SARM) data structure that was originally developed for the systematic identification and structural organization of analogue series. The SARM-based analogue search algorithm further extends the capacity of current substructure-based methods by (i) simultaneously considering existing and virtual analogues that populate chemical space around query compounds, (ii) permitting not only R-group replacements but also well-defined chemical modifications in core structures to further expand the analogue space, and (iii) automatically extracting all possible analogues from large pools. In addition, as a basis for analogue searching following the SARM concept, the Mega-SARM database is introduced. Mega-SARM is derived from nearly 3.7 million compounds and contains ∼250 000 matrices with structurally related analogue series and more than 1.5 million virtual candidate compounds.

Cascade reaction based synthetic strategies targeting biologically intriguing indole polycycles

In this review, cascade reaction based synthesis strategies delivering biologically intriguing indole polycycles are presented.

Synthetic approach to skeletally diverse nitrogen heterocycles from dicyano-2-methylenebut-3-enoates

Divergent synthesis of three types of azaheterocycles, including vinylaziridines, pyrroline and 2-aminopyridines, has been achieved through [2 + 1], formal-[4 + 1] and [5 + 1] annulations.

Regio- and stereoselective [3 + 2] cycloaddition reaction: access to isoxazole-dispirobisoxindoles featuring three contiguous stereocenters

A novel methodology toward the diversity-oriented asymmetric construction of densely functionalized isoxazole-dispirobisoxindoles was developed.

Bifunctional oxindole-chromone 4C building block directed asymmetric synthesis of bispirocyclic hexahydroxanthones featuring five contiguous stereocenters and two side-by-side oxindoles

Optically active small molecules based on privileged natural product frameworks and rich in three-dimensional complexity are in high demand.

Thermal-mediated catalyst-free heterolytic cleavage of 3-halooxindoles: rapid access to 3-functionalized-2-oxindoles

Herein a previously unreported catalyst-free S_N1 reaction of the 3-halooxindoles to build 3-functionalized-2-oxindoles is described.

Three-Component Reactions to Spirocyclic Pyrrolidinonylformimidamides: α-Isocyano Lactams as Two-Atom Unit in Silver-Catalyzed Formal [3 + 2] Cycloaddition Reactions

A facile approach to spirocyclic pyrrolidinonylformimidamides has been developed via three-component reactions of isocyanides, alkenes, and amines. The reaction proceeds through a sequence of two distinct reaction pathways; the base-catalyzed conjugate addition of α-isocyano lactams to electron-deficient alkenes and the Ag(I)-catalyzed amine insertion to the isocyanide moiety. Both reactions display markedly different reaction kinetics, allowing the one-pot three-component reactions to be performed in the presence of respective catalysts, a Brønsted base and a silver salt. The formation of spirocyclic pyrrolidin-2-ones represents an unusual use of α-isocyano lactam as a two-atom unit in a formal [3 + 2] cycloaddition reaction. The successful identification of ways to defy the typical three-atom unit role of α-isocyano carbonyl compounds in the [3 + 2] cycloaddition pathways manifests a rapid assembly of medicinally important spirocyclic scaffolds from readily available starting materials.