Design of Potent Poxvirus Inhibitors of the Heterodimeric Processivity Factor Required for Viral Replication

Palladium-Catalyzed C3-Carbaldehyde Directed Regioselective C2-Thioarylation of Indoles

Palladium-catalyzed thioarylation of indoles by diaryl disulfides in the presence of phenyliododiacetate is reported. The directing potential of weakly coordinating aldehyde group present at 3-position of indole was exploited for regioselective C2-H thioarylation over the possible C4-H functionalization. Mechanistic studies reveal that the process involves initial generation of thioaryl radical followed by sequential C-H activation, thiolate transfer, and reductive elimination.

Divergent Electrochemical Synthesis of Indoles through pKa Regulation of Amides: Synthetic and Mechanistic Insights

A divergent synthetic approach to access highly substituted indole scaffolds is illustrated. By virtue of a tunable electrochemical strategy, distinct control over the C-3 substitution pattern was achieved by employing two analogous 2-styrylaniline precursors. The chemoselectivity is governed by the fine-tuning of the acidity of the amide proton, relying on the appropriate selection of N-protecting groups, and assisted by the reactivity of the electrogenerated intermediates. Detailed mechanistic investigations based on cyclic voltametric experiments and computational studies revealed the crucial role of water additive, which assists the proton-coupled electron transfer event for highly acidic amide precursors, followed by an energetically favorable intramolecular C-N coupling, causing exclusive fabrication of the C-3 unsubstituted indoles. Alternatively, the implementation of an electrogenerated cationic olefin activator delivers the C-3 substituted indoles through the preferential nucleophilic nature of the N-acyl amides. This electrochemical approach of judicious selection of N-protecting groups to regulate pKa/E° provides an expansion in the domain of switchable generation of heterocyclic derivatives in a sustainable fashion, with high regio- and chemoselectivity.

Low-Valent-Tungsten-Catalyzed Aerobic Oxidative Cross-Dehydrogenative Coupling Reaction

A straightforward and convenient protocol was established for the synthesis of thiophosphates and 3-sulfenylated indoles via low-valent-tungsten-catalyzed aerobic oxidative cross-dehydrogenative coupling reactions. These reactions occur under mild conditions and simple operations with commercially available starting materials, processing the advantage of excellent atom and step economy, broad substrate scope, and good functional groups tolerance. Moreover, this transformation could be practiced on the gram scale, which exhibits great potential in the preparation of drug-derived or bioactive molecules.

Correlated Target Search by Vaccinia Virus Uracil-DNA Glycosylase, a DNA Repair Enzyme and a Processivity Factor of Viral Replication Machinery

The protein encoded by the vaccinia virus D4R gene has base excision repair uracil-DNA N-glycosylase (vvUNG) activity and also acts as a processivity factor in the viral replication complex. The use of a protein unlike PolN/PCNA sliding clamps is a unique feature of orthopoxviral replication, providing an attractive target for drug design. However, the intrinsic processivity of vvUNG has never been estimated, leaving open the question whether it is sufficient to impart processivity to the viral polymerase. Here, we use the correlated cleavage assay to characterize the translocation of vvUNG along DNA between two uracil residues. The salt dependence of the correlated cleavage, together with the similar affinity of vvUNG for damaged and undamaged DNA, support the one-dimensional diffusion mechanism of lesion search. Unlike short gaps, covalent adducts partly block vvUNG translocation. Kinetic experiments show that once a lesion is found it is excised with a probability ~0.76. Varying the distance between two uracils, we use a random walk model to estimate the mean number of steps per association with DNA at ~4200, which is consistent with vvUNG playing a role as a processivity factor. Finally, we show that inhibitors carrying a tetrahydro-2,4,6-trioxopyrimidinylidene moiety can suppress the processivity of vvUNG.

An Overview of Antivirals against Monkeypox Virus and Other Orthopoxviruses

The current monkeypox outbreaks during the COVID-19 pandemic have reignited interest in orthopoxvirus antivirals. Monkeypox belongs to the Orthopoxvirus genus of the Poxviridae family, which also includes the variola virus, vaccinia virus, and cowpox virus. Two orally bioavailable drugs, tecovirimat and brincidofovir, have been approved for treating smallpox infections. Given their human safety profiles and in vivo antiviral efficacy in animal models, both drugs have also been recommended to treat monkeypox infection. To facilitate the development of additional orthopoxvirus antivirals, we summarize the antiviral activity, mechanism of action, and mechanism of resistance of orthopoxvirus antivirals. This perspective covers both direct-acting and host-targeting antivirals with an emphasis on drug candidates showing in vivo antiviral efficacy in animal models. We hope to speed the orthopoxvirus antiviral drug discovery by providing medicinal chemists with insights into prioritizing proper drug targets and hits for further development.

Human mpox: Biology, epidemiology, therapeutic options, and development of small molecule inhibitors

Although monkeypox (mpox) has been endemic in Western and Central Africa for 50 years, it has not received sufficient prophylactic and therapeutical attention to avoid evolving into an epidemic. From January 2022 to January 2023, more than 84,000 of mpox cases were reported from 110 countries worldwide. Case numbers appear to be rising every day, making mpox an increasing global public health threat for the foreseeable future. In this perspective, we review the known biology and epidemiology of mpox virus, together with the latest therapeutic options available for mpox treatment. Further, small molecule inhibitors against mpox virus and the future directions in this field are discussed as well.

Silver-catalyzed direct selanylation of indoles: synthesis and mechanistic insights

Herein we describe the Ag(i)-catalyzed direct selanylation of indoles with diorganoyl diselenides. The reaction gave 3-selanylindoles with high regioselectivity and also allowed direct access to 2-selanylindoles when the C3 position of the indole ring was blocked via a process similar to Plancher rearrangement. Experimental analyses and density functional theory calculations were carried out in order to picture the reaction mechanism. Among the pathways considered (via concerted metalation-deprotonation, Ag(iii), radical, and electrophilic aromatic substitution), our findings support a classic electrophilic aromatic substitution via Lewis adducts between Ag(i) and diorganoyl diselenides. The results also afforded new insights into the interactions between Ag(i) and diorganoyl diselenides.

Divergent synthesis of 2-methylthioindole and 2-unsubstituted indole derivatives mediated by SOCl2 and dimethyl/diethyl sulfoxides

A metal-free divergent synthesis of indole compounds dependent on a reagent via intramolecular C(sp²)-H amination was described. The reaction of 2-vinylanilines with DMSO/SOCl₂ at 70 °C was found to give 2-thiomethylindoles, while replacing DMSO with diethyl sulfoxide afforded 2-unsubstituted indoles in a highly selective manner.

Palladium-Catalyzed Three-Component Cross-Coupling of Conjugated Dienes with Indoles Using Ethynylbenziodazolones as Electrophilic Alkynylating Reagents

A palladium-catalyzed regioselective 1,2-alkynyl-carbonalization of conjugated dienes with ethynylbenziodazolone (EBZ) and indoles has been developed for the first time. Various molecules containing alkenyl, alkynyl, and indole groups were readily obtained. Moreover, the resulting products can be applied to various derivatizations. This protocol uses EBZ as an electrophilic alkynylating reagent, avoiding the byproduct of dimerization of alkynes.

Discovery of a potent cytotoxic agent that promotes G2/M phase cell cycle arrest and apoptosis in a malignant human pharyngeal squamous carcinoma cell line

Squamous cell carcinoma is the major form of malignancy that arises in head and neck cancer. The modest improvement in the 5‑year survival rate underpins its complex etiology and provides the impetus for the discovery of new therapeutics. The present study describes the discovery of an indole‑based small molecule (24a) that was a potent cytotoxic agent with antiproliferative and pro‑apoptotic properties against a pharyngeal carcinoma cell line, Detroit 562, effectively killing the cells at a half‑maximal inhibitory concentration of 0.03 µM, as demonstrated using cell proliferation studies. The antiproliferative property of 24a was demonstrated by its ability to promote G₂/M blockade, as assessed by cell cycle analysis using flow cytometry and the monitoring of real‑time cell cycle progression by the fluorescence ubiquitination‑based cell cycle indicator. This pro‑apoptotic property is supported by the promotion of TUNEL‑staining and increase in the activities of caspases‑3/7 and ‑6, in addition to the expression of death receptors and the cleavage of poly (ADP‑ribose) polymerase 1 protein as demonstrated by western blotting. Given that Detroit 562 lacks functional p53, it is suggested that 24a acts independently of the tumor suppressor.

Visible-Light-Induced, Graphene Oxide-Promoted C3-Chalcogenylation of Indoles Strategy under Transition-Metal-Free Conditions

An efficient and general method for the synthesis of 3-sulfenylindoles and 3-selenylindoles employing visible-light irradiation with graphene oxide as a promoter at room temperature has been achieved. The reaction features are high yields, simple operation, metal-free and iodine-free conditions, an easy-to-handle oxidant, and gram-scalable synthesis. This simple protocol allows one to access a wide range of 3-arylthioindoles, 3-arylselenylindoles, and even 3-thiocyanatoindoles with good to excellent yields.

Cp*Co(III)-catalyzed C2-thiolation and C2,C3-dithiolation of substituted indoles with N-(arylthio)succinimide

A general and efficient Cp*Co^III-catalyzed C2-thiolation and C2,C3-dithiolation of indole derivatives has been achieved employing N-(aryl/alkylthio)succinimide as a thiolating reagent. This external oxidant-free method utilizes only catalytic amounts of additive and tolerates various functional groups to afford various thiolated products in good yields. Control experiments revealed the importance of the Cp*Co^III-catalyst for both C2- and C3-thiolation.

Transient Directing Groups in Metal-Organic Cooperative Catalysis

The direct functionalization of C-H bonds is among the most fundamental chemical transformations in organic synthesis. However, when the innate reactivity of the substrate cannot be utilized for the functionalization of a given single C-H bond, this selective C-H bond functionalization mostly relies on the use of directing groups that allow bringing the catalyst in close proximity to the C-H bond to be activated and these directing groups need to be installed before and cleaved after the transformation, which involves two additional undesired synthetic operations. These additional steps dramatically reduce the overall impact and the attractiveness of C-H bond functionalization techniques since classical approaches based on substrate pre-functionalization are sometimes still more straightforward and appealing. During the past decade, a different approach involving both the in situ installation and removal of the directing group, which can then often be used in a catalytic manner, has emerged: the transient directing group strategy. In addition to its innovative character, this strategy has brought C-H bond functionalization to an unprecedented level of usefulness and has enabled the development of remarkably efficient processes for the direct and selective introduction of functional groups onto both aromatic and aliphatic substrates. The processes unlocked by the development of these transient directing groups will be comprehensively overviewed in this review article.

Solution Structure of the C-terminal Domain of A20, the Missing Brick for the Characterization of the Interface between Vaccinia Virus DNA Polymerase and its Processivity Factor

Poxviruses are enveloped viruses with a linear, double-stranded DNA genome. Viral DNA synthesis is achieved by a functional DNA polymerase holoenzyme composed of three essential proteins. For vaccinia virus (VACV) these are E9, the catalytic subunit, a family B DNA polymerase, and the heterodimeric processivity factor formed by D4 and A20. The A20 protein links D4 to the catalytic subunit. High-resolution structures have been obtained for the VACV D4 protein in complex with an N-terminal fragment of A20 as well as for E9. In addition, biochemical studies provided evidence that a poxvirus-specific insertion (insert 3) in E9 interacts with the C-terminal residues of A20. Here, we provide solution structures of two different VACV A20 C-terminal constructs containing residues 304-426, fused at their C-terminus to either a BAP (Biotin Acceptor Peptide)-tag or a short peptide containing the helix of E9 insert 3. Together with results from titration studies, these structures shed light on the molecular interface between the catalytic subunit and the processivity factor component A20. The interface comprises hydrophobic residues conserved within the Chordopoxvirinae subfamily. Finally, we constructed a HADDOCK model of the VACV A20_304-426-E9 complex, which is in excellent accordance with previous experimental data.

DMSO/SOCl2-mediated C(sp2)-H amination: switchable synthesis of 3-unsubstituted indole and 3-methylthioindole derivatives

The reaction of 2-alkenylanilines with SOCl2 in DMSO was found to selectively afford 3-unsubstituted indoles and 3-methylthioindoles. This switchable approach was found to be temperature-dependent: at room temperature, the reaction afforded 3-unsubstituted indoles through intramolecular cyclization and elimination; while at higher temperature, the reaction gave 3-methylthioindoles via further electrophilic methylthiolation.

The direct C3 chalcogenylation of indolines using a graphene-oxide-promoted and visible-light-induced synergistic effect

A green methodology for the construction of carbon–chalcogen (S and Se) bonds via a GO-promoted and metal-free light-induced synergistic effect is demonstrated.

Palladium/Norbornene Cooperative Catalysis

Palladium/norbornene cooperative catalysis has emerged as a distinct approach to construct polyfunctionalized arenes from readily available starting materials. This Review provides a comprehensive overview of this field, including the early stoichiometric investigations, catalytic reaction developments, as well as the applications in the syntheses of bioactive compounds and polymers. The section of catalytic reactions is divided into two parts according to the reaction initiation mode: Pd(0)-initiated reactions and Pd(II)-initiated reactions.

Targeting uracil-DNA glycosylases for therapeutic outcomes using insights from virus evolution

Ung-type uracil-DNA glycosylases are frontline defenders of DNA sequence fidelity in bacteria, plants and animals; Ungs also directly assist both innate and humoral immunity. Critically important in viral pathogenesis, whether acting for or against viral DNA persistence, Ungs also have therapeutic relevance to cancer, microbial and parasitic diseases. Ung catalytic specificity is uniquely conserved, yet selective antiviral drugging of the Ung catalytic pocket is tractable. However, more promising precision therapy approaches present themselves via insights from viral strategies, including sequestration or adaptation of Ung for noncanonical roles. A universal Ung inhibition mechanism, converged upon by unrelated viruses, could also inform design of compounds to inhibit specific distinct Ungs. Extrapolating current developments, the character of such novel chemical entities is proposed.

AuBr3 -Catalyzed Chemoselective Annulation of Isocyanates with 2H-Azirine

The chemoselective cyclization of isocyanates with 2H-azirine was achieved with AuBr₃ as catalyst. This transfer sets the stage for the synthesis of aromatic oxazole-ureas in a tandem process. The addition of a catalytic amount of phosphite enhances the process enormously. The reaction can also be performed in a one-pot process using benzoyl azide instead of isocyanate under the same conditions. A detailed study on the role of the phosphite that was applied as an additive revealed that only non-coordinated phosphite can reduce gold(III) and that gold(I) coordinated phosphite is not oxidized. Accompanied by the reduction of gold, HBr is generated in situ, which turned out to be the actual promotor in combination with the remaining AuBr₃ . The positive effect of acid can be explained by a strong N-Au coordination, which tends to break more easily in the presence of small amount of protic acid in the reaction solution.

3-Selenocyanate-indoles as new agents for the treatment of superficial and mucocutaneous infections

The development of resistance to the current antifungal agents is an alarming problem.

Mutation and structure guided discovery of an antiviral small molecule that mimics an essential C-Terminal tripeptide of the vaccinia D4 processivity factor

The smallpox virus (variola) remains a bioterrorism threat since a majority of the human population has never been vaccinated. In the event of an outbreak, at least two drugs against different targets of variola are critical to circumvent potential viral mutants that acquire resistance. Vaccinia virus (VACV) is the model virus used in the laboratory for studying smallpox. The VACV processivity factor D4 is an ideal therapeutic target since it is both essential and specific for poxvirus replication. Recently, we identified a tripeptide (Gly-Phe-Ile) motif at the C-terminus of D4 that is conserved among poxviruses and is necessary for maintaining protein function. In the current work, a virtual screening for small molecule mimics of the tripeptide identified a thiophene lead that effectively inhibited VACV, cowpox virus, and rabbitpox virus in cell culture (EC₅₀ = 8.4-19.7 μM) and blocked in vitro processive DNA synthesis (IC₅₀ = 13.4 μM). Compound-binding to D4 was demonstrated through various biophysical methods and a dose-dependent retardation of the proteolysis of D4 proteins. This study highlights an inhibitor design strategy that exploits a susceptible region of the protein and identifies a novel scaffold for a broad-spectrum poxvirus inhibitor.

Copper-catalysed regioselective sulfenylation of indoles with sodium sulfinates

A copper-catalysed sulfenylation of indoles with sodium sulfinates that affords 3-sulfenylindoles in good-to-excellent yields in N,N-dimethyl formamide (DMF) is described. In the process, DMF serves not only as a solvent but also as a reductant. This transformation is easy to carry out and has mild reaction conditions and good functional group tolerance.

Cooperative catalysis by bovine serum albumin-iodine towards cascade oxidative coupling-C(sp(2))-H sulfenylation of indoles/hydroxyaryls with thiophenols on water

Cooperative cascade catalysis by bovine serum albumin (BSA)-iodine allows for the first time the performance of C(sp(2))-H sulfenylation of indole from readily available thiophenol (-SH bond) via in situ generation/cleavage of disulfide (S-S bond) in air under aqueous conditions, whereas BSA or I2 individually do not permit this two step sequence to occur in the same pot towards C-S bond formation. This green cooperative protocol is extendable to sulfenylation of hydroxyaryls (i.e. 2-naphthol or 4-hydroxycoumarin) with diverse thiols (aryl/heteroaryl) without using any toxic metal catalysts, bases or oxidants, thus rendering the process environmentally and economically reliable. Further, the gram scale synthesis of a COX-2 inhibitor (3-(pyridin-2-ylthio)-1H-indole), regioselectivity and recyclability (up to four cycles) are the additional merits of this cooperative cascade bio-chemocatalytic (BSA-I2) protocol. Moreover, HPLC and ESI-MS provide powerful insights into the mechanistic aspects of the above cascade sulfenylation reaction.

C-H alkylation reactions of indoles mediated by Pd(ii) and norbornene: applications and recent developments

The Catellani reaction enables an ortho-C-H activation based on oxidative addition of Pd(0) and an intermediary carbopalladation of norbornene. Among its variants, the recently developed C2-selective alkylation of indoles is particular as it employs Pd(ii) as the source of palladium. This review describes the mechanistic background of this transformation. Applications in total synthesis and in the synthesis of biologically relevant molecules are illustrated and further developments of the method are discussed.

Iron(ii)-catalyzed C-2 cyanomethylation of indoles and pyrroles via direct oxidative cross-dehydrogenative coupling with acetonitrile derivatives

A novel and efficient approach for the C(sp²)–H/C(sp³)–H oxidative coupling of indoles and pyrroles with acetonitrile derivatives was reported by using the Fe(ii) complex.

Dual vicinal functionalisation of heterocycles via an interrupted Pummerer coupling/[3,3]-sigmatropic rearrangement cascade

A dual vicinal functionalisation cascade involving the union of heterocycles and allyl sulfoxides is described. In particular, the approach provides efficient one-step access to biologically relevant and synthetically important C3 thio, C2 carbo substituted indoles. The reaction operates under mild, metal free conditions and without directing groups, via an interrupted Pummerer coupling of activated allyl sulfoxides, generating allyl heteroaryl sulfonium salts that are predisposed to a charge accelerated [3,3]-sigmatropic rearrangement.

Direct C2-Functionalization of Indoles Triggered by the Generation of Iminium Species from Indole and Sulfonium Salt

An indole core bearing a functional group on the C2 position is often found as a key structure in biologically active natural products and pharmaceuticals. Here, we report direct C2-functionalization of indoles triggered by the formation of an iminium species generated from indole and a sulfonium reagent. The reaction proceeded under very mild conditions to give the corresponding C2-substituted indole derivatives in good to high yields.

The vaccinia virus DNA polymerase and its processivity factor

Vaccinia virus is the prototypic poxvirus. The 192 kilobase double-stranded DNA viral genome encodes most if not all of the viral replication machinery. The vaccinia virus DNA polymerase is encoded by the E9L gene. Sequence analysis indicates that E9 is a member of the B family of replicative polymerases. The enzyme has both polymerase and 3'-5' exonuclease activities, both of which are essential to support viral replication. Genetic analysis of E9 has identified residues and motifs whose alteration can confer temperature-sensitivity, drug resistance (phosphonoacetic acid, aphidicolin, cytosine arabinsode, cidofovir) or altered fidelity. The polymerase is involved both in DNA replication and in recombination. Although inherently distributive, E9 gains processivity by interacting in a 1:1 stoichiometry with a heterodimer of the A20 and D4 proteins. A20 binds to both E9 and D4 and serves as a bridge within the holoenzyme. The A20/D4 heterodimer has been purified and can confer processivity on purified E9. The interaction of A20 with D4 is mediated by the N'-terminus of A20. The D4 protein is an enzymatically active uracil DNA glycosylase. The DNA-scanning activity of D4 is proposed to keep the holoenzyme tethered to the DNA template but allow polymerase translocation. The crystal structure of D4, alone and in complex with A20_1-50 and/or DNA has been solved. Screens for low molecular weight compounds that interrupt the A20_1-50/D4 interface have yielded hits that disrupt processive DNA synthesis in vitro and/or inhibit plaque formation. The observation that an active DNA repair enzyme is an integral part of the holoenzyme suggests that DNA replication and repair may be coupled.

A Conserved Tripeptide Sequence at the C Terminus of the Poxvirus DNA Processivity Factor D4 Is Essential for Protein Integrity and Function

Vaccinia virus (VACV) is a poxvirus, and the VACV D4 protein serves both as a uracil-DNA glycosylase and as an essential component required for processive DNA synthesis. The VACV A20 protein has no known catalytic function itself but associates with D4 to form the D4-A20 heterodimer that functions as the poxvirus DNA processivity factor. The heterodimer enables the DNA polymerase to efficiently synthesize extended strands of DNA. Upon characterizing the interaction between D4 and A20, we observed that the C terminus of D4 is susceptible to perturbation. Further analysis demonstrated that a conserved hexapeptide stretch at the extreme C terminus of D4 is essential for maintaining protein integrity, as assessed by its requirement for the production of soluble recombinant protein that is functional in processive DNA synthesis. From the known crystal structures of D4, the C-terminal hexapeptide is shown to make intramolecular contact with residues spanning the inner core of the protein. Our mutational analysis revealed that a tripeptide motif (²¹⁵GFI²¹⁷) within the hexapeptide comprises apparent residues necessary for the contact. Prediction of protein disorder identified the hexapeptide and several regions upstream of Gly²¹⁵ that comprise residues of the interface surfaces of the D4-A20 heterodimer. Our study suggests that ²¹⁵GFI²¹⁷ anchors these potentially dynamic upstream regions of the protein to maintain protein integrity. Unlike uracil-DNA glycosylases from diverse sources, where the C termini are disordered and do not form comparable intramolecular contacts, this feature may be unique to orthopoxviruses.

Poxvirus uracil-DNA glycosylase-An unusual member of the family I uracil-DNA glycosylases

Uracil-DNA glycosylases are ubiquitous enzymes, which play a key role repairing damages in DNA and in maintaining genomic integrity by catalyzing the first step in the base excision repair pathway. Within the superfamily of uracil-DNA glycosylases family I enzymes or UNGs are specific for recognizing and removing uracil from DNA. These enzymes feature conserved structural folds, active site residues and use common motifs for DNA binding, uracil recognition and catalysis. Within this family the enzymes of poxviruses are unique and most remarkable in terms of amino acid sequences, characteristic motifs and more importantly for their novel non-enzymatic function in DNA replication. UNG of vaccinia virus, also known as D4, is the most extensively characterized UNG of the poxvirus family. D4 forms an unusual heterodimeric processivity factor by attaching to a poxvirus-specific protein A20, which also binds to the DNA polymerase E9 and recruits other proteins necessary for replication. D4 is thus integrated in the DNA polymerase complex, and its DNA-binding and DNA scanning abilities couple DNA processivity and DNA base excision repair at the replication fork. The adaptations necessary for taking on the new function are reflected in the amino acid sequence and the three-dimensional structure of D4. An overview of the current state of the knowledge on the structure-function relationship of D4 is provided here.