Scaffolds In Medicinal Chemistry Research Articles

Computational Exploration of Molecular Scaffolds in Medicinal Chemistry.

The scaffold concept is widely applied in medicinal chemistry. Scaffolds are mostly used to represent core structures of bioactive compounds. Although the scaffold concept has limitations and is often viewed differently from a chemical and computational perspective, it has provided a basis for systematic investigations of molecular cores and building blocks, going far beyond the consideration of individual compound series. Over the past 2 decades, alternative scaffold definitions and organization schemes have been introduced and scaffolds have been studied in a variety of ways and increasingly on a large scale. Major applications of the scaffold concept include the generation of molecular hierarchies, structural classification, association of scaffolds with biological activities, and activity prediction. This contribution discusses computational approaches for scaffold generation and analysis, with emphasis on recent developments impacting medicinal chemistry. A variety of scaffold-based studies are discussed, and a perspective on scaffold methods is provided.

5-Substituted 3-isopropyl-7-[4-(2-pyridyl)benzyl]amino-1(2)H-pyrazolo[4,3-d]pyrimidines with anti-proliferative activity as potent and selective inhibitors of cyclin-dependent kinases

A series of 5-substituted 3-isopropyl-7-[4-(2-pyridyl)benzyl]amino-1(2)H-pyrazolo[4,3-d]pyrimidine derivatives was synthesized and evaluated for their cyclin-dependent kinase (CDK) inhibition activity. The most potent compounds contained various hydroxyalkylamines at the 5 position and possessed low nanomolar IC50 values for CDK2 and CDK5. Preliminary profiling of one of the most active compounds on a panel of 50 protein kinases revealed its high selectivity for CDKs. The compounds arrested cells in S and G2/M phases, and induced apoptosis in various cancer cell lines. Significant dephosphorylation of the C-terminus of RNA polymerase II and focal adhesion kinase (FAK), well-established substrates of CDKs, has been found in treated cells. Cleavage of PARP-1, down-regulation of Mcl-1 and activation of caspases correlated well with CDK inhibition and confirmed apoptosis as the primary type of cell death induced in cancer cells treated with the compounds in vitro. A comparison of known purine-based CDK inhibitor CR8 with its pyrazolo[4,3-d]pyrimidine bioisosteres confirmed that the novel compounds are more potent in cellular assays than purines. Therefore, pyrazolo[4,3-d]pyrimidine may emerge as a novel scaffold in medicinal chemistry and as a source of potent CDK inhibitors.

Direct Catalytic Synthesis of Unprotected 2-Amino-1-Phenylethanols from Alkenes by Using Iron(II) Phthalocyanine.

Aryl-substituted amino alcohols are privileged scaffolds in medicinal chemistry and natural products. Herein, we report that an exceptionally simple and inexpensive Fe(II) complex efficiently catalyzes the direct transformation of simple alkenes into unprotected amino alcohols in good yield and perfect regioselectivity. This new catalytic method was applied in the expedient synthesis of bioactive molecules and could be extended to aminoetherification.

DFT and Molecular Docking Studies on Biological Active Acridines: the Interaction with Bovine Serum Albumin

Acridine derivatives, especially 1,8-dioxo-9-aryl-decahydroacridine represent significant scaffolds in medicinal chemistry. Given the biological properties of such products which are used in drug development, they need to have appropriate carrier. Proteins are generally used as helpful tools in drug delivery. Consequently, molecular docking between these compounds and bovine serum albumin (BSA) has been taken into account. Furthermore, in order to achieve better results, the suggested compounds have been optimized using Gaussian 03 software.

Inhibition of guinea pig aldehyde oxidase activity by different flavonoid compounds: An in vitro study

Aldehyde oxidase (AO), a cytosolic molybdenum-containing hydroxylase, is predominantly active in liver and other tissues of mammalian species and involved in the metabolism of extensive range of aldehydes and nitrogen-containing compounds. A wide range of natural components including polyphenols are able to interfere with AO-catalyzed reactions. Polyphenols and flavonoids are one of the extensive secondary plant metabolites ubiquitously present in plants considered an important part of the human diet. The aim of the present study was to investigate inhibitory effect of selected phenolic compounds from three subclasses of aurone, flavanone and phenolic lactone compounds on the activity of AO, spectrophotometrically. AO enzyme was partially purified from liver of guinea pig. Then, inhibitory effects of 10 flavonoid compounds including 8 derivatives of 2-benzylidenebenzofuran-3(2H)-ones, as well as naringenin and ellagic acid on the activity of aldehyde oxidase were assessed compared with the specific inhibitor of AO, menadione. Among the phenolic compounds with inhibitory effects on the enzyme, ellagic acid (IC50=14.47μM) was the most potent agent with higher inhibitory action than menadione (IC50=31.84μM). The mechanisms by which flavonoid compounds inhibit AO activity have been also determined. The inhibitory process of the assessed compounds occurs via either a non-competitive or mixed mode. Although flavonoid compounds extensively present in the nature, mainly in dietary regimen, aurones with promising biological properties are not widely distributed in nature, so synthesis of aurone derivatives is of great importance. Additionally, aurones seem to provide a promising scaffold in medicinal chemistry for the skeleton of new developing drugs, so the results of the current study can be valuable in order to better understanding drug–food as well as drug–drug interaction and also appears to be worthwhile in drug development strategies.

Searching for novel applications of the benzohomoadamantane scaffold in medicinal chemistry: Synthesis of novel 11β-HSD1 inhibitors

The structural and physicochemical properties of the adamantane nucleus account for its use as a chemical scaffold in multiple drugs. In the last years, we have developed new polycyclic scaffolds as surrogates of the adamantane group with encouraging results in multiple targets. As adamantane is a common structural feature in several 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1) inhibitors, we have explored the ability of the 6,7,8,9,10,11-hexahydro-5H-5,9:7,11-dimethanobenzo[9]annulen-7-yl scaffold to act as a surrogate of the adamantane nucleus in a novel series of 11β-HSD1 inhibitors. Of note, within this family of compounds one derivative is endowed with submicromolar 11β-HSD1 inhibitory activity. Molecular modeling studies support the binding of the compounds to the active site of the enzyme. However, a fine tuning of the hydrophobicity of the size-expanded nucleus may be beneficial for the inhibitory potency.

Facile synthesis of 4-aryl and alkyl substituted, N6-alkylated pyridazine-3,6-diamines

Substituted pyridazine-3,6-diamines are attractive but poorly precedented scaffolds in medicinal chemistry and are challenging targets in terms of synthetic tractability. In the following communication we report the use of a Buchwald protocol for the facile synthesis of 4-aryl and alkyl substituted, N6-alkylated pyridazine-3,6-diamines. This approach utilises the unreactive nature of the pyridazine 3-amino group, negating the need for an additional protecting group in the transformation. The relevant precursors were prepared by selective Suzuki or Negishi transformations using commercially available 4-bromo-6-chloro-3-pyridazinamine.

Development of new 5-(chromene-3-yl)methylene-2,4-thiazolidinediones as antimicrobial agents.

Background and aimsIn the context of the increasing phenomenon of microbial resistance to usual drugs, the development of new treatment strategies and new therapeutic protocols is a constant need. Thiazolidinedione and chromone represent two important scaffolds in medicinal chemistry due to their large pharmacological applicability.MethodsWe synthesized a new 5-(chromene-3-yl)methylene-2,4-thiazolidinedione starting from 6,8-dichloro-4-oxo-4H-chromene-3-carbaldehyde. Then, by treating with different α-bromoalkylarylketones, we obtained N-substituted derivatives. All new compounds were investigated for their antimicrobial potential, using the diffusion method, against Listeria monocytogenes ATCC 13932, Staphylococcus aureus ATCC 49444, Escherichia coli ATCC 25922, Salmonella typhimurium ATCC 14028 and Candida albicans ATCC 10231. Three concentrations, 10 mg/ml, 5 mg/ml and 1 mg/ml of compounds were used. The results were evaluated by the measurement of the inhibition zone diameters and compared to those of gentamicin and fluconazole respectively, as reference drugs.ResultsAll new synthesized compounds were characterized using physico-chemical and spectrometric methods. They displayed modest to good antimicrobial activity. New molecules 8, 9 and 10 may represent promising candidates, showing zone inhibition diameters superior to those of reference drugs.ConclusionsThis work presents chemical synthesis, characterization and investigation of the antibacterial and antifungal potential of 5-(chromene-3-yl)methylene-2,4-thiazolidinedione derivatives, which may be worthy of future research for designing new chemical entities.

Synthesis of Heteroaryl ortho-Phenoxyethylamines via Suzuki Cross-Coupling: Easy Access to New Potential Scaffolds in Medicinal Chemistry

Heteroaryl <i>ortho</i>-phenoxyethylamines have been extensively employed in medicinal chemistry as privileged scaffolds for the design of highly potent and selective ligands. Herein an efficient, fast, and general method for the synthesis of heteroaryl phenoxyethylamines via Suzuki­ cross-coupling is reported. This approach offers the opportunity to obtain a large variety of biaryls incorporating five-membered (thiophene, furan, thiazole, pyrazole, imidazole) or six-membered (pyridine, pyrimidine) heteroaromatic rings for appropriate libraries of ligands. All the compounds presented here have never been synthesized before and a full structural characterization is given.

ChemInform Abstract: Direct Access to 2‐Aminopyrazolo[1,5‐a]pyridines via N‐Amination/Cyclization Reactions of 2‐Pyridineacetonitriles.

AbstractThe two‐step one‐pot procedure delivers substituted 2‐aminopyrazolo[1,5‐a]pyridines as scaffolds in medicinal chemistry.

Expedient stereoselective synthesis of new dihydropyrano- and dihydrofuranonaphthoquinones

Heterocyclic naphthoquinones represent valuable scaffolds in medicinal chemistry. In the present Letter, the efficient stereoselective synthesis of new dihydropyrano- and dihydrofuranonaphthoquinones by means of one-pot multicomponent reactions using 2-hydroxy-1,4-naphthoquinone, an aromatic aldehyde and ethyl 4,4,4-trifluoroacetoacetate or a pyridinium bromide, respectively, is described.

ChemInform Abstract: 2,5‐Diketopiperazines as Privileged Scaffolds in Medicinal Chemistry, Peptidomimetic Chemistry and Organocatalysis

AbstractReview: 124 refs.

ChemInform Abstract: Thiazolidine‐2,4‐diones as Multi‐targeted Scaffold in Medicinal Chemistry: Potential Anticancer Agents

AbstractReview: 99 refs.

The Cu(OTf)2 catalysed microwave assisted synthesis of a new scaffold, 7-aryl-7,8-dihydropyrido[4,3-c]pyridazin-5(6H)-one

The synthesis of novel 7-aryl-7,8-dihydropyrido[4,3-c]pyridazin-5(6H)-ones is described including a one-step Mannich-type reaction followed by intramolecular ring closure of ethyl 3-methylpyridazine-4- carboxylate and aldimines, catalysed by the Lewis acid Cu(OTf)2 under microwave heating. This synthesis opens up possibilities to access this unexplored scaffold for medicinal chemistry.

Synthesis of Pyrido-Annelated Seven-Membered N-Containing Heterocycles

Pharmaceutical industry is struggling with a lack of potential drugs in the pipe line. However, there is still a great opportunity to elaborate interesting scaffolds for medicinal chemistry. Various scaffolds that hold promise are rarely described in the literature. The last couple of decades, the wide range of biological activities of benzodiazepine derivatives have been investigated thoroughly and make the benzodiazepine scaffold, particularly the 1,4-benzodiazepine system, one of the most important structures for drug discovery. The substantial research on benzodiazepines has led to the synthesis of heterocycle-fused azepine derivatives with potentially new pharmacological activity. Some pyridoazepines are known to be active in the central nervous system and have a comparable activity to the well-known benzodiazepine scaffolds, which make the synthesis and study of pyridoazepines an important research topic.

Synthetic approaches, functionalization and therapeutic potential of quinazoline and quinazolinone skeletons: the advances continue.

The presence of N-heterocycles as an essential structural motif in a variety of biologically active substances has stimulated the development of new strategies and technologies for their synthesis. Among the various N-heterocyclic scaffolds, quinazolines and quinazolinones form a privileged class of compounds with their diverse spectrum of therapeutic potential. The easy generation of complex molecular diversity through broadly applicable, cost-effective, practical and sustainable synthetic methods in a straightforward fashion along with the importance of these motifs in medicinal chemistry, received significant attention from researchers engaged in drug design and heterocyclic methodology development. In this perspective, the current review article is an effort to recapitulate recent developments in the eco-friendly and green procedures for the construction of highly challenging and potentially bioactive quinazoline and quinazolinone compounds in order to help medicinal chemists in designing and synthesizing novel and potent compounds for the treatment of different disorders. The key mechanistic insights for the synthesis of these heterocycles along with potential applications and manipulations of the products have also been conferred. This article also aims to highlight the promising future directions for the easy access to these frameworks in addition to the identification of more potent and specific products for numerous biological targets.

ChemInform Abstract: 1,3,5‐Triazine‐Based Analogues of Purine: From Isosteres to Privileged Scaffolds in Medicinal Chemistry

AbstractReview: 201 refs.

Thiazolidine-2,4-diones as multi-targeted scaffold in medicinal chemistry: Potential anticancer agents.

A variety of substituents on the thiazolidine-2,4-dione(TZD) nucleus have provided a wide spectrum of biological activities by the using of different mechanism on various target sites. PPARγ ligands have recently been demonstrated to affect cell proliferation, differentiation and apoptosis of different cell types. Currently, some of the TZDs are designed for the treatment of human cancers expressing high levels of PPARγ because it is assumed that activation of PPARγ mediates their anticancer activity. Another site for TZDs is survival signaling pathways under growth factor loops have been implicated in cancer development, progression, and metastasis. The Raf/MEK/ERK, Wnt and PI3K/Akt signalling cascades are the most commonly up-regulated in human cancers. In the present review, various derivatives of thiazolidine-2,4-diones its SAR and different signaling pathways involved to produce anticancer activity been highlighted.

1,3,5-Triazine-based analogues of purine: From isosteres to privileged scaffolds in medicinal chemistry

Purines can be considered as the most ubiquitous and functional N-heterocyclic compounds in nature. Structural modifications of natural purines, particularly using isosteric ring systems, have been in the focus of many drug discovery programs. Fusion of 1,3,5-triazine ring with pyrrole, pyrazole, imidazole, 1,2,3-triazole or 1,2,4-triazole results in seven bicyclic heterocyclic systems isosteric to purine. Application of the isosterism concept for the development of new compounds with therapeutic potential in areas involving purinergic regulation or purine metabolism led to significant advances in medicinal chemistry of the azolo[1,3,5]triazines. These 1,3,5-triazine-based purine-like scaffolds significantly increase level of molecular diversity and allow covering chemical space in the important areas of medicinal chemistry. Some of these azolo[1,3,5]triazine systems have become privileged scaffolds in the development of inhibitors of various kinases, phosphodiesterase, xanthine oxidase, and thymidine phosphorylase, antagonists of adenosine and corticotropin-releasing hormone receptors, anticancer and antiviral agents.

Reaction between (Z)-arylchlorooximes and α-isocyanoacetamides: a procedure for the synthesis of aryl-α-ketoamide amides.

(Z)-Arylchlorooximes and α-isocyanoacetamides undergo a smooth reaction to produce 1,3-oxazol-2-oxime derivatives in good yields. Opening of the oxazole ring and deoximation reaction give a facile access to aryl-α-ketoamide amides, a class of privileged scaffolds in medicinal chemistry and important synthetic intermediates in organic chemistry.