Discovery of novel and selective IKK-beta serine-threonine protein kinase inhibitors. Part 1

CCR2 cooperativity promotes hematopoietic stem cell homing to the bone marrow

Cross-talk between hematopoietic stem and progenitor cells (HSPCs) and bone marrow (BM) cells is critical for homing and sustained engraftment after transplantation. In particular, molecular and physical adaptation of sinusoidal endothelial cells (ECs) promote HSPC BM occupancy; however, signals that govern these events are not well understood. Extracellular vesicles (EVs) are mediators of cell-cell communication crucial in shaping tissue microenvironments. Here, we demonstrate that integrin α4β7 on murine HSPC EVs targets uptake into ECs. In BM ECs, HSPC EVs induce up-regulation of C-C motif chemokine receptor 2 (CCR2) ligands that synergize with CXCL12-CXCR4 signaling to promote BM homing. In nonirradiated murine models, marrow preconditioning with HSPC EVs or recombinant CCR2 ligands improves homing and early graft occupancy after transplantation. These findings identify a role for HSPC EVs in remodeling ECs, newly define CCR2-dependent graft homing, and inform novel translational conditioning strategies to improve HSPC transplantation.

Evaluating the Physicochemical Properties-Activity Relationship and Discovering New 1,2-Dihydropyridine Derivatives as Promising Inhibitors for PIM1-Kinase: Evidence from Principal Component Analysis, Molecular Docking, and Molecular Dynamics Studies

In this study, we evaluated the physicochemical properties related to the previously reported anticancer activity of a dataset comprising thirty 1,2-dihydropyridine derivatives. We utilized Principal Component Analysis (PCA) to identify the most significant influencing factors. The PCA analysis showed that the first two principal components accounted for 59.91% of the total variance, indicating a strong correlation between the molecules and specific descriptors. Among the 239 descriptors analyzed, 18 were positively correlated with anticancer activity, clustering with the 12 most active compounds based on their IC50 values. Six of these variables-LogP, Csp3, b_1rotN, LogS, TPSA, and lip_don-are related to drug-likeness potential. Thus, we then ranked the 12 compounds according to these six variables and excluded those violating the drug-likeness criteria, resulting in a shortlist of nine compounds. Next, we investigated the binding affinity of these nine shortlisted compounds with the use of molecular docking towards the PIM-1 Kinase enzyme (PDB: 2OBJ), which is overexpressed in various cancer cells. Compound 6 exhibited the best docking score among the docked compounds, with a docking score of -11.77 kcal/mol, compared to -12.08 kcal/mol for the reference PIM-1 kinase inhibitor, 6-(5-bromo-2-hydroxyphenyl)-2-oxo-4-phenyl-1,2-dihydropyridine-3-carbonitrile. To discover new PIM-1 kinase inhibitors, we designed nine novel compounds featuring hybrid structures of compound 6 and the reference inhibitor. Among these, compound 31 displayed the best binding affinity, with a docking score of -13.11 kcal/mol. Additionally, we performed PubChem database mining using the structure of compound 6 and the similarity search tool, identifying 16 structurally related compounds with various reported biological properties. Among these, compound 52 exhibited the best binding affinity, with a docking score of -13.03 kcal/mol. Finally, molecular dynamics (MD) studies were conducted to confirm the stability of the protein-ligand complexes obtained from docking the studied compounds to PIM-1 kinase, validating the potential of these compounds as PIM-1 kinase inhibitors.

Inhibition of IKKβ via a DNA-Based In Situ Delivery System Improves Achilles Tendinopathy Healing in a Rat Model

BACKGROUND

The inhibition of IKKβ by the inhibitor 2-amino-6-[2-(cyclopropylmethoxy)-6-hydroxyphenyl]-4-(4-piperidinyl)-3-pyridine carbonitrile (ACHP) is a promising strategy for the treatment of Achilles tendinopathy. However, the poor water solubility of ACHP severely hinders its in vivo application. Moreover, the effective local delivery of ACHP to the tendon and its therapeutic effects have not been reported.

PURPOSE

To investigate the therapeutic effects of IKKβ inhibition via injection of ACHP incorporated into a DNA supramolecular hydrogel in a collagenase-induced tendinopathy rat model.

STUDY DESIGN

Controlled laboratory study.

METHODS

Dendritic DNA, a Y-shaped monomer, and a crosslinking monomer were mixed with ACHP and self-assembled into an ACHP-DNA supramolecular hydrogel (ACHP-Gel). The effects of ACHP-Gel in tendon stem/progenitor cells were investigated via RNA sequencing and validated using quantitative reverse transcription polymerase chain reaction (qRT-PCR). A total of 120 collagenase-induced rats were randomly assigned to 5 groups: blank, phosphate-buffered saline (PBS), DNA-Gel, ACHP, and ACHP-Gel. Healing outcomes were evaluated using biomechanic and histologic evaluations at 4 and 8 weeks.

RESULTS

ACHP-Gel enhanced the solubility of ACHP and sustained its release for ≥21 days in vivo, which significantly increased the retention time of ACHP and markedly reduced the frequency of administration. RNA sequencing and qRT-PCR showed that ACHP effectively downregulated genes related to inflammation and extracellular matrix remodeling and upregulated genes related to tenogenic differentiation. The cross-sectional area (P = .024), load to failure (P = .002), stiffness (P = .039), and elastic modulus (P = .048) significantly differed between the ACHP-Gel and PBS groups at 8 weeks. The ACHP-Gel group had better histologic scores than the ACHP group at 4 (P = .042) and 8 weeks (P = .009). Type I collagen expression (COL-I; P = .034) and the COL-I/collagen type III ratio (P = .015) increased while interleukin 6 expression decreased (P < .001) in the ACHP-Gel group compared with the ACHP group at 8 weeks.

CONCLUSION

DNA supramolecular hydrogel significantly enhanced the aqueous solubility of ACHP and increased its release-retention time. Injection frequency was markedly reduced. ACHP-Gel suppressed inflammation in Achilles tendinopathy and promoted tendon healing in a rat model.

CLINICAL RELEVANCE

ACHP-Gel injection is a promising strategy for the treatment of Achilles tendinopathy in clinical practice.

Novel Set of Highly Substituted Bis-pyridines: Synthesis, Molecular Docking and Drug-Resistant Antibacterial Profile

Aims: Development of antimicrobial agents having the ability to prevent bacterial biofilm formation which causes serious health problems, especially with antibiotic-resistant bacterial strains. Materials and methods: The use of 1,3-diaryl enones as structural motifs to access the pyridine core. Antimicrobial activities of the synthesized compounds against methicillin-susceptible Staphylococcus aureus, methicillin-resistant S. aureus and vancomycin-resistant S. aureus bacterial strains were investigated. Results: The newly synthesized bis-enones were used as building blocks to access some novel highly substituted bis-pyridine derivatives. Several novel bis-compounds showed great bacterial biofilm eradication activity. Conclusion: A new series of bis-chalcones was synthesized and their structural diversity was exploited to access the corresponding, more biologically active, pyridine core. These bis-pyridines showed respectable antibacterial activities against various drug-resistant bacterial strains: namely, methicillin-susceptible, methicillin-resistant and vancomycin-resistant S. aureus.

Alternative NF-κB Signaling Discriminates Induction of the Tumor Marker Fascin by the Viral Oncoproteins Tax-1 and Tax-2 of Human T-Cell Leukemia Viruses

Transcriptional regulation of the actin-bundling protein and tumor marker Fascin is highly diverse depending on cell and tumor type. Previously, we discovered that the viral oncoprotein Tax-1 of human T-cell leukemia virus type 1 (HTLV-1) considerably enhances Fascin expression in T-cells, depending on classical NF-κB signaling. In this study, we asked if the non-oncogenic Tax-2 of the related HTLV-2 is still able to induce Fascin by using luciferase assays, immunoblot, and qPCR. We found that Tax-2 only slightly induces Fascin expression compared to Tax-1; however, both Tax-1 and Tax-2 comparably activated a 1.6 kb fragment in the human Fascin promoter including Tax-responsive elements. Furthermore, we identified a link between Tax-induced activity of the alternative NF-κB pathway and Fascin induction. While treatment with the second mitochondria-derived activator of caspases (SMAC)-mimetic AZD5582, a compound known to robustly activate alternative NF-κB signaling, did not induce Fascin, combination of AZD5582 with activation of classical NF-κB signaling by Tax-2 significantly induced Fascin expression. In conclusion, our data demonstrate that both classical and alternative NF-κB activity are necessary for strong Fascin induction by the viral Tax oncoproteins, thus, shedding new light on the regulation of Fascin in T-cells and during viral transformation.

Cu(OAc)2/DABCO-mediated domino reaction of vinyl malononitriles with cyclic sulfamidate imines: access to 6-hydroxyaryl-2-aminonicotinonitriles

A novel Cu(II)-salt/DABCO-mediated one-pot access to a myriad of highly substituted biologically relevant 2-aminonicotinonitriles possessing a resourceful phenolic moiety with satisfactory yields is reported. This method involves cyclic sulfamidate imines as 1C1N sources and different kinds of acyclic/cyclic vinyl malononitriles as 4C sources for pyridine synthesis via a vinylogous Mannich-cycloaromatization sequence process, creating two new C-N bonds under mild conditions. Importantly, this de novo strategy is applicable to gram-scale syntheses, underlining the method's practicability and allowing for a wide range of substrates with excellent functional group tolerance.

Antibacterial Cellulose Acetate Microfibers Containing Pyridine Derivative Complexes

Pyridine (L1) and 2,4-dimethylpyridine (L2) halide complexes of the type of [ML2X2] were prepared and characterized via FT-IR and 1H NMR. The CA microfibers containing complexes were electrospun and investigated via FT-IR. The morphologies of the microfibers were investigated via FE-SEM. Antibacterial activities of the complexes and the fibers were investigated.

β-Cyclodextrin: a supramolecular catalyst for metal-free approach towards the synthesis of 2-amino-4,6-diphenylnicotinonitriles and 2,3-dihydroquinazolin-4(1H)-one

β-Cyclodextrin, a green and widespread supramolecular catalyst, has been explored as a highly proficient promoter for the metal-free one-pot multi-component synthesis of a vast range of highly functionalized bioactive heterocyclic moiety, 2-amino-4,6-diphenylnicotinonitriles and 2,3-dihydroquinazolin-4(1H)-one, from easily available precursor aldehydes. The main endeavor of these protocols is to explore this organic supramolecule in one-pot multi-component synthesis. Absence of metal catalyst or toxic acid and harsh reaction conditions, excellent functional group tolerance, inexpensive, greener and environmentally safe protocol are the key advantages of this work.

Venezuelan Equine Encephalitis Virus nsP3 Phosphorylation Can Be Mediated by IKKβ Kinase Activity and Abrogation of Phosphorylation Inhibits Negative-Strand Synthesis

Venezuelan equine encephalitis virus (VEEV), a mosquito transmitted alphavirus of the Togaviridae family, can cause a highly inflammatory and encephalitic disease upon infection. Although a category B select agent, no FDA-approved vaccines or therapeutics against VEEV currently exist. We previously demonstrated NF-κB activation and macromolecular reorganization of the IKK complex upon VEEV infection in vitro, with IKKβ inhibition reducing viral replication. Mass spectrometry and confocal microscopy revealed an interaction between IKKβ and VEEV non-structural protein 3 (nsP3). Here, using western blotting, a cell-free kinase activity assay, and mass spectrometry, we demonstrate that IKKβ kinase activity can directly phosphorylate VEEV nsP3 at sites 204/5, 142, and 134/5. Alanine substitution mutations at sites 204/5, 142, or 134/5 reduced VEEV replication by >30-100,000-fold corresponding to a severe decrease in negative-strand synthesis. Serial passaging rescued viral replication and negative-strand synthesis, and sequencing of revertant viruses revealed reversion to the wild-type TC-83 phosphorylation capable amino acid sequences at nsP3 sites 204/5, 142, and 135. Generation of phosphomimetic mutants using aspartic acid substitutions at site 204/5 resulted in rescue of both viral replication and negative-strand RNA production, whereas phosphomimetic mutant 134/5 rescued viral replication but failed to restore negative-strand RNA levels, and phosphomimetic mutant 142 did not rescue VEEV replication. Together, these data demonstrate that IKKβ can phosphorylate VEEV nsP3 at sites 204/5, 142, and 134/5, and suggest that phosphorylation is essential for negative-strand RNA synthesis at site 204/5, but may be important for infectious particle production at site 134/5.

Synthesis of cobalt tetra-2,3-pyridiniumporphyrazinato with sulfonic acid tags as an efficient catalyst and its application for the synthesis of bicyclic ortho-aminocarbonitriles, cyclohexa-1,3-dienamines and 2-amino-3-cyanopyridines

Cobalt tetra-2,3-pyridiniumporphyrazinato with sulfonic acid tag [Co(TPPASO3H)]Cl was produced and catalyzed the synthesis of ortho-aminocarbonitriles, cyclohexa-1,3-dienamines and 2-amino-3-cyanopyridines. The synthesis of 2-amino-3-cyanopyridines by using [Co(TPPASO3H)]Cl proceeded via a cooperative vinylogous anomeric based oxidation mechanism. [Co(TPPASO3H)]Cl can be recycled and reused six times with a marginal decreasing of its catalytic activity.

Nanocrystalline ZnO: A Competent and Reusable Catalyst for the Preparation of Pharmacology Relevant Heterocycles in the Aqueous Medium

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Nanoparticle catalyzed synthesis is a green and convenient method to achieve most of the chemical transformations in water or other green solvents. Nanoparticle ensures an easy isolation process of catalyst as well as products from the reaction mixture avoiding the hectic work up procedure. Zinc oxide is a biocompatible, environmentally benign and economically viable nanocatalyst with effectivity comparable to the other metal nanocatalyst employed in several reaction strategies. This review mainly focuses on the recent applications of zinc oxide in the synthesis of biologically important heterocyclic molecules under sustainable reaction conditions.

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Application of zinc oxide in organic synthesis: Considering the achievable advantages of this nanocatalyst, presently several research groups are paying attention in anchoring zincoxide or its modified structure in several types of organic conversions e.g. multicomponent reactions, ligand-free coupling reactions, cycloaddition reaction, etc. The advantages and limitations of this nanocatalyst are also demonstrated. The present study aims to highlight the recent multifaceted applications of ZnO towards the synthesis of diverse heterocyclic motifs. Being a promising biocompatible nanoparticle, this catalyst has an important contribution in the fields of synthetic chemistry and medicinal chemistry.

Synthesis, cytotoxic assessment, and molecular docking studies of 2,6-diaryl-substituted pyridine and 3,4- dihydropyrimidine-2(1H)-one scaffolds

Cancer is one of the main global health problems. In order to develop novel antitumor agents, we synthesized 3,4-dihydropyrimidine-2(1H)-one (DHPM) and 2,6-diaryl-substituted pyridine derivatives as potential antitumor structures and evaluated their cytotoxic effects against several cancer cell lines. An easy and convenient method is reported for the synthesis of these derivatives, employing cobalt ferrite (CoFe 2 O 4 @SiO 2 -SO 3 H) magnetic nanoparticles under microwave irradiation and solvent-free conditions. The structural characteristics of the prepared nanocatalyst were investigated by FTIR, XRD, SEM, and TGA techniques. In vitro cytotoxic effects of the synthesized products were assessed against the human breast adenocarcinoma cell line (MCF-7), gastric adenocarcinoma (AGS), and human embryonic kidney (HEK293) cells via MTT assay. The results indicated that compound 4r (DHPM derivative) was the most toxic molecule against the MCF-7 cell line (IC 50 of 0.17 μg/mL). Moreover, compounds 4j and 4r (DHPM derivatives) showed excellent cytotoxic activities against the AGS cell line, with an IC 50 of 4.90 and 4.97 μg/mL, respectively. Although they are pyridine derivatives, compounds 5g and 5m were more active against the MCF-7 cell line. Results showed that the candidate compounds exhibited low cytotoxicity against HEK293 cells. The kinesin Eg5 inhibitory potential of the candidate compounds was evaluated by molecular docking. The docking results showed that, among the pyridine derivatives, compound 5m had the most free energy of binding (-9.52 kcal/mol) and lowest Ki (0.105 μM), and among the pyrimidine derivatives, compound 4r had the most free energy of binding (-7.67 kcal/mol) and lowest Ki (2.39 μM). Ligand-enzyme affinity maps showed that compounds 4r and 5m had the potential to interact with the Eg5 binding site via H-bond interactions to GLU116 and GLY117 residues. The results of our study strongly suggest that DHPM and pyridine derivatives inhibit important tumorigenic features of breast and gastric cancer cells. Our results may be helpful in the further design of DHPMs and pyridine derivatives as potential anticancer agents.

The IκB Kinase Inhibitor ACHP Targets the STAT3 Signaling Pathway in Human Non-Small Cell Lung Carcinoma Cells

STAT3 is an oncogenic transcription factor that regulates the expression of genes which are involved in malignant transformation. Aberrant activation of STAT3 has been observed in a wide range of human malignancies and its role in negative prognosis is well-documented. In this report, we performed high-throughput virtual screening in search of STAT3 signaling inhibitors using a cheminformatics platform and identified 2-Amino-6-[2-(Cyclopropylmethoxy)-6-Hydroxyphenyl]-4-Piperidin-4-yl Nicotinonitrile (ACHP) as the inhibitor of the STAT3 signaling pathway. The predicted hit was evaluated in non-small cell lung cancer (NSCLC) cell lines for its STAT3 inhibitory activity. In vitro experiments suggested that ACHP decreased the cell viability and inhibited the phosphorylation of STAT3 on Tyr705 of NSCLC cells. In addition, ACHP imparted inhibitory activity on the constitutive activation of upstream protein tyrosine kinases, including JAK1, JAK2, and Src. ACHP decreased the nuclear translocation of STAT3 and downregulated its DNA binding ability. Apoptosis was evidenced by cleavage of caspase-3 and PARP with the subsequent decline in antiapoptotic proteins, including Bcl-2, Bcl-xl, and survivin. Overall, we report that ACHP can act as a potent STAT3 signaling inhibitor in NSCLC cell lines.

Protective effect of RNA interference targeting Ikkβ on hepatic fibrosis in rats

Nuclear factor-κB (NF-κB) is an important regulatory factor in cells. NF-κB has a wide range of biological activities. After activation, it participates in the transcription and regulation of many genes and plays a role in infection, inflammatory response, oxidative stress, cell multiplication, and apoptosis. The activation of the NF-κB signal pathway is dependent on the degradation of the IκB kinase β (IKKβ) complex. IKK β is the key kinase in the NF-κB activation pathway. After inhibition, it can block the activation of NF-κB. IKKβ is a key regulator of NF-κB activation, also an early regulator of inflammation in all stages of the immune response. This study aimed to investigate the effect of IKKβ-siRNA lentivirus vector treatment for hepatic fibrosis of rats. An IKKβ-siRNA expression plasmid was constructed and injected in the tail vein of rats. Then, IKKβ-siRNA distribution in the liver was observed by immunofluorescence, and the quantitative polymerase chain reaction was used to detect inflammation-related and fibrosis-related factors. IKKβ-siRNA lentiviruses could be delivered to the liver and significantly decrease carbon tetrachloride-induced hepatic fibrosis. Furthermore, serum transaminase levels significantly decreased, and inflammation-related and fibrosis-related factors decreased. IKKβ-siRNA can be an effective method of anti-fibrosis gene therapy for liver fibrosis.

Quantum chemical studies and spectroscopic investigations on 22-amino-3-methyl-5-nitropyridine by density functional theory

Quantum chemical calculations on energy and molecular structure of 2-amino-3-methyl-5-nitropyridine (2A3M5NP) have been attempted by implementing DFT/B3LYP method using 6-311G (d,p), 6-311G++ (d,p) and cc-pVTZ basis sets. The optimized geometry and the vibrational analysis for energetically most stable configuration, are carried out theoretically by using B3LYP/cc-pVTZ basis set. The computed vibrational frequencies were scaled by using scaling factors and compared with the experimental Fourier Transform Infra-Red (FTIR) solid phase spectrum in the region 4000-400 cm-1 and FT-Raman spectrum in the region 4000-100 cm-1. The complete vibrational assignments, analysis and correlation of fundamental modes of the compound have been carried out using the potential energy distribution (PED). The intramolecular charge transfer, hyperconjugative interaction of the compound is investigated from natural bonding orbital (NBO) analysis. The UV-Visible spectrum of 2A3M5NP was obtained with ethanol as a solvent. The electronic properties such as HOMO (Highest Occupied Molecular Orbital) and LUMO (Lowest Unoccupied Molecular Orbital) energies are determined by B3LYP/cc-pVTZ basis set. The electronic absorption spectrum of the compound was studied from UV-Visible analysis by using time-dependent density functional theory (TD-DFT). The electron density distribution and chemical reactive sites of 2A3M5NP were analyzed from molecular electrostatic potential (MEP) analysis and frontier molecular orbital (FMO) analysis.

Design, synthesis and antitumor activity of steroidal pyridine derivatives based on molecular docking

With steroid as a carrier nucleus and introducing a pyridine heterocycle as a pharmacophore on the D ring, a series of steroidal pyridine derivatives were designed and studied for their antitumor activity by molecular docking software. The compounds were synthesized as small molecule inhibitors and studied as anticancer agents. The synthesis of the analogs was performed in a one-pot multi-component reaction and the corresponding compounds were screened in vitro for their antitumor activity. Four adherently growing cancer cell lines were used and arranged before dosing. Among all compounds screened for their antitumor activity, compounds 2f and 2p were found to be the most active. Here, the most obvious changes in the morphology of the treated cells could be observed.

Development of mKO2 fusion proteins for real-time imaging and mechanistic investigation of the degradation kinetics of human IκBα in living cells

In resting cells, the nuclear factor kappa B (NF-κB) family of transcription factors is stabilized by complexation with the cytoplasmic inhibitor of kappa B alpha (IκBα). Extracellular stimuli, such as tumor necrosis factor alpha (TNFα) or bacterial lipopolysaccharide activate NF-κB through IκBα phosphorylation and ubiquitin-proteasomal degradation. Herein, we developed a novel biosensor, by fusing the monomeric fluorescent protein Kusabira-Orange 2 to IκBα (mKO2-IκBα), to study the dynamics and structure-activity relationship of IκBα degradation. Site-specific deletion studies on the IκBα sequence revealed that the C-terminal PEST domain is required in signal-induced proteasomal degradation of IκBα and functions independently from ankyrin repeats. Using deletion mutants, we show that IκBα ankyrin repeats do not affect IκBα degradability but affect its degradation rate. We demonstrate, by both real-time confocal microscopy and western blot analysis, that the half-life of mKO2-IκBα in response to TNFα is approximately 35 min, which is similar to the half-life of endogenous IκBα. Using this biosensor we also show that selective proteasome inhibitors, such as lactacystin and MG132, inhibit degradation and affect the kinetics of IκBα in a dose-dependent manner. The techniques described here can have a range of possible applications, such as facilitating studies associated with IκBα dynamics and biochemical characteristics, as well as the screening of potential proteasome inhibitors.

Gold Catalyzed Multicomponent Reactions beyond A³ Coupling

The preparation of complex architectures has inspired the search for new methods and new processes in organic synthesis. Multicomponent reactions have become an interesting approach to achieve such molecular diversity and complexity. This review intends to illustrate important gold-catalyzed examples for the past ten years leading to interesting skeletons involved in biologically active compounds.

Success stories of natural product-based hybrid molecules for multi-factorial diseases

Complex diseases comprises of highly complicated etiology resulting in limited applicability of conventional targeted therapies. Consequently, conventional medicinal compounds suffer major failure when used for such disease conditions. Additionally, development of multidrug resistance (MDR), adverse drug reactions and clinical specificity of single targeted drug therapy has increased thrust for novel drug therapy. In this rapidly evolving era, natural product-based discovery of hybrid molecules or multi-targeted drug therapies have shown promising results and are trending now a days. Historically, nature has blessed human with different sources viz. plant, animal, microbial, marine and ethnopharmaceutical sources which has given a wide variety of medicinally active compounds. These compounds from natural origin are always choice of interest of medicinal chemists because of their minimum side effects. Hybrid molecules synthesized by fusing or conjugating different active molecules obtained from these sources are reported to synergistically block different pathways which contribute in the pathogenesis of complex diseases. This review strives to encompass all natural product-derived hybrid molecules which act as multi-targeting agents striking various targets involved in different pathways of complex diseased conditions reported in literature.