Zachary Bacigalupa, Ph.D.’s Post

💥💥💥 Distinct conformational states enable transglutaminase 2 to promote cancer cell survival versus cell death. Transglutaminase 2 (TG2) is a GTP-binding, protein-crosslinking enzyme that has been investigated as a therapeutic target for Celiac disease, neurological disorders, and aggressive cancers. TG2 has been suggested to adopt two conformational states that regulate its functions: a GTP-bound, closed conformation, and a calcium-bound, crosslinking-active open conformation. TG2 mutants that constitutively adopt an open conformation are cytotoxic to cancer cells. Thus, small molecules that bind and stabilize the open conformation of TG2 could offer a new therapeutic strategy. Here, we investigate TG2, using static and time-resolved small-angle X-ray scattering (SAXS) and single-particle cryoelectron microscopy (cryo-EM), to determine the conformational states responsible for conferring its biological effects. We also describe a newly developed TG2 inhibitor, LM11, that potently kills glioblastoma cells and use SAXS to investigate how LM11 affects the conformational states of TG2. Using SAXS and cryo-EM, we show that guanine nucleotides bind and stabilize a monomeric closed conformation while calcium binds to an open state that can form higher order oligomers. SAXS analysis suggests how a TG2 mutant that constitutively adopts the open state binds nucleotides through an alternative mechanism to wildtype TG2. Furthermore, we use time resolved SAXS to show that LM11 increases the ability of calcium to bind and stabilize an open conformation, which is not reversible by guanine nucleotides and is cytotoxic to cancer cells. Taken together, our findings demonstrate that the conformational dynamics of TG2 are more complex than previously suggested and highlight how conformational stabilization of TG2 by LM11 maintains TG2 in a cytotoxic conformational state. 🛎️ 🛎️🛎️ Pay attention that compounds for this research have been purchased from Vitas M. #drugdiscovery #smallmolecules #Vitas #inhibitors #research #biotech #medicinalchemistry #drugspharmaceuticals #hitcompound #bioactivity #pharmaceuticalsciences #treatment #diseasetreatment #biotech #research #targets #leadgeneration

I'm thrilled to share our latest research published in the Turkish Journal of Biochemistry on the differential effects of choline on TLR2/4 mediated signaling through the regulation of Toll-interacting protein (TOLLIP) in hepatocellular carcinoma (HCC) cell lines. Our study with Ayşe Banu Demir, found that choline, known for its anti-inflammatory properties via the α7 nicotinic acetylcholine receptor (α7nAChR), exerts varying effects depending on the differentiation stage of HCC cells. Specifically, choline downregulated TOLLIP in both well-differentiated HEP3B and poorly differentiated SNU449 cells. It decreased the expression of α7nAChR, NF-κB, IL-6, TLR2, and TLR4 in well-differentiated cells, while increasing these markers in poorly differentiated cells. These findings suggest that choline could have therapeutic potential in the earlier stages of HCC by modulating TOLLIP and TLR2/4-dependent signaling pathways. This research highlights the complexity of choline's impact on HCC and opens new avenues for targeted therapies in liver cancer. 

🔬❗ A long-term collaboration between the Biomedical Research Foundation of the Academy of Athens, Pharmacology (BRFAA) and the Laboratory of Organic Chemistry at Aristotle University of Thessaloniki (AUTH), (Constantin Tamvakopoulos and Vasiliki Sarli labs) as well as the contribution of the Laboratory of Biological Chemistry at the University of Ioannina and the Biomedical Research Institute, Foundation for Research and Technology, Ioannina was underscored by the recent publication entitled “Developing Myc Degraders Bearing Von Hippel-Lindau Ligand to Target the ‘Undruggable’ Myc” in ACS Pharmacology & Translational Science ✍ 🔗 https://lnkd.in/dFVPtb4w This is an outstanding effort that emphasizes the importance of finding alternative methods to target "undruggable" proteins involved in many types of cancer, and other diseases through Protein Degrader Molecules: The degradation of the target protein is strategically achieved via the proteasome (a large protein complex whose main function is the regulation of proteins). The published work includes the synthesis of novel chimeric molecules (PROteolysis Targeting Chimeras, PROTACs) that target the c-MYC protein, studies of their pharmacological effects in prostate and breast cancer cells, and studies in preclinical stages. 👉 We hope that our findings will contribute to advancing the understanding and improvement of therapeutic approaches to cancer, offering more targeted and effective therapies. 👉 We aim to further expand the effort to include other targets and ultimately improve the quality of life and survival of patients. Constantin Tamvakopoulos https://lnkd.in/d2bWUH7C Christos Siokatas Alexandra Lampropoulou Alexandra Smina Theodoros Karampelas

Best Paper Award from MDPI🏆 I am thrilled to share that our paper, "LC–MS/MS Phytochemical Profiling, Antioxidant Activity, and Cytotoxicity of the Ethanolic Extract of Atriplex halimus L. against Breast Cancer Cell Lines: Computational Studies and Experimental Validation," has been honored with the Best Paper Award 2022 by the prestigious journal Pharmaceuticals MDPI (Impact Factor: 4.3, CiteScore: 6.1, Q1 in Pharmacology and Pharmacy). This award is a testament to the hard work and dedication of our research team and collaborators. Our study on Atriplex halimus, a halophytic shrub widely distributed across the Mediterranean, has opened new avenues for understanding its potential in breast cancer treatment through a combination of advanced LC–MS/MS phytochemical profiling and rigorous experimental validation. A heartfelt thank you to the editorial team at Pharmaceuticals and the award committee, led by Prof. Dr. Amélia Pilar Rauter, for recognizing our work among the many outstanding submissions. This accolade not only highlights the scientific merit and innovation of our research but also encourages us to continue pushing the boundaries of pharmacological science. A big thanks to my supervisor, Prof. Dr. Mohamed Addi, and my colleagues, especially Doc. Abdellah Baraich. A significant triumph in science is when your relentless effort and commitment are acknowledged, even amidst skepticism. 🔗 Link to the paper: https://lnkd.in/e3fqdYYG 🔗 Link of the announcement: https://lnkd.in/eaZDR87e #Research #Pharmacology #BreastCancerAwareness #ScientificAchievement #AtriplexHalimus #awardwinning {وَمَا تَوْفِيقِي إِلَّا بِاللَّهِ ۚ عَلَيْهِ تَوَكَّلْتُ وَإِلَيْهِ أُنِيبُ} [هود من الآية:88]

Three years ago, I started to develop an idea to accelerate the in vivo screening of targeting aptamers and oligonucleotides. Taking inspiration from the work of George Church, James Dahlman, and others in the field of DNA-encoded libraries (DEL), I wanted to generate a small library of barcoded aptamer formulations and determine their biodistribution in mice bearing xenograft lung cancer harboring oncogenic EGFR mutations. Together with my postdoc mentor, Burke-Aguero Donald and Brian Thomas, we demonstrated that barcoded aptamer technology enables rapid test of tissue targeting and tumor uptake in vivo. Our findings show no correlation between in vitro (cell culture) and in vivo models, suggesting the need of prioritizing studies in animals to improve translation of aptamers and oligonucleotide therapeutics. Our approach also minimizes the use of animals in agreement with the 3Rs since we tested 20 formulations (but could be hundreds or thousands) at once in just a single cohort of mice. This proof-of-principle study was recently published on the journal Nucleic Acid Therapeutics (see link below). I consider this work as a sort of scientific baby due to all love and passion I put into it (from idea crafting to manuscript preparation). Thanks to all co-authors for your help and support along the way. University of Missouri-Columbia #aptamers #RNAoligonucleotides #oligonucleotides #TumorTargeting #barcoding #NGS #RNAtherapeutics #RNA #EGFR #NSCLC

 Excited to share our latest research on the intricate relationship between mitogen-activated protein kinase 3 (MKK3) and MYC protooncogene protein (MYC) activation, and its implications for cancer progression, particularly in triple negative breast cancer (TNBC). Despite significant progress, discovering effective MYC-targeted drugs remains a challenge. Our study explores a promising approach to control MYC-dependent malignancies by disrupting the protein-protein interactions (PPIs) between MKK3 and MYC. This interaction is critical, as MKK3 activates MYC in diverse cell types, presenting a novel perspective for therapeutic interventions in MYC-driven pathways. In our study, we employed an innovative in silico strategy to screen small molecule libraries targeting the MKK3-MYC interaction. We developed dynamic structure-based pharmacophore models to screen these libraries, identifying compounds with favorable alignment to the defined pharmacophore features. A key highlight of our research is the use of steered molecular dynamics (sMD) simulations in virtual screening—a new direction in this field. We utilized sMD simulations to assess the correlation between the forces needed to dissociate candidate hit ligands from the binding pocket and their average binding free energies (MM/GBSA). Our comparative analysis showed that the identified compounds have promising predicted binding affinities compared to the reference molecule SGI-1027. These findings represent a crucial advancement in our ability to control MYC activation in cancer, potentially paving the way for new therapeutic interventions. https://lnkd.in/dVyS3-FY #CancerResearch #DrugDiscovery #MolecularBiology #TripleNegativeBreastCancer #Pharmacology #Bioinformatics #InSilico #DeepLearning #PharmaceuticalResearch #MolecularDynamics

The future of biobanking in precision oncology relies on technological advancements, data integration, and international collaboration. Read more: https://lnkd.in/dyqHp_yf #biobanking #precisiononcology #genomics #proteomics

Atypical TK fusions - Oncogenic formation and clinical implications for targeted therapy “Partner genes and exons in most TK fusions follow typical recurrent patterns, but the underlying mechanisms and clinical implications of these patterns are poorly understood. By developing Functionally Active Chromosomal Translocation Sequencing (FACTS), we discover that typical TK fusions involving ALK, ROS1, RET and NTRK1 are selected from pools of chromosomal rearrangements by two major determinants: active transcription of the fusion partner genes and protein stability. In contrast, atypical TK fusions that are rarely seen in patients showed reduced protein stability, decreased downstream oncogenic signaling, and were less responsive to inhibition. Consistently, patients with atypical TK fusions were associated with a reduced response to TKI therapies. Our findings highlight the principles of oncogenic TK fusion formation and selection in cancers, with clinical implications for guiding targeted therapy.” #targetedtherapy #fusion #TKfusion #transcription #genomicprofiling

The formation of protein corona (PC) around nanoparticles (NPs) has been reported inside biological media. This phenomenon alters biological identity, targeting capability, delivery capacity, biodistribution and the fate of all types of nano formulations in vivo studies. In the case of targeted nano-based drug delivery systems, it has been well characterized that different types of ligands, their density and physicochemical features dictate the PC content, affinity and quantity. Surprisingly, in a study conducted by our team unravelled that the targeting ability of folic acid (FA)-modified chitosan nanoparticles (FA-CS NPs) is significantly hampered by plasma proteins of breast cancer patients, compared to healthy donors ones! Also, our results showed that the complex of FA-CS NPs and patients plasma proteins are more efficiently removed by macrophages. https://lnkd.in/dzz5BaWb More interestingly, the same findings were published in ACS nano journal that demonstrated FA-modified liposomes are trapped by spleen and liver quickly in a species dependent manner, almost simultaneous to us (6 months before us)!! All together, these two studies strongly suggest that using FA as targeting ligand should be avoided for the future clinical settings. Meanwhile, folic acid has been used as one of the most well-known ligands for targeted delivery to various cancers in clinical settings! #Dr. Huile Gao #MahdiehNemati

Cancer patients are already going through enough without the drug meant to treat them potentially leading to severe to life-threatening toxicity. In collaboration with the Medical Laboratory Science Programme at the University of Otago, Awanui Labs have developed and validated a DPYD genotyping assay to identify patients who have variants in the DPYD gene and predict who might get side effects, and plan treatment accordingly.  Learn more here https://lnkd.in/g3e_FDHE