Library Of Analogues Research Articles

Abstract 4050: Effect of benzofuran pharmacophores on CYP-activated duocarmycin bioprecursors

Abstract Duocarmycins are natural DNA alkylators which have potent toxicity with no established mechanism of resistance. Prodrug versions need to be developed to ensure a sufficient therapeutic window for cancer treatment (1). A series of duocarmycin bioprecursors have been developed in-house which lack a key hydroxyl trigger group, required for spirocyclisation and subsequent activation. This hydroxyl group can be regioselectivity restored by specific Cytochrome P450 enzymes (CYPs), with a primary focus on cancer associated isoforms CYP1A1 and CYP2W1 (2). An exploratory library of analogues of our lead compound, ICT2700 (CYP1A1 and CYP2W1 activated), has been synthesized and elucidated aspects of the structure-activity relationship (SAR) between the compound and subsequent toxicity in CYP transfected and mock cell lines, using MTT assays. The data shows the importance of having an indole in the DNA recognition subunit (the non-alkylating subunit) for CYP1A1 and CYP2W1 activation. Further, a compound with thus far unexplained activity was identified. ICT11038 has a benzofuran instead of an indole in the recognition subunit and subsequently demonstrates inherent nanomolar toxicity consistently in all cell lines tested, including a range of cancerous and non-cancerous cells, which is not dependent on cytochrome expression. CYP1A1 has been shown to enhance the toxicity of ICT11038 further but is not required for nanomolar toxicity. Further SAR exploration and western blots confirm that the inherent toxicity is achieved through DNA damage despite lacking the key trigger group, suggesting a novel activation pathway. Additionally, our SAR studies show that replacing the indole of the DNA alkylation subunit with a benzofuran ablates CYP dependent activity, with one exception, ICT2724. ICT2724 is non-toxic in mock transfected cells but is toxic in CYP1A1 transfected cells, albeit it at higher concentration than ICT2700. ICT2724 is analogous to ICT2700, except for the direct indole to benzofuran substitution. Other compounds with benzofurans in the alkylating subunit compounds are not metabolized to a toxic compound by CYP1A1 or CYP2W1 despite their indole equivalents being good prodrug candidates. To conclude, the introduction of the benzofuran functional group into the CYP-activated duocarmycin bioprecursor pharmacophores produces an unexplained pattern of CYP activation and, in one example, an intrinsically toxic DNA damaging agent (ZYP-11038). References (1) Z. Jukes et al, Drug Discov Today, 2020, 26(2), 577-584, https://doi.org/10.1016/j.drudis.2020.11.020 (2) H. Sheldrake et al, J. Med. Chem, 2013, 56(16); 6273-6277, dx.doi.org/10.1021/jm4000209 Citation Format: Zoe H. Jukes. Effect of benzofuran pharmacophores on CYP-activated duocarmycin bioprecursors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4050.

Quadruple Functionalized Pyrazole Pharmacophores by One-pot Regioselective [3+2] Cycloaddition of Fluorinated Nitrile Imines and Dicyanoalkenes.

Here we present a quadruple functionalization approach for the modular construction of fully substituted N1 -aryl 3-di/trifluoro-methyl-4/5-cyanopyrazole pharmacophores from readily available hydrazonyl chlorides and dicyanoalkenes. The realization of this [3+2] cycloaddition reaction hinges upon the employment of N-aryl di/trifluoromethyl nitrile imines as the 1,3-dipoles to bypass external synthetic steps and dicyanoalkenes as the dipolarophiles to tune the regioselectivity. This one-pot strategy offers access to a divergent library of cyano analogues of prevalent 3-di/trifluoromethyl pyrazole pharmacophores, among which several compounds have shown potent inhibitory activity towards cyclooxygenase 2 (COX-2) compared with marketed drug Celecoxib.

Synthesis of triazinoindole bearing sulfonamide derivatives, in vitro α-amylase activity and their molecular docking study

• Synthesis of triazinoindole bearing sulfonamide analogues. • In vitro alpha-amylase activity. • Identification of a new class of alpha-amylase activity. • Limited structure activity relationship established. • Molecular docking study. Diabetes mellitus is one of the most chronic metabolic diseases. Since past few years, our research group had synthesized and evaluated libraries of heterocyclic analogues against α -amylase enzyme and found encouraging results. The current study comprises of evaluation of triazinoindole bearing sulfonamide as antidiabetic agents. A library of twenty three analogues ( 1–23 ) were synthesized, characterized through 1 HNMR, 13 C NMR and HREI-MS and evaluated for α -amylase inhibitory potential. Off twenty three, nine analogues 1, 2, 3, 6, 7, 8, 12, 13 and 14 displayed excellent inhibitory potential against α -amylase enzyme with IC 50 values 0.60 ± 0.05, 1.10 ± 0.05, 1.20 ± 0.05, 1.60 ± 0.10, 1.40 ± 0.10, 1.40 ± 0.10, 0.80 ± 0.05, 0.30 ± 0.05 and 1.50 ± 0.10 µ M, respectively. These analogues may potentially serve as lead for the development of new therapeutic representatives. Moreover, in silico docking study were carried out to investigate active binding mode of selected analogues with the target enzyme.

Microbial Surfactants: Bright Prospects for Innovation, New Product Categories, and Commercialization

Microbial Surfactants: Bright Prospects for Innovation, New Product Categories, and Commercialization

Expedient Access to Type II Kinase Inhibitor Chemotypes by Microwave-Assisted Suzuki Coupling

Functionalized pyrazole-urea scaffolds are a common type II chemotype for the inhibition of protein kinases (PKs), binding simultaneously into the ATP-binding pocket with an ATP bioisostere and into a vicinal allosteric pocket with a pyrazole group. Standard approaches to the scaffold require multi-step synthesis of the ATP bioisostere followed by phosgene or triphosgene-mediated coupling with the substituted pyrazole group. Here we report an expedient approach to the chemotype, characterized by an optimized MW-assisted Suzuki coupling on easily accessed bromo-phenyl pyrazole ureas. The new protocol allowed quick access a large library of target analogues covering a broad chemical space of putative protein kinases inhibitors (PKIs).

Optimization of the Natural Product Calothrixin A to Discover Novel Dual Topoisomerase I and II Inhibitors with Improved Anticancer Activity.

Calothrixin A (CAA) is a dual Topo I and II inhibitor but exhibits poor antiproliferative activities and water solubility. Herein, a library of novel CAA analogues was synthesized. Among them, compound F16 exhibited superior water solubility (>5 mg/mL) as compared to CAA (<5 μg/mL). The mechanism of action studies confirmed that F16 acted as a dual Topo I and II poison. Furthermore, F16 displayed potent antiproliferative activities against high Topo I and II expression cell lines A375 and HCT116, with IC50 values of 20 and 50 nM, respectively. In xenograft models, F16 reduced the tumor growth at a dose of 10 or 20 mg/kg without apparent effect on the mouse weight, while the clinically used Topo II inhibitor VP-16 dramatically reduced the mouse weight. Collectively, our data demonstrated that F16 could be a promising lead for the development of novel dual Topo I and II antitumor agents.

Structural Elucidation of Rift Valley Fever Virus L Protein towards the Discovery of Its Potential Inhibitors.

Rift valley fever virus (RVFV) is the causative agent of a viral zoonosis that causes a significant clinical burden in domestic and wild ruminants. Major outbreaks of the virus occur in livestock, and contaminated animal products or arthropod vectors can transmit the virus to humans. The viral RNA-dependent RNA polymerase (RdRp; L protein) of the RVFV is responsible for viral replication and is thus an appealing drug target because no effective and specific vaccine against this virus is available. The current study reported the structural elucidation of the RVFV-L protein by in-depth homology modeling since no crystal structure is available yet. The inhibitory binding modes of known potent L protein inhibitors were analyzed. Based on the results, further molecular docking-based virtual screening of Selleckchem Nucleoside Analogue Library (156 compounds) was performed to find potential new inhibitors against the RVFV L protein. ADME (Absorption, Distribution, Metabolism, and Excretion) and toxicity analysis of these compounds was also performed. Besides, the binding mechanism and stability of identified compounds were confirmed by a 50 ns molecular dynamic (MD) simulation followed by MM/PBSA binding free energy calculations. Homology modeling determined a stable multi-domain structure of L protein. An analysis of known L protein inhibitors, including Monensin, Mycophenolic acid, and Ribavirin, provide insights into the binding mechanism and reveals key residues of the L protein binding pocket. The screening results revealed that the top three compounds, A-317491, Khasianine, and VER155008, exhibited a high affinity at the L protein binding pocket. ADME analysis revealed good pharmacodynamics and pharmacokinetic profiles of these compounds. Furthermore, MD simulation and binding free energy analysis endorsed the binding stability of potential compounds with L protein. In a nutshell, the present study determined potential compounds that may aid in the rational design of novel inhibitors of the RVFV L protein as anti-RVFV drugs.

Dual therapeutic approach to modulate Glycogen Synthase kinase −3 beta (GSK-3Β) and inhibitor of nuclear factor kappa kinase-beta (IKK-β) receptors by in silico designing of inhibitors

Cancer malignancies require the application of advanced strategies leading to the development of novel theranostic. Quite often drugs target a variety of receptors in the cell signaling cascades that could be explored to combat aggressive tumors. Herein, two receptors that are over-expressed during the diagnosis of breast cancer are used as the primary drug targets, inclusively Glycogen Synthase kinase −3 beta (GSK-3Β) and Inhibitor of nuclear factor kappa kinase-beta (IKK-β). Dual-targeting inhibitors pave the way for a challenging pathway in the treatment of aberrant tumor progression. The present study involves the observation of similarities in the structure of the receptors, along with the designing of novel therapeutics that act on them by molecular docking followed by a pharmacokinetic screening approach. A 3D QSAR modeling study is performed to approach the functionality of the bioactive conformer molecules. Additionally, Molecular Dynamic Simulation parameters are used for the validation of the drug complexes. Already available inhibitors are used as reference compounds and a library of analogs generated for these compounds from the PubChem database has been used for in silico designing of novel inhibitors. Molecular Docking and ADME analysis narrowed down the vast library of compounds to two specific classes of chemical compounds. Molecular Dynamic simulation studies used for the selection of the novel moieties showed significant superiority in their stability studies and binding trajectories resulted in two novel molecules A6 and B3 that could inhibit the kinase receptors. The current work involves computational designing of therapeutics targeting two major oncogenic proteins.

Design, and Synthesis of Aryl Derivatives of Imidazopyridine‐Thiadiazoles as Possible Anticancer Agents

AbstractIn this article, we reported a new library of arylthiadiazole analogs of imidazopyridines (9 a–j) designed based on the structures of Nocodazole and Cefozopran. After characterization by spectroscopic data, the synthesized analogs were assessed for anticancer potential using MTT assay against PC3, A549, MCF‐7 and DU‐145 human cancer cell lines. Etoposide, an anticancer medication candidate, was employed as a positive control. The anticancer activity of the synthesized analogues was expressed in IC50 ranging from 0.01±0.008 μM to 19.3±7.65 μM and compared with positive control. Five compounds 9 d, 9 e, 9 g, 9 h and 9 j possessed more potent anticancer properties.

Synthesis of Novel Tubulin Inhibitor Candidates as Potential Anti‐Cancer Agents

Tubulin polymerization and depolymerization are vital for cellular processes, such as cell division, making tubulin inhibition a viable target for the development of anti‐cancer agents. Previous studies have confirmed that an indole‐containing heterocycle we synthesized exhibits anti‐cancer activity through a tubulin polymerization inhibitory mechanism. The heterocycle is structurally related to combretastatin A4, and is thought to interact with tubulin at the colchicine binding site. Our goal is to build upon the existing library of indole‐containing heterocyclic analogs and synthesize novel tubulin inhibitors with increased potency. Molecular docking studies with the colchicine binding site of tubulin informed the design of PY‐391‐Das a tubulin inhibitor candidate. Thus, we are working toward synthesizing this novel compound using modular synthetic strategies. Our synthetic strategy encompasses five reactions. Three out of the five synthetic steps toward PY‐391‐Dhave been completed in high yield. Two reactions that have been previously optimized by our research group have been applied to novel compounds en route to PY‐391‐D, demonstrating the wide applicability of our synthetic strategies. The optimization of the butyl‐group addition to the indole‐nitrogen through an SN2 mechanism was investigated in this study, and has been applied to other electrophiles. Reaction success has been monitored through compound characterization facilitated by 1H NMR spectroscopy analysis. The progress towards completing the streamlined synthesis to produce tubulin inhibition candidates, including PY‐391‐Dand structurally related analogs, are detailed in this study.

Structure Activity Relationships of Illicit Fentanyl Analogs

Fentanyl is a highly potent and efficacious mu opioid receptor (MOR) agonist with significant abuse potential. More than 70% of opioid overdose deaths involve fentanyl or one of its analogs; recently the DEA announced that 2 in 5 counterfeit prescription pills contain a lethal dose of fentanyl. However, little is known about the novel fentanyl analogs (fentalogs) flooding the illicit drug market. It is presumed that these novel fentalogs are also potent, highly efficacious MOR agonists and they are driving the increase in opioid overdoses, but pharmacological data on these compounds are scarce. We have determined the affinity for and agonist activity of a library of novel fentanyl analogs in vitro. We found that structure greatly alters affinity and agonist activity; in this library, affinity at MOR ranged from 0.4 nM to almost 400 nM – fentanyl displays 1.6 nM affinity for MOR. Based on the data collected from this library, we have been able to construct structure‐activity relationships which may allow us to predict which fentalogs are potent agonists and are likely to carry significant abuse liability. Conversely, we have discovered new high affinity, low efficacy compounds which could be developed into novel rescue therapies.

Strong Antibiotic Activity of the Myxocoumarin Scaffold in vitro and in vivo.

The increasing emergence of resistances against established antibiotics is a substantial threat to human health. The discovery of new compounds with potent antibiotic activity is thus of utmost importance. Within this work, we identify strong antibiotic activity of the natural product myxocoumarin B from Stigmatella aurantiaca MYX‐030 against a range of clinically relevant bacterial pathogens, including clinical isolates of MRSA. A focused library of structural analogs was synthesized to explore initial structure‐activity relationships and to identify equipotent myxocoumarin derivatives devoid of the natural nitro substituent to significantly streamline synthetic access. The cytotoxicity of the myxocoumarins as well as their potential to cure bacterial infections in vivo was established using a zebrafish model system. Our results reveal the exceptional antibiotic activity of the myxocoumarin scaffold and hence its potential for the development of novel antibiotics.

Novel Inhibitors of 2′-O-Methyltransferase of the SARS-CoV-2 Coronavirus

The COVID-19 pandemic is still affecting many people worldwide and causing a heavy burden to global health. To eliminate the disease, SARS-CoV-2, the virus responsible for the pandemic, can be targeted in several ways. One of them is to inhibit the 2′-O-methyltransferase (nsp16) enzyme that is crucial for effective translation of viral RNA and virus replication. For methylation of substrates, nsp16 utilizes S-adenosyl methionine (SAM). Binding of a small molecule in the protein site where SAM binds can disrupt the synthesis of viral proteins and, as a result, the replication of the virus. Here, we performed high-throughput docking into the SAM-binding site of nsp16 for almost 40 thousand structures, prepared for compounds from three libraries: Enamine Coronavirus Library, Enamine Nucleoside Mimetics Library, and Chemdiv Nucleoside Analogue Library. For the top scoring ligands, semi-empirical quantum-chemical calculations were performed, to better estimate protein–ligand binding enthalpy. Relying upon the calculated binding energies and predicted docking poses, we selected 21 compounds for experimental testing.

Front Cover: Scaffold Hopping from Amodiaquine to Novel Nurr1 Agonist Chemotypes via Microscale Analogue Libraries (ChemMedChem 8/2022)

The Front Cover shows a scaffold hop from amodiaquine to a new agonist of the neuroprotective transcription factor Nurr1 through library synthesis from rationally and computationally selected building blocks. The first library served to replace the diethylaminomethylphenol residue before the second set varied the chloroquinoline motif. The analogue libraries were prepared in microscale format in 1 mL glass tubes and tested for cellular Nurr1 activation after a simple workup. The most promising compounds of each library were synthesized in batch, isolated, and characterized to confirm Nurr1 agonism. Cover design by Sabine Willems. More information can be found in the Research Article by Sabine Willems, Marcel Müller, Daniel Merk et al.

Structure-Based Design of a Novel Class of Autotaxin Inhibitors Based on Endogenous Allosteric Modulators.

Autotaxin (ATX) facilitates the hydrolysis of lysophosphatidylcholine to lysophosphatidic acid (LPA), a bioactive phospholipid, which facilitates a diverse range of cellular effects in multiple tissue types. Abnormal LPA expression can lead to the progression of diseases such as cancer and fibrosis. Previously, we identified a potent ATX steroid-derived hybrid (partially orthosteric and allosteric) inhibitor which did not form interactions with the catalytic site. Herein, we describe the design, synthesis, and biological evaluation of a focused library of novel steroid-derived analogues targeting the bimetallic catalytic site, representing an entirely unique class of ATX inhibitors of type V designation, which demonstrate significant pathway-relevant biochemical and phenotypic biological effects. The current compounds modulated LPA-mediated ATX allostery and achieved indirect blockage of LPA1 internalization, in line with the observed reduction in downstream signaling cascades and chemotaxis induction. These novel type V ATX inhibitors represent a promising tool to inactivate the ATX-LPA signaling axis.

Synthesis and biological evaluation of imidamide analogs as selective anti-trypanosomal agents

Human African trypanosomiasis is caused by a protozoan parasite Trypanosoma brucei majorly infecting people living in sub-Saharan Africa. Current limited available treatments suffer from drug resistance, severe adverse effects, low efficacy, and costly administrative procedures in African countries with limited medical resources. Therefore, there is always a perpetual demand for advanced drug development and invention of new strategies to combat the disease. Previous work in our lab generated a library of sulfonamide analogs as selective tubulin inhibitors, based on the structural difference between mammalian and trypanosome tubulin proteins. Further lead derivatization was performed in the current study and generated 25 potential drug candidates to improve the drug efficacy and uptake by selectively targeting the parasite’s P2 membrane transporter protein with imidamide moiety. One of the newly synthesized analogs, compound 25 with a di-imidamide moiety, has shown greater potency with an IC50 of 1 nM to selectively inhibit the growth of trypanosome cells without affecting the viability of mammalian cells. Western blot analyses reveal that the compound suppressed tubulin polymerization in T. brucei cells. A detailed structure–activity relationship (SAR) was summarized that will be used to guide future lead optimization.

Potent Bactericidal Antimycobacterials Targeting the Chaperone ClpC1 Based on the Depsipeptide Natural Products Ecumicin and Ohmyungsamycin A.

Ohmyungsamycin A and ecumicin are structurally related cyclic depsipeptide natural products that possess activity against Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB). Herein, we describe the design and synthesis of a library of analogues of these two natural products using an efficient solid-phase synthesis and late-stage macrolactamization strategy. Lead analogues possessed potent activity against Mtb in vitro (minimum inhibitory concentration 125-500 nM) and were shown to inhibit protein degradation by the mycobacterial ClpC1-ClpP1P2 protease with an associated enhancement of ClpC1 ATPase activity. The most promising analogue from the series exhibited rapid bactericidal killing activity against Mtb, capable of sterilizing cultures after 7 days, and retained bactericidal activity against hypoxic non-replicating Mtb. This natural product analogue was also active in an in vivo zebrafish model of infection.

Positional scanning of natural product hispidol’s ring-B: discovery of highly selective human monoamine oxidase-B inhibitor analogues downregulating neuroinflammation for management of neurodegenerative diseases

Multifunctional molecules might offer better treatment of complex multifactorial neurological diseases. Monoaminergic pathways dysregulation and neuroinflammation are common convergence points in diverse neurodegenerative and neuropsychiatric disorders. Aiming to target these diseases, polypharmacological agents modulating both monoaminergic pathways and neuroinflammatory were addressed. A library of analogues of the natural product hispidol was prepared and evaluated for inhibition of monoamine oxidases (MAOs) isoforms. Several molecules emerged as selective potential MAO B inhibitors. The most promising compounds were further evaluated in vitro for their impact on microglia viability, induced production of proinflammatory mediators and MAO-B inhibition mechanism. Amongst tested compounds, 1p was a safe potent competitive reversible MAO-B inhibitor and inhibitor of microglial production of neuroinflammatory mediators; NO and PGE2. In-silico study provided insights into molecular basis of the observed selective MAO B inhibition. This study presents compound 1p as a promising lead compound for management of neurodegenerative disease.

Facile and Adaptable Synthesis of a Prazosin Analogue Library: Bringing Medicinal Chemistry into the Undergraduate Curriculum

Facile and Adaptable Synthesis of a Prazosin Analogue Library: Bringing Medicinal Chemistry into the Undergraduate Curriculum

Scaffold Hopping from Amodiaquine to Novel Nurr1 Agonist Chemotypes via Microscale Analogue Libraries.

Several lines of evidence suggest the ligand‐sensing transcription factor Nurr1 as a promising target to treat neurodegenerative diseases. Nurr1 modulators to validate and exploit this therapeutic potential are rare, however. To identify novel Nurr1 agonist chemotypes, we have employed the Nurr1 activator amodiaquine as template for microscale analogue library synthesis. The first set of analogues was based on the 7‐chloroquiolin‐4‐amine core fragment of amodiaquine and revealed superior N‐substituents compared to diethylaminomethylphenol contained in the template. A second library of analogues was subsequently prepared to replace the chloroquinolineamine scaffold. The two sets of analogues enabled a full scaffold hop from amodiaquine to a novel Nurr1 agonist sharing no structural features with the lead but comprising superior potency on Nurr1. Additionally, pharmacophore modeling based on the entire set of active and inactive analogues suggested key features for Nurr1 agonists.