Bicyclic Scaffold Research Articles

A bicyclic peptide scaffold promotes phosphotyrosine mimicry and cellular uptake

While peptides are promising as probes and therapeutics, targeting intracellular proteins will require greater understanding of highly structured, cell-internalized scaffolds. We recently reported BC1, an 11-residue bicyclic peptide that inhibits the Src homology 2 (SH2) domain of growth factor receptor-bound protein 2 (Grb2). In this work, we describe the unique structural and cell uptake properties of BC1 and similar cyclic and bicyclic scaffolds. These constrained scaffolds are taken up by mammalian cells despite their net neutral or negative charges, while unconstrained analogs are not. The mechanism of uptake is shown to be energy-dependent and endocytic, but distinct from that of Tat. The solution structure of BC1 was investigated by NMR and MD simulations, which revealed discrete water-binding sites on BC1 that reduce exposure of backbone amides to bulk water. This represents an original and potentially general strategy for promoting cell uptake.

Carboxybenzyl group as an o-nucleophile in the C-H allylic oxidation: total synthesis of (-)-castanospermine.

The first palladium-mediated C-H allylic oxidation with a Cbz group acting as an O-nucleophile is reported. It was found that this transformation is promoted by rare-earth metal triflates: Yb(OTf)(3) or Sc(OTf)(3). A possible catalytic cycle is proposed. This reaction was applied in the synthesis of a d-xylose derived oxazolidinon, a versatile intermediate used further in the stereoselective synthesis of unnatural (-)-castanospermine. Cyclization of the key intermediate with PhSeBr afforded the desired bicyclic scaffold. In an alternative route, hydroboration/oxidation followed by DPPA-mediated cyclization was used.

Multicomponent, Mannich-type assembly process for generating novel, biologically-active 2-arylpiperidines and derivatives

A multicomponent, Mannich-type assembly process commencing with commercially available bromobenzaldehydes was sequenced with [3+2] dipolar cycloaddition reactions involving nitrones and azomethine ylides to generate collections of fused, bicyclic scaffolds based on the 2-arylpiperidine subunit. Use of the 4-pentenoyl group, which served both as an activator in the Mannich-type reaction and a readily-cleaved amine protecting group, allowed sub-libraries to be prepared through piperidine N-functionalization and cross-coupling of the aryl bromide. A number of these derivatives displayed biological activities that had not previously been associated with this substructure. Methods were also developed that allowed rapid conversion of these scaffolds to novel, polycyclic dihydroquinazolin-2-ones, 2-imino-1,3-benzothiazinanes, dihydroisoquinolin-3-ones, and bridged tetrahydroquinolines.

ChemInform Abstract: Highly Selective Janus Kinase 3 Inhibitors Based on a Pyrrolo[2,3‐d]pyrimidine Scaffold: Evaluation of WO2013085802

AbstractReview: 24 refs.

Optimization of peptidomimetic boronates bearing a P3 bicyclic scaffold as proteasome inhibitors

A new series of pseudopeptide boronate proteasome inhibitors (2–3) was developed, through optimization of our previously described analogs of bortezomib, bearing a bicyclic 1,6-naphthyridin-5(6H)-one scaffold as P3 fragment (1). The biological evaluation on human 20S proteasome displayed a promising inhibition profile, especially for compounds bearing a P2 ethylene fragment, which exhibited Ki values in the nanomolar range for the ChT-L activity (e.g. 2a, Ki = 0.057 μM) and considerable selectivity for proteasome over bovine pancreatic α-chymotrypsin. Docking experiments into the yeast 20S proteasome revealed that the ligands are accommodated predominantly into the ChT-L site and that they covalently bind to the active site threonine residue via boron atom. Within the cellular assays performed against a 60 cancer cell line panel, compounds 3e and 3f demonstrated also good antiproliferative activity and compound 3f emerged as promising lead compound for the development of anticancer agents targeting melanoma and non-small cell lung cancer.

Scaffold-switching: An exploration of 5,6-fused bicyclic heteroaromatics systems to afford antituberculosis activity akin to the imidazo[1,2-a]pyridine-3-carboxylates

A set of 5,6-fused bicyclic heteroaromatic scaffolds were investigated for their in vitro anti-tubercular activity versus replicating and non-replicating strains of Mycobacterium tuberculosis (Mtb) in an attempt to find an alternative scaffold to the imidazo[1,2-a]pyridine and imidazo[1,2-a]pyrimidines that were previously shown to have potent activity against replicating and drug resistant Mtb. The five new bicyclic heteroaromatic scaffolds explored in this study include a 2,6-dimethylimidazo[1,2-b]pyridazine-3-carboxamide (7), a 2,6-dimethyl-1H-indole-3-carboxamide (8), a 6-methyl-1H-indazole-3-carboxamide (9), a 7-methyl-[1,2,4]triazolo[4,3-a]pyridine-3-carboxamide (10), and a 5,7-dimethyl-[1,2,4]triazolo[1,5-a]pyrimidine-2-carboxamide (11). Additionally, imidazo[1,2-a]pyridines isomers (2 and 12) and a homologous imidazo[1,2-a]pyrimidine isomer (6) were prepared and compared. Compounds 2 and 6 were found to be the most potent against H37Rv Mtb (MIC’s of 0.1μM and 1.3μM) and were inactive (MIC >128μM) against Staphylococcus aureus, Escherichia coli and Candida albicans. Against other non-tubercular mycobacteria strains, compounds 2 and 6 had activity against Mycobacterium avium (16 and 122μM, respectively), Mycobacterium kansasii (4 and 19μM, respectively), Mycobacterium bovis BCG (1 and 8μM, respectively) while all the other scaffolds were inactive (>128μM).

Catalytic enantioselective 1,3-dipolar cycloadditions of azomethine ylides for biology-oriented synthesis.

ConspectusCycloaddition reactions are among the most powerful methods for the synthesis of complex compounds. In particular, the development and application of the 1,3-dipolar cycloaddition, an important member of this reaction class, has grown immensely due to its powerful ability to efficiently build various five-membered heterocycles. Azomethine ylides are commonly used as dipoles for the synthesis of the pyrrolidine scaffold, which is an important motif in natural products, pharmaceuticals, and biological probes. The reaction between azomethine ylides and cyclic dipolarophiles allows access to polycyclic products with considerable complexity. The extensive application of the 1,3-dipolar cycloaddition is based on the fact that the desired products can be obtained with high yield in a regio- and stereocontrolled manner. The most attractive feature of the 1,3-dipolar cycloaddition of azomethine ylides is the possibility to generate pyrrolidines with multiple stereocenters in a single step. The development of enantioselective cycloadditions became a subject of intensive and impressive studies in recent years. Among many modes of stereoinduction, the application of chiral metal–ligand complexes has emerged as the most viable option for control of enantioselectivity.In chemical biology research based on the principle of biology-oriented synthesis (BIOS), compound collections are prepared inspired by natural product scaffolds. In BIOS, biological relevance is employed as the key criterion to generate hypotheses for the design and synthesis of focused compound libraries. In particular, the underlying scaffolds of natural product classes provide inspiration for BIOS because they define the areas of chemical space explored by nature, and therefore, they can be regarded as “privileged”. The scaffolds of natural products are frequently complex and rich in stereocenters, which necessitates the development of efficient enantioselective methodologies.This Account highlights examples, mostly from our work, of the application of 1,3-dipolar cycloaddition reactions of azomethine ylides for the catalytic enantioselective synthesis of complex products. We successfully applied the 1,3-dipolar cycloaddition in the synthesis of spiro-compounds such as spirooxindoles, for kinetic resolution of racemic compounds in the synthesis of an iridoid inspired compound collection and in the synthesis of a nitrogen-bridged bicyclic tropane scaffold by application of 1,3-fused azomethine ylides. Furthermore, we performed the synthesis of complex molecules with eight stereocenters using tandem cycloadditions. In a programmable sequential double cycloaddition, we demonstrated the synthesis of both enantiomers of complex products by simple changes in the order of addition of chemicals. Complex products were obtained using enantioselective higher order [6 + 3] cycloaddition of azomethine ylides with fulvenes followed by Diels–Alder reaction. The bioactivity of these compound collections is also discussed.

3D Pharmacophore modeling in the molecules of 5,7-dimethyl-6-phenylazo-3H-thiazolo[4,5-b]pyridine-2-one derivatives

Flexible molecular docking studies for 5,7-dimethyl-6-phenylazo-3H-thiazolo[4,5-b]pyridin-2-ones have been performed with the purpose to reveal their potency as enzymes involved in the arachidonic acid (AA) cascade inhibitors: both cyclooxygenase isoforms (COX-1 and COX-2), and microsomal prostaglandin E synthase-1 (mPGES-1). The protein-ligand interaction fingerprint (PLIF) tool implemented in MOE software has been used for summarizing the interactions between ligands and the abovementioned enzymes. Receptor interaction fingerprints have been generated from the docked poses of the virtual screening hits with COX-1,2 and mPGES-1 active sites coordinates. 3D pharmacophore models containing two and three points queries as the combination of their structures steric and electronic parameters have been generated and it provides the affinity and inhibitory activity of the novel compounds towards multiply receptors. The analysis of the pharmacophore models obtained indicates the functionality of fused bicyclic thiazolopyridine scaffold which provides the steric placement of at least one of these heterocycles atoms in the respective pharmacophore centres. The fused thiazolo[4,5-b]pyridine-2-one system may be considered as a promosing scaffold for creating diverse combinatorial libraries of potential biologically active substances. The final conclusion has been confirmed by the results of the virtual screening procedures and pharmacophore centres modeling in molecules of novel thiazolo [4,5-b]pyridine-2-one.

Highly Stereoselective Generation of Complex Oxy-Bicyclic Scaffolds via an Atom-Economic Pd(II)-Catalyzed Hydroalkynylation, Isomerization and Diels–Alder Cycloaddition Sequence

An atom-economic tandem Pd(II)-catalyzed hydroalkynylation, alkyne-allene isomerization, and Diels-Alder cycloaddition is reported. The reaction employs readily available starting substrates, proceeds in a highly ordered fashion, features high regio- and stereoselectivity, and tolerates a wide range of functionality and structural motifs, thus offering an attractive strategy for producing new molecular complexity and diversity from easily available starting materials. A mechanistic study with density functional theoretical calculations was conducted to rationalize the observed stereoselectivity.

Stereoselectivity through a network of non-classical CH weak interactions: a prospective study of a bicyclic organocatalytic scaffold

The preferred stereoisomeric product of this catalytic Diels–Alder reaction is in part determined by noncovalent CH⋯π interactions.

Highly selective Janus kinase 3 inhibitors based on a pyrrolo[2,3-d]pyrimidine scaffold: evaluation of WO2013085802

A series of pyrrolo[2,3-d]pyrimidine derivatives have previously been claimed as Janus kinase (JAK) 1 selective inhibitors. Introduction of a 4-aryl substituent onto this bicyclic scaffold modulates the JAK selectivity profile, thus providing JAK3 selective inhibitors. This patent application claims such compounds as JAK3 inhibitors. Many of the compounds exemplified show > 100,000-fold selectivity for JAK3 over JAK2. The inhibitors are claimed to be useful in the treatment of respiratory diseases, arthritis and cancer.

Synthesis and biological evaluation of 5-carbamoyl-2-phenylpyrimidine derivatives as novel and potent PDE4 inhibitors

5-Carbamoyl-2-phenylpyrimidine derivative 2 has been identified as a phosphodiesterase 4 (PDE4) inhibitor with moderate PDE4B inhibitory activity (IC50=200nM). Modification of the carboxylic acid moiety of 2 gave N-neopentylacetamide derivative 10f, which had high in vitro PDE4B inhibitory activity (IC50=8.3nM) and in vivo efficacy against lipopolysaccharide (LPS)-induced pulmonary neutrophilia in mice (ID50=16mg/kg, ip). Furthermore, based on the X-ray crystallography of 10f bound to the human PDE4B catalytic domain, we designed 7,8-dihydro-6H-pyrido[4,3-d]pyrimidin-5-one derivative 39 which has a fused bicyclic lactam scaffold. Compound 39 exhibited excellent inhibitory activity against LPS-induced tumor necrosis factor alpha (TNF-α) production in mouse splenocytes (IC50=0.21nM) and in vivo anti-inflammatory activity against LPS-induced pulmonary neutrophilia in mice (41% inhibition at a dose of 1.0mg/kg, i.t.).

Synthetic studies of centromere-associated protein-E (CENP-E) inhibitors: 1.Exploration of fused bicyclic core scaffolds using electrostatic potential map

Centromere-associated protein-E (CENP-E), a mitotic kinesin that plays an important role in mitotic progression, is an attractive target for cancer therapeutic drugs. For the purpose of developing novel CENP-E inhibitors as cancer therapeutics, we investigated a fused bicyclic compound identified by high throughput screening, 4-oxo-4,5-dihydrothieno[3,4-c]pyridine-6-carboxamide 1a. Based on this scaffold, we designed inhibitors for efficient binding at the L5 site in CENP-E utilizing homology modeling as well as electrostatic potential map (EPM) analysis to enhance CENP-E inhibitory activity. This resulted in a new lead, 5-bromoimidazo[1,2-a]pyridine 7, which showed potent CENP-E enzyme inhibition (IC50: 50nM) and cellular activity with accumulation of phosphorylated histone H3 in HeLa cells. Our homology model and EPM analysis proved to be useful tools for the rational design of CENP-E inhibitors.

Increasing the Efficiency of Ligands for FK506-Binding Protein 51 by Conformational Control

The design of efficient ligands remains a key challenge in drug discovery. In the quest for lead-like ligands for the FK506-binding protein 51 (FKBP51), we designed two new classes of bicyclic sulfonamides to probe the contribution of conformational energy in these ligands. The [4.3.1] scaffold had consistently higher affinity compared to the [3.3.1] or monocyclic scaffolds, which could be attributed to better preorganization of two key recognition motifs. Surprisingly, the binding of the rigid [4.3.1] scaffold was enthalpy-driven and entropically disfavored compared to the flexible analogues. Cocrystal structures at atomic resolution revealed that the sulfonamide nitrogen in the bicyclic scaffolds can accept an unusual hydrogen bond from Tyr(113) that mimics the putative FKBP transition state. This resulted in the first lead-like, functionally active ligand for FKBP51. Our work exemplifies how atom-efficient ligands can be achieved by careful conformational control even in very open and thus difficult binding sites such as FKBP51.

Abstract 2456: Discovery of orally active 4-amino-6-arylaminopyrimidine-5-carbaldehyde oximes with dual EGFR and HER2 inhibitory activity.

Abstract Growth factor receptors of the ErbB family, especially ErbB1 (EGFR) and ErbB2 (HER2), have attracted considerable attention in recent years as therapeutic targets for the treatment of numerous malignancies including cancers of the lung, colon, and breast, either through blockade of the extracellular ligand binding site by monoclonal antibodies (e.g. anti-EGFR antibodies cetuximab and panitumumab, and anti-HER2 antibody trastuzumab) or inhibition of the intracellular tyrosine kinase domain by small molecule inhibitors (e.g. EGFR kinase inhibitors gefitinib and erlotinib, and dual EGFR/HER2 inhibitor lapatinib). The abundance of small molecule kinase inhibitors in clinical development or on the market attests to the acceptance of ErbB inhibition as a clinically relevant paradigm. Nevertheless, the emergence of resistance mechanisms in ErbB driven or dependent tumors indicates that continued research is required to discover more effective drugs. We previously reported the discovery of JNJ-28871063, a potent inhibitor of EGFR and HER2 kinases in vitro that also showed excellent antitumor efficacy in EGFR (A431 epidermoid carcinoma) and HER2 (N87 gastric carcinoma) overexpressing xenograft models and significant extension of survival in a mouse intracranial tumor model. This compound is a 4-amino-6-arylaminopyrimidine-5-carbaldehyde oxime, a monocyclic chemotype that mimics the traditional bicyclic quinazoline scaffold via an intramolecular hydrogen-bonded pseudocycle involving the adjacent 4-amino and 5-oximino groups. In this study, we present results of a structure-guided analog program designed to optimize in vitro kinase potency and in vivo antitumor efficacy of the pyrimidine-oximes. While substituents on the 6-arylamino group are critical for ErbB inhibitory potency and kinase selectivity, substitution on the oxime oxygen may be changed to modify physico-chemical properties and bioavailability. We will discuss structure-activity relationships for the 5-oximino and 6-arylamino groups as well as the important role played by O-aminoalkyl oxime substituents in improving in vivo activity. Citation Format: Peter J. Connolly, Mary Adams, Amanda K. Beck, Stuart L. Emanuel, Angel R. Fuentes-Pesquera, Lee M. Greenberger, Robert H. Gruninger, Terry V. Hughes, Stephen A. Middleton, Sandra Moreno-Mazza, Niranjan Pandey, Steven K. Wetter, Guozhang Xu. Discovery of orally active 4-amino-6-arylaminopyrimidine-5-carbaldehyde oximes with dual EGFR and HER2 inhibitory activity. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2456. doi:10.1158/1538-7445.AM2013-2456

A general synthesis of tetrahydropyrazolo[3,4-d]thiazoles

A short three-step synthesis of tetrasubstituted 3,3a,5,6-tetrahydro-2H-pyrazolo[3,4-d]thiazoles has been worked out. This relatively unknown heterobicyclic system is assembled from two carbonyl compounds, an amine, a hydrazine, and mercaptoacetic acid ester. These versatile starting materials allow the introduction of a broad range of alkyl, haloalkyl, cycloalkyl, aryl, and heteroaryl substituents into four different positions of the bicyclic scaffold. The efficiency of the synthesis route is proven by the fact, that two of the three steps are a multicomponent reaction or a cascade reaction, respectively, and that it can further be shortened to two consecutive one-pot processes.

Skeletal Diversification via Heteroatom Linkage Control: Preparation of Bicyclic and Spirocyclic Scaffolds from N-Substituted Homopropargyl Alcohols

The discovery and application of a new branching pathway synthesis strategy that rapidly produces skeletally diverse scaffolds is described. Two different scaffold types, one a bicyclic iodo-vinylidene tertiary amine/tertiary alcohol and the other, a spirocyclic 3-furanone, are each obtained using a two-step sequence featuring a common first step. Both scaffold types lead to intermediates that can be orthogonally diversified using the same final components. One of the scaffold types was obtained in sufficiently high yield that it was immediately used to produce a 97-compound library.

2-Arylpyrazolo[4,3-d]pyrimidin-7-amino Derivatives As New Potent and Selective Human A3 Adenosine Receptor Antagonists. Molecular Modeling Studies and Pharmacological Evaluation

On the basis of our previously reported 2-arylpyrazolo[4,3-d]pyrimidin-7-ones, a set of 2-arylpyrazolo[4,3-d]pyrimidin-7-amines were designed as new human (h) A3 adenosine receptor (AR) antagonists. Lipophilic groups with different steric bulk were introduced at the 5-position of the bicyclic scaffold (R5 = Me, Ph, CH2Ph), and different acyl and carbamoyl moieties (R7) were appended on the 7-amino group, as well as a para-methoxy group inserted on the 2-phenyl ring. The presence of acyl groups turned out to be of paramount importance for an efficient and selective binding at the hA3 AR. In fact, most of the 7-acylamino derivatives showed low nanomolar affinity (Ki = 2.5-45 nM) and high selectivity toward this receptor. A few selected pyrazolo[4,3-d]pyrimidin-7-amides were effective in counteracting oxaliplatin-induced apoptosis in rat astrocyte cell cultures, an in vitro model of neurotoxicity. Through an in silico receptor-driven approach the obtained binding data were rationalized and the molecular bases of the observed hA3 AR affinity and hA3 versus hA2A AR selectivity were explained.

Design and synthesis of novel pyrimido[4,5-b]azepine derivatives as HER2/EGFR dual inhibitors

A novel 7,6 fused bicyclic scaffold, pyrimido[4,5-b]azepine was designed to fit into the ATP binding site of the HER2/EGFR proteins. The synthesis of this scaffold was accomplished by an intramolecular Claisen-type condensation. As the results of optimization lead us to 4-anilino and 6-functional groups, we discovered 6-substituted amide derivative 19b, which has a 1-benzothiophen-4-yloxy group attached to the 4-anilino group. An X-ray co-crystal structure of 19b with EGFR demonstrated that the N-1 and N-3 nitrogens of the pyrimido[4,5-b]azepine scaffold make hydrogen-bonding interactions with the main chain NH of Met793 and the side chain of Thr854 via a water-mediated hydrogen bond network, respectively. In addition, the NH proton at the 9-position makes an additional hydrogen bond with the carbonyl group of Met793, as we expected. Compound 19b revealed potent HER2/EGFR kinase (IC50: 24/36nM) and BT474 cell growth (GI50: 18nM) inhibitory activities based on its pseudo-irreversible (PI) profile.

Design and synthesis of bicyclic pyrazinone and pyrimidinone amides as potent TF–FVIIa inhibitors

Bicyclic pyrazinone and pyrimidinone amides were designed and synthesized as potent TF–FVIIa inhibitors. SAR demonstrated that the S2 and S3 pockets of FVIIa prefer to bind small, lipophilic groups. An X-ray crystal structure of optimized compound 9b bound in the active site of FVIIa showed that the bicyclic scaffold provides 5 hydrogen bonding interactions in addition to projecting groups for interactions within the S1, S2 and S3 pockets. Compound 9b showed excellent FVIIa potency, good selectivity against FIXa, Xa, XIa and chymotrypsin, and good clotting activity.