Potential Inhibitors Research Articles

Synthesis, Biological Evaluation, and Docking Study of a New Series of Thiophene Derivatives Based on 3‐Oxobutanamidothiophene as an Anticancer Agent

AbstractHerein, the constructing synthon 3‐oxobutanamidothiophene derivatives 2 a and 2 b were synthesized and utilized for building a wide variety of pyran, thiazole, pyrazole or pyrimidine ring heterocyclic compounds that can be used as anticancer medications. 3‐Oxobutanamidothiophene derivatives 2 a,b were coupled with 4‐substitutedphenyl diazonium chloride to produce the corresponding hydrazones derivatives 3 a–f. Various thiophene‐pyran derivatives 4 a,b were synthesized through the treatment of thiophene components 2 a,b with different arylidene‐malononitrile. 2‐Aminothiophene derivatives 5 were prepared via Gewald's reaction between 2 a,b, elemental sulfur, and various activated nitrile derivatives. The 3‐oxobutanamidothiophene derivatives 2 a,b were reacted with PhNCS and the potassium salt intermediates 6 a,b with ethyl bromoacetate to pick up the corresponding thiophene‐thiazolidin‐4‐one derivatives 7. Treatment of the conforming thiocarbamoyl compounds 8 a,b, which undergo heating with three types of α‐halogenated reagents to afford the corresponding substitutedthiophene‐3‐carboxamides 9 a,b. Condensation of keteneN,S‐acetals 10 a,b with hydrazines furnished the thiophene‐pyrazole‐4‐carboxamide hybrids 11 a,b, while condensation with urea and/or thiourea afforded the corresponding thiophene‐pyrimidine‐5‐carboxamides 12 a,b. The recently synthesized thiophene compounds were characterized there in vitro anticancer properties against HepG2 (hepatocellular carcinoma) and MDA‐MB‐231 (breast cancer) were evaluated. Molecular docking was also performed to predict the binding modes of synthesized derivatives with the good anticancer results designed as potential inhibitors for a specific target.

Computational insights into allosteric inhibition of focal adhesion kinase: A combined pharmacophore modeling and molecular dynamics approach

Focal adhesion kinase (FAK) is a non-receptor tyrosine kinase that modulates integrin and growth factor signaling pathways and is implicated in cancer cell migration, proliferation, and survival. Over the past decade various, FAK kinase, FERM, and FAT domain inhibitors have been reported and a few kinase domain inhibitors are under clinical consideration. However, few of them were identified as multikinase inhibitors. In kinase drug design selectivity is always a point of concern, to improve selectivity allosteric inhibitor development is the best choice. The current research utilized a pharmacophore modeling (PM) approach to identify novel allosteric inhibitors of FAK. The all-available allosteric inhibitor bound 3D structures with PDB ids 4EBV, 4EBW, and 4I4F were utilized for the pharmacophore modeling. The validated PM models were utilized to map a database of 770,550 compounds prepared from ZINC, EXIMED, SPECS, ASINEX, and InterBioScreen, aiming to identify potential allosteric inhibitors. The obtained compounds from screening step were forwarded to molecular docking (MD) for the prediction of binding orientation inside the allosteric site and the results were evaluated with the known FAK allosteric inhibitor (REF). Finally, 14 FAK-inhibitor complexes were selected from the docking study and were studied under molecular dynamics simulations (MDS) for 500 ns. The complexes were ranked according to binding free energy (BFE) and those demonstrated higher affinity for allosteric site of FAK than REF inhibitors were selected. The selected complexes were further analyzed for intermolecular interactions and finally, three potential allosteric inhibitor candidates for the inhibition of FAK protein were identified. We believe that identified scaffolds may help in drug development against FAK as an anticancer agent.

α-Glucosidase inhibitory potential of Oroxylum indicum using molecular docking, molecular dynamics, and in vitro evaluation

BackgroundAccording to the International Diabetes Federation, there will be 578 million individuals worldwide with diabetes by 2030 and 700 million by 2045. One of the promising drug targets to fight diabetes is α-glucosidase (AG), and its inhibitors may be used to manage diabetes by reducing the breakdown of complex carbohydrates into simple sugars. The study aims to identify and validate potential AG inhibitors in natural sources to combat diabetes. MethodsComputational techniques such as structure-based virtual screening and molecular dyncamic simulation were employed to predict potential AG inhibitors from compounds of Oroxylum indicum. Finally, in silico results were validated by in vitro analysis using n-butanol fraction of crude methanol extracts. ResultsThe XP glide scores of top seven hits OI_13, OI_66, OI_16, OI_44, OI_43, OI_20, OI_78 and acarbose were –14.261, –13.475, –13.074, –13.045, –12.978, –12.659, –12.354 and –12.296 kcal/mol, respectively. These hits demonstrated excellent binding affinity towards AG, surpassing the known AG inhibitor acarbose. The MM-GBSA dG binding energies of OI_13, OI_66, and acarbose were −69.093, −62.950, and −53.055 kcal/mol, respectively. Most of the top hits were glycosides, indicating that active compounds lie in the n-butanol fraction of the extract. The IC50 value for AG inhibition by n-butanol fraction was 248.1 μg/ml, and for that of pure acarbose it was 89.16 μg/ml. The predicted oral absorption rate in humans for the top seven hits was low like acarbose, which favors the use of these compounds as anti-diabetes in the small intestine. ConclusionIn summary, the study provides promising insights into the use of natural compounds derived from O. indicum as potential AG inhibitors to manage diabetes. However, further research, including clinical trials and pharmacological studies, would be necessary to validate their efficacy and safety before clinical use.

Potential dual inhibitors of Hexokinases and mitochondrial complex I discovered through machine learning approach

Hexokinases (Hks) and mitochondrial complex I (MCI) are involved in the energy metabolism of cells; glycolysis/fermentation and oxidative phosphorylation. Both Hks and MCI are known to play critical roles in either division of metabolic plasticity which enables tumor progression and proliferation in the presence of chemotherapies. Therefore, targeting these enzymes are important in cancer drug resistance. Here, computational models for the prediction of inhibition of Hks were developed based on experimental data and an optimal feature subset that was selected by the Boruta algorithm (a wrapper feature selection algorithm coupled with random forest). Out of the seven models that were explored, a random forest classifier gave the best prediction (GA = 0.84, FNR = 0.12 and AUC = 0.96 for the external dataset). Fragmentation analysis led to the identification of the unique structural scaffolds that characterize hexokinase inhibitors and non-inhibitors. The best Hks inhibition model predicted that 23 molecules out of the 191 dataset of MCI actives (IC50 ≤ 10 µM) that were screened, have more than 60 % probability of exhibiting Hk inhibitory activity. Hence, they are possible dual inhibitors of both targets. Furthermore, the 23 molecules’ core structures are members of the scaffolds that are unique to Hk inhibitors earlier predicted by fragment analysis. The need for dual targeting agents in cancer therapy, particularly in combating cancer drug resistance, highlights the relevance of these findings.

Synthesis, design, and antiproliferative evaluation of 6-(N-Substituted-methyl)pyrazolo[3,4-d]pyrimidines as the potent anti-leukemia agents

Pyrazolopyrimidine derivatives, including pyrazolopyrimidines, 6-aminopyrazolopyrimidines, 6-[(formyloxy)methyl]pyrazolopyrimidines, 6-(hydroxymethyl)pyrazolopyrimidine, and 6-(aminomethyl)pyrazolopyrimidines have been successfully prepared and tested against NCI-H226, NPC-TW01, and Jurkat cancer cell lines. Among the tested pyrazolopyrimidine compounds, we found 6-aminopyrazolopyrimidines and 6-(aminomethyl)pyrazolopyrimidines with essential o-ClPh or p-ClPh substituted moieties on N-1 pyrazole ring exhibited the best IC50 inhibition activity for Jurkat cells. Furthermore, optimization of the SAR study on the C-6 position of pyrazolopyrimidine ring demonstrated that 6-(N-substituted-methyl)pyrazolopyrimidines 17b, 17d, and 19d possessed the significant IC50 inhibitory activity for the different leukemia cell lines, especially for Jurkat, K-562, and HL-60. On the other hand, further SAR inhibition and docking model studies revealed that compound 19d, which has a 3-(1H-imidazol-1-yl)propan-1-amino side-chain on the C-6 position, was able to form four hydrogen bonds with residues Ala226, Leu152, and Glu194 and specifically extended into the P1 pocket subsite with Aurora A, resulting in improved inhibitory activity almost similar to SNS-314. To explore the anti-cancer mechanism, compound 19d was measured by Western blot analysis in Jurkat T-cells, however, it showed non-responsibility to Aurora B. For the further structural modifications on the lateral chain of compound 19d, compounds 24 with longer lateral chain were designed and synthesized for testing leukemia cell lines. However, compounds 24 was significantly decrease inhibition potency against leukemia cell lines. Based on the in-vitro results, compounds 17b and 19d could be considered to be the best potential lead drug in our study for the development of new and effective therapies for leukemia treatment. On the other hand, the DHFR inhibition results indicated compound 19d possessed good inhibitory activity and better than the reported naphthalene derivative. Through further comparisons of the model superposition of three-dimensional (3D) conformations in DHFR, compound 19d presented a similar structural alignment to Methotrexate and the reported naphthalene derivative and led to similar drug-like functional relationships. As a results, compound 19d would be a potential DHFR inhibitor for anti-leukemia drug candidate.

Discovery of a novel chemotype as DYRK1A inhibitors against Alzheimer's disease: Computational modeling and biological evaluation

Dual-specificity tyrosine phosphorylation-regulated kinase 1 A (DYRK1A) plays an essential role in Tau and Aβ pathology closely related to Alzheimer's disease (AD). Accumulative evidence has demonstrated DYRK1A inhibition is able to reduce the pathological features of AD. Nevertheless, there is no approved DYRK1A inhibitor for clinical use as anti-AD therapy. This is somewhat due to the lack of effective and safe chemotypes of DYRK1A inhibitors. To address this issue, we carried out in silico screening, in vitro assays and in vivo efficacy evaluation with the aim to discover a new class of DYRK1A inhibitors for potential treatment of AD. By in silico screening, we selected and purchased 16 potential DYRK1A inhibitors from the Specs chemical library. Among them, compound Q17 (Specs ID: AO-476/40829177) potently inhibited DYRK1A. The hydrogen bonds between compound Q17 and two amino acid residues named GLU239 and LYS188, were uncovered by molecular docking and molecular dynamics simulation. The cell-based assays showed that compound Q17 could protect the SH-SY5Y human neuroblastoma cell line from okadaic acid (OA)-induced injury by targeting DYRK1A. More importantly, compound Q17 significantly improved cognitive dysfunction of 3 × Tg-AD mice, ameliorated pathological changes, and attenuated Tau hyperphosphorylation as well as Aβ deposition. In summary, our computational modeling strategy is effective to identify novel chemotypes of DYRK1A inhibitors with great potential to treat AD, and the identified compound Q17 in this study is worthy of further study.

Essential role of glycoprotein Ibα in platelet activation

Glycoprotein (GP) Ibα, the ligand-binding subunit of platelet GPIb-IX complex, interacts with von Willebrand factor (VWF) exposed at the injured vessel wall, initiating platelet adhesion, activation, hemostasis, and thrombus formation. The cytoplasmic tail of GPIbα interacts with 14-3-3ζ, regulate ng the VWF-GPIbα-elicited signal transduction and VWF binding function of GPIbα. However, we unexpectedly found that the GPIbα-14-3-3ζ association, beyond VWF-dependent function, is essential for general platelet activation. We found that the GPIbα cytoplasmic tail peptide MPαC, a potential GPIbα inhibitor, by itself induced platelet aggregation, integrin αIIbβ3 activation, granule secretion, and phosphatidylserine (PS) exposure. Conversely, the deletion of the cytoplasmic tail of GPIbα in mouse platelets (10aa-/-) decreased platelet aggregation, integrin αIIbβ3 activation, granule secretion, and PS exposure induced by various physiological agonists. Phosphoproteome-based kinase activity profiling revealed significantly upregulated protein kinase C (PKC) activity in MPαC-treated platelets. MPαC-induced platelet activation was abolished by the pan-PKC inhibitor and PKCα deletion. Decreased PKC activity was observed in both resting and agonist-stimulated 10aa-/- platelets. GPIbα regulates PKCα activity by sequestering 14-3-3ζ from PKCα. In vivo, the deletion of the GPIbα cytoplasmic tail impaired mouse hemostasis and thrombus formation and protected against platelet-dependent pulmonary thromboembolism. Therefore, our findings demonstrate an essential role for the GPIbα cytoplasmic tail in regulating platelet general activation and thrombus formation beyond the VWF-GPIbα axis.

Identification of prognostic stemness-related genes in kidney renal papillary cell carcinoma

BackgroundKidney renal papillary cell carcinoma (KIRP) is the second most prevalent malignant cancer originating from the renal epithelium. Nowadays, cancer stem cells and stemness-related genes (SRGs) are revealed to play important roles in the carcinogenesis and metastasis of various tumors. Consequently, we aim to investigate the underlying mechanisms of SRGs in KIRP.MethodsRNA-seq profiles of 141 KIRP samples were downloaded from the TCGA database, based on which we calculated the mRNA expression-based stemness index (mRNAsi). Next, we selected the differentially expressed genes (DEGs) between low- and high-mRNAsi groups. Then, we utilized weighted gene correlation network analysis (WGCNA) and univariate Cox analysis to identify prognostic SRGs. Afterwards, SRGs were included in the multivariate Cox regression analysis to establish a prognostic model. In addition, a regulatory network was constructed by Pearson correlation analysis, incorporating key genes, upstream transcription factors (TFs), and downstream signaling pathways. Finally, we used Connectivity map analysis to identify the potential inhibitors.ResultsIn total, 1124 genes were characterized as DEGs between low- and high-RNAsi groups. Based on six prognostic SRGs (CCKBR, GPR50, GDNF, SPOCK3, KC877982.1, and MYO15A), a prediction model was established with an area under curve of 0.861. Furthermore, among the TFs, genes, and signaling pathways that had significant correlations, the CBX2-ASPH-Notch signaling pathway was the most significantly correlated. Finally, resveratrol might be a potential inhibitor for KIRP.ConclusionsWe suggested that CBX2 could regulate ASPH through activation of the Notch signaling pathway, which might be correlated with the carcinogenesis, development, and unfavorable prognosis of KIRP.

Computational Screening of Some Phytochemicals to Identify Best Modulators for Ligand Binding Domain of Estrogen Receptor Alpha.

The peculiar aim of this study is to discover and identify the most effective and potential inhibitors against the most influential target ERα receptor by in silico studies of 45 phytochemicals from six diverse ayurvedic medicinal plants. The molecular docking investigation was carried out by the genetic algorithm program of AutoDock Vina. The molecular dynamic (MD) simulation investigations were conducted using the Desmond tool of Schrödinger molecular modelling. This study identified the top ten highest binding energy phytochemicals that were taken for drug-likeness test and ADMET profile prediction with the help of the web-based server QikpropADME. Molecular docking study revealed that ellagic acid (-9.3 kcal/mol), emodin (-9.1 kcal/mol), rhein (-9.1 kcal/mol), andquercetin (-9.0 kcal/mol) phytochemicals showed similar binding affinity as standard tamoxifen towards the target protein ERα. MD studies showed that all four compounds possess comparatively stable ligand-protein complexes with ERα target compared to the tamoxifen-ERα complex. Among the four compounds, phytochemical rhein formed a more stable complex than standard tamoxifen. ADMET studies for the top ten highest binding energy phytochemicals showed a better safety profile. Additionally, these compounds are being reported for the first time in this study as possible inhibitors of ERα for treating breast cancer, according to the notion of drug repurposing. Hence, these phytochemicals can be further studied and used as a parent core molecule to develop innovative lead molecules for breast cancer therapy.

Abstract PO2-04-14: Dual Inhibition of WEE1 and PKMYT1 Synergistically Overcomes CDK4/6 Inhibitor Resistance in Breast Cancer

Abstract Cyclin-dependent kinase 4/6 inhibitors (CDK4/6i) are approved for the treatment of advanced estrogen receptor-positive, HER2-negative (ER+ve) breast cancer when combined with endocrine therapy. However, the emergence of resistance to CDK4/6 inhibitors poses a significant clinical challenge. This study investigates the mechanisms underlying CDK4/6 inhibitor resistance and identifies a common occurrence of high replication stress in triple-negative breast cancer (TNBC) and CDK4/6 inhibitor-resistant ER+ve breast cancers. While ER+ve breast cancer patients have benefited from targeted therapy, TNBC patients, particularly those without germline BRCA1/2 or PALB2 mutations, lack effective treatment options. TNBC and CDK4/6 inhibitor-resistant ER+ve breast cancer cells exhibit an increased dependence on cell cycle arrest to repair replication stress-induced DNA damage. Failure to exit the cell cycle results in excessive DNA damage, thereby limiting their proliferative potential. Based on these findings, we hypothesize that dual inhibition of WEE1 and PKMYT1, two kinases involved in G2/M cell cycle transition and crucial for cell cycle arrest and DNA damage repair, could synergistically inhibit tumor growth. Although WEE1 and PKMYT1 share a common function in promoting G2/M cell cycle transition through CDK1 phosphorylation, their functions are not entirely redundant, suggesting that targeting both kinases may elicit a synergistic response. Recent clinical trials have shown resistance to WEE1-targeted monotherapies, emphasizing the need for combining WEE1 inhibitors with other agents, such as PKMYT1 inhibitors. We demonstrate the synergistic effects of WEE1 inhibitor (MK1775/AZD1775) and PKMYT1 inhibitor (RP6306) in a panel of TNBC and ER+ve breast cancer cells with acquired palbociclib resistance (PalboR). Combination treatment with both inhibitors leads to excessive unrepaired DNA damage, as indicated by increased γH2AX foci following 48 hours of combination treatment, whereas single-agent treatments induce significantly lower levels of DNA damage. Furthermore, we observed the AZD1775/RP6306 combination decreases the expression of the DNA repair protein Rad51 in PalboR cells. To evaluate the clinical potential of dual WEE1 and PKMYT1 inhibition, we generated organoids from metastatic breast cancer lesions of patients who had progressed on CDK4/6 inhibitors for ex vivo studies. Our results demonstrate that dual inhibition of WEE1 and PKMYT1 is more effective than single-agent treatments in eliminating CDK4/6 inhibitor-resistant organoids. Additionally, using patient-derived xenograft mouse models from patients who had progressed on palbociclib and endocrine treatment, we show that the AZD1775/RP6306 combination exhibits superior tumor suppression effects compared to single agents. Overall, this study highlights the potential therapeutic benefits of dual inhibition of WEE1 and PKMYT1 in overcoming CDK4/6 inhibitor resistance in TNBC and ER+ve breast cancer patients. These findings provide a rationale for future clinical trials aimed at exploring the clinical utility of this combination therapy. Citation Format: Mei-Kuang Chen, Grace DeAlessandro, Tuyen Bui, Khandan Keyomarsi. Dual Inhibition of WEE1 and PKMYT1 Synergistically Overcomes CDK4/6 Inhibitor Resistance in Breast Cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-04-14.

Abstract PO1-20-04: STX-478-101: A phase 1/2, first-in-human study of STX-478 monotherapy or in combination with fulvestrant in patients with breast cancer or other advanced solid tumors (trial in progress)

Abstract Background: The phosphoinositide 3-kinase-alpha (PI3Kα)/AKT/mTOR pathway is one of the major pathways in oncogenesis. PI3Kα alterations are especially prevalent in breast, gynecological, and head and neck squamous cell carcinomas. PI3Kα oncogenic mutations are highly enriched for kinase (H1047X) and helical (E542K, E545K) domain hotspots. The therapeutic potential of isoform-selective PI3Kα inhibition in PI3Kα-mutant cancers was established with alpelisib, which shows equipotent activity against both wild-type (WT) and mutant PI3Kα. However, alpelisib use is limited by toxicities induced by WT PI3Kα inhibition, e.g. hyperglycemia and mucositis. This suggests that mutant-selective PI3Kα inhibitors have the potential to improve efficacy while sparing WT-related toxicity. STX-478 is an investigational allosteric, mutant-selective PI3Kα inhibitor. Preclinical testing in human breast cancer xenografts bearing helical- or kinase-domain mutant PI3Kα demonstrated that STX-478 monotherapy and combinations with fulvestrant and/or CDK4/6 inhibitors provided robust efficacy without the metabolic dysfunction observed with alpelisib. Trial Design: This first-in-human, multicenter, phase 1/2 study (NCT05768139) evaluates the optimal dosing, safety, and preliminary efficacy of STX-478 as monotherapy in patients with locally-advanced or metastatic HR+/HER2− breast cancer or other solid tumor types with PI3Kα H1047X mutations, other kinase domain mutations, or helical domain mutations (Part 1), and STX-478 in combination with fulvestrant in patients with locally-advanced or metastatic HR+/HER2− breast cancer with PI3Kα H1047X or other kinase domain mutations (Part 2). Part 1 comprises 2 subparts (Table 1) to define the optimally biologically active dose (OBD) and maximum tolerated dose (MTD) in Part 1.1, and recommended phase 2 dose (RP2D) of STX-478 monotherapy in Part 1.2. At the conclusion of each dose-level in Part 1.1 (3 + 3 design), a backfill cohort will be initiated in patients with HR+/HER2− breast cancer with PI3Kα H1047X mutations or other kinase domain mutations, who will receive STX-478 at the determined safe dose. Part 2 comprises two subparts (Table 2) to define RP2D and assess the initial efficacy of STX-478 in combination with fulvestrant in patients with HR+/HER2− breast cancer expressing PI3Kα H1047X or other kinase domain mutations. Key Eligibility Criteria: Adults with a PI3Kα-mutant advanced or refractory solid tumor malignancy that is metastatic or locally advanced and unresectable, ECOG performance status score of 0–1, and no prior PI3K/AKT/mTOR inhibitor(s) use (except with prior intolerance) are eligible. Individuals with diabetes mellitus type 1 or uncontrolled diabetes mellitus type 2 are excluded. Cohort-specific eligibility criteria are provided in Tables 1 and 2. Endpoints: Efficacy, safety, pharmacokinetics, pharmacodynamics, patient-reported quality of life, and biomarkers (e.g., glucose metabolism, circulating tumor DNA) will be assessed. Trial Status: Recruitment opened April 2023 in the US and is ongoing, with potential for ex-US site expansion. Contact clinicaltrials@scorpiontx.com for additional information. Table 1. Part 1 Dose Escalation, RP2D Selection, and RP2D Expansion (STX-478 Monotherapy) Table 2. Part 2 RP2D Selection and Expansion (STX-478 + Fulvestrant Combination Therapy) Citation Format: Alberto Montero, Douglas Orr, Pamela Munster, Patricia LoRusso, Komal Jhaveri, Timothy Pluard, Ira Winer, Michael Streit, Monica Patterson, Simon Roberts, Stefani Corsi-Travali, Courtney Ewert, Dejan Juric. STX-478-101: A phase 1/2, first-in-human study of STX-478 monotherapy or in combination with fulvestrant in patients with breast cancer or other advanced solid tumors (trial in progress) [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO1-20-04.

A versatile immunoassay based on functionalized nanoparticles for botulinum neurotoxin detection and sensor development

Botulinum neurotoxins (BoNTs) serotypes A and B are the two most common of the four BoNTs that cause the high mortality botulism disease in individuals consuming contaminated foods. The gold standard assay for BoNT detection is the live mouse bioassay, which has several major disadvantages, including tedious procedures and animal sacrifice requirements. In this study, we developed an immuno-based assay using magnetic streptavidin nanoparticles (mSNP) functionalized with specific synthetic biotinylated, 6xHis-tagged peptide substrates (Peptides A, PA and B, PB) designed for BoNT/A and BoNT/B proteolytic reactions, respectively. In the presence of active toxins that possess endopeptidase activity, upon cleavage, the released fragments with His-tag were dotted on a blotting membrane, ultimately producing color signals after incubation with anti-His antibody, alkaline phosphatase (AP)-conjugated antibody, and then AP substrates. The results showed that the efficiency of peptide-mSNP complex formation reached up to 81%, and the dot blot immunoassay allowed peptide detection from 10 ng of His-tagged peptides. Preliminary testing with the extracellular extracts from the isolated Clostridium botulinum strains indicated that the botulinum toxin in the 2020 botulism outbreak in Vietnam belonged to serotype A, the most potent BoNT. The established assay could be applied to construct a portable biosensor for BoNT detection and a high throughput device to screen potential BoNT inhibitors for drug development.

Abstract PO3-25-08: Artificial Intelligence-based screening of small molecule inhibitors of phosphoenolpyruvate carboxykinase 2 (PCK2), a novel cancer therapeutic target

Abstract Background: Metabolic rewiring is a hallmark of cancer that is often mediated by alterations in metabolic isozyme expression. Isozymes that are overexpressed in cancer and catalyze rate limiting steps in key metabolic processes are potential therapeutic targets. We previously identified phosphoenolpyruvate carboxykinase 2 (PCK2) as cancer dominant isoform, required for maintaining high metabolic activity and proliferation of lung, prostate, and breast cancer (BC) cells in vitro and in vivo. No PCK2 specific small molecule inhibitors exist. Methods: mRNA expression levels were assessed in the TCGA data. PCK2 MISSION shRNAs (Millipore) were used to knock-down expression of PCK2 in BC cells. Alterations in metabolic flux caused by PCK2 down-regulation were examined via 13C-labeling and mass spectrometry using a SCIEX 5500 QTRAP and SelexION instrument for mobility separation of metabolites. The AtomNetTM (Atomwise Inc.) deep convolutional neural network structure-based drug design software was used to identify candidate small molecule PCK2 inhibitors which were tested in PCK1 and PCK2 in vitro enzyme activity assays. The lead compound was assessed for drug-like properties by QickPropV4.0.001w, and its growth inhibitory activity was tested in MDA-MB-321 and BT-549 cells. Results: Analysis of mRNA levels in TNBC samples revealed a significant decrease in PCK1 expression compared to normal tissues, while PCK2 expression remained elevated or even increased. Quantification of mRNA levels in TNBC cell lines confirmed the higher expression of PCK2 compared to PCK1. To assess functional significance of PCK2 expression, we downregulated PCK2 using shRNA constructs in TNBC cell lines. Western blot analysis confirmed efficient knockdown of PCK2 protein without affecting PCK1 expression. Clonogenic assays demonstrated that PCK2-depleted BT-549 and MDA-MB-231 cells exhibited impaired proliferation, with reduced colony number and size compared to control cells. Metabolic analysis of PCK2-depleted TNBC cells demonstrated decreased levels of glycolytic and TCA intermediates and reduced flux through pyruvate carboxylase, indicating altered metabolic pathways upon PCK2 depletion. To identify potential inhibitors of PCK2, virtual screening was conducted using compound structures. We used a PCK2 protein structure homology model and designated the 3-mercaptopicolinic acid-binding site of the PCK1 structure as the site of interest to perform virtual drug screening of 7 million diverse compounds. The first screen yielded 86 structures to be tested in vitro, of which 5 demonstrated > 16% PCK2 inhibition. The top hit (IC50=2.4µM) was used to refine a second round of in silico screen that yielded 87 second-round candidates that were assessed for PCK2 inhibition in vitro. 3-(3,4-dihydroxyphenyl)-2-hydroxypropanoate emerged as the lead compound. QickProp predicted favorable absorption, distribution, metabolism, and excretion properties, but relatively low cell permeability (apparent Caco-2 and MDCK2 cell permeabilities 18 nm/sec and 8 nm/sec, respectively). The specificity of 3-(3,4-dihydroxyphenyl)-2-hydroxypropanoate was tested in PCK1 and PCK2 enzymatic assays and revealed IC50 of 500nM on PCK1 and an IC50 of 3 nM on PCK2. We next tested the cell growth inhibitory effect of 3-(3,4-dihydroxyphenyl)-2-hydroxypropanoate on parental MDA-MB-231 and BT-549 cells and their PCK2 knockdown clones. Cell growth and viability significantly decreased in the MDA-MD-231 and BT-549 parental cells (the IC50 for MDA-MB-231 was 173 μM) and in shRNA non-targeting control cells, but not in the PCK2 depleted clones, demonstrating PCK2-dependent inhibitory effect. Conclusion: We identified 3-(3,4-dihydroxyphenyl)-2-hydroxypropanoate as a high affinity selective PCK2 enzyme inhibitor. This compound also has significant growth inhibitory activity in BC cell lines in vitro and represents a novel therapeutic lead compound. Citation Format: Alejandro Rios Hoyo, Naing Lin Shan, Hao-Kuen Lin, Gerson Espinoza Campos, Mostafa Ahmed, Sheila Umlauf, Rebecca Cardone, Yulia V. Surovtseva, Vignesh Gunasekharan, Lajos pusztai. Artificial Intelligence-based screening of small molecule inhibitors of phosphoenolpyruvate carboxykinase 2 (PCK2), a novel cancer therapeutic target [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO3-25-08.

Phytochemicals: Promising Inhibitors of Human Rhinovirus Type 14 3C Protease as a Strategy to Fight the Common Cold.

Human rhinovirus 3C protease (HRV-3Cpro) plays a crucial role in viral proliferation, establishing it as a prime target for antiviral therapy. However, research on identifying HRV-3Cpro inhibitors is still limited. This study had two primary objectives: first, to validate the efficacy of an end-point colorimetric assay, previously developed by our team, for identifying potential inhibitors of HRV-3Cpro; and second, to discover phytochemicals in medicinal plants that inhibit the enzyme's activity. Rupintrivir, a well-known inhibitor of HRV-3Cpro, was used to validate the colorimetric assay. Following this, we conducted a two-step in silico screening of 2532 phytochemicals, which led to the identification of eight active compounds: apigenin, carnosol, chlorogenic acid, kaempferol, luteolin, quercetin, rosmarinic acid, and rutin. We subsequently evaluated these candidates in vitro. To further investigate the inhibitory potential of the most promising candidates, namely, carnosol and rosmarinic acid, molecular docking studies were performed to analyze their binding interactions with HRV-3Cpro. The colorimetric assay we previously developed is effective in identifying compounds that selectively inhibit HRV-3Cpro. Carnosol and rosmarinic acid emerged as potent inhibitors, inhibiting HRV-3Cpro activity in vitro by over 55%. Our analysis indicated that carnosol and rosmarinic acid exert their inhibitory effects through a competitive mechanism. Molecular docking confirmed their competitive binding to the enzyme's active site. Carnosol and rosmarinic acid warrant additional investigation for their potential in the development of cold treatment. By highlighting these compounds as effective HRV-3Cpro inhibitors, our study presents a promising approach for discovering phytochemical inhibitors against proteases from similar pathogens.

Rapid screening of potential α-glucosidase inhibitors from the waste leaves of Rheum tanguticum by activity-oriented extraction and enrichment optimization, UPLC-QTOF-MS/MS, molecular docking and in vitro validation

In the present study, an efficient strategy has been established for rapid screening of potential α-glucosidase inhibitors from the waste leaves of Rheum tanguticum by activity-oriented extraction and enrichment optimization, UPLC-QTOF-MS/MS, molecular docking, and in vitro validation. With α-glucosidase inhibitory activity as the evaluation index, the extraction process was optimized by response surface methodology and the enrichment process by macroporous resins was optimized by adsorption and desorption experiments. The active flavonoids yield was 8.85 mg/g under the optimized extraction conditions. After AB-8 macroporous resins enrichment, the active flavonoids purity increased from 2.89 % to 47.6 %, a 17-fold increase, while the IC50 of α-glucosidase reduced from 13.97 mg/mL to 412 μg/mL, a 33.9-fold reduction. Thirty-six flavonoids in the active flavonoids fraction were identified by UPLC-QTOF-MS/MS. Molecular docking screening, in vitro activity assay and multispectral approaches verification confirmed the potential of six flavonoids as novel α-glucosidase inhibitors.

Natural compound screening predicts novel GSK-3 isoform-specific inhibitors

Glycogen synthase kinase-3 (GSK-3) plays important roles in the pathogenesis of cardiovascular, metabolic, neurological disorders and cancer. Isoform-specific loss of either GSK-3α or GSK-3β often provides cytoprotective effects under such clinical conditions. However, available synthetic small molecule inhibitors are relatively non-specific, and their chronic use may lead to adverse effects. Therefore, screening for natural compound inhibitors to identify the isoform-specific inhibitors may provide improved clinical utility. Here, we screened 70 natural compounds to identify novel natural GSK-3 inhibitors employing comprehensive in silico and biochemical approaches. Molecular docking and pharmacokinetics analysis identified two natural compounds Psoralidin and Rosmarinic acid as potential GSK-3 inhibitors. Specifically, Psoralidin and Rosmarinic acid exhibited the highest binding affinities for GSK-3α and GSK-3β, respectively. Consistent with in silico findings, the kinase assay-driven IC50 revealed superior inhibitory effects of Psoralidin against GSK-3α (IC50=2.26 μM) vs. GSK-3β (IC50=4.23 μM) while Rosmarinic acid was found to be more potent against GSK-3β (IC50=2.24 μM) than GSK-3α (IC50=5.14 μM). Taken together, these studies show that the identified natural compounds may serve as GSK-3 inhibitors with Psoralidin serving as a better inhibitor for GSK-3α and Rosmarinic for GSK-3β isoform, respectively. Further characterization employing in vitro and preclinical models will be required to test the utility of these compounds as GSK-3 inhibitors for cardiometabolic and neurological disorders and cancers.

Synthesis, antidiabetic activity and in silico studies of benzo[b]thiophene based small molecule α-amylase inhibitors

Benzo[b]thiophene has been implicated as molecular framework in the drug discovery against broad spectrum of biological targets. In the antidiabetic drug regime, benzo[b]thiophene based SGLT2 and ALR2 inhibitors have been recently developed but their potential towards α-amylase inhibition remained unexplored to date. In this context, a series of novel small molecule benzo[b]thiophene-2-carboxylic acid derivatives (3a-p) was synthesized, characterized, and evaluated for antidiabetic activity as α-amylase inhibitors. We found that, all benzo[b]thiophene derivatives exhibited significant α-amylase inhibition with IC50 value ranging from 5.37 ± 0.25 μM to 29.89 ± 0.68 μM. The SAR studies showed benzo[b]thiophene carboxylate bearing bis(2-hydroxyethyl)amino group (3b) was most potent with IC50 5.37 ± 0.25 μM compared to standard drug Acarbose (IC50 = 6.40 ± 0.14 μM). Further, the enzyme inhibition mechanism study regarded 3b as competitive inhibitor of α-amylase with Ki value of 1.76 μM. A detailed in silico study was also performed in order to estimate binding properties, drug likeness and predict toxicity profile of these agents. It was demonstrated that novel small molecule benzo[b]thiophene derivative (3b) can effectively bind through H-bonding, hydrophobic and π-stacking interactions within α-amylase active site. Moreover, drug likeness and toxicity prediction studies suggested compound 3b as potential & safter α-amylase inhibitor. Overall, our present study disclosed a novel class of benzo[b]thiophene based α-amylase inhibitors and opened a template for further lead optimization and development.

Virtual Screening of Small Molecules Targeting BCL2 with Machine Learning, Molecular Docking, and MD Simulation

This study aimed to identify potential BCL-2 small molecule inhibitors using deep neural networks (DNN) and random forest (RF), algorithms as well as molecular docking and molecular dynamics (MD) simulations to screen a library of small molecules. The RF model classified 61% (2355/3867) of molecules as ‘Active’. Further analysis through molecular docking with Vina identified CHEMBL3940231, CHEMBL3938023, and CHEMBL3947358 as top-scored small molecules with docking scores of −11, −10.9, and 10.8 kcal/mol, respectively. MD simulations validated these compounds’ stability and binding affinity to the BCL2 protein.

A Novel Tetramethylpyrazine Chalcone Hybrid- HCTMPPK, as a Potential Anti-Lung Cancer Agent by Downregulating MELK.

Lung adenocarcinoma currently ranks the leading causes of cancer-related mortality worldwide. Many anti-inflammation herbs, like tetramethylpyrazine, have shown their anti-tumor potentials. Here, we evaluated the role of a novel chalcone derivative of tetramethylpyrazine ((E) -1- (E) -1- (2-hydroxy-5-chlorophenyl) -3- (3,5,6-trimethylpyrazin-2-yl) -2-propen-1, HCTMPPK) in lung adenocarcinoma. The effects of HCTMPPK on cell proliferation, apoptosis, and invasion were investigated by in-vitro assays, including CCK-8, colony formation assay, flow cytometry, transwell assay, and wound-healing assay. The therapeutic potential of HCTMPPK in vivo was evaluated in xenograft mice. To figure out the target molecules of HCTMPPK, a network pharmacology approach and molecular docking studies were employed, and subsequent experiments were conducted to confirm these candidate molecules. HCTMPPK effectively suppressed the proliferative activity and migration, as well as enhanced the apoptosis of A549 cells in a concentration-dependent manner. Consistent with this, tumor growth was inhibited by HCTMPPK significantly in vivo. Regarding the mechanisms, HCTMPPK down-regulated Bcl-2 and MMP-9 and up-regulating Bax and cleaved-caspase-3. Subsequently, we identified 601 overlapping DEGs from LUAD patients in TCGA and GEO database. Then, 15 hub genes were identified by PPI network and CytoHubba. Finally, MELK was verified to be the HCTMPPK targeted site, through the molecular docking studies and validation experiments. Overall, our study indicates HCTMPPK as a potential MELK inhibitor and may be a promising candidate for the therapy of lung cancer.

The artificial neural network selects saccharides from natural sources a promise for potential FimH inhibitor to prevent UTI infections.

The online version contains supplementary material available at 10.1007/s40203-024-00212-5.