Inhibitors of HIV-1 Protease by Using In Situ Click Chemistry

Palladium-Catalyzed Tandem Reactions via Allene Intermediates for the Rapid Synthesis of a Fused Indenone-Indole Scaffold

A palladium-catalyzed tandem reaction of 1-(2-iodophenyl)-3-arylprop-2-yn-1-ones and 1-(2-azidophenyl)propargyl ethers is developed to provide the rapid construction of a fused polycyclic indenone-indole scaffold under mild conditions. The reaction proceeds via a highly ordered process involving Sonogashira coupling, propargyl-allenyl isomerization, allene-azide cycloaddition, denitrogenation, and diradical coupling. The proposed reaction mechanism is supported by experimental and computational studies.

Introduction and characterization of a novel Cu(ii)-based quaternary deep eutectic solvent and its application in the efficient synthesis of triazoles and tetrazoles under mild conditions as an inexpensive, reusable, benign, and dual solvent/catalyst medium

Deep eutectic solvents consist of hydrogen bond donor and acceptor components. They are a new type of ionic liquids, and they have attracted the attention of many chemists in recent years. In this work, a quaternary deep eutectic solvent (QDES) was prepared using choline chloride, glycerol, l-arginine, and copper acetate. Its physicochemical properties were determined by Fourier transform infrared spectroscopy (FT-IR), thermal analysis (TGA), differential scanning calorimetry (DSC), hydrogen potential (pH), cyclic voltammetry (CV), viscosity, density, refractive index, ionic conductivity and spectrophotometer ultraviolet-visible (UV-Vis). Further, as a novel benign solvent/catalyst for the synthesis of 1,4-disubstituted-1,2,3-triazole, 4-substituted-1H-1,2,3-triazole, and 5-substituted-1H-tetrazole derivatives were used in a click reaction strategy. The special features of this method include mild conditions, a non-toxic environment, short reaction time, easy operation, biodegradability, deep eutectic solvent/catalyst recovery, access to cheaper raw materials, and environmental compatibility.

Design and development of an isatin-1,2,3-triazole hybrid analogue as a potent anti-inflammatory agent with enhanced efficacy and gene expression modulation

Isatin (1H-indole-2,3-dione) and its derivatives have been found to exhibit various biological activities, including anticancer and antidiabetic properties. In this study, a series of nine isatin-1,2,3-triazole conjugates were synthesized and evaluated for their anti-inflammatory potential via in vitro experiments. Their synthesis involved the propargylation of isatin 1 with propargyl bromide to obtain N-propargyl isatin 2, which was subjected to click reactions with different aromatic azides to yield isatin-N-1,2,3-triazoles (3a-i). The structures of all the compounds were confirmed via NMR and HR-MS. The final isatin analogues were tested for their ability to attenuate the production of proinflammatory cytokines in the lipopolysaccharide (LPS)-induced human leukemia monocytic THP-1 cells. Importantly, none of the compounds had any negative effect on THP-1 cell viability at the tested concentrations of 4 mM and 8 mM. LPS induced the production of the cytokines: Tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6) and monocyte chemoattractant protein-1 (MCP-1) by 351.4, 7.9 and 14.3 fold, respectively, in THP-1 cells. However, treatment with compound 3e markedly attenuated the levels of TNF-α (by 6.6 fold and 1.5 fold), IL-6 (by 1.03 fold and 1.41 fold) and MCP-1 (by 3.3 fold and 1.7 fold) by several fold at concentrations of 4 mM and 8 mM, respectively. Furthermore, in the gene expression modulation studies, 3e was found to downregulate the genes responsible for the production of TNF-α (24 and 25 fold), IL-6 (148 and 502 fold) and MCP-1 (50 and 25 fold) at the two tested concentrations compared with their expression in the LPS-induced THP-1 cells (135 fold, 6612 fold, and 68.8 fold, respectively). Thus, 3e markedly attenuated the secretion of TNF-α, IL-6 and MCP-1 from LPS-treated THP-1 cells, and also the expression of the concerned genes. At the lowest dose tested, i.e., 4 mM, 3e had the greatest effect on both gene expression and marker secretion.

Chemically Induced Dimerization via Nanobody Binding Facilitates in Situ Ligand Assembly and On-Demand GPCR Activation

Methods that enable the on-demand synthesis of biologically active molecules offer the potential for a high degree of control over the timing and context of target activation; however, such approaches often require extensive engineering to implement. Tools to restrict the localization of assembly also remain limited. Here we present a new approach for stimulus-induced ligand assembly that helps to address these challenges. This methodology relies on the high affinity and specificity recognition exhibited by antibody fragments (nanobodies, Nbs). By using Nbs that recognize short peptide epitopes to create semisynthetic conjugates, we develop a bioengineering platform termed peptide epitope dimerization (PED) in which the addition of heterodimeric peptide composed of two Nb epitopes stimulates the proximity-induced synthesis of a functional ligand for the parathyroid hormone receptor-1, a G protein-coupled receptor. We further demonstrate that high efficiency assembly can be achieved on the cell surface via Nb-based delivery of template. This approach opens the door for the on-demand generation of bioactive receptor ligands preferentially at a desired biological niche.

Miniaturized Modular Click Chemistry-enabled Rapid Discovery of Unique SARS-CoV-2 Mpro Inhibitors With Robust Potency and Drug-like Profile

The COVID-19 pandemic has required an expeditious advancement of innovative antiviral drugs. In this study, focused compound libraries are synthesized in 96- well plates utilizing modular click chemistry to rapidly discover potent inhibitors targeting the main protease (Mpro) of SARS-CoV-2. Subsequent direct biological screening identifies novel 1,2,3-triazole derivatives as robust Mpro inhibitors with high anti-SARS-CoV-2 activity. Notably, C5N17B demonstrates sub-micromolar Mpro inhibitory potency (IC50 = 0.12 µM) and excellent antiviral activity in Calu-3 cells determined in an immunofluorescence-based antiviral assay (EC50 = 0.078 µM, no cytotoxicity: CC50 > 100 µM). C5N17B shows superior potency to nirmatrelvir (EC50 = 1.95 µM) and similar efficacy to ensitrelvir (EC50 = 0.11 µM). Importantly, this compound displays high antiviral activities against several SARS-CoV-2 variants (Gamma, Delta, and Omicron, EC50 = 0.13 - 0.26 µM) and HCoV-OC43, indicating its broad-spectrum antiviral activity. It is worthy that C5N17B retains antiviral activity against nirmatrelvir-resistant strains with T21I/E166V and L50F/E166V mutations in Mpro (EC50 = 0.26 and 0.15 µM, respectively). Furthermore, C5N17B displays favorable pharmacokinetic properties. Crystallography studies reveal a unique, non-covalent multi-site binding mode. In conclusion, these findings substantiate the potential of C5N17B as an up-and-coming drug candidate targeting SARS-CoV-2 Mpro for clinical therapy.

Miniaturized click chemistry and direct screening facilitate the discovery of triazole piperazine SARS-CoV-2 Mpro inhibitors with improved metabolic stability

The continuous mutational nature of SARS-CoV-2 and its inter-species' similarities emphasize the urgent need to design and develop more direct-acting antiviral agents against highly infectious variants. Herein, we report on the efficient discovery of potent non-covalent non-peptide-derived Mpro inhibitors using miniaturized click chemistry and direct screening. Based on the privileged piperazine scaffold, 68 triazole-containing derivatives were assembled and screened. Notably, representative compound C1N46 (IC50 = 1.87 μM, EC50 = 6.99 μM, CC50 > 100 μM) displayed potent inhibition activity against Mpro and showed promising anti-SARS-CoV-2 properties in vitro. Additionally, C1N46 exhibited improved liver microsome stability compared to lead compound GC-14. Docking studies predicted a multi-site binding mode of the triazole-based compounds. In conclusion, our studies validate the efficacy and feasibility of click chemistry in rapidly discovering antiviral agents.

Protein-Templated Click Ligation Reaction Triggered by Protein-Split Aptamer Interactions

DNA-templated reactions have found wide applications in sensing and drug discovery. However, this strategy has been limited to the use of nucleic acids as templating elements to direct the proximity effect. Herein, we describe a versatile protein-templated split aptamer click ligation reaction (PT-SpA-CLR) in which the protein template-induced covalent proximity ligation of split aptamer elements enables translating protein/aptamer binding events into the output of ligated DNA products. A ligation yield of >80% is observed for three model protein templates, including VEGF165, PDGF-BB, and SARS-CoV-2 S1. The ligation reaction compensates for the weakness of reduced binding affinity resulting from splitting the aptamer, as evidenced by an approximately 2-fold lower dissociation constant than the non-ligated system. This newly developed PT-SpA-CLR strategy is further integrated with colorimetric or fluorescent reporting mechanisms to achieve easy-to-use and low-cost biosensors utilizing ligation to produce a fully active G-quadruplex or an RNA-cleaving DNAzyme to report protein binding. Both assays can achieve specific detection of an intended protein target with a limit of detection at the picomolar level even when challenged in biological samples. The combined PT-SpA-CLR and versatile sensing strategies offer attractive universal platforms for efficient detection of protein biomarkers.

Synthesis of New Chroman-4-one Based 1,2,3-Triazole Analogues as Antioxidant and Anti-Inflammatory Agents

A library of new chroman-4-one based 1,2,3-triazole analogues were synthesized involving a series of condensation, cyclization, Suzuki coupling and copper catalysed click chemistry protocols. The newly synthesized compounds 8a-l were screened for their invitro antioxidant and anti-inflammatory activities by employing Ascorbic acid and Diclofenac as reference drugs respectively. The compound without any substituent on benzyl ring (8a), compound with -Cl substituent in para position of benzyl ring (8i), and compound with ethoxy substituent in para position of benzyl ring (8k) exhibited potent antioxidant and anti-inflammatory activities with higher percentage of inhibition. To understand their binding affinities, molecular docking study of these three compounds performed against NADPH oxidase with presented outstanding docking scores and promising binding interactions like H-bond and hydrophobic.

Cu-catalyzed click reaction in synthesis of eugenol derivatives as potent antimalarial agents

Eugenol(1), a terpenoid found in Ocimum, has various biological activities. The present study aims at extraction, isolation of the plant secondary metabolite eugenol (1), it's derivatisation and structure identification as bioactive molecules. Synthesis and antiplasmodial activity (in-vitro and in-vivo), of a series of fourteen novel eugenol-based 1,2,3-triazole derivatives was done in the present study. Derivatives 5a-5n showed good antimalarial activity against the strain Plasmodium falciparum NF54. Derivative 5 m, IC50 at 2.85 µM was found to be several times better than its precursor 1 (106.82 µM) whereas the derivative 5n showed three fold better activity than compound 1, in vitro. The structure-activity relationship of the synthesised compounds indicated that the presence of triazole ring in eugenol analogues is responsible for their good activity. Compound 5m, was further evaluated for in-vivo antimalarial activity which showed about 79% parasitemia suppression. It is the first report on antimalarial activity of triazole eugenol derivatives.

Protein-templated ligand discovery via the selection of DNA-encoded dynamic libraries

DNA-encoded chemical libraries (DELs) have become a powerful technology platform in drug discovery. Dual-pharmacophore DELs display two sets of small molecules at the termini of DNA duplexes, thereby enabling the identification of synergistic binders against biological targets, and have been successfully applied in fragment-based ligand discovery and affinity maturation of known ligands. However, dual-pharmacophore DELs identify separate binders that require subsequent linking to obtain the full ligands, which is often challenging. Here we report a protein-templated DEL selection approach that can identify full ligand/inhibitor structures from DNA-encoded dynamic libraries (DEDLs) without the need for subsequent fragment linking. Our approach is based on dynamic DNA hybridization and target-templated in situ ligand synthesis, and it incorporates and encodes the linker structures in the library, along with the building blocks, to be sampled by the target protein. To demonstrate the performance of this method, 4.35-million- and 3.00-million-member DEDLs with different library architectures were prepared, and hit selection was achieved against four therapeutically relevant target proteins.

Click chemistry-aided drug discovery: A retrospective and prospective outlook

Click chemistry has emerged as a valuable tool for rapid compound synthesis, presenting notable advantages and convenience in the exploration of potential drug candidates. In particular, in situ click chemistry capitalizes on enzymes as reaction templates, leveraging their favorable conformation to selectively link individual building blocks and generate novel hits. This review comprehensively outlines and introduces the extensive use of click chemistry in compound library construction, and hit and lead discovery, supported by specific research examples. Additionally, it discusses the limitations and precautions associated with the application of click chemistry in drug discovery. Our intention for this review is to contribute to the development of a modular synthetic approach for the rapid identification of drug candidates.

Shotgun Kinetic Target-Guided Synthesis Approach Enables the Discovery of Small-Molecule Inhibitors against Pathogenic Free-Living Amoeba Glucokinases

Pathogenic free-living amoebae (pFLA) can cause life-threatening central nervous system (CNS) infections and warrant the investigation of new chemical agents to combat the rise of infection from these pathogens. Naegleria fowleri glucokinase (NfGlck), a key metabolic enzyme involved in generating glucose-6-phosphate, was previously identified as a potential target due to its limited sequence similarity with human Glck (HsGlck). Herein, we used our previously demonstrated multifragment kinetic target-guided synthesis (KTGS) screening strategy to identify inhibitors against pFLA glucokinases. Unlike the majority of previous KTGS reports, our current study implements a "shotgun" approach, where fragments were not biased by predetermined binding potentials. The study resulted in the identification of 12 inhibitors against 3 pFLA glucokinase enzymes─NfGlck, Balamuthia mandrillaris Glck (BmGlck), and Acanthamoeba castellanii Glck (AcGlck). This work demonstrates the utility of KTGS to identify small-molecule binders for biological targets where resolved X-ray crystal structures are not readily accessible.

Strategies for the Discovery of Oxazolidinone Antibacterial Agents: Development and Future Perspectives

Oxazolidinones represent a significant class of synthetic bacterial protein synthesis inhibitors that are primarily effective against Gram-positive bacteria. The commercial success of linezolid, the first FDA-approved oxazolidinone antibiotic, has motivated researchers to develop more potent oxazolidinones by employing various drug development strategies to fight against antimicrobial resistance, some of which have shown promising results. Thus, this Perspective aims to discuss the strategies employed in constructing oxazolidinone-based antibacterial agents and summarize recent advances in discovering oxazolidinone antibiotics to provide valuable insights for potentially developing next-generation oxazolidinone antibacterial agents or other pharmaceuticals.

Linkers in fragment-based drug design: an overview of the literature

INTRODUCTION

In fragment-based drug design, fragment linking is a popular strategy where two fragments binding to different sub-pockets of a target are linked together. This attractive method remains challenging especially due to the design of ideal linkers.

AREAS COVERED

The authors review the types of linkers and chemical reactions commonly used to the synthesis of linkers, including those utilized in protein-templated fragment self-assembly, where fragments are directly linked in the presence of the protein. Finally, they detail computational workflows and software including generative models that have been developed for fragment linking.

EXPERT OPINION

The authors believe that fragment linking offers key advantages for compound design, particularly for the design of bivalent inhibitors linking two distinct pockets of the same or different subunits. On the other hand, more studies are needed to increase the potential of protein-templated approaches in FBDD. Important computational tools such as structure-based de novo software are emerging to select suitable linkers. Fragment linking will undoubtedly benefit from developments in computational approaches and machine learning models.

Semi-quantification and Potency Verification of the HIV Protease Inhibitor Based on the Matrix-Capsid Protein Immobilized Nickel (II)/NTA-Tol/Graphene Oxide/SPCE Electrochemical Biosensor

Human immunodeficiency virus (HIV) causing acquired immune deficiency syndrome (AIDS) is still a global issue. Long-term drug treatment and nonadherence to medication increase the spread of drug-resistant HIV strains. Therefore, the identification of new lead compounds is being investigated and is highly desirable. Nevertheless, a process generally necessitates a significant budget and human resources. In this study, a simple biosensor platform for semi-quantification and verification of the potency of HIV protease inhibitors (PIs) based on electrochemically detecting the cleavage activity of the HIV-1 subtype C-PR (C-SA HIV-1 PR) was proposed. An electrochemical biosensor was fabricated by immobilizing His6-matrix-capsid (H₆MA-CA) on the electrode surface via the chelation to Ni²⁺-nitrilotriacetic acid (NTA) functionalized GO. The functional groups and the characteristics of modified screen-printed carbon electrodes (SPCE) were characterized by Fourier transform infrared (FTIR) spectroscopy, scanning electron microscopy (SEM), and energy-dispersive X-ray spectroscopy (EDS). C-SA HIV-1 PR activity and the effect of PIs were validated by recording changes in electrical current signals of the ferri/ferrocyanide redox probe. The detection of PIs, i.e., lopinavir (LPV) and indinavir (IDV), toward the HIV protease was confirmed by the decrease in the current signals in a dose-dependent manner. In addition, our developed biosensor demonstrates the ability to distinguish the potency of two PIs to inhibit C-SA HIV-1 PR activities. We anticipated that this low-cost electrochemical biosensor would increase the efficiency of the lead compound screening process and accelerate the discovery and development of new HIV drugs.

Angular Regioselective Synthesis of Varied Functionalized Hexahydro-1,2,4-triazolo[4,3-a]quinazolin-9-ones and Their Antiproliferative Action

New 2-thioxopyrimidin-4-ones capable of participating in regioselective reactions with functionally diverse hydrazonoyl chlorides towards angular regioisomers, rather than linear ones, were designed and synthesized to form stereoisomeric cis- and trans-hexahydro [1,2,4]triazolo[4,3-a]quinazolin-9-ones to be tested as antitumor candidates. The angular regiochemistry of the products was verified through crystallographic experiments and NMR studies. In addition, the regioselectivity of the reaction was found to be independent of the stereochemistry of the used 2-thioxopyrimidin-4-one. Only compound 4c demonstrated satisfactory growth inhibition against all the cancer cells used among all the produced drugs.

Going beyond Binary: Rapid Identification of Protein-Protein Interaction Modulators Using a Multifragment Kinetic Target-Guided Synthesis Approach

Kinetic target-guided synthesis (KTGS) is a powerful screening approach that enables identification of small molecule modulators for biomolecules. While many KTGS variants have emerged, a majority of the examples suffer from limited throughput and a poor signal/noise ratio, hampering reliable hit detection. Herein, we present our optimized multifragment KTGS screening strategy that tackles these limitations. This approach utilizes selected reaction monitoring liquid chromatography tandem mass spectrometry for hit detection, enabling the incubation of 190 fragment combinations per screening well. Consequentially, our fragment library was expanded from 81 possible combinations to 1710, representing the largest KTGS screening library assembled to date. The expanded library was screened against Mcl-1, leading to the discovery of 24 inhibitors. This work unveils the true potential of KTGS with respect to the rapid and reliable identification of hits, further highlighting its utility as a complement to the existing repertoire of screening methods used in drug discovery.

Mutual leveraging of proximity effects and click chemistry in chemical biology

Nature has the remarkable ability to realize reactions under physiological conditions that normally would require high temperature and other forcing conditions. In doing so, often proximity effects such as simultaneous binding of two reactants in the same pocket and/or strategic positioning of catalytic functional groups are used as ways to achieve otherwise kinetically challenging reactions. Though true biomimicry is challenging, there have been many beautiful examples of how to leverage proximity effects in realizing reactions that otherwise would not readily happen under near-physiological conditions. Along this line, click chemistry is often used to endow proximity effects, and proximity effects are also used to further leverage the facile and bioorthogonal nature of click chemistry. This review brings otherwise seemingly unrelated topics in chemical biology and drug discovery under one unifying theme of mutual leveraging of proximity effects and click chemistry and aims to critically analyze the biomimicry use of such leveraging effects as powerful approaches in chemical biology and drug discovery. We hope that this review demonstrates the power of employing mutual leveraging proximity effects and click chemistry and inspires the development of new strategies that will address unmet needs in chemistry and biology.

Erlotinib-Modified BODIPY Photosensitizers for Targeted Photodynamic Therapy

Photodynamic therapy (PDT) is an innovative, non-invasive and highly selective therapeutic modality for tumours and non-malignant diseases. BODIPY based molecules can function as new generation photosensitizers (PSs) in various PDT applications. Despite numerous conjugated PS systems are available, BODIPYs containing erlotinib lagged behind other photosensitizer units. In this study, smart photosensitizers containing BODIPY, erlotinib and hydrophilic units were prepared for the first time, their physicochemical properties and PDT effects were investigated. Compared with non-halogenated compound, halogenated derivatives possessed much lower fluorescence profile as well as the good ROS generation ability under red light. In vitro PDT studies were performed on both healthy (PNT1a) and prostate cancerous cells (PC3) to determine the selectivity of the compounds on cancerous cells and their effects under light. The halogenated conjugates, exposed to low dose of light illumination exhibited potent activity on cancer cell viability and the calculated IC₅₀ values proved the high phototoxicity of the photosensitizers. It was also determined that the PSs have very low dark toxicity and that the light illumination and ROS formation are required for the initiation of the cell death mechanism. As a result, erlotinib modified BODIPYs could serve as promising agents in anticancer photodynamic therapy.

Mechanochemical Approach towards Multi-Functionalized 1,2,3-Triazoles and Anti-Seizure Drug Rufinamide Analogs Using Copper Beads

Highly regiospecific, copper-salt-free and neat conditions have been demonstrated for the 1,3-dipolar azide-alkyne cycloaddition (AAC) reactions under mechanochemical conditions. A group of structurally challenging alkynes and heterocyclic derivatives was efficiently implemented to achieve highly functionalized 1,4-disubstituted-1,2,3-triazoles in good to excellent yield by using the Cu beads without generation of unwanted byproducts. Furthermore, the high-speed ball milling (HSBM) strategy has also been extended to the synthesis of the commercially available pharmaceutical agent, Rufinamide, an antiepileptic drug (AED) and its analogues. The same strategy was also applied for the synthesis of the Cl-derivative of Rufinamide. Analysis of the single crystal XRD data of the triazole was also performed for the final structural confirmation. The Cu beads are easily recoverable from the reaction mixture and used for the further reactions without any special treatment.

Design, Synthesis, in vitro and in silico Characterization of 2-Quinolone-L-alaninate-1,2,3-triazoles as Antimicrobial Agents

Due to the ever-increasing antimicrobial resistance there is an urgent need to continuously design and develop novel antimicrobial agents. Inspired by the broad antibacterial activities of various heterocyclic compounds such as 2-quinolone derivatives, we designed and synthesized new methyl-(2-oxo-1,2-dihydroquinolin-4-yl)-L-alaninate-1,2,3-triazole derivatives via 1,3-dipolar cycloaddition reaction of 1-propargyl-2-quinolone-L-alaninate with appropriate azide groups. The synthesized compounds were obtained in good yield ranging from 75 to 80 %. The chemical structures of these novel hybrid molecules were determined by spectroscopic methods and the antimicrobial activity of the compounds was investigated against both bacterial and fungal strains. The tested compounds showed significant antimicrobial activity and weak to moderate antifungal activity. Despite the evident similarity of the quinolone moiety of our compounds with fluoroquinolones, our compounds do not function by inhibiting DNA gyrase. Computational characterization of the compounds shows that they have attractive physicochemical and pharmacokinetic properties and could serve as templates for developing potential antimicrobial agents for clinical use.

Scientific and Technological Prospecting of 1H-1,2,3-Triazoles

Abstract:

The use of 1H-1,2,3-triazoles has become an important scaffold for applications in different technological sectors. Therefore, we sought to carry out a technological monitoring to understand the international scenario involving 1H-1,2,3-triazoles from the patents filed, in addition to evaluating the relationship between the growth in the number of patents and the improvement of strategies for obtaining of these compounds via a metal-catalyzed azide-alkyne cycloaddition reaction. Technological monitoring was performed with the support of the PatentInspiration® platform, using the keywords "1,2,3-triazol", "1,2,3-triazole", and "1,2,3-triazolyl". A total of 960 registered patents were found, most for the years 2014 and 2019. The main filers were prestigious multinational companies such as Syngenta, Merck, Sandoz, Pfizer, and Bayer. The United States, China, Japan, and Germany lead patent registrations, mainly addressing innovations in chemistry and metallurgy, human needs, and new technologies. These results help to understand the state of innovation for this topic, pointing out the characteristics of the main discoveries concerning 1H-1,2,3-triazole derivatives.

New 1,2,3-Triazoles from (R)-Carvone: Synthesis, DFT Mechanistic Study and In Vitro Cytotoxic Evaluation

Aseries of novel 1,4-disubstituted 1,2,3-triazoles were synthesized from an (R)-carvone terminal alkyne derivative via a Cu (I)-catalyzed azide–alkyne cycloaddition reaction using CuSO₄,5H₂O as the copper (II) source and sodium ascorbate as a reducing agent which reduces Cu (II) into Cu (I). All the newly synthesized 1,2,3-triazoles 9a–h were fully identified on the basis of their HRMS and NMR spectral data and then evaluated for their cell growth inhibition potential by MTS assay against HT-1080 fibrosarcoma, A-549 lung carcinoma, and two breast adenocarcinoma (MCF-7 and MDA-MB-231) cell lines. Compound 9d showed notable cytotoxic effects against the HT-1080 and MCF-7 cells with IC₅₀ values of 25.77 and 27.89 µM, respectively, while compound 9c displayed significant activity against MCF-7 cells with an IC₅₀ value of 25.03 µM. Density functional calculations at the B3LYP/6-31G* level of theory were used to confirm the high reactivity of the terminal alkyne as a dipolarophile. Quantum calculations were also used to investigate the mechanism of both the uncatalyzed and copper (I)-catalyzed azide–alkyne cycloaddition reaction (CuAAC). The catalyzed reaction gives complete regioselectivity via a stepwise mechanism streamlining experimental observations. The calculated free-energy barriers 4.33 kcal/mol and 29.35 kcal/mol for the 1,4- and 1,5-regioisomers, respectively, explain the marked regioselectivity of the CuAAC reaction.

Azide-Alkyne "Click" Reaction in Water Using Parts-Per-Million Amine-Functionalized Azoaromatic Cu(I) Complex as Catalyst: Effect of the Amine Side Arm

A series of Cu(II) complexes, 1-4 and 6, were synthesized through a reaction of amine-functionalized pincer-like ligands, HL^1,2, L^a,b, and a bidentate ligand L¹ with CuCl₂·2H₂O. The chemical reduction of complex 1 using 1 equiv of sodium l-ascorbate resulted in a dimeric Cu(I) complex 5 in excellent yield. All of the complexes, 1-6, were thoroughly characterized using various physicochemical characterization techniques, single-crystal X-ray structure determination, and density functional theory calculations. Ligands HL^1,2 and L^a,b behaved as tridentated donors by the coordination of the amine side arm in their respective Cu(II) complexes, and the amine side arm remained as a pendant in Cu(I) complexes. All of these complexes (1-6) were explored for copper(I)-catalyzed 1,3-dipolar azide-alkyne cycloaddition (CuAAC) reaction at room temperature in water under air. Complex 5 directly served as an active catalyst; however, complexes 1-4 and 6 required 1 equiv of sodium l-ascorbate to generate their corresponding active Cu(I) catalyst. It has been observed that azo-based ligand-containing Cu(I)-complexes are air-stable and were highly efficient for the CuAAC reaction. The amine side arm in the ligand backbone has a dramatic role in accelerating the reaction rate. Mechanistic investigations showed that the alkyne C-H deprotonation was the rate-limiting step and the pendant amine side arm intramolecularly served as a base for Cu-coordinated alkyne deprotonation, leading to the azide-alkyne 2 + 3 cycloaddition reaction. Thus, variation of the amine side arm in complexes 1-4 and use of the most basic diisopropyl amine moiety in complex 4 has resulted in an unique amine-functionalized azoaromatic Cu(I) system for CuAAC reaction upon sodium l-ascorbate reduction. The complex 4 has shown excellent catalysis at its low parts-per-million level loading in water. The catalytic protocol was versatile and exhibited very good functional group tolerance. It was also employed efficiently to synthesize a number of useful functional triazoles having medicinal, catalytic, and targeting properties.

Chemical Evolution of Antivirals Against Enterovirus D68 through Protein-Templated Knoevenagel Reactions

The generation of bioactive molecules from inactive precursors is a crucial step in the chemical evolution of life, however, mechanistic insights into this aspect of abiogenesis are scarce. Here, we investigate the protein-catalyzed formation of antivirals by the 3C-protease of enterovirus D68. The enzyme induces aldol condensations yielding inhibitors with antiviral activity in cells. Kinetic and thermodynamic analyses reveal that the bioactivity emerges from a dynamic reaction system including inhibitor formation, alkylation of the protein target by the inhibitors, and competitive addition of non-protein nucleophiles to the inhibitors. The most active antivirals are slowly reversible inhibitors with elongated target residence times. The study reveals first examples for the chemical evolution of bio-actives through protein-catalyzed, non-enzymatic C-C couplings. The discovered mechanism works under physiological conditions and might constitute a native process of drug development.

Metabolic and conformational stabilization of a VEGF-mimetic beta-hairpin peptide by click-chemistry

HPLW is a Vascular Endothelial Growth Factor (VEGF)-mimicking beta-hairpin peptide endowed of proangiogenic effect and showing valuable biomedical application in the proangiogenic therapy. However, the translational potential of HPLW is limited by its low metabolic stability, which would shorten the in vivo efficacy of the molecule. Here, we developed a peptide analog of HPLW, named HPLW2, that retains the structural and biological properties of the original peptide but features an impressive resistance to degradation by human serum proteases. HPLW2 was obtained by covalently modifying the chemical structure of the peptide with molecular tools known to impart protease resistance. Notably, the peptide was cyclized by installing an interstrand triazole bridge through Cu(I)-catalyzed azide-alkyne 1,3-dipolar cycloaddition (CuAAC) reaction. HPLW2 appears as a novel and promising drug candidate with potential biomedical application in the proangiogenic therapy as a low molecular weight drug, alternative to the use of VEGF. Our work points out the utility of the interstrand triazole bridge as effective chemical platform for the conformational and metabolic stabilization of beta-hairpin bioactive peptides.

Triazole, imidazole, and thiazole-based compounds as potential agents against coronavirus

The expansion of the novel coronavirus known as SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), COVID-19 (coronavirus disease 2019), or 2019-nCoV (2019 novel coronavirus) is a global concern over its pandemic potential. The need for therapeutic alternatives to stop this new pandemic is urgent. Nowadays, no efficacious therapy is available, and vaccines and drugs are underdeveloped to cure or prevent SARS-CoV-2 infections in many countries. Some vaccines candidates have been approved; however, a number of people are still skeptical of this coronavirus vaccines. Probably because of issues related to the quantity of the vaccine and a possible long-term side effects which are still being studied. The previous pandemics of infections caused by coronavirus, such as SARS-CoV in 2003, the Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012, HCoV-229E, and HCoV-OC43 were described in the 1960 s, -HCoV-NL63 isolated in 2004, and HCoV-HKU1identified in 2005 prompted researchers to characterize many compounds against these viruses. Most of them could be potentially active against the currently emerging novel coronavirus. Five membered nitrogen heterocycles with a triazole, imidazole, and thiazole moiety are often found in many bioactive molecules such as coronavirus inhibitors. This present work summarizes to review the biological and structural studies of these compound types as coronavirus inhibitors.

Synthesis, in vitro and computational studies of novel glycosyl-1, 2, 3-1H-triazolyl methyl benzamide derivatives as potential α-glucosidase inhibitory activity

A series of novel glycosyl-1,2,3-1H-triazolyl methyl benzamide analogues were synthesized by the unambiguous strategy and evaluated for α-glucosidase inhibitory activity. Glycosyl benzamide exhibited a dose-dependent inhibition of α-glucosidase activity. The In-vitro α-glucosidase inhibition activity results indicated that all the synthesized triazolyl methyl benzamide compounds (IC₅₀ values ranging from 25.3 ± 0.8 to 118.5 ± 5.3 μM) exhibited more inhibitory activity in comparison with the standard drug acarbose (IC₅₀ = 750.0 ± 12.5 μM). Among all, the 3 deacetylated glycosyl methyl benzamide derivatives (4c, 4d and 4f) showed promising α-glucosidase enzyme inhibitory activities with IC₅₀ value 25.3 ± 0.8, 26.1 ± 1.5 and 30.6 ± 2.1 respectively. Furthermore, these compounds were subjected to molecular docking and molecular dynamics simulation studies. The molecular docking studies were performed between (PDB ID: 3A4A) target protein and these synthesized molecules. The compounds displayed good docking energies in the range of -7.5 to -7.8 Kcal/mol. This work could be used as an initial approach in identifying potential novel molecules with the promising activity of type-2 diabetes mellitus.

Bioactive 1,2,3-Triazoles: An Account on their Synthesis, Structural Diversity and Biological Applications

The triazole heterocycle is a privileged scaffold in medicinal chemistry, since its structure is present in a large number of biologically active molecules, including several drugs currently in the market. Due to their vast applications, a wide variety of methods are described for their preparation, such as the 1,3-dipolar cycloaddition and processes involving diazo compounds and diazo transfer reactions. Considering the significant number of contributions from our research group to this chemistry in recent decades, in this account we discuss both the development of new methods for the synthesis of 1,2,3-triazoles and the preparation of new triazole-functionalized biologically active molecules using classical approaches.

Kinetic Target-Guided Synthesis of Small-Molecule G-Quadruplex Stabilizers

The formation of a G-quadruplex motif in the promoter region of the c-MYC protooncogene prevents its expression. Accordingly, G-quadruplex stabilization by a suitable ligand may be a viable approach for anticancer therapy. In our study, we used the 4-(4-methylpiperazin-1-yl)aniline molecule, previously identified as a fragment library screen hit, as a template for the SAR-guided design of a new small library of clickable fragments and subjected them to click reactions, including kinetic target-guided synthesis in the presence of a G-quadruplex forming oligonucleotide Pu24. We tested the clickable fragments and products of click reactions for their G-quadruplex stabilizing activity and determined their mode of binding to the c-MYC G-quadruplex by NMR spectroscopy. The enhanced stabilizing potency of click products in biology assays (FRET, Polymerase extension assay) matched the increased yields of in situ click reactions. In conclusion, we identified the newly synthesized click products of bis-amino derivatives of 4-(4-methylpiperazin-1-yl)aniline as potent stabilizers of c-MYC G-quadruplex, and their further evolution may lead to the development of an efficient tool for cancer treatment.

Protein-Templated Hit Identification through an Ugi Four-Component Reaction*

Kinetic target-guided synthesis represents an efficient hit-identification strategy, in which the protein assembles its own inhibitors from a pool of complementary building blocks via an irreversible reaction. Herein, we pioneered an in situ Ugi reaction for the identification of novel inhibitors of a model enzyme and binders for an important drug target, namely, the aspartic protease endothiapepsin and the bacterial β-sliding clamp DnaN, respectively. Highly sensitive mass-spectrometry methods enabled monitoring of the protein-templated reaction of four complementary reaction partners, which occurred in a background-free manner for endothiapepsin or with a clear amplification of two binders in the presence of DnaN. The Ugi products we identified show low micromolar activity on endothiapepsin or moderate affinity for the β-sliding clamp. We succeeded in expanding the portfolio of chemical reactions and biological targets and demonstrated the efficiency and sensitivity of this approach, which can find application on any drug target.

Decarboxylative Alkyl Coupling Promoted by NADH and Blue Light

Photoexcited dihydronicotinamides like NADH and analogues have been found to generate alkyl radicals upon reductive decarboxylation of redox-active esters without auxiliary photocatalysts. This principle allowed aliphatic photocoupling between redox-active carboxylate derivatives and electron-poor olefins, displaying surprising water and air-tolerance and unusually high coupling rates in dilute conditions. The orthogonality of the reaction in the presence of other carboxylic acids and its utility in the functionalization of DNA is presented, notably using visible light in combination with NADH, the ubiquitous reductant of life.

Synthesis and Antitrypanosomal Activity of 1,4-Disubstituted Triazole Compounds Based on a 2-Nitroimidazole Scaffold: a Structure-Activity Relationship Study

Chagas disease affects 6-8 million people worldwide, remaining a public health concern. Toxicity, several adverse effects and inefficiency in the chronic stage of the disease are the major challenges regarding the available treatment protocols. This work involved the synthesis of twenty-two 1,4-disubstituted-1,2,3-triazole analogues of benznidazole (BZN), by using a click chemistry strategy. Analogues were obtained in moderate to good yields (40-97 %). Antitrypanosomal activity was evaluated against the amastigote forms of Trypanosoma cruzi. Compound 8 a (4-(2-nitro-1H-imidazol-1-yl)methyl)-1-phenyl-1H-1,2,3-triazole) without substituents on phenyl ring showed similar biological activity to BZN (IC₅₀ =3.0 μM, SI>65.3), with an IC₅₀ =3.1 μM and SI>64.5. Compound 8 o (3,4-di-OCH₃ -Ph) with IC₅₀ = 0.65 μM was five-fold more active than BZN, and showed an excellent selectivity index (SI>307.7). Compound 8 v (3-NO₂ , 4-CH₃ -Ph) with IC₅₀ =1.2 μM and relevant SI>166.7, also exhibited higher activity than BZN. SAR analysis exhibited a pattern regarding antitrypanosomal activity relative to BZN, in compounds with electron-withdrawing groups (Hammett σ+) at position 3, and electron-donating groups (Hammett σ-) at position 4, as observed in 8 o and 8 v. Further research might explore in vivo antitrypanosomal activity of promising analogues 8 a, 8 o, and 8 v. Overall, this study indicates that approaches such as the bioisosteric replacement of amide group by 1,2,3-triazole ring, the use of click chemistry as a synthesis strategy, and design tools like Craig-plot and Topliss tree are promising alternatives to drug discovery.

Helical Self-Assembly of Optically Active Glycoconjugated Phthalocyanine J-Aggregates

Four galactoconjugated zinc(II) phthalocyanines (Pcs) have been prepared and fully characterized. The carbohydrate-containing phthalonitrile precursors of the Pcs were synthesized through a copper-catalysed azide-alkyne cycloaddition (CuAAC). The Pcs show a remarkable aggregation behaviour in solution, depending on the nature of the solvent, the temperature and the substitution position on the phthalocyanine. Solvent-dependent CD-spectroscopy experiments show that these Pcs aggregate as chiral helices in solution. Crystal structure data of a phthalocyanine bearing two carbohydrate units substantiate the properties shown by CD spectroscopy. Furthermore, the 1,2,3-triazole moieties of the Pcs play a decisive role in the formation of supramolecular aggregates. The glycoconjugated zinc(II) phthalocyanines described here show molar extinction coefficients ϵ_max >10⁵  M^-1  cm^-1 and absorption maxima λ_max >680 nm, which make them attractive photosensitizers for Photodynamic Therapy (PDT).

Target-Directed Azide-Alkyne Cycloaddition for Assembling HIV-1 TAR RNA Binding Ligands

The highly conserved HIV-1 transactivation response element (TAR) binds to the trans-activator protein Tat and facilitates viral replication in its latent state. The inhibition of Tat-TAR interactions by selectively targeting TAR RNA has been used as a strategy to develop potent antiviral agents. Therefore, HIV-1 TAR RNA represents a paradigmatic system for therapeutic intervention. Herein, we have employed biotin-tagged TAR RNA to assemble its own ligands from a pool of reactive azide and alkyne building blocks. To identify the binding sites and selectivity of the ligands, the in situ cycloaddition has been further performed using control nucleotide (TAR DNA and TAR RNA without bulge) templates. The hit triazole-linked thiazole peptidomimetic products have been isolated from the biotin-tagged target templates using streptavidin beads. The major triazole lead generated by the TAR RNA presumably binds in the bulge region, shows specificity for TAR RNA over TAR DNA, and inhibits Tat-TAR interactions.

Synthesis of 1,4-Biphenyl-triazole Derivatives as Possible 17β-HSD1 Inhibitors: An in Silico Study

Triazoles occupy an important position in medicinal chemistry because of their various biological activities. The structural features of 1,2,3-triazoles enable them to act as a bioisostere of different functional groups such as amide, ester, carboxylic acid, and heterocycle, being capable of forming hydrogen bonds and π-π interactions or coordinate metal ions with biological targets. In this work, the synthesis of 1,2,3-triazole derivatives via copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) is reported. Overexpression of 17β-hydroxysteroid dehydrogenase type 1 (17β-HSD1) is often found in breast cancer cells. Molecular similarity and docking analysis were used to evaluate the potential inhibitory activity of 1,2,3-triazoles synthesized over 17β-HSD1 for the treatment of mammary tumors. Our in silico analysis shows that compounds 4c, 4d, 4f, 4g, and 4j are good molecular scaffold candidates as 17β-HSD1 inhibitors.