Heteroaromatic rings of the future

Review and Theoretical Analysis of Fluorinated Radicals in Direct CAr-H Functionalization of (Hetero)arenes

We highlight key contributions in the field of direct radical CAr- H (hetero)aromatic functionalization involving fluorinated radicals. A compilation of Functional Group Transfer Reagents and their diverse activation mechanisms leading to the release of radicals are discussed. The substrate scope for each radical is analyzed and classified into three categories according to the electronic properties of the substrates. Density functional theory computational analysis provides insights into the chemical reactivity of several fluorinated radicals through their electrophilicity and nucleophilicity parameters. Theoretical analysis of their reduction potentials also highlights the remarkable correlation between electrophilicity and oxidizing ability. It is also established that highly fluorinated radicals (e.g. ⋅OCF3) are capable of engaging in single-electron transfer (SET) processes rather than radical addition, which is in good agreement with experimental literature data. A reactivity scale, based on activation barrier of addition of these radicals to benzene is also elaborated using the high accuracy DLPNO-(U)CCSD(T) method.

Greener Approach for Synthesis of δ-MnO2 Nanoparticles: Access to Pharmaceutically Important Pyrimidines and their Antimicrobial Activity Studies

A sustainable approach for pharmaceutically important pyrimidine derivatives is achieved by using biogenically produced single-phase δ-MnO2 NPs under external ligand-free conditions. The phytochemicals that comprise the extract of Areca Nut Husk (ANH) have been discovered to serve as reducing agents. The role of phytochemicals is not only to aid in the reduction of Mn(VII) into Mn(IV), but they also have an important role in stabilizing the catalyst. The establishment of δ-MnO2 NPs was confirmed inveterate by FE-SEM, p-XRD, ICP-OES (Mn content = 43.17% w/w), EDX, and with an active Mn content of 43.17% w/w. A series of pyrimidine derivatives were prepared in good yields using a one-pot multicomponent synthesis approach under atmospheric conditions. In addition, hot filtration tests, control experiments, gram-scale synthesis, and mechanistic investigations were demonstrated. Additionally, antimicrobial activity studies of δ-MnO2 NPs and pyrimidine derivatives against the Gram-negative bacteria E. coli, growth curve and minimum inhibitory concentration were studied.

Database of 4 Million Medicinal Chemistry-Relevant Ring Systems

Central ring systems are the most important part of bioactive molecules. They determine molecule shape, keep substituents in their proper positions, and also influence global molecular properties. In the present study, a database of 4 million medicinal chemistry-relevant ring systems has been created, not by crude random enumeration but by applying a set of rules derived by analyzing rings present in bioactive molecules. The aromatic properties and tautomer stability of generated rings have also been considered to ensure that the rings in the database are stable and chemically reasonable. 99.2% of these rings are novel and not included in molecules in the ChEMBL or PubChem databases. This large database of ring systems has been created with the goal to provide support for bioisosteric design and scaffold hopping as well as to be used in generative chemistry applications. The complete set of created rings is available for download in the SMILES format from https://peter-ertl.com/molecular/data/.

Recent advances in Pd-catalyzed asymmetric cyclization reactions

Over the past few decades, there have been major developments in transition metal-catalyzed asymmetric cyclization reactions, enabling the convenient access to a wide spectrum of structurally diverse chiral carbo- and hetero-cycles, common skeletons found in fine chemicals, natural products, pharmaceuticals, agrochemicals, and materials. In particular, a plethora of enantioselective cyclization reactions have been promoted by chiral palladium catalysts owing to their outstanding features. This review aims to collect the latest advancements in enantioselective palladium-catalyzed cyclization reactions over the past eleven years, and it is organized into thirteen sections depending on the different types of transformations involved.

Direct Amino-α-C-H Heteroarylation of Amides under Electrochemical Conditions

An electrochemical hydrogen atom transfer (HAT) strategy for the direct amino-α-C-H heteroarylation of amides is described. The cheap TMSN3 acts as a hydrogen atom transfer reagent. A series of heteroarenes including quinoxalin-2(1H)-ones, 4-methylquinoline, isoquinoline, 2-methylquinoxaline, benzothiazole, etc., and various readily available amides/lactams were suitable. The reaction has the characteristics of a wide range of substrates, good regioselectivity, chemical oxidant-free conditions, etc.

Synthesis and vectorial functionalisation of pyrazolo[3,4-c]pyridines

Heterocycles are a cornerstone of fragment-based drug discovery (FBDD) due to their prevalence in biologically active compounds. However, novel heterocyclic fragments are only valuable if they can be suitably elaborated to compliment a chosen target protein. Here we describe the synthesis of 5-halo-1H-pyrazolo[3,4-c]pyridine scaffolds and demonstrate how these compounds can be selectively elaborated along multiple growth-vectors. Specifically, N-1 and N-2 are accessed through protection-group and N-alkylation reactions; C-3 through tandem borylation and Suzuki-Miyaura cross-coupling reactions; C-5 through Pd-catalysed Buchwald-Hartwig amination; and C-7 through selective metalation with TMPMgCl.LiCl followed by reaction with electrophiles or transmetalation to ZnCl2 and Negishi cross-coupling. Linking multiple functionalisation strategies emulates a hit-to-lead pathway and demonstrates the utility of pyrazolo[3,4-c]pyridines to FBDD.

Orthogonal Dual Photocatalysis of Single Atoms on Carbon Nitrides for One-Pot Relay Organic Transformation

Single-atom photocatalysis has shown potential in various single-step organic transformations, but its use in multistep organic transformations in one reaction systems has rarely been achieved. Herein, we demonstrate atomic site orthogonality in the M1/C3N4 system (where M = Pd or Ni), enabling a cascade photoredox reaction involving oxidative and reductive reactions in a single system. The system utilizes visible-light-generated holes and electrons from C3N4, driving redox reactions (e.g., oxidation and fluorination) at the surface of C3N4 and facilitating cross-coupling reactions (e.g., C-C and C-O bond formation) at the metal site. The concept is generalized to different systems of Pd and Ni, thus making the catalytic site-orthogonal M1/C3N4 system an ideal photocatalyst for improving the efficiency and selectivity of multistep organic transformations.

Calculation-assisted regioselective functionalization of the imidazo[1,2-a]pyrazine scaffold via zinc and magnesium organometallic intermediates

Straightforward calculations such as determinations of pKa values and N-basicities have allowed the development of a set of organometallic reactions for the regioselective functionalization of the underexplored fused N-heterocycle imidazo[1,2-a]pyrazine. Thus, regioselective metalations of 6-chloroimidazo[1,2-a]pyrazine using TMP-bases (TMP = 2,2,6,6-tetramethylpiperidyl) such as TMPMgCl·LiCl and TMP2Zn·2MgCl2·2LiCl provided Zn- and Mg-intermediates, that after quenching with various electrophiles gave access to polyfunctionalized imidazopyrazine heterocycles. Additionally, the use of TMP2Zn·2MgCl2·2LiCl as base for the first metalation allowed an alternative regioselective metalation. Nucleophilic additions at position 8 as well as selective Negishi cross-couplings complete the set of methods for selectively decorating this heterocycle of the future.

DASH: Dynamic Attention-Based Substructure Hierarchy for Partial Charge Assignment

We present a robust and computationally efficient approach for assigning partial charges of atoms in molecules. The method is based on a hierarchical tree constructed from attention values extracted from a graph neural network (GNN), which was trained to predict atomic partial charges from accurate quantum-mechanical (QM) calculations. The resulting dynamic attention-based substructure hierarchy (DASH) approach provides fast assignment of partial charges with the same accuracy as the GNN itself, is software-independent, and can easily be integrated in existing parametrization pipelines, as shown for the Open force field (OpenFF). The implementation of the DASH workflow, the final DASH tree, and the training set are available as open source/open data from public repositories.

Molecular Editing of Pyrroles via a Skeletal Recasting Strategy

Heterocyclic scaffolds are commonly found in numerous biologically active molecules, therapeutic agents, and agrochemicals. To probe chemical space around heterocycles, many powerful molecular editing strategies have been devised. Versatile C-H functionalization strategies allow for peripheral modifications of heterocyclic motifs, often being specific and taking place at multiple sites. The past few years have seen the quick emergence of exciting "single-atom skeletal editing" strategies, through one-atom deletion or addition, enabling ring contraction/expansion and structural diversification, as well as scaffold hopping. The construction of heterocycles via deconstruction of simple heterocycles is unknown. Herein, we disclose a new molecular editing method which we name the skeletal recasting strategy. Specifically, by tapping on the 1,3-dipolar property of azoalkenes, we recast simple pyrroles to fully substituted pyrroles, through a simple phosphoric acid-promoted one-pot reaction consisting of dearomative deconstruction and rearomative reconstruction steps. The reaction allows for easy access to synthetically challenging tetra-substituted pyrroles which are otherwise difficult to synthesize. Furthermore, we construct N-N axial chirality on our pyrrole products, as well as accomplish a facile synthesis of the anticancer drug, Sutent. The potential application of this method to other heterocycles has also been demonstrated.

Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field

We introduce the Open Force Field (OpenFF) 2.0.0 small molecule force field for drug-like molecules, code-named Sage, which builds upon our previous iteration, Parsley. OpenFF force fields are based on direct chemical perception, which generalizes easily to highly diverse sets of chemistries based on substructure queries. Like the previous OpenFF iterations, the Sage generation of OpenFF force fields was validated in protein-ligand simulations to be compatible with AMBER biopolymer force fields. In this work, we detail the methodology used to develop this force field, as well as the innovations and improvements introduced since the release of Parsley 1.0.0. One particularly significant feature of Sage is a set of improved Lennard-Jones (LJ) parameters retrained against condensed phase mixture data, the first refit of LJ parameters in the OpenFF small molecule force field line. Sage also includes valence parameters refit to a larger database of quantum chemical calculations than previous versions, as well as improvements in how this fitting is performed. Force field benchmarks show improvements in general metrics of performance against quantum chemistry reference data such as root-mean-square deviations (RMSD) of optimized conformer geometries, torsion fingerprint deviations (TFD), and improved relative conformer energetics (ΔΔE). We present a variety of benchmarks for these metrics against our previous force fields as well as in some cases other small molecule force fields. Sage also demonstrates improved performance in estimating physical properties, including comparison against experimental data from various thermodynamic databases for small molecule properties such as ΔHmix, ρ(x), ΔGsolv, and ΔGtrans. Additionally, we benchmarked against protein-ligand binding free energies (ΔGbind), where Sage yields results statistically similar to previous force fields. All the data is made publicly available along with complete details on how to reproduce the training results at https://github.com/openforcefield/openff-sage.

Conjugation as a Tool in Therapeutics: Role of Amino Acids/Peptides-Bioactive (Including Heterocycles) Hybrid Molecules in Treating Infectious Diseases

Peptide-based drugs are gaining significant momentum in the modern drug discovery, which is witnessed by the approval of new drugs by the FDA in recent years. On the other hand, small molecules-based drugs are an integral part of drug development since the past several decades. Peptide-containing drugs are placed between small molecules and the biologics. Both the peptides as well as the small molecules (mainly heterocycles) pose several drawbacks as therapeutics despite their success in curing many diseases. This gap may be bridged by utilising the so called 'conjugation chemistry', in which both the partners are linked to one another through a stable chemical bond, and the resulting conjugates are found to possess attracting benefits, thus eliminating the stigma associated with the individual partners. Over the past decades, the field of molecular hybridisation has emerged to afford us new and efficient molecular architectures that have shown high promise in medicinal chemistry. Taking advantage of this and also considering our experience in this field, we present herein a review concerning the molecules obtained by the conjugation of peptides (amino acids) to small molecules (heterocycles as well as bioactive compounds). More than 125 examples of the conjugates citing nearly 100 references published during the period 2000 to 2022 having therapeutic applications in curing infectious diseases have been covered.

CIPDB: A biological structure databank for studying cation and π interactions

As major forces for modulating protein folding and molecular recognition, cation and π interactions are extensively identified in protein structures. They are even more competitive than hydrogen bonds in molecular recognition, thus, are vital in numerous biological processes. In this review, we introduce the methods for the identification and quantification of cation and π interactions, provide insights into the characteristics of cation and π interactions in the natural state, and reveal their biological function together with our developed database (Cation and π Interaction in Protein Data Bank; CIPDB; http://chemyang.ccnu.edu.cn/ccb/database/CIPDB). This review lays the foundation for the in-depth study of cation and π interactions and will guide the use of molecular design for drug discovery.

Structure of a HIV-1 IN-Allosteric inhibitor complex at 2.93 Å resolution: Routes to inhibitor optimization

HIV integrase (IN) inserts viral DNA into the host genome and is the target of the strand transfer inhibitors (STIs), a class of small molecules currently in clinical use. Another potent class of antivirals is the allosteric inhibitors of integrase, or ALLINIs. ALLINIs promote IN aggregation by stabilizing an interaction between the catalytic core domain (CCD) and carboxy-terminal domain (CTD) that undermines viral particle formation in late replication. Ongoing challenges with inhibitor potency, toxicity, and viral resistance motivate research to understand their mechanism. Here, we report a 2.93 Å X-ray crystal structure of the minimal ternary complex between CCD, CTD, and the ALLINI BI-224436. This structure reveals an asymmetric ternary complex with a prominent network of π-mediated interactions that suggest specific avenues for future ALLINI development and optimization.

A Copper-Catalyzed Interrupted Domino Reaction for the Synthesis of Fused Triazolyl Benzothiadiazine-1-oxides

Copper(I)-catalyzed domino reactions of 2-azido sulfoximines with 1-iodoalkynes yield fused triazolyl-containing benzothiadiazine-1-oxides. The protocol features the synthesis of two fused heterocyclic rings in one step with good to excellent yields and a broad functional group tolerance. Detailed mechanistic investigations indicate that a copper π-complex initiates a cycloaddition and oxidative C-N coupling reaction sequence. The results suggest an interrupted domino process involving an iodinated triazole as a key intermediate.

Copper-Catalyzed Trifluoromethylation of (Hetero)aryl Boronic Acid Pinacol Esters with YlideFluor

A copper-catalyzed trifluoromethylation of (hetero)arylboronic acid pinacol esters with YlideFluor for the preparation of trifluoromethylated (hetero)arenes was described. The reaction conditions are mild and compatible with a broad range of functional groups. Heteroaryl boronic acid pinacol esters could also be trifluoromethylated in high yields. Application of this protocol for trifluoromethylation of drug and OLED molecules was demonstrated.

End-to-end differentiable construction of molecular mechanics force fields

Molecular mechanics (MM) potentials have long been a workhorse of computational chemistry. Leveraging accuracy and speed, these functional forms find use in a wide variety of applications in biomolecular modeling and drug discovery, from rapid virtual screening to detailed free energy calculations. Traditionally, MM potentials have relied on human-curated, inflexible, and poorly extensible discrete chemical perception rules (atom types) for applying parameters to small molecules or biopolymers, making it difficult to optimize both types and parameters to fit quantum chemical or physical property data. Here, we propose an alternative approach that uses graph neural networks to perceive chemical environments, producing continuous atom embeddings from which valence and nonbonded parameters can be predicted using invariance-preserving layers. Since all stages are built from smooth neural functions, the entire process-spanning chemical perception to parameter assignment-is modular and end-to-end differentiable with respect to model parameters, allowing new force fields to be easily constructed, extended, and applied to arbitrary molecules. We show that this approach is not only sufficiently expressive to reproduce legacy atom types, but that it can learn to accurately reproduce and extend existing molecular mechanics force fields. Trained with arbitrary loss functions, it can construct entirely new force fields self-consistently applicable to both biopolymers and small molecules directly from quantum chemical calculations, with superior fidelity than traditional atom or parameter typing schemes. When adapted to simultaneously fit partial charge models, espaloma delivers high-quality partial atomic charges orders of magnitude faster than current best-practices with low inaccuracy. When trained on the same quantum chemical small molecule dataset used to parameterize the Open Force Field ("Parsley") openff-1.2.0 small molecule force field augmented with a peptide dataset, the resulting espaloma model shows superior accuracy vis-á-vis experiments in computing relative alchemical free energy calculations for a popular benchmark. This approach is implemented in the free and open source package espaloma, available at https://github.com/choderalab/espaloma.

Synthetic Pathways to Pyrido[3,4-c]pyridazines and Their Polycyclic Derivatives

Pyrido[3,4-c]pyridazines are nitrogen-containing scaffolds that have been described as being promising in medicinal chemistry, but they are rather rare chemicals. In this review article, the literature on synthetic pathways towards pyrido[3,4-c]pyridazines is listed exhaustively, first with the bicyclic systems themselves that are obtained starting either from pyridines, pyridazines or other heterocycles. Then, the reports on the related tricyclic derivatives are discussed, again according to the source heterocycle, and finally we mention some examples on polycyclic systems.

On drug discovery against infectious diseases and academic medicinal chemistry contributions

This perspective is an attempt to document the problems that medicinal chemists are facing in drug discovery. It is also trying to identify relevant/possible, research areas in which academics can have an impact and should thus be the subject of grant calls. Accordingly, it describes how hit discovery happens, how compounds to be screened are selected from available chemicals and the possible reasons for the recurrent paucity of useful/exploitable results reported. This is followed by the successful hit to lead stories leading to recent and original antibacterials which are, or about to be, used in human medicine. Then, illustrated considerations and suggestions are made on the possible inputs of academic medicinal chemists. This starts with the observation that discovering a “good” hit in the course of a screening campaign still rely on a lot of luck – which is within the reach of academics –, that the hit to lead process requires a lot of chemistry and that if public–private partnerships can be important throughout these stages, they are absolute requirements for clinical trials. Concerning suggestions to improve the current hit success rate, one academic input in organic chemistry would be to identify new and pertinent chemical space, design synthetic accesses to reach these and prepare the corresponding chemical libraries. Concerning hit to lead programs on a given target, if no new hits are available, previously reported leads along with new structural data can be pertinent starting points to design, prepare and assay original analogues. In conclusion, this text is an actual plea illustrating that, in many countries, academic research in medicinal chemistry should be more funded, especially in the therapeutic area neglected by the industry. At the least, such funds would provide the intensive to secure series of hopefully relevant chemical entities which appears to often lack when considering the results of academic as well as industrial screening campaigns.

Exploring the anti-SARS-CoV-2 main protease potential of FDA approved marine drugs using integrated machine learning templates as predictive tools

Since the inception of COVID-19 pandemic in December 2019, socio-economic crisis begins to rise globally and SARS-CoV-2 was responsible for this outbreak. With this outbreak, currently, world is in need of effective and safe eradication of COVID-19. Hence, in this study anti-SAR-Co-2 potential of FDA approved marine drugs (Biological macromolecules) data set is explored computationally using machine learning algorithm of Flare by Cresset Group, Field template, 3D-QSAR and activity Atlas model was generated against FDA approved M-pro SARS-CoV-2 repurposed drugs including Nafamostat, Hydroxyprogesterone caporate, and Camostat mesylate. Data sets were categorized into active and inactive molecules on the basis of their structural and biological resemblance with repurposed COVID-19 drugs. Then these active compounds were docked against the five different M-pro proteins co-crystal structures. Highest LF VS score of Holichondrin B against all main protease co-crystal structures ranked it as lead drug. Finally, this new technique of drug repurposing remained efficient to explore the anti-SARS-CoV-2 potential of FDA approved marine drugs.

Rings in Clinical Trials and Drugs: Present and Future

We present a comprehensive analysis of all ring systems (both heterocyclic and nonheterocyclic) in clinical trial compounds and FDA-approved drugs. We show 67% of small molecules in clinical trials comprise only ring systems found in marketed drugs, which mirrors previously published findings for newly approved drugs. We also show there are approximately 450 000 unique ring systems derived from 2.24 billion molecules currently available in synthesized chemical space, and molecules in clinical trials utilize only 0.1% of this available pool. Moreover, there are fewer ring systems in drugs compared with those in clinical trials, but this is balanced by the drug ring systems being reused more often. Furthermore, systematic changes of up to two atoms on existing drug and clinical trial ring systems give a set of 3902 future clinical trial ring systems, which are predicted to cover approximately 50% of the novel ring systems entering clinical trials.

Reliable Functionalization of 5,6‐Fused Bicyclic N‐Heterocycles Pyrazolopyrimidines and Imidazopyridazines via Zinc and Magnesium Organometallics

DFT‐calculations allow prediction of the reactivity of uncommon N‐heterocyclic scaffolds of pyrazolo[1,5‐a]pyrimidines and imidazo[1,2‐b]pyridazines and considerably facilitate their functionalization. The derivatization of these N‐heterocycles was realized using Grignard reagents for nucleophilic additions to 5‐chloropyrazolo[1,5‐a]pyrimidines and TMP₂Zn ⋅ 2 MgCl₂  ⋅ 2 LiCl allowed regioselective zincations. In the case of 6‐chloroimidazo[1,2‐b]pyridazine, bases such as TMP₂Zn ⋅ MgCl₂  ⋅ 2 LiCl, in the presence or absence of BF₃  ⋅ OEt₂, led to regioselective metalations at positions 3 or 8. Subsequent functionalizations were achieved with TMPMgCl ⋅ LiCl, producing various polysubstituted derivatives (up to penta‐substitution). X‐ray analysis confirmed the regioselectivity for key functional heterocycles.

Analysing a billion reactions with the RInChI

The RInChI is a canonical identifier for reactions which is widely used in reaction databases. It can be used to handle large collections of reactions and to link information from diverse data sources. How much information can it handle? Studies of the SAVI database, which contains more than a billion reactions, demonstrate that the RInChI is useful in analysing such a large collection of molecular data, and the reduced form of the Web-RInChIKey contains enough information to be an effective differentiator of reactions. Issues of NH tautomerism and stereochemistry are handled effectively. The RInChI illustrates that some of the properties of the algorithmically-generated SAVI database differ from SPRESI, which is a collection of experimental data. The RInChI has different properties to Reaction SMILES and both approaches provide useful and distinct information. We recommend that the RInChI be included in data models for reactions.

Excited-State Copper Catalysis for the Synthesis of Heterocycles

Heterocycles are one of the largest groups of organic moieties with significant medicinal, chemical, and industrial applications. Herein, we report the discovery and development of visible-light-induced, synergistic excited-state copper catalysis using a combination of Cu(IPr)I as a catalyst and rac-BINAP as a ligand, which produces more than 10 distinct classes of heterocycles. The reaction tolerates a broad array of functional groups and complex molecular scaffolds, including derivatives of peptides, natural products, and marketed drugs. Preliminary mechanistic investigation suggests in situ generations of [Cu(BINAP)₂ ]⁺ and [Cu(IPr)₂ ]⁺ catalysts that work cooperatively under visible-light irradiation to facilitate catalytic carbo-aroylation of unactivated alkenes, affording a wide range of useful heterocycles.

Hydration patterns of rings in drugs and relationship to lipophilicity: A DFT study

Rings are one of the major scaffold components of drugs in medicinal chemistry, due to their unique electronic distribution, scaffold rigidity, and three-dimensionality while lipophilicity is considered as a vital parameter of rings that can influence the reactivity, metabolic stability, and toxicity. We have analyzed the electronic features, hydration patterns, solvation effect and lipophilicity data for 51 most widely used ring systems in drugs. Molecular electrostatic potential (MESP) topology analysis has been used to assess the electronic distribution in rings which provided an easy interpretation of the most suitable hydration patterns of the ring with H₂ O molecule. Further, the global minimum of ring…H₂ O complex has been utilized to predict lipophilicity (logP) with the incorporation of implicit solvation effect. Classification of ring systems based on their molecular weight into four categories, viz. small ring 'sr', medium ring 'mr', large ring 'lr' and extra large ring 'xlr' systems has led to the finding of strong correlations between logP and hydration energy with R = 0.942, 0.933, 0.968 and 0.933, respectively. The micro solvation model is found to be useful for locating the hydrophobic-hydrophilic border for each category of rings in terms of hydration energy whereas the implicit solvation model used for two solvents, n-octanol and water on the most stable hydrated structure led to a global correlation between logP and solvation energy ratio. This correlation predicts a limiting logP value -7.03 for the most hydrophilic ring system and also suggests a clear partitioning of the ring molecules into hydrophobic and hydrophilic classes. The MESP topology-guided approach to understand the electronic features and hydration patterns of rings in drugs lead to powerful predictions on their lipophilicity behavior.

Growth vector elaboration of fragments: regioselective functionalization of 5-hydroxy-6-azaindazole and 3-hydroxy-2,6-naphtyridine

This article discusses the reactivity of an 6-azaindazole (1) and a 2,6-naphthyridine (2), proposed to be “heteroaromatic rings of the future” which would be useful for fragment-based drug discovery (FBDD)...

MassGenie: A Transformer-Based Deep Learning Method for Identifying Small Molecules from Their Mass Spectra

The 'inverse problem' of mass spectrometric molecular identification ('given a mass spectrum, calculate/predict the 2D structure of the molecule whence it came') is largely unsolved, and is especially acute in metabolomics where many small molecules remain unidentified. This is largely because the number of experimentally available electrospray mass spectra of small molecules is quite limited. However, the forward problem ('calculate a small molecule's likely fragmentation and hence at least some of its mass spectrum from its structure alone') is much more tractable, because the strengths of different chemical bonds are roughly known. This kind of molecular identification problem may be cast as a language translation problem in which the source language is a list of high-resolution mass spectral peaks and the 'translation' a representation (for instance in SMILES) of the molecule. It is thus suitable for attack using the deep neural networks known as transformers. We here present MassGenie, a method that uses a transformer-based deep neural network, trained on ~6 million chemical structures with augmented SMILES encoding and their paired molecular fragments as generated in silico, explicitly including the protonated molecular ion. This architecture (containing some 400 million elements) is used to predict the structure of a molecule from the various fragments that may be expected to be observed when some of its bonds are broken. Despite being given essentially no detailed nor explicit rules about molecular fragmentation methods, isotope patterns, rearrangements, neutral losses, and the like, MassGenie learns the effective properties of the mass spectral fragment and valency space, and can generate candidate molecular structures that are very close or identical to those of the 'true' molecules. We also use VAE-Sim, a previously published variational autoencoder, to generate candidate molecules that are 'similar' to the top hit. In addition to using the 'top hits' directly, we can produce a rank order of these by 'round-tripping' candidate molecules and comparing them with the true molecules, where known. As a proof of principle, we confine ourselves to positive electrospray mass spectra from molecules with a molecular mass of 500Da or lower, including those in the last CASMI challenge (for which the results are known), getting 49/93 (53%) precisely correct. The transformer method, applied here for the first time to mass spectral interpretation, works extremely effectively both for mass spectra generated in silico and on experimentally obtained mass spectra from pure compounds. It seems to act as a Las Vegas algorithm, in that it either gives the correct answer or simply states that it cannot find one. The ability to create and to 'learn' millions of fragmentation patterns in silico, and therefrom generate candidate structures (that do not have to be in existing libraries) directly, thus opens up entirely the field of de novo small molecule structure prediction from experimental mass spectra.

Deep scaffold hopping with multimodal transformer neural networks

Scaffold hopping is a central task of modern medicinal chemistry for rational drug design, which aims to design molecules of novel scaffolds sharing similar target biological activities toward known hit molecules. Traditionally, scaffolding hopping depends on searching databases of available compounds that can't exploit vast chemical space. In this study, we have re-formulated this task as a supervised molecule-to-molecule translation to generate hopped molecules novel in 2D structure but similar in 3D structure, as inspired by the fact that candidate compounds bind with their targets through 3D conformations. To efficiently train the model, we curated over 50 thousand pairs of molecules with increased bioactivity, similar 3D structure, but different 2D structure from public bioactivity database, which spanned 40 kinases commonly investigated by medicinal chemists. Moreover, we have designed a multimodal molecular transformer architecture by integrating molecular 3D conformer through a spatial graph neural network and protein sequence information through Transformer. The trained DeepHop model was shown able to generate around 70% molecules having improved bioactivity together with high 3D similarity but low 2D scaffold similarity to the template molecules. This ratio was 1.9 times higher than other state-of-the-art deep learning methods and rule- and virtual screening-based methods. Furthermore, we demonstrated that the model could generalize to new target proteins through fine-tuning with a small set of active compounds. Case studies have also shown the advantages and usefulness of DeepHop in practical scaffold hopping scenarios.

Synthesis of P-Substituted 5- and 6-Membered Benzo-Phostams: 2,3-Dihydro-1H-1,2-benzazaphosphole 2-Oxides and 2,3-Tetrahydro-1H-1,2-benzazaphosphinine 2-Oxides

Several approaches were developed for the preparation of phosphorus-substituted 5- and 6-membered benzophostams. Carbodiimide-promoted cyclization of zwitterionic aminophosphinates derived from a nitrobenzene precursor accomplished the cyclization in good yields. Alternatively, a novel copper-catalyzed cross-coupling between a phosphonamide and a bromobenzene precursor produced the heterocycles in moderate to good yields. Three different methods are compared for the synthesis of the P-ethoxy-substituted 5-membered benzophostam.

Three-Dimensional Heterocycles by 5-exo-dig Cyclizations of S-Methyl-N-ynonylsulfoximines

Upon treatment with Cs₂CO₃, S-methyl-N-ynonylsulfoximines undergo 5-exo-dig cyclizations to give three-dimensional heterocycles. The reactions proceed at ambient temperature with a wide range of substrates affording the corresponding products in good to excellent yields.

Selective functionalization of the 1H-imidazo[1,2-b]pyrazole scaffold. A new potential non-classical isostere of indole and a precursor of push-pull dyes

We report the selective functionalization of the 1H-imidazo[1,2-b]pyrazole scaffold using a Br/Mg-exchange, as well as regioselective magnesiations and zincations with TMP-bases (TMP = 2,2,6,6-tetramethylpiperidyl), followed by trapping reactions with various electrophiles. In addition, we report a fragmentation of the pyrazole ring, giving access to push-pull dyes with a proaromatic (1,3-dihydro-2H-imidazol-2-ylidene)malononitrile core. These functionalization methods were used in the synthesis of an isostere of the indolyl drug pruvanserin. Comparative assays between the original drug and the isostere showed that a substitution of the indole ring with a 1H-imidazo[1,2-b]pyrazole results in a significantly improved solubility in aqueous media.

Infrared, Electronic Absorption, and Emission Spectra of Tris (4-methyl-1-(1- methyl-1H-benzo [d]imidazol-2-yl)-4H-benzo [d]imidazo[1,5-a]imid- azole-3-yl) methyl: Roles of Molecular Electronic States and Axial Substitution

In order to comparing and explaining the experimental infrared, electronic absorption, and emission spectra of tris (4-methyl-1-(1-methyl-1H-benzo [d] imidazol-2-yl) -4H-benzo [d] imidazo[1,5-a]imid- azole-3-yl) methyl (L6), density functional theory calculations were performed to systematically study the spectral properties of several species with different electronic states (L6⁺ , L6, and HL6⁺ ) as well as the axial substituted derivative with methoxy group (L6-OCH₃ ). The main peaks in the vibrational, electronic absorption, and emission spectra were assigned in detail. Roles of molecular electronic states and axial substitution on the spectral properties are revealed. The calculated spectra are compared with experimental results to distinguish the nature of L6 in crystal and solvent. This work combing experiment and theoretical calculations would be good example for clarifying molecular electronic states and thus promising the practice application of such kind of novel molecules.

Synthesis of Polysubstituted Fused Pyrroles by Gold-Catalyzed Cycloisomerization/1,2-Sulfonyl Migration of Yndiamides

Yndiamides (bis-N-substituted alkynes) are valuable precursors to azacycles. Here we report a cycloisomerization/1,2-sulfonyl migration of alkynyl-yndiamides to form tetrahydropyrrolopyrroles, unprecedented heterocyclic scaffolds that are relevant to medicinal chemistry. This functional group tolerant transformation can be achieved using Au(I) catalysis that proceeds at ambient temperature, and a thermally promoted process. The utility of the products is demonstrated by a range of reactions to functionalize the fused pyrrole core.

Vinylation of α-Aminoazoles with Triethylamine: A General Strategy to Construct Azolo[1,5-a]pyrimidines with a Nonsubstituted Ethylidene Fragment

A new general synthesis of pharmaceutically important azolo[1,5-a]pyrimidines starting from widely available 3(5)-aminoazoles, aldehydes, and triethylamine is developed. The key is to enable the vinylation reaction that allows the in situ generation of elusive acyclic enamines and the subsequent annulation reaction to occur. This direct and practical strategy is capable of constructing a range of 5,6-unsubstituted pyrazolo[1,5-a]pyrimidines and [1,2,4]triazolo[1,5-a]pyrimidines. More importantly, this protocol provides a concise synthetic route to prepare the clinically used zaleplon.

Iridium-Catalysed C-H Borylation of Heteroarenes: Balancing Steric and Electronic Regiocontrol

The iridium-catalysed borylation of aromatic C-H bonds has become the preferred method for the synthesis of aromatic organoboron compounds. The reaction is highly efficient, tolerant of a broad range of substituents and can be applied to both carbocyclic and heterocyclic substrates. The regioselectivity of C-H activation is dominated by steric considerations and there have been considerable efforts to develop more selective processes for less constrained substrates. However, most of these have focused on benzenoid-type substrates and in contrast, heteroarenes remain much desired but more challenging substrates with the position and/or nature of the heteroatom(s) significantly affecting reactivity and regioselectivity. This review will survey the borylation of heteroarenes, focusing on the influence of steric and electronic effects on regiochemical outcome and, by linking to current mechanistic understandings, will provide insights to what is currently possible and where further developments are required.

Catalytic Asymmetric 1,3-Dipolar Cycloaddition of α,β-Unsaturated Amide and Azomethine Imine

α,β-Unsaturated amides were incorporated as viable dipolarophiles in a catalytic asymmetric 1,3-dipolar cycloaddition of azomethine imines. The use of a 7-azaindoline auxiliary was essential to acquire sufficient reactivity with excellent diastereoselectivity, likely due to the chelating activation of the amide by the In(III)/bishydroxamic acid complex. Although the enantioselectivity remains unsatisfactory, this work is an important step toward the development of an asymmetric catalysis utilizing stable and low-reactive substrates.