Potent Hit Compound Research Articles

Structure-based Virtual Screening and Molecular Dynamic Simulation Approach for the Identification of Terpenoids as Potential DPP-4 Inhibitors.

Diabetes mellitus is a metabolic disorder where insulin secretion is compromised, leading to hyperglycemia. DPP-4 is a viable and safer target for type 2 diabetes mellitus. Computational tools have proven to be an asset in the process of drug discovery. In the present study, tools like structure-based virtual screening, MM/GBSA, and pharmacokinetic parameters were used to identify natural terpenoids as potential DPP-4 inhibitors for treating diabetes mellitus. Structure-based virtual screening, a cumulative mode of elimination technique, was adopted, identifying the top five potent hit compounds depending on the docking score and nonbonding interactions. According to the docking data, the most important contributors to complex stability are hydrogen bonding, hydrophobic interactions, and Pi-Pi stacking interactions. The dock scores ranged from -6.492 to -5.484 kcal/mol, indicating robust ligand-protein interactions. The pharmacokinetic characteristics of top-scoring hits (CNP0309455, CNP0196061, CNP0122006, CNP0 221869, CNP0297378) were also computed in this study, confirming their safe administration in the human body. Also, based on the synthetic accessibility score, all top-scored hits are easily synthesizable. Compound CNP0309455 was quite stable during molecular dynamic simulation studies. Virtual database screening yielded new leads for developing DPP-4 inhibitors. As a result, the findings of this study can be used to design and develop natural terpenoids as DPP-4 inhibitors for the medication of diabetes mellitus.

Identification of 1,3,8-Triazaspiro[4.5]Decane-2,4-Dione Derivatives as a Novel δ Opioid Receptor-Selective Agonist Chemotype.

δ opioid receptors (DORs) hold potential as a target for neurologic and psychiatric disorders, yet no DOR agonist has proven efficacious in critical phase II clinical trials. The exact reasons for the failure to produce quality drug candidates for the DOR are unclear. However, it is known that certain DOR agonists can induce seizures and exhibit tachyphylaxis. Several studies have suggested that those adverse effects are more prevalent in delta agonists that share the (+)-4-[(αR)-α-((2S,5R)-4-allyl-2,5-dimethyl-1-piperazinyl)-3-methoxybenzyl]-N,N-diethylbenzamide (SNC80)/4-[(αR*)-α-((2S*,5R*)-4-allyl-2,5-dimethyl-1-piperazinyl)-3-hydroxybenzyl]-N,N-diethylbenzamide chemotype. There is a need to find novel lead candidates for drug development that have improved pharmacological properties to differentiate them from the current failed delta agonists. Our objective in this study was to identify novel DOR agonists. We used a β-arrestin assay to screen a small G-protein coupled receptors (GPCR)-focused chemical library. We identified a novel chemotype of DOR agonists that appears to bind to the orthosteric site based of docking and molecular dynamic simulation. The most potent agonist hit compound is selective for the DOR over a panel of 167 other GPCRs, is slightly biased toward G-protein signaling and has anti-allodynic efficacy in a complete Freund's adjuvant model of inflammatory pain in C57BL/6 male and female mice. The newly discovered chemotype contrasts with molecules like SNC80 that are highly efficacious β-arrestin recruiters and may suggest this novel class of DOR agonists could be expanded on to develop a clinical candidate drug. SIGNIFICANCE STATEMENT: δ opioid receptors are a clinical target for various neurological disorders, including migraine and chronic pain. Many of the clinically tested delta opioid agonists share a single chemotype, which carries risks during drug development. Through a small-scale high-throughput screening assay, this study identified a novel δ opioid receptor agonist chemotype, which may serve as alternative for the current analgesic clinical candidates.

Structure-Based Discovery of High-Affinity Small Molecule Ligands and Development of Tool Probes to Study the Role of Chitinase-3-Like Protein 1.

Chitinase-3-like-1 (CHI3L1), also known as YKL-40, is a glycoprotein linked to inflammation, fibrosis, and cancer. This study explored CHI3L1's interactions with various oligosaccharides using microscale thermophoresis (MST) and AlphaScreen (AS). These investigations guided the development of high-throughput screening assays to assess interference of small molecules in binding between CHI3L1 and biotinylated small molecules or heparan sulfate-based probes. Small molecule binders of YKL-40 were identified in our chitotriosidase inhibitors library with MST and confirmed through X-ray crystallography. Based on cocrystal structures of potent hit compounds with CHI3L1, small molecule probes 19 and 20 were designed for an AS assay. Structure-based optimization led to compounds 30 and 31 with nanomolar activities and drug-like properties. Additionally, an orthogonal AS assay using biotinylated heparan sulfate as a probe was developed. The compounds' affinity showed a significant correlation in both assays. These screening tools and compounds offer novel avenues for investigating the role of CHI3L1.

N-Substituted piperazine-coupled imidazo[2,1-b]thiazoles as inhibitors of Mycobacterium tuberculosis: Synthesis, evaluation, and docking studies.

An innovative series of N-substituted piperazine-linked imidazothiazole derivatives 7(a-x) were synthesized, and their antitubercular effectiveness was evaluated. A three-step reaction sequence involving the condensation of 1,3-dichloroacetone and thiourea, coupling with substituted piperazines to give the intermediates 5(a-d) and cyclization with substituted α-bromoacetophenones produced the desired imidazothiazole derivatives 7(a-x) in excellent yields. In vitro screening of new derivatives against Mycobacterium tuberculosis H37Rvresulted in 7k (minimum inhibitory concentration [MIC]: 0.78 μg/mL) and 7g and 7h (MIC: 1.56 μg/mL) as potent hit compounds. Further, the docking studies of the promising compounds7k, 7g, and 7h revealed that the best molecular interactions are with the DprE1 in complex with sulfonyl PBTZ of M. tuberculosis as the target protein (PDB ID: 6G83).

Hit Identification Driven by Combining Artificial Intelligence and Computational Chemistry Methods: A PI5P4K-β Case Study.

Computer-aided drug design (CADD), especially artificial intelligence-driven drug design (AIDD), is increasingly used in drug discovery. In this paper, a novel and efficient workflow for hit identification was developed within the ID4Inno drug discovery platform, featuring innovative artificial intelligence, high-accuracy computational chemistry, and high-performance cloud computing. The workflow was validated by discovering a few potent hit compounds (best IC50 is ∼0.80 μM) against PI5P4K-β, a novel anti-cancer target. Furthermore, by applying the tools implemented in ID4Inno, we managed to optimize these hit compounds and finally obtained five hit series with different scaffolds, all of which showed high activity against PI5P4K-β. These results demonstrate the effectiveness of ID4inno in driving hit identification based on artificial intelligence, computational chemistry, and cloud computing.

Virtual screening, pharmacokinetic, and DFT studies of anticancer compounds as potential V600E-BRAF kinaseinhibitors

ObjectivesV600E-BRAF kinase is an essential therapeutic target in melanoma and other types of tumors. Because of its resistance to known inhibitors and the adverse effects of some identified inhibitors, investigation of new potent inhibitors is necessary. MethodsIn the present work, in silico strategies such as molecular docking simulation, pharmacokinetic evaluation, and density functional theory (DFT) computations were used to identify potential V600E-BRAF inhibitors from a set of 72 anticancer compounds in the PubChem database. ResultsFive top-ranked molecules (12, 15, 30, 31, and 35) with excellent docking scores (MolDock score ≥90 kcal mol−1, Rerank score ≥60 kcal mol−1) were selected. Several potential binding interactions were discovered between the molecules and V600E-BRAF. The formation of H-bonds and hydrophobic interactions with essential residues of V600E-BRAF suggested the high stability of these complexes. The selected compounds had excellent pharmacological properties according to the drug likeness rules (bioavailability) and pharmacokinetic properties. Similarly, the energy for the frontier molecular orbitals, such as the HOMO, LUMO, energy gap, and other reactivity parameters, was computed with DFT. The frontier molecular orbital surfaces and electrostatic potentials were investigated to demonstrate the charge-density distributions potentially associated with anticancer activity. ConclusionThe identified compounds were found to be potent hit compounds for V600E-BRAF inhibition with superior pharmacokinetic properties; therefore, they may be promising cancer drug candidates.

Exploration of a Large Virtual Chemical Space: Identification of Potent Inhibitors of Lactate Dehydrogenase-A against Pancreatic Cancer.

It is imperative to explore the gigantic available chemical space to identify new scaffolds for drug lead discovery. Identifying potent hits from virtual screening of large chemical databases is challenging and computationally demanding. Rather than the traditional two-dimensional (2D)/three-dimensional (3D) approaches on smaller chemical libraries of a few hundred thousand compounds, we screened a ZINC library of 15 million compounds using multiple computational methods. Here, we present the successful application of a virtual screening methodology that identifies several chemotypes as starting hits against lactate dehydrogenase-A (LDHA). From 29 compounds identified from virtual screening, 17 (58%) showed IC50 values < 63 μM, two showed single-digit micromolar inhibition, and the most potent hit compound had IC50 down to 117 nM. We enriched the database and employed an ensemble approach by combining 2D fingerprint similarity searches, pharmacophore modeling, molecular docking, and molecular dynamics. WaterMap calculations were carried out to explore the thermodynamics of surface water molecules and gain insights into the LDHA binding pocket. The present work has led to the discovery of two new chemical classes, including compounds with a succinic acid monoamide moiety or a hydroxy pyrimidinone ring system. Selected hits block lactate production in cells and inhibit pancreatic cancer cell lines with cytotoxicity IC50 down to 12.26 μM against MIAPaCa-2 cells and 14.64 μM against PANC-1, which, under normoxic conditions, is already comparable or more potent than most currently available known LDHA inhibitors.

Novel pyrimidine-piperazine hybrids as potential antimicrobial agents: in-vitro antimicrobial and in-silico studies

A series of new pyrimidine-piperazine hybrid molecules ware designed and synthesized as possible antimicrobial agents. The synthesized compounds (20 derivatives) were characterized using 1HNMR, 13C NMR, MS and elemental analysis and then the activity of the new compounds were compared with that of antibiotics.Various pathogenic bacteria including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumonia, Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli, as well as standard antibiotics such as ampicillin/tetracycline, ceftazidime, and vancomycin, as recommended by the clinical and laboratory standards institute (CLSI). Compounds N-(4-(4-(5-fluoropyrimidin-2-yl)piperazin-1-yl) phenyl) cyclobutanecarboxamide (9 g), 1-cyclopropyl-3-(4-(4-(5-fluoropyrimidin-2-yl) piperazin-1-yl) phenyl) urea (7c) and 1-cyclobutyl-3-(4-(4-(5-fluoropyrimidin-2-yl) piperazin-1-yl) phenyl) urea (7d) exhibited strong antimicrobial activity against K. pneumonia, with an IC50 of 27.1, 32.4, and 32.4 μg/ml, respectively. 1-cyclohexyl-3-(4-(4-(5-fluoropyrimidin-2-yl) piperazin-1-yl) phenyl) urea (7 h) and 1-ethyl-3-(4-(4-(5-fluoropyrimidin-2-yl) piperazin-1-yl) phenyl) urea (7i) showed potent antimicrobial activity against E. faecium, with an IC50 of 26.2 and 34.2 μg/ml, respectively. Notably, 1-(4-(4-(5-fluoropyrimidin-2-yl) piperazin-1-yl) phenyl)-3-phenylurea (7f) displayed excellent antimicrobial activity against P. aeruginosa, with an IC50 of 9.8 μg/mL. Moreover, molecular docking studies were carried out to determine the binding affinity and ligand interactions of the compounds with the penicillin-binding protein3. The pharmacokinetic properties (ADME) of the synthesized compounds were predicted, and a high percentage of human oral absorption was found for most of the compounds. Lipinski's rule was adhered by the majority of the compounds. Furthermore, the most potent antibacterial hit compounds, N-(4-(4-(5-fluoropyrimidin-2-yl) piperazin-1-yl) phenyl)-2-naphthamide (9e) and 1-(4-(4-(5-fluoropyrimidin-2-yl)piperazin-1-yl)phenyl)-3-phenylurea (7f) were selected for MD simulation studies using the Desmond (2022–4) module of Schrodinger software.

Substrate-Based Design of Cytosolic Nucleotidase IIIB Inhibitors and Structural Insights into Inhibition Mechanism.

Cytosolic nucleotidases (cNs) catalyze dephosphorylation of nucleoside 5’-monophosphates and thereby contribute to the regulation of nucleotide levels in cells. cNs have also been shown to dephosphorylate several therapeutically relevant nucleotide analogues. cN-IIIB has shown in vitro a distinctive activity towards 7-mehtylguanosine monophosphate (m7GMP), which is one key metabolites of mRNA cap. Consequently, it has been proposed that cN-IIIB participates in mRNA cap turnover and prevents undesired accumulation and salvage of m7GMP. Here, we sought to develop molecular tools enabling more advanced studies on the cellular role of cN-IIIB. To that end, we performed substrate and inhibitor property profiling using a library of 41 substrate analogs. The most potent hit compounds (identified among m7GMP analogs) were used as a starting point for structure–activity relationship studies. As a result, we identified several 7-benzylguanosine 5’-monophosphate (Bn7GMP) derivatives as potent, unhydrolyzable cN-IIIB inhibitors. The mechanism of inhibition was elucidated using X-ray crystallography and molecular docking. Finally, we showed that compounds that potently inhibit recombinant cN-IIIB have the ability to inhibit m7GMP decay in cell lysates.

172 Discovery of small molecule compounds with readthrough potency at premature termination codon

Nagashima-type palmoplantar keratosis (NPPK) is the most common palmoplantar keratoderma in the East Asian populations. NPPK is caused by biallelic loss-of-function mutations in SERPINB7. Notably, almost all NPPK patients carry the TGAA nonsense mutation c.796C>T (p.Arg266Ter) in SERPINB7, which creates a premature termination codon (PTC) and leads to highly reduced production of full-length, functional SERPINB7 polypeptides. The suppression of a PTC, also known as ‘readthrough’, is able to restore the full-length protein. As the currently available drugs, including topical vitamin D3 and topical keratolytic, yield very limited improvement of NPPK skin phenotypes, we sought to tackle the disease by the readthrough therapy. We first performed a high- throughput screening of 19,992 small molecule compounds for readthrough activity using firefly luciferase assay. A total of 64 compounds survived retest screening and were shortlisted as potential readthrough candidates. Next, we generated a FLAG-tagged mutant SERPINB7 cDNA vector which contains the nonsense mutation c.796C>T and perform single and multiple concentrations screening using this vector for the selected 64 compounds. 2 hit compounds were identified with readthrough efficiency at their optimal concentration. Additional small molecule compounds with similar chemical structures of the 2 hit compounds were purchased for hit expansion; the process in which derivatives with similar chemical structure are selected from databases. Along with the hit expansion compounds, they have shown to induce a higher readthrough potency than the currently available drugs such as gentamicin and ataluren (Translarna®). As approximately 10% of all described gene lesions in genetic diseases are caused by nonsense mutations, the discovery of potent hit compounds can benefit not only NPPK patients but also patients who suffer from diseases caused by nonsense mutations.

Pyrrolidine-based 3-deoxysphingosylphosphorylcholine analogs as possible candidates against neglected tropical diseases (NTDs): identification of hit compounds towards development of potential treatment of Leishmania donovani

A rational-based process was adopted for repurposing pyrrolidine-based 3-deoxysphingosylphosphorylcholine analogs bearing variable acyl chains, different stereochemical configuration and/or positional relationships. Structural features were highly influential on activity. Amongst, enantiomer 1e having 1,2-vicinal relationship for the -CH2O- and the N-acyl moieties, a saturated palmitoyl chain and an opposite stereochemical configuration to natural sphingolipids was the most potent hit compound against promastigotes showing IC50 value of 28.32 µM. The corresponding enantiomer 1a was 2-fold less potent showing a eudismic ratio of 0.54 in promastigotes. Compounds 1a and 1e inhibited the growth of amastigotes more potently relative to promastigotes. Amongst, enantiomer 1a as the more selective and safer. In silico docking study using a homology model of Leishmania donovani inositol phosphoceramide synthase (IPCS) provided plausible reasoning for the molecular factors underlying the found activity. Collectively, this study suggests compounds 1a and 1e as potential hit compounds for further development of new antileishmanial agents.

The translocator protein ligands as mitochondrial functional modulators for the potential anti-Alzheimer agents

Small molecule modulators of mitochondrial function have been attracted much attention in recent years due to their potential therapeutic applications for neurodegenerative diseases. The mitochondrial translocator protein (TSPO) is a promising target for such compounds, given its involvement in the formation of the mitochondrial permeability transition pore in response to mitochondrial stress. In this study, we performed a ligand-based pharmacophore design and virtual screening, and identified a potent hit compound, 7 (VH34) as a TSPO ligand. After validating its biological activity against amyloid-β (Aβ) induced mitochondrial dysfunction and in acute and transgenic Alzheimer’s disease (AD) model mice, we developed a library of analogs, and we found two most active compounds, 31 and 44, which restored the mitochondrial membrane potential, ATP production, and cell viability under Aβ-induced mitochondrial toxicity. These compounds recovered learning and memory function in acute AD model mice with improved pharmacokinetic properties.

Metacytofilin has potent anti-malarial activity.

Metacytofilin (MCF) was isolated from the fungus Metarhizium sp. TA2759. Although MCF possesses anti-Toxoplasma activity, the effects of this compound against other parasites are unknown. Here, we evaluated the in vitro anti-malarial activity of MCF against the 3D7 strain and the chloroquine-resistant K1 strain of Plasmodium falciparum. The half maximal inhibitory concentrations (IC50) of MCF against the 3D7 and K-1 strains following culture for 48h were 666nM and 605nM, respectively. Artemisinin was more potent than MCF against both strains (3D7 IC50: 17.4nM; K-1 IC50: 18.3nM), while chloroquine was ineffective against the chloroquine-resistant strain (3D7 IC50: 39.1nM; K-1 IC50: 1.62μM). MCF affected the ring stage of the parasites, resulting in their death as shown by spots within red blood cells. MCF also inhibited parasite growth following culture for 72h (3D7 IC50, 285nM). Four optical isomers of cyclo[Leu-Phe]-diketopiperazine derivatives with modified methoxy and/or hydroxyl groups lost anti-malarial activity, suggesting that the spatial positions of the methoxy and hydroxyl groups in MCF play an important role in its anti-malarial effects. Together, these data suggest that MCF may represent a promising lead compound for treatment of drug-resistant malarial parasites.

Design and development of Tetrahydro-Quinoline derivatives as dual mTOR-C1/C2 inhibitors for the treatment of lung cancer

Lung cancer is one of the most prevailed cancer worldwide. Many genes get mutated in lung cancer but the involvement of EGFR, KRAS, PTEN and PIK3CA are more common. Unavailability of potent drugs and resistance to the available drugs are major concern in the treatment of lung cancer. In the present research, mTOR was selected as an important alternative target for the treatment of lung cancer which involves the PI3K/AKT/mTOR pathway. We studied binding interactions of AZD-2014 with the mTOR protein to identify important interactions required to design potent mTOR inhibitors which was supported by QSAR studies. Pharmacophore based virtual screening studies provided core scaffold, THQ. Based on molecular docking interactions, 31 THQ derivatives were synthesized and characterized. All compounds were screened for cellular mTOR enzyme assay along with antiproliferative activity against the panel of cancerous cell lines, from which 6 compounds were further screened for colony forming assay. Two most potent compounds, HB-UC-1 and HB-UC-5, were further screened for flow cytometry analysis, gene expression study and western blot analysis. Gene expression study revealed the efficiency of compound HB-UC-1 against both mTORC1 and mTORC2 by affecting downstream regulators of mTORC1 (E4BP4, eIF4EBP1) and mTORC2 (PCK1), respectively. In western blot analysis, both compounds, inhibited phosphorylation of AKT S473 which proved the efficiency these compounds against the mTORC2. These two compounds were further screened for in-vivo biological evaluation. Both compounds increased lifespan of cancer-bearing animals with improvement in mean survival time. Further, in bezopyrene induced lung cancer animal model, both compounds showed effectiveness through the biochemical parameters and histopathological evaluation of the lung tissue. In future, potent hit compound from this series could be modified to develop lead mTOR inhibitors for the treatment of lung cancer.

Discovery of a Chiral DNA‐Targeted Platinum–Acridine Agent with Potent Enantioselective Anticancer Activity

AbstractA structure–activity relationship study was performed for a set of rigidified platinum–acridine anticancer agents containing linkers derived from chiral pyrrolidine and piperidine scaffolds. Screening a library of microscale reactions and selected resynthesized compounds in non‐small‐cell lung cancer (NSCLC) cells showed that cytotoxicities varied by more than three orders of magnitude. A potent hit compound was discovered containing a (R)‐N‐(piperidin‐3‐yl) linker (P2‐6R), which killed NCI‐H460 and A549 lung cancer cells 100 times more effectively than the S enantiomer (P2‐6S). P2‐6R accumulated in A549 cells significantly faster and produced 50‐fold higher DNA adduct levels than P2‐6S. Ligand similarity analysis suggests that only module 6R may be compatible with strainless monofunctional intercalative binding. NCI‐60 screening and COMPARE analysis highlights the spectrum of activity and potential utility of P2‐6R for treating NSCLC and other solid tumors.

Discovery of a Chiral DNA-Targeted Platinum-Acridine Agent with Potent Enantioselective Anticancer Activity.

A structure-activity relationship study was performed for a set of rigidified platinum-acridine anticancer agents containing linkers derived from chiral pyrrolidine and piperidine scaffolds. Screening a library of microscale reactions and selected resynthesized compounds in non-small-cell lung cancer (NSCLC) cells showed that cytotoxicities varied by more than three orders of magnitude. A potent hit compound was discovered containing a (R)-N-(piperidin-3-yl) linker (P2-6R), which killed NCI-H460 and A549 lung cancer cells 100 times more effectively than the S enantiomer (P2-6S). P2-6R accumulated in A549 cells significantly faster and produced 50-fold higher DNA adduct levels than P2-6S. Ligand similarity analysis suggests that only module 6R may be compatible with strainless monofunctional intercalative binding. NCI-60 screening and COMPARE analysis highlights the spectrum of activity and potential utility of P2-6R for treating NSCLC and other solid tumors.

Synthesis, Molecular Docking Studies and Antibacterial Activities of Novel Monocationic Indole-benzimidazole Derivatives.

Finding efficient therapy against hospital-acquired MRSA infections has become rather important in the last decade. To this end, inhibition of the enzyme pyruvate kinase (PK) is being investigated for antibacterial activity, since this enzyme controls energy generation and metabolic flux distribution. Our main scaffold consists of benzimidazole and indole rings fused together. Both rings are famous for antibacterial properties and promising anti-MRSA compounds including indole ring. Several 1-substituted-2-(1H-indol-3-yl)-N-substituted-1H-benzimidazole-5-carboxamidine analogues were developed, synthesized and their antibacterial activities were evaluated against Staphylococcus aureus (ATCC 25923), Methicillin resistant Staphylococcus aureus (MRSA) (ATCC 43300), and Staphylococcus epidermidis (ATCC 12228) by using tube dilution method. Molecular docking analysis with a characteristic protein called MRSA- Pyruvate Kinase has been conducted for the assessment of the activities of our compounds against Methicillinresistant S. aureus (MRSA). Among all the tested compounds, the most potent compound 36 had MIC values as 3.12, 3.12 and 6.25 μg/mL against S. aureus, Methicillin-resistant S. aureus (MRSA), and S. epidermidis, respectively. This compound had much better docking energy value than standard ampicillin and also created the link between two residues in different monomers of PK. This approach of using indol-amidine conjugate systems as anti-MRSA agents may include MRSA-PK as potential target. To further increase the affinity, some other H-bonding parts may be added. By doing so, another bridge with Ile361 residues on both sides can be created. Our compounds tend to violate log P limit of Lipinski, therefore some optimizations with formulation can be made. This study mainly includes the design, synthesis and optimization of indolebenzimidazole- amidine derivatives. Docking studies confirmed our results, since our most potent hit compound 36 created the necessary interactions between two chains of MRSA-PK. Further optimization can be considered to increase drug ability.

Discovery of Novel 5-Lipoxygenase-Activating Protein (FLAP) Inhibitors by Exploiting a Multistep Virtual Screening Protocol.

Leukotrienes (LTs) are proinflammatory mediators derived from arachidonic acid (AA), which play significant roles in inflammatory diseases. The 5-lipoxygenase-activating protein (FLAP) is an integral membrane protein, which is essential for the initial step in LT biosynthesis. The aim of this study was to discover novel and chemically diverse FLAP inhibitors for treatment of inflammatory diseases requiring anti-LT therapy. Both ligand- and structure-based approaches were applied to explain the activities of known FLAP inhibitors in relation to their predicted binding modes. We gained valuable insights into the binding modes of the inhibitors by molecular modeling and generated a multistep virtual screening (VS) workflow in which 6.2 million compounds were virtually screened, and the molecular hypotheses were validated by testing VS-hit compounds biologically. The most potent hit compounds showed significant inhibition of FLAP-dependent cellular LT biosynthesis with IC50 values in the range from 0.13 to 0.87 μM. Collectively, this study provided novel bioactive chemotypes with potential for further development as effective anti-inflammatory drugs.

A domino annulation approach to 3,4-diacylpyrrolo[1,2-a]pyrazines: decoration of pyrazine units.

A new one-pot, sequential three-component access to 3,4-diacylpyrrolo[1,2-a]pyrazine was achieved from the reaction of an α-haloketone, azide, and N-substituted pyrrole-2-carboxaldehyde under mild reaction conditions, through which a polysubstitution pattern on the pyrazine moiety of the scaffold was realized. The formation of multiple bonds (one C-C and two C-N) was enabled by this domino process involving the in situ generation of α-iminoketones, intermolecular Mannich reaction, intramolecular imine formation, and aromatization. Construction of the relevant 3,4-diacylpyrazino[1,2-a]indole and further expansion of this chemical space via synthetic elaboration of the resulting products were demonstrated as well. Preliminary biological screening of the synthesized derivatives against oral adenosquamous carcinoma cells (CAL-27) and triple negative human breast cancer cells (MDA-MB-231) led us to identify a potent hit compound (7o) having ∼3 times stronger in vitro anticancer activity than that of the anticancer agent, capecitabine.

DDIS-27. TARGETING ATP DOCKING AND P35/P25 BINDING OF CDK5 IN GLIOMA STEM CELLS USING SYNTHETIC INHIBITORS

Abstract The survival advantage of glioma stem cells (GSCs) represents a critical mechanism for growth, therapy resistance and recurrence in glioblastoma. So far, targeting GSCs has not been highly specific, since these cells co-opt the normal developmental signaling pathways. We have demonstrated that the activated CDK5-CREB1 signaling axis regulates GSC self-renewal and also promotes radiation-resistance. Thus targeting CDK5 signaling is highly rational, yet there are challenges. Most of the available CDK5 inhibitors also target other CDKs non-specifically. In collaboration with The Center for Molecular Evolution and Drug Discovery, we are developing novel CDK5 inhibitors that are highly potent and specific. METHODOLOGY: The CKD5-p25 crystal structure (pdb code 1UNL) was used to conduct a virtual high throughput screen (vHTS). A library of 10 million commercially available compounds which had been filtered to ensure they possessed good drug-like properties was screened against the crystal structure. The top 33 compounds based on their predicted target binding, synthetic feasibility and availability were tested in an in vitro kinase assay to measure CDK5 inhibition. RESULTS: Of the 33 potential hit, 11 compounds showed a CDK5 inhibition of &lt; 50 µM. These 11 hits represent 4 distinct chemical scaffolds. Two of them have IC50 &lt; 1 µM, with one compound having an IC50 &lt; 0.4 µM. The vHTS and subsequent in vitro testing have therefore confirmed the identification of several new series of potent CDK5 hit compounds. We are now characterizing the kinase selectivity of our different hit series and evaluating their activity in cell-based assays. This will help focus efforts on the most promising 1–2 scaffolds for further medicinal chemistry optimization to improve the compounds’ potency, selectivity and brain penetration. Ultimately, our optimized compounds will be tested in GBM models to demonstrate their effectiveness in inhibiting CDK5 as a new approach for treating GBM.