Structure-based design of potent and selective inhibitors of collagenase-3 (MMP-13)

Chemodivergent mechanosynthesis of cyclopentenyl and pyrrolinyl spirobarbiturates from unsaturated barbiturates and enamino esters

A novel and interesting controllable spirocyclization of unsaturated barbiturates with enamino esters for the assembly of cyclopentenyl and pyrrolinyl spirobarbiturates has been developed under ball-milling conditions. The present protocol features high chemoselectivity and efficiency, excellent functional group tolerance and mild reaction conditions.

Small molecular exogenous modulators of active forms of MMPs

Matrix metalloproteinases (MMPs) are endopeptidases, and their activity depends on calcium and zinc metal ions. These enzymes are expressed originally in zymogenic form, where the active site of proteins is closed by a prodomain which is removed during activation. A homeostatic balance of their activity is primarily regulated by a 'cysteine switch' located on a consensus sequence of the prodomain and natural endogenous inhibitors, called tissue inhibitors of metalloproteinases (TIMPs). Breakage of this homeostasis may lead to various pathological conditions, which may require further activation and/or inhibition of these enzymes to regenerate that balance. Here, we report four modulators, more specifically, three inhibitors (I1, I2 and I3), and one exogenous activator (L) of the active form of human collagenase MMP-1 (without prodomain). The results were confirmed by binding studies using fluorescence-based enzyme assays.

Novel benzimidazole-linked (thio)barbiturates as non-hydroxamate HDAC6 inhibitors targeting leukemia: Design, synthesis, and structure-activity relationship

Based on the well-established pharmacophoric features required for histone deacetylase (HDAC) inhibition, novel easy-to-prepare benzimidazole-linked (thio)barbiturate derivatives were designed and synthesized as HDAC6 inhibitors. The proposed structures of the title compounds were confirmed based on their spectral data and elemental analyses. The newly synthesized compounds were screened in vitro against HDAC6. All tested compounds showed potent HDAC6 inhibition at the nanomolar level. Several compounds displayed a remarkable HDAC6 inhibitory activity (IC₅₀  = 48.85-75.62 nM), superior to that of the reference drug suberoylanilide hydroxamic acid (SAHA; IC₅₀  = 91.73 nM). The most potent derivatives were further assessed for their in vitro anticancer activity against two human leukemia cell lines. Thiobarbiturate 3e was two times more potent than SAHA against the tested cells. The detailed structure-activity relationship was also described. Furthermore, molecular docking simulation revealed the ability of the title compounds to chelate the catalytic Zn⁺² ion located within the binding pocket of HDAC6. In silico evaluation of physicochemical properties indicated that the target compounds are promising candidates in terms of pharmacokinetic aspects.

A review of the synthetic strategies toward spirobarbiturate-fused 3- to 7-membered rings

Spiro-connected hexahydropyrimidine-2,4,6-trione heterocyclic rings have received increasing attention from the viewpoint of biological activity and synthetic methods due to the importance of the rigid heterocyclic system and unique orientation of the functional substituents. Since 1900, numerous studies have exploited the synthesis of various spirobarbiturate-fused carbo- and heterocycles by applying different strategies. Due to the importance of barbiturate-based olefins as activated alkenes, these substrates have been utilized in many reactions. In addition, the nucleophilic addition of 1,3-disubstituted barbituric acid to different electrophiles has been applied to prepare highly functionalized spirobarbiturate scaffolds. This short review highlights various strategies for synthesizing spirobarbiturate-fused 3- to 7-membered carbo- and heterocyclic rings and some catalytic diastereoselective and enantioselective chemical reactions to access chiral compounds. The sections are divided by the incorporation of 3- to 7-membered heterocyclic or carbocyclic rings into a spirobarbiturate scaffold, and are presented in different subsections depending on the mechanistic details.

Biological Evaluation of 3-Azaspiro[Bicyclo[3.1.0]Hexane-2,5′-Pyrimidines] as Potential Antitumor Agents

A series of heterocyclic compounds containing spirofused barbiturate and 3-azabicyclo[3.1.0]hexane frameworks have been studied as potential antitumor agents. Antiproliferative activity of products was screened in human erythroleukemia (K562), T lymphocyte (Jurkat), and cervical carcinoma (HeLa) as well as mouse colon carcinoma (CT26) and African green monkey kidney epithelial (Vero) cell lines. The most effective among the screened compounds show IC50 in the range from 4.2 to 24.1 μM for all tested cell lines. The screened compounds have demonstrated a significant effect of the distribution of HeLa and CT26 cells across the cell cycle stage, with accumulation of cells in SubG1 phase and induced apoptosis. It was found, using a confocal microscopy, that actin filaments disappeared and granular actin was distributed diffusely in the cytoplasm of up to 90% of HeLa cells and up to 64% of CT26 cells after treatment with tested 3-azaspiro[bicyclo [3.1.0]hexane-2,5′-pyrimidines]. We discovered that the number of HeLa cells with filopodium-like membrane protrusions was reduced significantly (from 91% in control cells to 35%) after treatment with the most active compounds. A decrease in cell motility was also noticed. Preliminary in vivo experiments on the impact of the studied compounds on the dynamics of CT26 tumor growth in Balb/C mice were also performed.

Multicomponent Electrocatalytic Selective Approach to Unsymmetrical Spiro[furo[3,2-c]pyran-2,5′-pyrimidine] Scaffold under a Column Chromatography-Free Protocol at Room Temperature

Electrochemical synthesis suggested a mild, green and atom-efficient route to interesting and useful molecules, thus avoiding harsh chemical oxidizing and reducing agents used in traditional synthetic methods. Organic electrochemistry offers an excellent alternative to conventional methods of organic synthesis and creates a modern tool for carrying out organic synthesis, including cascade and multicomponent ones. In this research, a novel electrocatalytic multicomponent transformation was found: the electrochemical multicomponent assembly of arylaldehydes, N,N′-dimethylbarbituric acid and 4-hydroxy-6-methyl-2H-pyran-2-one in one pot reaction was carried out in alcohols in an undivided cell in the presence of alkali metal halides with the selective formation of substituted unsymmetrical 1′,3′,6-trimethyl-3-aryl-2′H,3H,4H-spiro[furo[3,2-c]pyran-2,5′-pyrimidine]-2′,4,4′,6′(1′H,3′H)-tetraones in 73–82% yields. This new electrocatalytic process is a selective, facile and efficient way to obtain spiro[furo[3,2-c]pyran-2,5′-pyrimidines]. According to screening molecular docking data using a self-made Python script in Flare, all synthesized compounds may be prominent for different medical applications, such as breast cancer, neurodegenerative diseases and treatments connected with urinary tract, bones and the cardiovascular system.

An Experimental and Theoretical Study of the 1,3-Dipolar Cyclo­addition of Alloxan-Derived Azomethine Ylides to Cyclopropenes

A diastereoselective synthesis of biologically interesting spirobarbiturates has been achieved via [3+2] cycloaddition of alloxan-derived azomethine ylides to 3-R-1,2-diphenylcyclopropenes. With this approach, a range of spirobarbiturate-3-azabicyclo[3.1.0]hexanes and spirobarbiturate-cyclopropa[a]pyrrolizines were obtained in moderate to good yields with excellent diastereoselectivities. DFT calculations (M11 density functional theory) were carried out to shed light on the molecular mechanism of 1,3-dipolar cycloaddition of alloxan-derived azomethine ylides to cyclopropenes. The cytotoxic activity of some obtained compounds against human erythroleukemia (K562) cell line was evaluated in vitro by MTS-assay.

Bifunctional thiourea-catalyzed asymmetric [3 + 2] annulation reactions of 2-isothiocyanato-1-indanones with barbiturate-based olefins

Bifunctional thiourea-catalyzed asymmetric [3 + 2] annulation reactions of 2-isothiocyanato-1-indanones with barbiturate-based olefins have been developed to afford chiral dispiro[indene-pyrrolidine-pyrimidine]s. Through this strategy, the target products could be obtained in good to excellent yields with excellent stereoselectivities. In addition, the synthetic utility was verified through a gram-scale synthesis, one-pot three-component reactions and further transformation experiments of the products.

Applications of fluorine to the construction of bioisosteric elements for the purposes of novel drug discovery

Introduction There continues to be an exponential rise in the number of small molecule drugs that contain either a fluorine atom or a fluorinated fragment. While the unique properties of fluorine enable the precise modulation of a molecule's physicochemical properties, strategic bioisosteric replacement of fragments with fluorinated moieties represents an area of significant growth.Areas covered This review discusses the strategic employment of fluorine substitution in the design and development of bioisosteres in medicinal chemistry. In addition, the classic exploitation of trifluoroethylamine group as an amide bioisostere is discussed. In each of the case studies presented, emphasis is placed on the context-dependent influence of the fluorinated fragment on the overall properties/binding of the compound of interest.Expert opinion Whereas utilization of bioisosteric replacements to modify molecular structures is commonplace within drug discovery, the overarching lesson to be learned is that the chances of success with this strategy significantly increase as the knowledge of the structure/environment of the biological target grows. Coupled to this, breakthroughs and learnings achieved using bioisosteres within a specific program are context-based, and though may be helpful in guiding future intuition, will not necessarily be directly translated to future programs. Another important point is to bear in mind what implications a structural change based on a bioisosteric replacement will have on the candidate molecule. Finally, the development of new methods and reagents for the controlled regioselective introduction of fluorine and fluorinated moieties into biologically relevant compounds particularly in drug discovery remains a contemporary challenge in organic chemistry.

Chemoselective synthesis of 5,4'-imidazolinyl spirobarbiturates via NBS-promoted cyclization of unsaturated barbiturates and amidines

A selective cyclization of unsaturated barbiturates and amidines promoted by N-bromosuccinimide has been successfully developed to afford a vast variety of 5,4'-imidazolinyl spirobarbiturates in moderate to good yields. The present protocol features broad substrate scope, facile work-up procedure and mild reaction conditions, providing a novel strategy for the highly selective and efficient construction of structurally diverse spiroimidazolines.

Efficient Electrocatalytic Approach to Spiro[Furo[3,2-b]pyran-2,5′-pyrimidine] Scaffold as Inhibitor of Aldose Reductase

A continuously growing interest in convenient and ‘green’ reaction techniques encourages organic chemists to elaborate on new synthetic methodologies. Nowadays, organic electrochemistry is a new useful method with important synthetic and ecological advantages. The employment of an electrocatalytic methodology in cascade reactions is very promising because it provides the combination of the synthetic virtues of the cascade strategy with the ecological benefits and convenience of electrocatalytic procedures. In this research, a new type of the electrocatalytic cascade transformation was found: the electrochemical cyclization of 1,3-dimethyl-5-[[3-hydroxy-6-(hydroxymethyl)-4-oxo-4H-pyran-2-yl](aryl)methyl]pyrimidine-2,4,6(1H,3H,5H)-triones was carried out in alcohols in an undivided cell in the presence of sodium halides with the selective formation of spiro[furo[3,2-b]pyran-2,5′-pyrimidines] in 59-95% yields. This new electrocatalytic process is a selective, facile, and efficient way to create spiro[furo[3,2-b]pyran-2,5′-pyrimidines], which are pharmacologically active heterocyclic systems with different biomedical applications. Spiro[furo[3,2-b]pyran-2,5′-pyrimidines] were found to occupy the binding pocket of aldose reductase and inhibit it. The values of the binding energy and Lead Finder’s Virtual Screening scoring function showed that the formation of protein–ligand complexes was favorable. The synthesized compounds are promising for the inhibition of aldose reductase. This makes them interesting for study in the treatment of diabetes or similar diseases.

A novel substrate directed multicomponent reaction for the syntheses of tetrahydro-spiro[pyrazolo[4,3-f]quinoline]-8,5′-pyrimidines and tetrahydro-pyrazolo[4,3-f]pyrimido[4,5-b]quinolines via selective multiple C–C bond formation under metal-free conditions

Substrate selectivity in the novel multi-component reaction of 5-aminoindazole, barbituric acid derivatives and aldehyde is explored.

Synthesis of spirobarbiturate-pyrrolidinones via a domino aza-Michael/SN2 cyclization of barbiturate-derived alkenes with N-alkoxy α-haloamides

A highly efficient domino aza-MIRC (Michael Induced Ring Closure) reaction between barbiturate-derived alkenes and N-alkoxy α-haloamides has been achieved in moderate to excellent yields. This reaction proceeds smoothly under mild conditions via a domino aza-Michael addition/intramolecular SN2 sequence, providing a practical tool in the synthesis of bioactive molecules spirobarbiturate-3-pyrrolidinones.

Chemoselective syntheses of spirodihydrofuryl and spirocyclopropyl barbiturates via cascade reactions of barbiturate-based olefins and acetylacetone

The Michael addition initiated ring closure reaction of barbiturate-based olefins and acetylacetone with NBS has been explored. The efficient and chemoselective approach for the synthesis of barbiturate-fused spirocycles was established. Spirodihydrofuryl barbiturates and spirocyclopropyl barbiturates were synthesized selectively via cascade reactions under different basic conditions in moderate to excellent yields. The structure of 2-(4-chlorophenyl)-1,1-diacetyl-5,7-dimethyl-5,7-diazaspiro[2,5]octane-4,6,8-trione was confirmed by single crystal X-ray diffraction analysis.

Enantioselective Catalytic Transformations of Barbituric Acid Derivatives

Since the beginning of the 20th century, numerous research efforts made elegant use of barbituric acid derivatives as building blocks for the elaboration of more complex and useful molecules in the field of pharmaceutical chemistry and material sciences. However, the construction of chiral scaffolds by the catalytic enantioselective transformation of barbituric acid and derivatives has only emerged recently. The specific properties of these rather planar scaffolds, which also encompass either a high Brønsted acidity concerning the native barbituric acid or the marked electrophilic character of alkylidene barbituric acids, required specific developments to achieve efficient asymmetric processes. This review covers the enantioselective catalytic reactions developed for barbituric acid platforms using an organocatalytic and metal-based enantioselective sequences. These achievements currently allow several unique addition and annulation reactions towards the construction of high valued chiral heterocycles from barbituric acid derivatives along with innovative enantioselective developments.

Matrix Metalloproteinase Inhibitors as Investigational and Therapeutic Tools in Unrestrained Tissue Remodeling and Pathological Disorders

Matrix metalloproteinases (MMPs) are zinc-dependent proteolytic enzymes that degrade various proteins in the extracellular matrix (ECM). MMPs may also regulate the activity of membrane receptors and postreceptor signaling mechanisms and thereby affect cell function. The MMP family includes collagenases, gelatinases, stromelysins, matrilysins, membrane-type MMPs, and other MMPs. Inactive proMMPs are cleaved by other MMPs or proteases into active MMPs, which interact with various protein substrates in ECM and cell surface. MMPs regulate important biological processes such as vascular remodeling and angiogenesis and may be involved in the pathogenesis of cardiovascular disorders such as hypertension, atherosclerosis, and aneurysm. The role of MMPs is often assessed by measuring their mRNA expression, protein levels, and proteolytic activity using gel zymography. MMP inhibitors are also used to assess the role of MMPs in different biological processes and pathological conditions. MMP activity is regulated by endogenous tissue inhibitors of metalloproteinases (TIMPs), and the MMP/TIMP balance could determine the net MMP activity, ECM turnover, and tissue remodeling. Also, several synthetic MMP inhibitors have been developed. Synthetic MMP inhibitors include a large number of zinc-binding globulins (ZBGs), in addition to non-ZBGs and mechanism-based inhibitors. MMP inhibitors have been proposed as potential tools in the management of osteoarthritis, cancer, and cardiovascular disorders. However, most MMP inhibitors have broad-spectrum actions on multiple MMPs and could cause undesirable musculoskeletal side effects. Currently, doxycycline is the only MMP inhibitor approved by the Food and Drug Administration. New generation biological and synthetic MMP inhibitors may show greater MMP specificity and fewer side effects and could be useful in targeting specific MMPs, reducing unrestrained tissue remodeling, and the management of MMP-related pathological disorders.

Stereoselective cascade assembling of benzylidenecyanoacetates and 1,3-dimethylbarbituric acid into (1R*,2S*)-1-cyano-5,7-dialkyl-4,6,8-trioxo-2-aryl-5,7-diazaspiro[2.5]octane-1-carboxylates

A new stereoselective cascade reaction of benzylidenecyanoacetates and 1,3-dimethylbarbituric acid by the action of bromine in the presence of a base into substituted (barbituric acid)-5-spirocyclopropanes is described. The yields are in the range of 60%–75%. Nuclear magnetic resonance (NMR) studies indicate that this cascade transformation results in the stereoselective formation of spiro products with trans-configuration of aryl and alkoxycarbonyl substituents in the cyclopropane ring. The products are a perspective class of compounds with prominent pharmacological and physiological activity.

Phosphine-catalyzed [3 + 2] and [4 + 2] annulation reactions of ynones with barbiturate-derived alkenes

The phosphine-catalyzed [3 + 2] annulation reaction of ynones and barbiturate-derived alkenes has been developed with the assistance of a weak acid, giving functionalized spirobarbiturate-cyclopentanones.

Design, synthesis, and biological activity of novel, potent, and highly selective fused pyrimidine-2-carboxamide-4-one-based matrix metalloproteinase (MMP)-13 zinc-binding inhibitors

Matrix metalloproteinase-13 (MMP-13), a member of the collagenase family of enzymes, has been implicated to play a key role in the pathology of osteoarthritis. Recently, we have reported the discovery of a series of quinazoline-2-carboxamide based non-zinc-binding MMP-13 selective inhibitors, as exemplified by compound 1. We then continued our research of a novel class of zinc-binding inhibitors to obtain follow-up compounds with different physicochemical, pharmacokinetic, and biological activity profiles. In order to design selective MMP-13 inhibitors, we adopted a strategy of connecting a zinc-binding group with the quinazoline-2-carboxamide system, a unique S1' binder, by an appropriate linker. Among synthesized compounds, a triazolone inhibitor 35 exhibited excellent potency (IC₅₀=0.071nM) and selectivity (greater than 170-fold) over other MMPs (MMP-1, 2, 3, 7, 8, 9, 10, 12, and 14) and tumor necrosis factor-α converting enzyme (TACE). In this article, the design, synthesis, and biological activity of novel zinc-binding MMP-13 inhibitors are described.

Antibacterial, antiurease, and antioxidant activities of some arylidene barbiturates

Some series of arylidene barbiturates and thiobarbiturates were evaluated for their antibacterial, antioxidant, and urease inhibition activities. The arylidene barbiturates and thiobarbiturates were tested for antimicrobial activity using the agar well diffusion technique against 13 bacteria. The synthesized compounds (1a-g) were screened for antiurease and antioxidant activities. The results showed that the synthesized compounds (1a-g) had effective antiurease, antioxidant, and antibacterial activities.