SARS-CoV-2 Main Protease Inhibitors from Natural Product Repository as Therapeutic Candidates for the Treatment of Coronaviridae Infections.

BACKGROUND: The main protease (Mpro) is a crucial enzyme for the life cycle of SARS-CoV-2 and a validated target for the treatment of COVID-19 infection. Natural products have been a proper alternative for treating viral diseases by modulating different steps of the life cycle of many viruses. OBJECTIVE: This review article is designed to summarize the cumulative information of natural-derived Mpro inhibitors that are validated by experimental biological testing. METHODS: The natural-derived Mpro inhibitors of SARS-CoV-2 that have been discovered since the emergence of the COVID-19 pandemic are reviewed in this article. Only natural products with experimental validation are reported in this article. Collected compounds are classified according to their chemical identity into flavonoids, phenolic acids, quinones, alkaloids, chromones, stilbenes, tannins, lignans, terpenes, and other polyphenolic and miscellaneous natural-derived Mpro inhibitors. CONCLUSION: These compounds could serve as scaffolds for further lead-structure optimization for desirable potency, a larger margin of safety, and better oral activity.

Discovery of natural-derived Mpro inhibitors as therapeutic candidates for COVID-19: Structure-based pharmacophore screening combined with QSAR analysis.

The main protease (Mpro ) is an essential enzyme for the life cycle of SARS-CoV-2 and a validated target for treatment of COVID-19 infection. Structure-based pharmacophore modeling combined with QSAR calculations were employed to identify new chemical scaffolds of Mpro inhibitors from natural products repository. Hundreds of pharmacophore models were manually built from their corresponding X-ray crystallographic structures. A pharmacophore model that was validated by receiver operating characteristic (ROC) curve analysis and selected using the statistically optimum QSAR equation was implemented as a 3D-search tool to mine AnalytiCon Discovery database of natural products. Captured hits that showed the highest predicted inhibitory activities were bioassayed. Three active Mpro inhibitors (pseurotin A, lactupicrin, and alpinetin) were successfully identified with IC50 values in low micromolar range.

An Electrochemical Sensor for the Detection of Albendazole Using Glassy Carbon Electrode Modified with Platinum-Palladium Nanocomposites.

An electroanalytical electrode for the detection of albendazole (ABZ) active ingredient in pharmaceutical dosage form and in contaminated animal-derived products was developed using a glassy carbon electrode modified with platinum-palladium nanoparticles. The electro-catalytic performance of the bimetallic-modified glassy carbon electrode was compared with its bare counterpart. Under optimized conditions, the modified electrode revealed two well-resolved anodic peak currents at 1.10 and 1.23 V using differential pulse voltammetry. Pure ABZ, as well as ABZ in spiked foods (milk and chicken), were detected with little interference from the food matrix. This electrode demonstrated high sensitivity and applicability, with a lower limit of detection of 0.08 µmol L-1 in aqueous solution and 10 µmol L-1 in the contaminated ground chicken and 100 µmol L-1 in the contaminated milk sample. The fabricated sensor is low in cost and appropriate for the estimation of albendazole in tablet dosage forms and biological samples, and so can act as a quality control tool in the pharmaceutical and food industry.

Synthesis and Biological Evaluation of Thiazole-Based Fibroblast Growth Factor Receptor-1 Inhibitors.

BACKGROUND: The Fibroblast Growth Factor Receptor-1 (FGFR-1) is a tyrosine kinase and a validated target for treatment of different cancer types. OBJECTIVE: Design and synthesis of novel thiazole-based analogues of anticancer agents. METHODS: Series of 2-aryl-5-methylthiazole analogues linked to structurally variable basic heads were synthesized as novel anticancer agents. Developed compounds were tested for their cytotoxic activities against several cancer cell lines. RESULTS: Many analogues exhibited strong antiproliferative activities against breast cancer cell lines, with higher potency towards the highly metastatic form (MDA-MB-231). Pharmacophoric profiling using in-house pharmacophore database identified FGFR-1 as a molecular target of active analogues. Synthesized compounds were bioassayed for their FGFR-1 inhibitory activities and many hits exhibited IC50 values in the low micromolar to nanomolar range. CONCLUSION: The 2-aryl-5-methylthiazole linked to a basic head is a novel chemical scaffold of ATP-competitive inhibitor of FGFR-1 with potential therapeutic activities against different types of cancer.

Oxadiazol-based mTOR inhibitors with potent antiproliferative activities: synthetic and computational modeling.

Series of N-aryl-1,3,4-oxadiazole-2-amines and 3-aryl-1,2,4-oxadiazole-5-carboxamides derivatives were synthesized as novel chemotherapeutic agents. Synthesized compounds were evaluated for their anticancer activities against several cancer cell lines. Many analogues of 1,3,4-oxadiazole scaffold showed potent antiproliferative activities against breast cancer cell lines, with higher activities toward the metastatic breast cancer cell line (MDA-MB-231). Active analogues were profiled using in-house pharmacophore database in search for molecular target. Active analogues (2j and 2k) were found to fit the pharmacophoric map of ATP-competitive inhibitors of mTOR. The mTOR inhibitory activities of the most active compounds were confirmed with IC50 values in nanomolar range. The N-aryl-1,3,4-oxadiazole-2-amines linked to a basic head is a novel ATP-competitive inhibitors of mTOR with potential activities for treatment of different types of cancer.

Structure-based Pharmacophore Screening Coupled with QSAR Analysis Identified Potent Natural-product-derived IRAK-4 Inhibitors.

Interleukin-1 Receptor-Associated Kinase 4 (IRAK-4) has crucial functions in inflammation, innate immunity, and malignancy. Structure-based pharmacophore modeling integrated with validated QSAR analysis was implemented to discover structurally novel IRAK-4 inhibitors from natural products database. The QSAR model combined molecular descriptors with structure-based pharmacophore capable of explaining bioactivity variation of structurally diverse IRAK-4 inhibitors. Manually built pharmacophore model, validated with receiver operating characteristic curve, and selected using the statistically optimum QSAR equation, was applied as a 3D-search query to mine AnalytiCon Discovery database of natural products. Experimental in vitro testing of highest-ranked hits identified uvaretin, saucerneol, and salvianolic acid B as active IRAK-4 inhibitors with IC50 values in low micromolar range.

Discovery of Potent Natural-Product-Derived SIRT2 Inhibitors Using Structure- Based Exploration of SIRT2 Pharmacophoric Space Coupled With QSAR Analyses.

BACKGROUND: SIRT2 belongs to a class III of Histone Deacetylase (HDAC) and has crucial roles in neurodegeneration and malignancy. OBJECTIVE: The objective of this study is to discover structurally novel natural-product-derived SIRT2 inhibitors. METHODS: Structure-based pharmacophore modeling integrated with validated QSAR analysis was implemented to discover structurally novel SIRT2 inhibitors from the natural products database. The targeted QSAR model combined molecular descriptors with structure-based pharmacophore capable of explaining bioactivity variation of structurally diverse SIRT2 inhibitors. Manually built pharmacophore model, validated with receiver operating characteristic curve, and selected using the statistically optimum QSAR equation, was applied as a 3Dsearch query to mine AnalytiCon Discovery database of natural products. RESULTS: Experimental in vitro testing of highest-ranked hits identified asperphenamate and salvianolic acid B as active SIRT2 inhibitors with IC50 values in low micromolar range. CONCLUSION: New chemical scaffolds of SIRT2 inhibitors have been identified that could serve as a starting point for lead-structure optimization.

Reversible Small Molecule Inhibitors of MAO A and MAO B with Anilide Motifs.

BACKGROUND: Ligands consisting of two aryl moieties connected via a short spacer were shown to be potent inhibitors of monoamine oxidases (MAO) A and B, which are known as suitable targets in treatment of neurological diseases. Based on this general blueprint, we synthesized a series of 66 small aromatic amide derivatives as novel MAO A/B inhibitors. METHODS: The compounds were synthesized, purified and structurally confirmed by spectroscopic methods. Fluorimetric enzymological assays were performed to determine MAO A/B inhibition properties. Mode and reversibility of inhibition was determined for the most potent MAO B inhibitor. Docking poses and pharmacophore models were generated to confirm the in vitro results. RESULTS: N-(2,4-Dinitrophenyl)benzo[d][1,3]dioxole-5-carboxamide (55, ST-2043) was found to be a reversible competitive moderately selective MAO B inhibitor (IC50 = 56 nM, Ki = 6.3 nM), while N-(2,4-dinitrophenyl)benzamide (7, ST-2023) showed higher preference for MAO A (IC50 = 126 nM). Computational analysis confirmed in vitro binding properties, where the anilides examined possessed high surface complementarity to MAO A/B active sites. CONCLUSION: The small molecule anilides with different substitution patterns were identified as potent MAO A/B inhibitors, which were active in nanomolar concentrations ranges. These small and easily accessible molecules are promising motifs, especially for newly designed multitargeted ligands taking advantage of these fragments.

Metabolomic Profiling and Cytotoxic Tetrahydrofurofuran Lignans Investigations from Premna odorata Blanco.

Metabolomic profiling of different Premna odorata Blanco (Lamiaceae) organs, bark, wood, young stems, flowers, and fruits dereplicated 20, 20, 10, 20, and 20 compounds, respectively, using LC-HRESIMS. The identified metabolites (1-34) belonged to different chemical classes, including iridoids, flavones, phenyl ethanoids, and lignans. A phytochemical investigation of P. odorata bark afforded one new tetrahydrofurofuran lignan, 4ß-hydroxyasarinin 35, along with fourteen known compounds. The structure of the new compound was confirmed using extensive 1D and 2D NMR, and HRESIMS analyses. A cytotoxic investigation of compounds 35-38 against the HL-60, HT-29, and MCF-7 cancer cell lines, using the MTT assay showed that compound 35 had cytotoxic effects against HL-60 and MCF-7 with IC50 values of 2.7 and 4.2 µg/mL, respectively. A pharmacophore map of compounds 35 showed two hydrogen bond acceptor (HBA) aligning the phenoxy oxygen atoms of benzodioxole moieties, two aromatic ring features vectored on the two phenyl rings, one hydrogen bond donor (HBD) feature aligning the central hydroxyl group and thirteen exclusion spheres which limit the boundaries of sterically inaccessible regions of the target's active site.

Discovery of potent IRAK-4 inhibitors as potential anti-inflammatory and anticancer agents using structure-based exploration of IRAK-4 pharmacophoric space coupled with QSAR analyses.

Interleukin-1 Receptor-Associated Kinase 4 (IRAK-4) has an important role in immunity, inflammation, and malignancy. The significant role of IRAK-4 makes it an interesting target for the discovery and development of potent small molecule inhibitors. In the current study, multiple linear regression -based QSAR analyses coupled with structure-based pharmacophoric exploration was applied to reveal the structural and physiochemical properties required for IRAK-4 inhibition. Manually built pharmacophoric models were initially validated with receiver operating characteristic curve, and best-ranked models were subsequently integrated in QSAR analysis along with other physiochemical descriptors. The pharmacophore model, selected using the statistically optimum QSAR equation, was implied as a 3D-search filter to mine the National Cancer Institute database for novel IRAK-4 inhibitors. Whereas the associated QSAR model prioritized the bioactivities of captured hits for in vitro evaluation. Experimental validation identified several potent IRAK-4 inhibitors of novel structural scaffolds. The most potent captured hit exhibited an IC50 value of 157 nM.

Lab on a Chip for the Colorimetric Determination of Nitrite in Processed Meat Products in the Jordanian Market.

Nitrite and Nitrate have been used extensively as additives in various meat products to enhance flavor, color, and to preserve the meat from the bacterial growth. High concentrations of nitrite can threat human health since several studies in the literature claim that nitrite is associated with cancer incidences, leukemia, and brain tumors. Therefore, it is vital to measure the nitrite concentrations in processed meat products. In this study, an in-lab miniaturized photometric detection system is fabricated to inspect the nitrite concentration in processed meat products in Jordan. The analytical performance of nitrite detection is evaluated based on three key statistical parameters; linearity, limit of detection, and limit of quantitation. Respectively, for the fabricated system, the three values are found to be equal to 0.995, 1.24 × 10-2 ppm, and 4.12 × 10-2 ppm. Adherence to Beer's law is found over the investigated range from 2.63 ppm to 96.0 ppm. The developed system is utilized for photometric detection of nitrite in processed meat products available in the Jordanian market like pastrami, salami, and corned beef. In all of the analyzed samples, the nitrite content is found to be lower than 150 ppm, which represents the maximum allowable nitrite limit.

New Pim-1 Kinase Inhibitor From the Co-culture of Two Sponge-Associated Actinomycetes.

Saccharomonospora sp. UR22 and Dietzia sp. UR66, two actinomycetes derived from the Red Sea sponge Callyspongia siphonella, were co-cultured and the induced metabolites were monitored by HPLC-DAD and TLC. Saccharomonosporine A (1), a novel brominated oxo-indole alkaloid, convolutamydine F (2) along with other three known induced metabolites (3-5) were isolated from the EtOAc extract of Saccharomonospora sp. UR22 and Dietzia sp. UR66 co-culture. Additionally, axenic culture of Saccharomonospora sp. UR22 led to isolation of six known microbial metabolites (6-11). A kinase inhibition assay results showed that compounds 1 and 3 were potent Pim-1 kinase inhibitors with an IC50 value of 0.3 ± 0.02 and 0.95 ± 0.01 µM, respectively. Docking studies revealed the binding mode of compounds 1 and 3 in the ATP pocket of Pim-1 kinase. Testing of compounds 1 and 3 displayed significant antiproliferative activity against the human colon adenocarcinoma HT-29, (IC50 3.6 and 3.7 µM, respectively) and the human promyelocytic leukemia HL-60, (IC50 2.8 and 4.2 µM, respectively). These results suggested that compounds 1 and 3 act as potential Pim-1 kinase inhibitors that mediate the tumor cell growth inhibitory effect. This study highlighted the co-cultivation approach as an effective strategy to increase the chemical diversity of the secondary metabolites hidden in the genomes of the marine actinomycetes.

Design, synthesis, and biological evaluation of novel oxadiazole- and thiazole-based histamine H3R ligands.

Histamine H3 receptor (H3R) is largely expressed in the CNS and modulation of the H3R function can affect histamine synthesis and liberation, and modulate the release of many other neurotransmitters. Targeting H3R with antagonists/inverse agonists may have therapeutic applications in neurodegenerative disorders, gastrointestinal and inflammatory diseases. This prompted us to design and synthesize azole-based H3R ligands, i.e. having oxadiazole- or thiazole-based core structures. While ligands of oxadiazole scaffold were almost inactive, thiazole-based ligands were very potent and several exhibited binding affinities in a nanomolar concentration range. Ligands combining 4-cyanophenyl moiety as arbitrary region, para-xylene or piperidine carbamoyl linkers, and/or pyrrolidine or piperidine basic heads were found to be the most active within this series of thiazole-based H3R ligands. The most active ligands were in silico screened for ADMET properties and drug-likeness. They fulfilled Lipinski's and Veber's rules and exhibited potential activities for oral administration, blood-brain barrier penetration, low hepatotoxicity, combined with an overall good toxicity profile.

Discovery of potent polyphosphate kinase 1 (PPK1) inhibitors using structure-based exploration of PPK1Pharmacophoric space coupled with docking analyses.

Inorganic polyphosphate (polyP) is present in all living forms of life. Studied mainly in prokaryotes, polyP and its associated enzymes are vital in diverse metabolic activities, in some structural functions, and most importantly in stress responses. Bacterial species, including many pathogens, encode a homolog of a major polyP synthesis enzyme, Poly Phosphate Kinase (PPK) with 2 different genes coding for PPK1 and PPK2. Genetic deletion of the ppk1 gene leads to reduced polyP levels and the consequent loss of virulence and stress adaptation responses. This far, no PPK1 homolog has been identified in higher-order eukaryotes, and, therefore, PPK1 represents a novel target for chemotherapy. The aim of the current study is to investigate PPK1 from Escherichia coli with comprehensive understanding of the enzyme's structure and binding sites, which were used to design pharmacophores and screen a library of compounds for potential discovery of selective PPK1 inhibitors. Verification of the resultant inhibitors activities was conducted using a combination of mutagenic and chemical biological approaches. The metabolic phenotypic maps of the wild type E. coli (WT) and ppk1 knockout mutant were generated and compared with the metabolic map of the chemically inhibited WT. In addition, biofilm formation ability was measured in WT, ppk1 knockout mutant, and the chemically inhibited WT. The results demonstrated that chemical inhibition of PPK1, with the designed inhibitors, was equivalent to gene deletion in altering specific metabolic pathways, changing the metabolic fingerprint, and suppressing the ability of E. coli to form a biofilm.

Low Cost Lab on Chip for the Colorimetric Detection of Nitrate in Mineral Water Products.

The diagnostics of health status and the quality of drinking water are among the most important United Nations sustainable development goals. However, in certain areas, wars and instability have left millions of people setting in refugee camps and dangerous regions where infrastructures are lacking and rapid diagnostics of water quality and medical status are critical. In this work, microfluidic testing chips and photometric setups are developed in cheap and portable way to detect nitrate concentrations in water. The performed test is designed to work according to the Griess procedure. Moreover, to make it simple and usable in areas of low resource settings, commercially available Arduino mega and liquid crystal display (LCD) shield are utilized to process and display results, respectively. For evaluation purposes, different local products of tap water, bottled drinking water, and home-filter treated water samples were tested using the developed setup. A calibration curve with coefficient of determination (R²) of 0.98 was obtained when absorbance of the prepared standard solutions was measured as a function of the concentrations. In conclusion, this is the first step towards a compact, portable, and reliable system for nitrate detection in water for point-of-care applications.

Unsupervised pharmacophore modeling combined with QSAR analyses revealed novel low micromolar SIRT2 inhibitors.

Situin 2 (SIRT2) enzyme is a histone deacetylase that has important role in neuronal development. SIRT2 is clinically validated target for neurodegenerative diseases and some cancers. In this study, exhaustive unsupervised pharmacophore modeling was combined with quantitative structure-activity relationship (QSAR) analysis to explore the structural requirements for potent SIRT2 inhibitors using 146 known SIRT2 ligands. A computational workflow that combines genetic function algorithm with k-nearest neighbor or multiple linear regression was implemented to build self-consistent and predictive QSAR models based on combinations of pharmacophores and physicochemical descriptors. Successful pharmacophores were complemented with exclusion spheres to optimize their receiver operating characteristic curve profiles. Optimal QSAR models and their associated pharmacophore hypotheses were experimentally validated by identification and in vitro evaluation of several new promising SIRT2 inhibitory leads retrieved from the National Cancer Institute structural database. The most potent hit illustrated IC50 value of 5.4µM. The chemical structures of active hits were validated by proton nuclear magnetic resonance and mass spectroscopy.

A prodrug approach to enhance azelaic acid percutaneous availability.

Azelaic acid is a dicarboxylic acid compound used in treatment of acne vulgaris. However, high concentration (ca 20%) is needed to guarantee the drug availability in the skin. The latter increases the incidence of side effects such as local irritation. The prodrug strategy to enhance azelaic acid diffusion through skin was not reported before. Thus, a lipophilic prodrug of azelaic acid (diethyl azelate [DEA]) was synthesized and investigated to improve percutaneous availability of azelaic acid, with a subsequent full physical, chemical, and biological characterization. Expectedly, DEA exhibited a significant increase in diffusion compared to azelaic acid through silicone membrane. In contrast, the diffusion results through human stratum corneum (SC) displayed weaker permeation for DEA with expected retention in the SC. Therefore, a desorption study of DEA from SC was conducted to examine the reservoir behavior in SC. Results showed an evidence of sustained release behavior of DEA from SC. Consequently, enhancement of keratolytic effect is expected due to azelaic acid produced from enzymatic conversion of DEA released from SC.

Discovery of Potent Bruton's Tyrosine Kinase Inhibitors Using Ligand Based Modeling.

BACKGROUND: Bruton's Tyrosine Kinase (BTK) is a one of the Tec tyrosine kinase family. It has an essential role in B-cell development and function. Activation of BTK has been associated with the pathogenesis of many types of lymphomas and leukemia, and involved in non-life threatening autoimmune diseases. OBJECTIVE: In this study, exhaustive pharmacophore modeling was combined with QSAR analyses to examine the structural requirements for anti-BTK activities. METHOD: Genetic function algorithm (GFA) was coupled with multiple linear regression (MLR) analysis to select the best combinations of physicochemical descriptors and pharmacophoric hypothesis capable of generating predictive and self-consistent QSAR models. The optimum pharmacophores were decorated with exclusion volumes to improve their receiver operating characteristic (ROC) curve properties. The best predictive QSAR model and its corresponding pharmacophore models were validated by discovering of novel promising BTK inhibitors retrieved from the National Cancer Institute (NCI) database. RESULTS: Several potent hits exhibited anti-proliferative activities on U-937 cell-line in low micromolar IC50, and one active compound showed nontoxic activities on normal fibroblast cell line. CONCLUSION: Our efforts culminated in the identification of potent BTK ligands having desired inhibitory activities and structurally distinct from known active reference compounds (i.e., training compounds) and represent new chemotypes.

Discovery of potent NEK2 inhibitors as potential anticancer agents using structure-based exploration of NEK2 pharmacophoric space coupled with QSAR analyses.

High expression of Nek2 has been detected in several types of cancer and it represents a novel target for human cancer. In the current study, structure-based pharmacophore modeling combined with multiple linear regression (MLR)-based QSAR analyses was applied to disclose the structural requirements for NEK2 inhibition. Generated pharmacophoric models were initially validated with receiver operating characteristic (ROC) curve, and optimum models were subsequently implemented in QSAR modeling with other physiochemical descriptors. QSAR-selected models were implied as 3D search filters to mine the National Cancer Institute (NCI) database for novel NEK2 inhibitors, whereas the associated QSAR model prioritized the bioactivities of captured hits for in vitro evaluation. Experimental validation identified several potent NEK2 inhibitors of novel structural scaffolds. The most potent captured hit exhibited an [Formula: see text] value of 237 nM.

Computer-aided discovery of new FGFR-1 inhibitors followed by in vitro validation.

AIM: FGFR-1 is an oncogenic kinase involved in several cancers. FGFR1-specific inhibitors have shown promising results against several human cancers prompting us to model this interesting target. Toward the end, we implemented elaborate ligand-based and structure-based computational workflows to explore the pharmacophoric requirements for potent FGFR-1 inhibitors. Results & methodology: Structure-based and ligand-based modeling applied on 59 diverse FGFR-1 inhibitors yielded novel pharmacophore and quantitative structure-activity relationship models that were used to scan the National Cancer Institute's structural database for novel leads. Four potent hits were captured, with the most active having IC50 of 426 nM. Identities and purities of active hits were established using nuclear magnetic resonance and mass spectroscopy. CONCLUSION: Elaborate ligand-based (pharmacophore/quantitaive structure-activity relationship) and structure-based (docking-based comparative intermolecular contacts analysis) modeling provided deep understanding of ligand binding within FGFR-1 as evidenced by the virtually captured new potent leads.