Programmed Heterocycle Synthesis Using Halomucononitriles as Pyridinimine Precursors

Herein we report a method to convert primary amines, ubiquitous motifs found in pharmaceutical libraries, to either imidazo[1,2-a]pyridines or 7-alkyl azaindoles in two steps from known compounds. Using halomucononitrile reagents, we can directly access 5-bromo-6-imino-1-alkyl-1,6-dihydropyridine-2-carbonitriles (pyridinimines) in a single step from primary amines (25-93% yield) through the cyclization of transient aminomucononitrile intermediates. We then demonstrate that these compounds can be readily converted to 7-alkylazaindoles using Sonogashira cross-coupling conditions (13 examples, up to 91% yield). Under oxidative conditions, the pyridinimines serve as directing groups for C-H functionalization reactions to afford imidazo[1,2-a]pyridines. We also studied the mechanism of the cyclization event using DFT calculations and propose that this takes place via sequential base-mediated E/Z isomerization and cyclization steps.

Efficient and metal-free synthesis of 2-aroyl 7-azaindoles via thermally induced denitrogenative intramolecular annulation of 1,2,3,4-tetrazolopyridines

A facile and metal-free intramolecular denitrogenative annulation strategy for the preparation of novel 2-aroyl 7-azaindoles has been developed from 3-(tetrazolo[1,5-a]pyridin-8-yl)prop-2-en-1-one in the presence of the deep eutectic solvent Dowtherm A. The valuable features of the protocol include a short reaction time, absence of any metal catalyst, utilization of a eutectic solvent, easy product isolation, and very good yields of novel 2-aroyl 7-azaindoles.

Recent advances in pyruvate dehydrogenase kinase inhibitors: Structures, inhibitory mechanisms and biological activities

Metabolism is reprogrammed in a variety of cancer cells to ensure their rapid proliferation. Cancer cells prefer to utilize glycolysis to produce energy as well as to provide large amounts of precursors for their division. In this process, cancer cells inhibit the activity of pyruvate dehydrogenase complex (PDC) by upregulating the expression of pyruvate dehydrogenase kinases (PDKs). Inhibiting the activity of PDKs in cancer cells can effectively block this metabolic transition in cancer cells, while also activating mitochondrial oxidative metabolism and promoting apoptosis of cancer cells. To this day, the study of PDKs inhibitors has become one of the research hotspots in the field of medicinal chemistry. Novel structures targeting PDKs are constantly being discovered, and some inhibitors have entered the clinical research stage. Here, we reviewed the research progress of PDKs inhibitors in recent years and classified them according to the PDKs binding sites they acted on, aiming to summarize the structural characteristics of inhibitors acting on different binding sites and explore their clinical application value. Finally, the shortcomings of some PDKs inhibitors and the further development direction of PDKs inhibitors are discussed.

Multistage in silico approach to identify novel quinoline derivatives as potential c-kit kinase inhibitors

The type II-C-KIT signaling network has been extensively studied for its potential as a target for cancer treatment, leading to the investigation of quinoline derivatives as compounds with inhibitory effects on c-Kit kinase. In this study, a multistage approach was employed, including the creation of pharmacophore models, 3D QSAR analysis, virtual screening, docking investigations, and molecular dynamics stimulation. The pharmacophore evaluation included a data set of 29 ligands, which resulted in the generation of the ADDHR_1pharmacophore model as the most promising, with a survival score of 5.6812. The main objective was to utilize the atom-based 3D-QSAR approach for generating robust 3D-QSAR models aimed at identifying new TypeII-C-kit kinase inhibitors. The evaluations of these models have convincingly demonstrated their high predictive power (Q2 = 0.6547, R2 = 0.9947). Using atom-based 3D-QSAR data, a total of 7564 novel compounds were generated from R-group enumeration. Molecular docking and MM-GBSA study revealed that compound A1 exhibited the highest binding score of -9.30 kcal/mol and a Δ GBind value of -90.56 kcal/mol. The ZINC compounds were then screened using the pharmacophore model, followed by virtual screening, which identified ZINC65798256, ZINC09317958, ZINC73187176, and ZINC76176670 as potential candidates with promising docking scores. Among these, ZINC65798256 demonstrated the best binding interactions with amino acid residues, ASP810, LYS623, CYS673, and THR670 (PDB ID: 1T46). To further analyze the structural features and molecular interactions, molecular dynamics simulation was conducted for a time scale of 100 ns.Communicated by Ramaswamy H. Sarma.

Recent advances in the development of Rho kinase inhibitors (2015-2021)

Rho-associated coiled-coil kinases (ROCKs) are key downstream effectors of small GTPases. ROCK plays a central role in diverse cellular events with accumulating evidence supporting the concept that ROCK is important in tumor development and progression. Numerous ROCK inhibitors have been investigated for their therapeutic potential in the treatment of cancers. In this article, we review recent research progress on ROCK inhibitors, especially those with potential for the treatment of cancers, reported in the literature from 2015 to 2021. Most ROCK inhibitors show potent in vitro and in vivo antitumor activities and have potential in the treatment of cancers.

Design, synthesis and SAR of novel 7-azaindole derivatives as potential Erk5 kinase inhibitor with anticancer activity

The extracellular signal-regulated kinase 5 (Erk5) signaling plays a crucial role in cancer, and regulating its activity may have potential in cancer chemotherapy. In this study, a series of novel 7-azaindole derivatives (4a-5o) were designed and synthesized. Their antitumor activities on human lung cancer A549 cells was evaluated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, 4',6-diamidino-2-phenylindole (DAPI) staining and colony formation assay. Among them, compounds 4a, 4 h, 5d and 5j exhibited good anti-proliferative activity with the IC50 values of 6.23 µg/mL, 8.52 µg/mL, 7.33 µg/mL and 4.56 µg/mL, respectively, equivalent to Erk5 positive control XMD8-92 (IC50 = 5.36 µg/mL). The results of structure-activity relationships (SAR) showed that double bond on the piperidine ring and N atoms at the N7 position of 7-azaindole was essential for their antiproliferative activity. Furthermore, compounds 4a and 5j exhibited good inhibition on Erk5 kinase through Western blot analysis and possible action site of compounds with Erk5 kinase was elucidated by molecular docking.

Laser spectroscopic characterization of supersonic jet cooled 2,7-diazaindole

We report the first gas phase comprehensive study of the electronic spectroscopy of 2,7-diazaindole molecule in the ground and excited states. Single vibronic level fluorescence spectroscopy (SVLF) was performed to determine the ground state vibrations of the molecule, which depicted a large Franck-Condon activity beyond 2600 cm-1. For the excited state characterization, laser-induced fluorescence (LIF) and two-color resonant two-photon ionization spectroscopy (2C-R2PI) were performed. The band origin (000) for S1 ← S0 transition appeared at 33910 ± 1 cm-1 which was red shifted by 718 cm-1 and 1322 cm-1 compared to that of 7-azaindole and indole respectively. The Franck-Condon active vibrational modes in the spectra were seen till the (000) + 1600 cm-1 region. The IR-UV hole burning spectroscopy confirmed the absence of any other isomeric species in the molecular beam. The ionization energy (IE) of the molecule was measured as 8.921 ± 0.001 eV, recorded using photoionization efficiency spectroscopy. The above IE value was significantly higher than that of the related indole derivatives, suggesting the higher photostability of the 27DAI molecule due to N(2) insertion. The ground and excited state N-H stretching frequencies of the molecule were determined using fluorescence-dip infrared spectroscopy (FDIR) and resonant ion-dip infrared spectroscopy (IDIR), and the values are 3523 and 3467 cm-1, respectively. The lower value of νNH in the electronic excited state implied the increased photoacidity of the group. A comparative analysis of the experimental LIF/2C-R2PI spectra was done against Franck-Condon simulated spectra at three different levels of theory. The vibrational frequencies calculated at B3LYP-D4/def2-TZVPP showed the most accurate prediction in comparison with the experimentally detected symmetric modes in the ground state. However, in the excited state, the lower energy asymmetric modes simulated at the B3LYP/def-SVP level of theory provided the best agreement with the experiment. This is most probably due to the distortion observed at the pyrazolyl ring leading to the appearance of asymmetric vibrational modes. The above study highlights the possibility to appropriately tune the excitation wavelengths as well as alter the photostability of the organic chromophores via additional N-insertion in the molecular systems.

Unlocking New Prenylation Modes: Azaindoles as a New Substrate Class for Indole Prenyltransferases

Aza-substitution, the replacement of aromatic CH groups with nitrogen atoms, is an established medicinal chemistry strategy for increasing solubility, but current methods of accessing functionalized azaindoles are limited. In this work, indole-alkylating aromatic prenyltransferases (PTs) were explored as a strategy to directly functionalize azaindole-substituted analogs of natural products. For this, a series of aza-l-tryptophans (Aza-Trp) featuring N-substitution of every aromatic CH position of the indole ring and their corresponding cyclic Aza-l-Trp-l-proline dipeptides (Aza-CyWP), were synthesized as substrate mimetics for the indole-alkylating PTs FgaPT2, CdpNPT, and FtmPT1. We then demonstrated most of these substrate analogs were accepted by a PT, and the regioselectivity of each prenylation was heavily influenced by the position of the N-substitution. Remarkably, FgaPT2 was found to produce cationic N-prenylpyridinium products, representing not only a new substrate class for indole PTs but also a previously unobserved prenylation mode. The discovery that nitrogenous indole bioisosteres can be accepted by PTs thus provides access to previously unavailable chemical space in the search for bioactive indolediketopiperazine analogs.

Competing Excited-State Hydrogen and Proton-Transfer Processes in 6-Azaindole-S3,4 and 2,6-Diazaindole-S3,4 Clusters (S=H2 O, NH3 )

Excited state hydrogen (ESHT) and proton (ESPT) transfer reaction pathways in the three and four solvent clusters of 6-azaindole (6AI-S3,4 ) and 2,6-diazaindole (26DAI-S3,4 )(S=H2 O, NH3 ) were computationally investigated to understand the fate of photo-excited biomolecules. The ESHT energy barriers in (H2 O)3 complexes (39.6-41.3 kJmol-1 ) were decreased in (H2 O)4 complexes (23.1-20.2 kJmol-1 ). Lengthening the solvent chain lowered the barrier because of the relaxed transition states geometries with reduced angular strains. Replacing the water molecule with ammonia drastically decreased the energy barriers to 21.4-21.3 kJmol-1 in (NH3 )3 complexes and 8.1-9.5 kJ mol-1 in (NH3 )4 complexes. The transition states were identified as Ha atom attached to the first solvent molecule. The formation of stronger hydrogen bonds in (NH3 )3,4 complexes resulted in facile ESHT reaction than that in the (H2 O)3,4 complexes. The ESPT energy barriers in 6AI-S3,4 and 26DAI-S3,4 were found to range between 40-73 kJmol-1 . The above values were significantly higher than that of the ESHT processes and hence are considered as a minor channel in the process. The effect of N(2) insertion was explored for the very first time in the isolated solvent clusters using local vibrational mode analysis. In DAI-S4 , the higher Ka (Ha ⋯Sa ) values depicted the increased photoacidity of the N(1)-Ha group which may facilitate the hydrogen transfer reaction. However, the increased N(6)⋯Hb bond length elevated the reaction barriers. Therefore, in the ESHT reaction channel, the co-existence of two competing factors led to a marginal/no change in the overall energy barriers due to the N(2) insertion. In the ESPT reaction pathway, the energy barriers showed notable increase upon N(2) insertion because of the increased N(6)⋯Hb bond length.

Azaindole derivatives as potential kinase inhibitors and their SARs elucidation

Currently, heterocycles have occupied an important position in the fields of drug design. Among them, azaindole moiety is regarded as one privileged scaffold to develop therapeutic agents. Since two nitrogen atoms of azaindole increase the possibility to form hydrogen bonds in the adenosine triphosphate (ATP)-binding site, azaindole derivatives are important sources of kinase inhibitors. Moreover, some of them have been on the market or in clinical trials for the treatment of some kinase-related diseases (e.g., vemurafenib, pexidartinib, decernotinib). In this review, we focused on the recent development of azaindole derivatives as potential kinase inhibitors based on kinase targets, such as adaptor-associated kinase 1 (AAK1), anaplastic lymphoma kinase (ALK), AXL, cell division cycle 7 (Cdc7), cyclin-dependent kinases (CDKs), dual-specificity tyrosine (Y)-phosphorylation regulated kinase 1A (DYRK1A), fibroblast growth factor receptor 4 (FGFR4), phosphatidylinositol 3-kinase (PI3K) and proviral insertion site in moloney murine leukemia virus (PIM) kinases. Meanwhile, the structure-activity relationships (SARs) of most azaindole derivatives were also elucidated. In addition, the binding modes of some azaindoles complexed with kinases were also investigated during the SARs elucidation. This review may offer an insight for medicinal chemists to rationally design more potent kinase inhibitors bearing the azaindole scaffold.

Exploiting Coordination Behavior of 7-Azaindole for Mechanistic Investigation of Chan-Lam Coupling and Application to 7-Azaindole Based Pharmacophores

Multiple spectroscopic techniques, along with single-crystal X-ray analysis, have been used to reveal the detailed structural and electronic information on reaction intermediates of a new copper(II)-DBU catalytic system for the N-arylation of 7-Azaindole. The reaction mixture of Chan-Lam cross-coupling yields two dimeric copper(II)-7-azaindole complexes, including one attached with DBU, prior to adding arylboronic acid and are confirmed structurally and spectroscopically. A suitable mechanism has been proposed using the dimeric copper(II) complex as a catalyst for the coupling reactions. The role of DBU as a base and also as an auxiliary ligand in the course of the reaction has been established. The transmetalated monomeric aryl-copper(II) species generated from the dimeric unit is oxidized by another equivalent of copper(II) to yield an aryl-copper(III) intermediate for facile N-arylation, which has been authenticated with UV-vis spectroscopy. The regeneration of the copper(II)-catalyst by aerial oxidation of colorless copper(I) species (generated via reductive elimination and disproportionation step) is confirmed by mass and absorption spectroscopy. Detailed DFT and TD-DFT calculations help to rationalize the proposed reaction intermediates and their corresponding electronic transitions. Moreover, the confirmation of copper(I)-7-azaindole intermediate via HRMS reaffirmed the involvement of Cu(II)/Cu(III)/Cu(I) species in the Chan-Lam type of coupling. A medicinally-important 7-azaindole-based SHP2 inhibitor has been synthesized via sequential arylation.

1,2,4-Amino-triazine derivatives as pyruvate dehydrogenase kinase inhibitors: Synthesis and pharmacological evaluation

Among the different hallmarks of cancer, deregulation of cellular metabolism turned out to be an essential mechanism in promoting cancer resistance and progression. The pyruvate dehydrogenase kinases (PDKs) are well known as key regulators in cells metabolic process and their activity was found to be overexpressed in different metabolic alerted types of cancer, including the high aggressive pancreatic ductal adenocarcinoma (PDAC). To date few PDK inhibitors have been reported, and the different molecules developed are characterized by structural chemical diversity. In an attempt to find novel classes of potential PDK inhibitors, the molecular hybridization approach, which combine two or more active scaffolds in a single structure, was employed. Herein we report the synthesis and the pharmacological evaluation of the novel hybrid molecules, characterized by the fusion of three different pharmacophoric sub-units such as 1,2,4-amino triazines, 7-azaindoles and indoles, in a single structure. The synthesized derivatives demonstrated a promising ability in hampering the enzymatic activity of PDK1 and 4, further confirmed by docking studies. Interestingly, these derivatives retained a strong antiproliferative activity against pancreatic cancer cells either in 2D and 3D models. Mechanistic studies in highly aggressive PDAC cells confirmed their ability to hamper PDK axis and to induce cancer cell death by apoptosis. Moreover, in vivo translational studies in a murine syngeneic solid tumor model confirmed the ability of the most representative compounds to target the PDK system and highlight the ability to reduce the tumor growth without inducing substantial body weight changes in the treated mice.

Current Fragment-to-lead Approaches Starting from the 7-azaindole: The Pharmacological Versatility of a Privileged Molecular Fragment

Fragment-based drug discovery is one of the most powerful paradigms in the recent context of medicinal chemistry and is being widely practiced by academic and industrial researchers. Currently, azaindoles are among the most exploited molecular fragments in pharmaceutical innovation projects inspired by fragment-to-lead strategies. The 7-azaindole is the most prominent representative within this remarkable family of pyrrolopyridine fragments, as it is present in the chemical structure of several approved antitumor drugs and also of numerous therapeutic candidates. In this paper, a brief overview on existing proofs of concept in the literature will be presented, as well as some recent works that corroborate 7-azaindole as a privileged and pharmacologically versatile molecular fragment.

Chemoenzymatic Synthesis of Indole-Containing Acyloin Derivatives

Indole-containing acyloins are either key intermediates of many antimicrobial/antiviral natural products or building blocks in the synthesis of biologically active molecules. As such, access to structurally diverse indole-containing acyloins has attracted considerable attention. In this report, we present a pilot study of using biotransformation to provide acyloins that contain various indole substituents. The biotransformation system contains the tryptophan synthase standalone β-subunit variant, PfTrpB⁶, generated from directed evolution in the literature; a commercially available L-amino acid oxidase (LAAO); and the thiamine-diphosphate (ThDP)-dependent enzyme NzsH, encoded in the biosynthetic gene cluster (nzs) of the bacterial carbazole alkaloid natural product named neocarazostatin A. The utilization of the first two enzymes, the PfTrpB variant and LAAO, is designed to provide structurally diverse indole 3-pyruvate derivatives as donor substrates for NzsH-catalysed biotransformation to provide acyloin derivatives. Our results demonstrate that NzsH displays a considerable substrate profile toward donor substrates for production of acyloins with different indole ring systems, suggesting that NzsH could be further explored as a potential biocatalyst via directed evolution to improve the catalytic efficiency in the future.

Enabling Suzuki-Miyaura coupling of Lewis-basic arylboronic esters with a nonprecious metal catalyst

The high cost and negative environmental impact of precious metal catalysts has led to increased demand for nonprecious alternatives for widely practiced reactions such as the Suzuki-Miyaura coupling (SMC). Ni-catalyzed versions of this reaction have failed to achieve high reactivity with Lewis-basic arylboron nucleophiles, especially pinacolboron esters. We describe the development of (PPh2Me)2NiCl2 as an inexpensive and air-stable precatalyst that addresses this challenge. Under activation by n-BuMgCl, this complex can catalyze the coupling of synthetically important heteroaryl pinacolborons with heteroaryl halides. Mildly basic conditions (aqueous K3PO4) allow the reaction to tolerate sensitive functional groups that were incompatible with other Ni-SMC methods. Experimental and computational studies suggest that catalyst inhibition by substitution of PPh2Me from Ni(ii) intermediates by Lewis basic reactants and products is disfavored relative to more commonly employed ligands in the Ni-SMC, which allows it to operate efficiently in the presence of Lewis bases such as unhindered pyridines.

A New 7-azaindole Structure Analog: Molecular Docking, Synthesis and Preliminary Biological Activity in vitro for Anticancer

In this work, a series of 7-azaindole analogs was designed by the bioisosteric principle based on pharmacodynamic parent nucleus. Moreover, 5-Chloro-3-{[2-({[6-(trifluoromethyl) pyridin-3-yl]methyl}amino)pyrimidin-5-yl]methyl}-1H-pyrrolo[2,3-b]pyridine (compound P1 ) with the strongest interaction with colony-stimulating factor 1 receptor (CSF-1R) was screened by molecular docking. Compound P1 was successfully prepared by the six-step reaction with HPLC purity of 99.26% and characterized by 1 H NMR and ESI-MS spectra. In vitro bioactivity study showed that compound P1 appeared the cytotoxicity to MCF-7 and A549 cells, especially to HOS cells (IC 50 = 88.79 ± 8.07 nM), while it had lower toxicity to normal L929 cells (IC 50 = 140.49 ± 8.03 μM). In addition, compound P1 could induce HOS cell death by apoptosis and blocking the G0/G1 phase at nanomolar concentrations. The obtained results indicated that compound P1 might be a promising candidate compound for anticancer drug.

Fragment-Based and Structural Investigation for Discovery of JNK3 Inhibitors

The c-Jun N-terminal kinases (JNKs) are members of the mitogen-activated protein kinase (MAPK) family and are related to cell proliferation, gene expression, and cell death. JNK isoform 3 (JNK3) is an important therapeutic target in varieties of pathological conditions including cancers and neuronal death. There is no approved drug targeting JNKs. To discover chemical inhibitors of JNK3, virtual fragment screening, the saturation transfer difference (STD) NMR, in vitro kinase assay, and X-ray crystallography were employed. A total of 27 fragments from the virtually selected 494 compounds were identified as initial hits via STD NMR and some compounds showed the inhibition of the activity of JNK3 in vitro. The structures of JNK3 with a fragment and a potent inhibitor were determined by X-ray crystallography. The fragment and inhibitor shared a common JNK3-binding feature. The result shows that fragment screening by NMR spectroscopy is a very efficient method to screen JNK3 binders and the structure of JNK3-inhibitor complex can be used to design and develop more potent inhibitors.

Identification of Novel Aryl Carboxamide Derivatives as Death-Associated Protein Kinase 1 (DAPK1) Inhibitors with Anti-Proliferative Activities: Design, Synthesis, In Vitro, and In Silico Biological Studies

Death-associated protein kinase 1 (DAPK1) is a serine/threonine protein kinase involved in diverse fundamental cellular processes such as apoptosis and autophagy. DAPK1 isoform plays an essential role as a tumor suppressor and inhibitor of metastasis. Consequently, DAPK1 became a promising target protein for developing new anti-cancer agents. In this work, we present the rational design and complete synthetic routes of a novel series of eighteen aryl carboxamide derivatives as potential DAPK1 inhibitors. Using a custom panel of forty-five kinases, a single dose of 10 µM of the picolinamide derivative 4a was able to selectively inhibit DAPK1 kinase by 44.19%. Further investigations revealed the isonicotinamide derivative 4q as a promising DAPK1 inhibitory lead compound with an IC₅₀ value of 1.09 µM. In an in vitro anticancer activity assay using a library of 60 cancer cell lines including blood, lung, colon, CNS, skin, ovary, renal, prostate, and breast cancers, four compounds (4d, 4e, 4o, and 4p) demonstrated high anti-proliferative activity with mean % GI ~70%. Furthermore, the most potent DAPK1 inhibitor (4q) exhibited remarkable activity against leukemia (K-562) and breast cancer (MDA-MB-468) with % GI of 72% and 75%, respectively.

Development of Azaindole-Based Frameworks as Potential Antiviral Agents and Their Future Perspectives

The azaindole (AI) framework continues to play a significant role in the design of new antiviral agents. Modulating the position and isosteric replacement of the nitrogen atom of AI analogs notably influences the intrinsic physicochemical properties of lead compounds. The intra- and intermolecular interactions of AI derivatives with host receptors or viral proteins can also be fine tuned by carefully placing the nitrogen atom in the heterocyclic core. This wide-ranging perspective article focuses on AIs that have considerable utility in drug discovery programs against RNA viruses. The inhibition of influenza A, human immunodeficiency, respiratory syncytial, neurotropic alpha, dengue, ebola, and hepatitis C viruses by AI analogs is extensively reviewed to assess their plausible future potential in antiviral drug discovery. The binding interaction of AIs with the target protein is examined to derive a structural basis for designing new antiviral agents.

Approaches for discovery of small-molecular antivirals targeting to influenza A virus PB2 subunit

Influenza is an acute respiratory infectious disease caused by influenza virus, leading to huge morbidity and mortality in humans worldwide. Despite the availability of antivirals in the clinic, the emergence of resistant strains calls for antivirals with novel mechanisms of action. The PB2 subunit of the influenza A virus polymerase is a promising target because of its vital role in the 'cap-snatching' mechanism. In this review, we summarize the technologies and medicinal chemistry strategies for hit identification, hit-to-lead and lead-to-candidate optimization, and current challenges in PB2 inhibitor development, as well as offering insights for the fight against drug resistance.

Fragment-Based Drug Discovery by NMR. Where Are the Successes and Where can It Be Improved?

Over the last century, the definitions of pharmaceutical drug and drug discovery have changed considerably. Evolving from an almost exclusively serendipitous approach, drug discovery nowadays involves several distinct, yet sometimes interconnected stages aimed at obtaining molecules able to interact with a defined biomolecular target, and triggering a suitable biological response. At each of the stages, a wide range of techniques are typically employed to obtain the results required to move the project into the next stage. High Throughput Screening (HTS) and Fragment Based Drug Design (FBDD) are the two main approaches used to identify drug-like candidates in the early stages of drug discovery. Nuclear Magnetic Resonance (NMR) spectroscopy has many applications in FBDD and is used extensively in industry as well as in academia. In this manuscript, we discuss the paths of both successful and unsuccessful molecules where NMR had a crucial part in their development. We specifically focus on the techniques used and describe strengths and weaknesses of each stage by examining several case studies. More precisely, we examine the development history from the primary screening to the final lead optimisation of AZD3839 interacting with BACE-1, ABT-199 interacting with BCL2/XL and S64315 interacting with MCL-1. Based on these studies, we derive observations and conclusions regarding the FBDD process by NMR and discuss its potential improvements.

Novel Substituted Purine Isosteres: Synthesis, Structure-Activity Relationships and Cytotoxic Activity Evaluation

A number of pyrrolo[2,3-c]pyridines, pyrrolo[3,2-d]pyrimidines and pyrazolo[4,3-d]pyrimidines were designed and synthesized as antiproliferative agents. The target compounds possessed selected substituents in analogous positions on the central scaffold that allowed the extraction of interesting SARs. The cytotoxic activity of the new derivatives was evaluated against prostatic (PC-3) and colon (HCT116) cell lines, and the most potent analogues showed IC₅₀ values in the nM to low µM range, while they were found to be non-toxic against normal human fibroblasts (WI-38). Flow cytometric analysis of DNA content revealed that the most promising derivative 14b caused a statistically significant accumulation of PC-3 cells at G₂/M phase and induced apoptosis in PC-3 cells.

Design, synthesis and biological evaluation of novel aminopyrazole- and 7-azaindole-based Nek1 inhibitors and their effects on zebrafish kidney development

NIMA-related protein kinase Nek1 is crucially involved in cell cycle regulation, DNA repair and microtubule regulation and dysfunctions of Nek1 play key roles in amyotrophic lateral sclerosis (ALS), polycystic kidney disease (PKD) and several types of radiotherapy resistant cancer. Targeting of Nek1 could reveal a new class of radiosensitizing substances and provide useful tools to better understand the aforementioned diseases. In this report we explore substituted aminopyrazoles and 7-azaindoles as potent inhibitors for the Nek1 kinase domain and examine their effect on kidney organogenesis in Danio rerio.

New fused pyrroles with rA1/A2A antagonistic activity as potential therapeutics for neurodegenerative disorders

In a pilot study, eleven pyrrolopyridine and pyrrolopyrimidine derivatives (specifically, 7-azaindole and 7-deazapurine derivatives) were synthesised by Suzuki cross-coupling reactions and evaluated via radioligand binding assays as potential adenosine receptor (AR) antagonists in order to further investigate the structure-activity relationships of these compounds. 6-Chloro-4-phenyl-1H-pyrrolo[2,3-b]pyridine, with a 7-azaindole scaffold, was identified as a selective A₁ AR antagonist with a rA₁K_i value of 0.16 µM, and interestingly, the addition of a N-atom to the aforementioned fused heterocyclic ring system, creating corresponding 7-deazapurines, led to a dual A₁/A_2A AR ligand (2-chloro-4-phenyl-7H-pyrrolo[2,3-d]pyrimidine: rA₁K_i: 0.19 ± 0.02 µM; rA_2AK_i: 0.43 ± 0.01 µM). Introducing an additional N-atom into the heterocyclic ring system was tolerable for rA₁ AR affinity and also led to rA_2A AR affinity. This pilot study concluded that new 7-azaindole and 7-deazapurine derivatives represent interesting scaffolds for design of A₁ and/or A_2A AR antagonists.

Fragment-based lead discovery of indazole-based compounds as AXL kinase inhibitors

AXL is a member of the TAM (TYRO3, AXL, MER) subfamily of receptor tyrosine kinases. It is upregulated in a variety of cancers and its overexpression is associated with poor disease prognosis and acquired drug resistance. Utilizing a fragment-based lead discovery approach, a new indazole-based AXL inhibitor was obtained. The indazole fragment hit 11, identified through a high concentration biochemical screen, was expeditiously improved to fragment 24 by screening our in-house expanded library of fragments (ELF) collection. Subsequent fragment optimization guided by docking studies provided potent inhibitor 54 with moderate exposure levels in mice. X-ray crystal structure of analog 50 complexed with the I650M mutated kinase domain of Mer revealed the key binding interactions for the scaffold. The good potency coupled with reasonable kinase selectivity, moderate in vivo exposure levels, and availability of structural information for the series makes it a suitable starting point for further optimization efforts.

Design and development of a photoswitchable DFG-out kinase inhibitor

We report the synthesis and characterisation of a photoswitchable DFG-out kinase inhibitor. Photocontrol of the target kinase in both enzymatic and living cell assays is demonstrated.

Iridium-catalyzed C3-selective asymmetric allylation of 7-azaindoles with secondary allylic alcohols

The development of efficient synthetic methods of 7-azaindoles has been desired due to the useful biological activities and physical properties. We report the first example of the iridium-catalyzed C3-selective asymmetric allylation of 7-azaindoles with racemic secondary allylic alcohols to give only branched allylation products in good to high yields with high enantioselectivity (up to >99.5% ee). Allylic alcohols and 7-azaindoles with a variety of functional groups including halogen and heteroaromatic groups are compatible with the reaction conditions. Furthermore, transformations of the obtained allylation products are demonstrated without a significant loss of enantiomeric excess.

Hinge Binder Scaffold Hopping Identifies Potent Calcium/Calmodulin-Dependent Protein Kinase Kinase 2 (CAMKK2) Inhibitor Chemotypes

CAMKK2 is a serine/threonine kinase and an activator of AMPK whose dysregulation is linked with multiple diseases. Unfortunately, STO-609, the tool inhibitor commonly used to probe CAMKK2 signaling, has limitations. To identify promising scaffolds as starting points for the development of high-quality CAMKK2 chemical probes, we utilized a hinge-binding scaffold hopping strategy to design new CAMKK2 inhibitors. Starting from the potent but promiscuous disubstituted 7-azaindole GSK650934, a total of 32 compounds, composed of single-ring, 5,6-, and 6,6-fused heteroaromatic cores, were synthesized. The compound set was specifically designed to probe interactions with the kinase hinge-binding residues. Compared to GSK650394 and STO-609, 13 compounds displayed similar or better CAMKK2 inhibitory potency in vitro, while compounds 13g and 45 had improved selectivity for CAMKK2 across the kinome. Our systematic survey of hinge-binding chemotypes identified several potent and selective inhibitors of CAMKK2 to serve as starting points for medicinal chemistry programs.

Exploration of 7-azaindole-coumaranone hybrids and their analogues as protein kinase inhibitors

7-Azaindole has been labelled a privileged scaffold for the design of new potent inhibitors of protein kinases. In this paper, we determined the inhibition profiles of novel mono- and disubstituted derivatives of 7-azaindole-coumaranone hybrids on various disease-related protein kinases. Eight hit compounds were identified, including a potent Haspin inhibitor with an IC₅₀ value of 0.15 μM. An interesting observation was that all active monosubstituted compounds displayed dual inhibition for Haspin and GSK-3β, while disubstituted derivatives inhibited GSK-3β and LmCK1 from Leishmania major parasite. Analyses of structure activity relationships (SARs) also revealed that mono-substitution with para-fluorobenzyloxy ring produced an equipotent inhibition of Haspin and GSK-3β. Haspin and GSK-3β are relevant targets for developing new anticancer agents while LmCK1 is an innovative target for leishmanicidal drugs. Novel compounds reported in this paper constitute promising starting points for the development of new anticancer and leishmanicidal drugs.

Rhodium(III)-catalyzed oxidative alkylation of N-aryl-7-azaindoles with cyclopropanols

An efficient Rh(iii)-catalyzed C-H oxidative alkylation of N-aryl-7-azaindoles with cyclopropanols by merging tandem C-H and C-C cleavage was developed. This transformation features mild reaction conditions, high regioselectivity, and excellent functional group compatibility. The resulting β-aryl ketone derivatives can be readily transformed into 7-azaindole-containing π-extended polycyclic heteroarenes.

From Pyrazolones to Azaindoles: Evolution of Active-Site SHP2 Inhibitors Based on Scaffold Hopping and Bioisosteric Replacement

The tyrosine phosphatase SHP2 controls the activity of pivotal signaling pathways, including MAPK, JAK-STAT, and PI3K-Akt. Aberrant SHP2 activity leads to uncontrolled cell proliferation, tumorigenesis, and metastasis. SHP2 signaling was recently linked to drug resistance against cancer medications such as MEK and BRAF inhibitors. In this work, we present the development of a novel class of azaindole SHP2 inhibitors. We applied scaffold hopping and bioisosteric replacement concepts to eliminate unwanted structural motifs and to improve the inhibitor characteristics of the previously reported pyrazolone SHP2 inhibitors. The most potent azaindole 45 inhibits SHP2 with an IC₅₀ = 0.031 μM in an enzymatic assay and with an IC₅₀ = 2.6 μM in human pancreas cells (HPAF-II). Evaluation in a series of cellular assays for metastasis and drug resistance demonstrated efficient SHP2 blockade. Finally, 45 inhibited proliferation of two cancer cell lines that are resistant to cancer drugs and diminished ERK signaling.

Photosensitized Intramolecular [2+2] Cycloaddition of 1H-Pyrrolo[2,3-b]pyridines Enabled by the Assistance of Lewis Acids

The [2+2] photocycloaddition of alkenyl-tethered 1H-pyrrolo[2,3-b]pyridine derivatives sensitized with 3',4'-dimethoxyacetophenone under irradiation by a high-pressure mercury lamp through Pyrex glass was dramatically accelerated by the addition of Lewis acids, preferably Mg(OTf)₂, to give the products stereoselectively in high yields. The reaction without a Lewis acid gave only small amounts of the [2+2] cycloaddition products. Conformational fixation of the substrates by coordination with a Lewis acid was presumed to facilitate the cycloaddition.

Azaindole therapeutic agents

Azaindole structural framework is an integral part of several biologically active natural and synthetic organic molecules; and several FDA approved drugs for various diseases. In the last decade, quite a number of literature reports appeared describing the pharmacology, biological activity and therapeutic applications of a variety of azaindole molecules. This prompted the organic and medicinal chemistry community to develop novel synthetic methods for various azaindoles and test them for a bioactivity against a variety of biological targets. Herein, we have summarized the biological activity of therapeutically advanced clinical candidates and several preclinical candidate drugs that contain azaindole structural moiety.

Many small steps towards a COVID-19 drug

A large-scale screening campaign has yielded dozens of crystal structures of small molecule fragments that bind to the main protease of SARS-CoV-2. The global research community is encouraged to pursue these as drug discovery starting points for COVID-19.

Development of Potent PfCLK3 Inhibitors Based on TCMDC-135051 as a New Class of Antimalarials

The protein kinase PfCLK3 plays a critical role in the regulation of malarial parasite RNA splicing and is essential for the survival of blood stage Plasmodium falciparum. We recently validated PfCLK3 as a drug target in malaria that offers prophylactic, transmission blocking, and curative potential. Herein, we describe the synthesis of our initial hit TCMDC-135051 (1) and efforts to establish a structure-activity relationship with a 7-azaindole-based series. A total of 14 analogues were assessed in a time-resolved fluorescence energy transfer assay against the full-length recombinant protein kinase PfCLK3, and 11 analogues were further assessed in asexual 3D7 (chloroquine-sensitive) strains of P. falciparum parasites. SAR relating to rings A and B was established. These data together with analysis of activity against parasites collected from patients in the field suggest that TCMDC-135051 (1) is a promising lead compound for the development of new antimalarials with a novel mechanism of action targeting PfCLK3.

Regioselective C-H sulfenylation of N-sulfonyl protected 7-azaindoles promoted by TBAI: a rapid synthesis of 3-thio-7-azaindoles

This paper describes the regioselective C-3 sulfenylation of N-sulfonyl protected 7-azaindoles with sulfonyl chlorides. In this transformation, dual roles of TBAI serving as both promoter and desulfonylation reagent have been demonstrated. The reaction proceeded smoothly under simple conditions to afford 3-thio-7-azaindoles in moderate to good yields with broad substrate scopes. This protocol refrains from using transition-metal catalysts, strong oxidants or bases, and shows its practical synthetic value in organic synthesis.

A novel, practical and highly regioselective TBAI promoted C-3 sulfenylation reaction of N-sulfonyl protected 7-azaindoles with sulfonyl chlorides is presented here.

Levoglucosenone and Its Pseudoenantiomer iso-Levoglucosenone as Scaffolds for Drug Discovery and Development

The bioderived platform molecule levoglucosenone (LGO, 1) and its readily prepared pseudoenantiomer (iso-LGO, 2) have each been subjected to α-iodination reactions with the product halides then being engaged in palladium-catalyzed Ullmann cross-coupling reactions with various bromonitropyridines. The corresponding α-pyridinylated derivatives such as 11 and 24, respectively, are produced as a result. Biological screening of such products reveals that certain of them display potent and selective antimicrobial and/or cytotoxic properties. In contrast, the azaindoles obtained by reductive cyclization of compounds such as 11 and 12 are essentially inactive in these respects. Preliminary mode-of-action studies are reported.

Microwave-assisted synthesis of 7-azaindoles via iron-catalyzed cyclization of an o-haloaromatic amine with terminal alkynes

An efficient and practical procedure was developed to prepare 7-azaindole, starting from an o-haloaromatic amine and corresponding terminal alkynes under microwave irradiation and the scope was demonstrated with a number of examples. The valuable features of this procedure included the iron-catalyzed cyclization, short reaction times and convenient operation. Furthermore, iron catalysis is an interesting alternative to homogeneous catalysis for the synthesis of heterocycles.

An efficient and practical procedure was developed to prepare 7-azaindole, starting from an o-haloaromatic amine and corresponding terminal alkynes under microwave irradiation and the scope was demonstrated with a number of examples.

Solvent-Free C-3 Coupling of Azaindoles with Cyclic Imines

By direct coupling 7-azaindole and cyclic imines, such as 3,4-dihydroisoquinoline, 6,7-dihydrothieno[3,2-c]pyridine, 3,4-dihydro-β-carboline, and 4,5-dihydro-3H-benz[c]azepine, new 3-substituted 7-azaindole derivatives have been synthesized. The reaction was extended to 4-azaindoles and 6-azaindoles, as electron-rich aromatic compounds. The lowest reactivity was observed in the case of C-3 substitution of 5-azaindole. In this case, the aza-Friedel-Crafts reaction took place by using 10 mol % of p-toluenesulfonic acid (p-TSA) as the catalyst. The role of the acid catalyst can be explained by the different pKa values of the azaindoles. All reactions were performed in solvent-free conditions by using both classical heating and microwave irradiation. In all cases, microwave heating proved to be more convenient to synthesize new C-3-substituted azaindole derivatives.