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Brauer NR, Kempen AL, Hernandez D, Sintim HO. Non-kinase off-target inhibitory activities of clinically-relevant kinase inhibitors. Eur J Med Chem 2024; 275:116540. [PMID: 38852338 PMCID: PMC11243610 DOI: 10.1016/j.ejmech.2024.116540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/07/2024] [Accepted: 05/26/2024] [Indexed: 06/11/2024]
Abstract
Protein kinases are responsible for a myriad of cellular functions, such as cell cycle, apoptosis, and proliferation. Because of this, kinases make excellent targets for therapeutics. During the process to identify clinical kinase inhibitor candidates, kinase selectivity profiles of lead inhibitors are typically obtained. Such kinome selectivity screening could identify crucial kinase anti-targets that might contribute to drug toxicity and/or reveal additional kinase targets that potentially contribute to the efficacy of the compound via kinase polypharmacology. In addition to kinome panel screening, practitioners also obtain the inhibition profiles of a few non-kinase targets, such as ion-channels and select GPCR targets to identify compounds that might possess potential liabilities. Often ignored is the possibility that identified kinase inhibitors might also inhibit or bind to the other proteins (greater than 20,000) in the cell that are not kinases, which may be relevant to toxicity or even additional mode of drug action. This review highlights various inhibitors, which have been approved by the FDA or are currently undergoing clinical trials, that also inhibit other non-kinase targets. The binding poses of the drugs in the binding sites of the target kinases and off-targets are analyzed to understand if the same features of the compounds are critical for the polypharmacology.
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Affiliation(s)
- Nickolas R Brauer
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Allison L Kempen
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Delmis Hernandez
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Herman O Sintim
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA; Purdue Institute for Drug Discovery, 720 Clinic Drive, West Lafayette, IN, 47907, USA; Purdue Institute for Cancer Research, 201 S. University St., West Lafayette, IN, 47907, USA.
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2
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Ramalho S, Dopler A, Faller W. Ribosome specialization in cancer: a spotlight on ribosomal proteins. NAR Cancer 2024; 6:zcae029. [PMID: 38989007 PMCID: PMC11231584 DOI: 10.1093/narcan/zcae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 06/11/2024] [Accepted: 06/19/2024] [Indexed: 07/12/2024] Open
Abstract
In the past few decades, our view of ribosomes has changed substantially. Rather than passive machines without significant variability, it is now acknowledged that they are heterogeneous, and have direct regulatory capacity. This 'ribosome heterogeneity' comes in many flavors, including in both the RNA and protein components of ribosomes, so there are many paths through which ribosome specialization could arise. It is easy to imagine that specialized ribosomes could have wide physiological roles, through the translation of specific mRNA populations, and there is now evidence for this in several contexts. Translation is highly dysregulated in cancer, needed to support oncogenic phenotypes and to overcome cellular stress. However, the role of ribosome specialization in this is not clear. In this review we focus on specialized ribosomes in cancer. Specifically, we assess the impact that post-translational modifications and differential ribosome incorporation of ribosomal proteins (RPs) have in this disease. We focus on studies that have shown a ribosome-mediated change in translation of specific mRNA populations, and hypothesize how such a process could be driving other phenotypes. We review the impact of RP-mediated heterogeneity in both intrinsic and extrinsic oncogenic processes, and consider how this knowledge could be leveraged to benefit patients.
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Affiliation(s)
- Sofia Ramalho
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Anna Dopler
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - William James Faller
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, Netherlands
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3
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Nemr MTM, Elshewy A, Ibrahim ML, El Kerdawy AM, Halim PA. Design, synthesis, antineoplastic activity of new pyrazolo[3,4-d]pyrimidine derivatives as dual CDK2/GSK3β kinase inhibitors; molecular docking study, and ADME prediction. Bioorg Chem 2024; 150:107566. [PMID: 38896936 DOI: 10.1016/j.bioorg.2024.107566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/06/2024] [Accepted: 06/14/2024] [Indexed: 06/21/2024]
Abstract
In the current study, novel pyrazolo[3,4-d]pyrimidine derivatives 5a-h were designed and synthesized as targeted anti-cancer agents through dual CDK2/GSK-3β inhibition. The designed compounds demonstrated moderate to potent activity on the evaluated cancer cell lines (MCF-7 and T-47D). Compounds 5c and 5 g showed the most promising cytotoxic activity against the tested cell lines surpassing that of the used reference standard; staurosporine. On the other hand, both compounds showed good safety and tolerability on normal fibroblast cell line (MCR5). The final compounds 5c and 5 g showed a promising dual CDK2/GSK-3β inhibitory activity with IC50 of 0.244 and 0.128 μM, respectively, against CDK2, and IC50 of 0.317 and 0.160 μM, respectively, against GSK-3β. Investigating the effect of compounds 5c and 5 g on CDK2 and GSK-3β downstream cascades showed that they reduced the relative cellular content of phosphorylated RB1 and β-catenin compared to that in the untreated MCF-7 cells. Moreover, compounds 5c and 5 g showed a reasonable selective inhibition against the target kinases CDK2/GSK-3β in comparison to a set of seven off-target kinases. Furthermore, the most potent compound 5 g caused cell cycle arrest at the S phase in MCF-7 cells preventing the cells' progression to G2/M phase inducing cell apoptosis. Molecular docking studies showed that the final pyrazolo[3,4-d]pyrimidine derivatives have analogous binding modes in the target kinases interacting with the hinge region key amino acids. Molecular dynamics simulations confirmed the predicted binding mode by molecular docking. Moreover, in silico predictions indicated their favorable physicochemical and pharmacokinetic properties in addition to their promising cytotoxic activity.
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Affiliation(s)
- Mohamed T M Nemr
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, P.O. Box 11562, Egypt
| | - Ahmed Elshewy
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, P.O. Box 11562, Egypt; Department of Medicinal Chemistry, Faculty of Pharmacy, Galala University, New Galala 43713, Egypt.
| | - Mohammed L Ibrahim
- Department of Biochemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, P.O. Box 11562, Egypt
| | - Ahmed M El Kerdawy
- School of Pharmacy, College of Health and Science, University of Lincoln, Joseph Banks Laboratories, Green Lane, Lincoln, United Kingdom; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, P.O. Box 11562, Egypt
| | - Peter A Halim
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, P.O. Box 11562, Egypt
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Morez M, Lara Ordóñez AJ, Melnyk P, Liberelle M, Lebègue N, Taymans JM. Leucine-rich repeat kinase 2 (LRRK2) inhibitors for Parkinson's disease: a patent review of the literature to date. Expert Opin Ther Pat 2024; 34:773-788. [PMID: 39023243 DOI: 10.1080/13543776.2024.2378076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 07/04/2024] [Indexed: 07/20/2024]
Abstract
INTRODUCTION Nearly two decades after leucine rich repeat kinase 2 (LRRK2) was discovered as a genetic determinant of Parkinson's disease (PD), LRRK2 has emerged a priority therapeutic target in PD and inhibition of its activity is hypothesized to be beneficial. AREAS COVERED LRRK2 targeting agents, in particular kinase inhibitors and agents reducing LRRK2 expression show promise in model systems and have progressed to phase I and phase II clinical testing for PD. Several additional targeting strategies for LRRK2 are emerging, based on promoting specific 'healthy' LRRK2 quaternary structures, heteromeric complexes and conformations. EXPERT OPINION It can be expected that LRRK2 targeting strategies may proceed to phase III clinical testing for PD in the next five years, allowing the field to discover the real clinical value of LRRK2 targeting strategies.
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Affiliation(s)
- Margaux Morez
- University Lille, Inserm, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | | | - Patricia Melnyk
- University Lille, Inserm, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | - Maxime Liberelle
- University Lille, Inserm, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | - Nicolas Lebègue
- University Lille, Inserm, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | - Jean-Marc Taymans
- University Lille, Inserm, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
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Bhattacharjee A, Bagchi A, Sarkar S, Bawali S, Bhattacharya A, Biswas A. Repurposing approved protein kinase inhibitors as potent anti-leishmanials targeting Leishmania MAP kinases. Life Sci 2024; 351:122844. [PMID: 38897344 DOI: 10.1016/j.lfs.2024.122844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 06/03/2024] [Accepted: 06/12/2024] [Indexed: 06/21/2024]
Abstract
AIMS Leishmaniasis, caused by the protozoan parasite poses a significant health burden globally. With a very few specific drugs, increased drug resistance it is important to look for drug repurposing along with the identification of pre-clinical candidates against visceral leishmaniasis. This study aims to identify potential drug candidates against visceral leishmaniasis by targeting leishmanial MAP kinases and screening FDA approved protein kinase inhibitors. MATERIALS AND METHODS MAP kinases were identified from the Leishmania genome. 12 FDA approved protein kinase inhibitors were screened against Leishmania MAP kinases. Binding affinity, ADME and toxicity of identified drug candidates were profiled. The anti-proliferative effects and mechanism of action were assessed in Leishmania, including changes in cell morphology, flagellar length, cell cycle progression, reactive oxygen species (ROS) generation, and intra-macrophage parasitic burden. KEY FINDINGS 23 MAP kinases were identified from the Leishmania genome. Sorafenib and imatinib emerged as repurposable drug candidates and demonstrated excellent anti-proliferative effects in Leishmania. Treatment with these inhibitors resulted in significant changes in cell morphology, flagellar length, and cell cycle arrest. Furthermore, sorafenib and imatinib promoted ROS generation and reduced intra-macrophage parasitic burden, and elicited anti-leishmanial activity in in vivo experimental VL models. SIGNIFICANCE Collectively, these results imply involvement of MAP kinases in infectivity and survival of the parasite and can pave the avenue for repurposing sorafenib and imatinib as anti-leishmanial agents. These findings contribute to the exploration of new treatment options for visceral leishmaniasis, particularly in the context of emerging drug resistance.
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Affiliation(s)
- Anindita Bhattacharjee
- Cell and Molecular Biology Laboratory, Department of Zoology, University of Kalyani, Kalyani, Nadia 741235, India
| | - Arka Bagchi
- Cell and Molecular Biology Laboratory, Department of Zoology, University of Kalyani, Kalyani, Nadia 741235, India
| | - Solanki Sarkar
- Cell and Molecular Biology Laboratory, Department of Zoology, University of Kalyani, Kalyani, Nadia 741235, India
| | - Sriparna Bawali
- Cell and Molecular Biology Laboratory, Department of Zoology, University of Kalyani, Kalyani, Nadia 741235, India
| | - Arijit Bhattacharya
- AMR Research Laboratory, Department of Biological Sciences, Adamas University, Kolkata 700126, India.
| | - Arunima Biswas
- Cell and Molecular Biology Laboratory, Department of Zoology, University of Kalyani, Kalyani, Nadia 741235, India.
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Choithramani A, Das R, Bothra G, Patel Vatsa P, Muthukumar V, Bhuvana BKS, Kapoor S, Moola D, Chowdhury MG, Mandoli A, Shard A. Targeted suppression of oral squamous cell carcinoma by pyrimidine-tethered quinoxaline derivatives. RSC Med Chem 2024; 15:2729-2744. [PMID: 39149105 PMCID: PMC11324040 DOI: 10.1039/d4md00042k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 05/17/2024] [Indexed: 08/17/2024] Open
Abstract
Oral cancer (OC) stands as a prominent cause of global mortality. Despite numerous efforts in recent decades, the efficacy of novel therapies to extend the lifespan of OC patients remains disappointingly low. Consequently, the demand for innovative therapeutic agents has become all the more pressing. In this context, we present our work on the design and synthesis of twenty-five novel quinoxaline-tethered imidazopyri(mi)dine derivatives. This was followed by comprehensive investigations into the impact of these molecules on the OC cell line. The in vitro cytotoxicity studies performed in CAL-27 and normal oral epithelial (NOE) cell lines revealed that some of the synthesized molecules like 12d have potent antiproliferative activity specifically towards OC cells with an IC50 of 0.79 μM and show negligible cytotoxicity over NOE cells. Further, 12d arrested cell growth in the S phase of the cell cycle and induced cell death by early apoptosis. The in silico studies validated that 12d binds to the activator binding site on pyruvate kinase M2 (PKM2) overexpressed in OC while the lactate dehydrogenase (LDH)-coupled enzyme assay established 12d as a potent PKM2 activator with an AC50 of 0.6 nM. Hence, this study provides fruitful evidence for the designed compounds as anticancer agents against OC.
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Affiliation(s)
- Asmita Choithramani
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A) Opposite Airforce Station, Palaj Gandhinagar Gujarat - 382355 India
| | - Rudradip Das
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A) Opposite Airforce Station, Palaj Gandhinagar Gujarat - 382355 India
| | - Gourav Bothra
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A) Opposite Airforce Station, Palaj Gandhinagar Gujarat - 382355 India
| | - Priyanka Patel Vatsa
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A) Opposite Airforce Station, Palaj Gandhinagar Gujarat - 382355 India
| | - Venkatesh Muthukumar
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A) Opposite Airforce Station, Palaj Gandhinagar Gujarat - 382355 India
| | - Bombothu Kavya Sai Bhuvana
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A) Opposite Airforce Station, Palaj Gandhinagar Gujarat - 382355 India
| | - Saumya Kapoor
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A) Opposite Airforce Station, Palaj Gandhinagar Gujarat - 382355 India
| | - Deepshika Moola
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A) Opposite Airforce Station, Palaj Gandhinagar Gujarat - 382355 India
| | - Moumita Ghosh Chowdhury
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A) Opposite Airforce Station, Palaj Gandhinagar Gujarat - 382355 India
| | - Amit Mandoli
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A) Opposite Airforce Station, Palaj Gandhinagar Gujarat - 382355 India
| | - Amit Shard
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A) Opposite Airforce Station, Palaj Gandhinagar Gujarat - 382355 India
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7
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Choi KM, Kim SJ, Ji MJ, Kim E, Kim JS, Park HM, Kim JY. Activity-based protein profiling and global proteome analysis reveal MASTL as a potential therapeutic target in gastric cancer. Cell Commun Signal 2024; 22:397. [PMID: 39138495 PMCID: PMC11323684 DOI: 10.1186/s12964-024-01783-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 08/08/2024] [Indexed: 08/15/2024] Open
Abstract
BACKGROUND Gastric cancer (GC) is a prevalent malignancy with limited therapeutic options for advanced stages. This study aimed to identify novel therapeutic targets for GC by profiling HSP90 client kinases. METHODS We used mass spectrometry-based activity-based protein profiling (ABPP) with a desthiobiotin-ATP probe, combined with sensitivity analysis of HSP90 inhibitors, to profile kinases in a panel of GC cell lines. We identified kinases regulated by HSP90 in inhibitor-sensitive cells and investigated the impact of MASTL knockdown on GC cell behavior. Global proteomic analysis following MASTL knockdown was performed, and bioinformatics tools were used to analyze the resulting data. RESULTS Four kinases-MASTL, STK11, CHEK1, and MET-were identified as HSP90-regulated in HSP90 inhibitor-sensitive cells. Among these, microtubule-associated serine/threonine kinase-like (MASTL) was upregulated in GC and associated with poor prognosis. MASTL knockdown decreased migration, invasion, and proliferation of GC cells. Global proteomic profiling following MASTL knockdown revealed NEDD4-1 as a potential downstream mediator of MASTL in GC progression. NEDD4-1 was also upregulated in GC and associated with poor prognosis. Similar to MASTL inhibition, NEDD4-1 knockdown suppressed migration, invasion, and proliferation of GC cells. CONCLUSIONS Our multi-proteomic analyses suggest that targeting MASTL could be a promising therapy for advanced gastric cancer, potentially through the reduction of tumor-promoting proteins including NEDD4-1. This study enhances our understanding of kinase signaling pathways in GC and provides new insights for potential treatment strategies.
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Affiliation(s)
- Kyoung-Min Choi
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Sung-Jin Kim
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Mi-Jung Ji
- Advanced Analysis and Data Center, Korea Institute of Science and Technology (KIST), Seoul, 02456, Republic of Korea
| | - Eunjung Kim
- Natural Product Informatics Center, Korea Institute of Science and Technology (KIST), Gangneung, 25451, Republic of Korea
| | - Jae-Sung Kim
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul, 01812, Republic of Korea
| | - Hyun-Mee Park
- Advanced Analysis and Data Center, Korea Institute of Science and Technology (KIST), Seoul, 02456, Republic of Korea
| | - Jae-Young Kim
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea.
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Whittaker MK, Bendzunas GN, Shirani M, LeClair TJ, Shebl B, Dill TC, Coffino P, Simon SM, Kennedy EJ. Targeted Degradation of Protein Kinase A via a Stapled Peptide PROTAC. ACS Chem Biol 2024. [PMID: 39137166 DOI: 10.1021/acschembio.4c00237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Proteolysis-targeting chimeras (PROTACs) are bifunctional molecules that bind and recruit an E3 ubiquitin ligase to a targeted protein of interest, often through the utilization of a small molecule inhibitor. To expand the possible range of kinase targets that can be degraded by PROTACs, we sought to develop a PROTAC utilizing a hydrocarbon-stapled peptide as the targeting agent to bind the surface of a target protein of interest. In this study, we describe the development of a proteolysis-targeting chimera, dubbed Stapled Inhibitor Peptide - PROTAC or StIP-TAC, linking a hydrocarbon-stapled peptide with an E3 ligase ligand for targeted degradation of Protein Kinase A (PKA). This StIP-TAC molecule stimulated E3-mediated protein degradation of PKA, and this effect could be reversed by the addition of the proteasomal inhibitor MG-132. Further, StIP-TAC treatment led to a significant reduction in PKA substrate phosphorylation. Since many protein targets of interest lack structural features that make them amenable to small molecule targeting, development of StIP-TACs may broaden the potential range of protein targets using a PROTAC-mediated proteasomal degradation approach.
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Affiliation(s)
- Matthew K Whittaker
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
| | - George N Bendzunas
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
| | - Mahsa Shirani
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York 10065, United States
| | - Timothy J LeClair
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
| | - Bassem Shebl
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York 10065, United States
| | - Taylor C Dill
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
| | - Philip Coffino
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York 10065, United States
| | - Sanford M Simon
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York 10065, United States
| | - Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
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Joglekar T, Chin A, Voskanian-Kordi A, Baek S, Raja A, Rege A, Huang W, Kane M, Laiho M, Webb TR, Fan X, Rubenstein M, Bieberich CJ, Li X. Deep PIM kinase substrate profiling reveals new rational cotherapeutic strategies for acute myeloid leukemia. Blood Adv 2024; 8:3880-3892. [PMID: 38739710 PMCID: PMC11321302 DOI: 10.1182/bloodadvances.2022008144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 03/05/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
ABSTRACT Provirus integration site for Moloney murine leukemia virus (PIM) family serine/threonine kinases perform protumorigenic functions in hematologic malignancies and solid tumors by phosphorylating substrates involved in tumor metabolism, cell survival, metastasis, inflammation, and immune cell invasion. However, a comprehensive understanding of PIM kinase functions is currently lacking. Multiple small-molecule PIM kinase inhibitors are currently being evaluated as cotherapeutics in patients with cancer. To further illuminate PIM kinase functions in cancer, we deeply profiled PIM1 substrates using the reverse in-gel kinase assay to identify downstream cellular processes targetable with small molecules. Pathway analyses of putative PIM substrates nominated RNA splicing and ribosomal RNA (rRNA) processing as PIM-regulated cellular processes. PIM inhibition elicited reproducible splicing changes in PIM-inhibitor-responsive acute myeloid leukemia (AML) cell lines. PIM inhibitors synergized with splicing modulators targeting splicing factor 3b subunit 1 (SF3B1) and serine-arginine protein kinase 1 (SRPK1) to kill AML cells. PIM inhibition also altered rRNA processing, and PIM inhibitors synergized with an RNA polymerase I inhibitor to kill AML cells and block AML tumor growth. These data demonstrate that deep kinase substrate knowledge can illuminate unappreciated kinase functions, nominating synergistic cotherapeutic strategies. This approach may expand the cotherapeutic armamentarium to overcome kinase inhibitor-resistant disease that limits durable responses in malignant disease.
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Affiliation(s)
- Tejashree Joglekar
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD
| | - Alexander Chin
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD
| | - Alin Voskanian-Kordi
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD
| | - Seungchul Baek
- Department of Mathematics and Statistics, University of Maryland, Baltimore County, Baltimore, MD
| | - Azim Raja
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD
| | - Apurv Rege
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD
| | - Weiliang Huang
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Baltimore, MD
| | - Maureen Kane
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Baltimore, MD
| | - Marikki Laiho
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Xiaoxuan Fan
- Department of Microbiology and Immunology, University of Maryland Baltimore School of Medicine, Baltimore, MD
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD
| | - Michael Rubenstein
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD
| | - Charles J. Bieberich
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD
- Department of Microbiology and Immunology, University of Maryland Baltimore School of Medicine, Baltimore, MD
| | - Xiang Li
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD
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10
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Joshi DC, Sharma A, Prasad S, Singh K, Kumar M, Sherawat K, Tuli HS, Gupta M. Novel therapeutic agents in clinical trials: emerging approaches in cancer therapy. Discov Oncol 2024; 15:342. [PMID: 39127974 PMCID: PMC11317456 DOI: 10.1007/s12672-024-01195-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
Novel therapeutic agents in clinical trials offer a paradigm shift in the approach to battling this prevalent and destructive disease, and the area of cancer therapy is on the precipice of a trans formative revolution. Despite the importance of tried-and-true cancer treatments like surgery, radiation, and chemotherapy, the disease continues to evolve and adapt, making new, more potent methods necessary. The field of cancer therapy is currently witnessing the emergence of a wide range of innovative approaches. Immunotherapy, including checkpoint inhibitors, CAR-T cell treatment, and cancer vaccines, utilizes the host's immune system to selectively target and eradicate malignant cells while minimizing harm to normal tissue. The development of targeted medicines like kinase inhibitors and monoclonal antibodies has allowed for more targeted and less harmful approaches to treating cancer. With the help of genomics and molecular profiling, "precision medicine" customizes therapies to each patient's unique genetic makeup to maximize therapeutic efficacy while minimizing unwanted side effects. Epigenetic therapies, metabolic interventions, radio-pharmaceuticals, and an increasing emphasis on combination therapy with synergistic effects further broaden the therapeutic landscape. Multiple-stage clinical trials are essential for determining the safety and efficacy of these novel drugs, allowing patients to gain access to novel treatments while also furthering scientific understanding. The future of cancer therapy is rife with promise, as the integration of artificial intelligence and big data has the potential to revolutionize early detection and prevention. Collaboration among researchers, and healthcare providers, and the active involvement of patients remain the bedrock of the ongoing battle against cancer. In conclusion, the dynamic and evolving landscape of cancer therapy provides hope for improved treatment outcomes, emphasizing a patient-centered, data-driven, and ethically grounded approach as we collectively strive towards a cancer-free world.
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Affiliation(s)
- Deepak Chandra Joshi
- Department of Pharmacy, School of Chemical Sciences and Pharmacy, Central University of Rajasthan, Bandar Sindri, Dist., Ajmer, Rajasthan, India.
| | - Anurag Sharma
- Invertis Institute of Pharmacy, Invertis University Bareilly Uttar Pradesh, Bareilly, India
| | - Sonima Prasad
- Chandigarh University, Ludhiana-Chandigarh State Highway, Gharuan, Mohali, Punjab, 140413, India
| | - Karishma Singh
- Institute of Pharmaceutical Sciences, Faculty of Engineering and Technology, University of Lucknow, Lucknow, India
| | - Mayank Kumar
- Himalayan Institute of Pharmacy, Road, Near Suketi Fossil Park, Kala Amb, Hamidpur, Himachal Pradesh, India
| | - Kajal Sherawat
- Meerut Institute of Technology, Meerut, Uttar Pradesh, India
| | - Hardeep Singh Tuli
- Department of Bio-Sciences & Technology, Maharishi Markandeshwar Engineering College, Maharishi Markandeshwar (Deemed to Be University), Mullana, Ambala, India
| | - Madhu Gupta
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, New Delhi, India.
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Verma J, Vashisth H. Molecular basis for differential recognition of an allosteric inhibitor by receptor tyrosine kinases. Proteins 2024; 92:905-922. [PMID: 38506327 PMCID: PMC11222054 DOI: 10.1002/prot.26685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/08/2024] [Accepted: 03/06/2024] [Indexed: 03/21/2024]
Abstract
Understanding kinase-inhibitor selectivity continues to be a major objective in kinase drug discovery. We probe the molecular basis of selectivity of an allosteric inhibitor (MSC1609119A-1) of the insulin-like growth factor-I receptor kinase (IGF1RK), which has been shown to be ineffective for the homologous insulin receptor kinase (IRK). Specifically, we investigated the structural and energetic basis of the allosteric binding of this inhibitor to each kinase by combining molecular modeling, molecular dynamics (MD) simulations, and thermodynamic calculations. We predict the inhibitor conformation in the binding pocket of IRK and highlight that the charged residues in the histidine-arginine-aspartic acid (HRD) and aspartic acid-phenylalanine-glycine (DFG) motifs and the nonpolar residues in the binding pocket govern inhibitor interactions in the allosteric pocket of each kinase. We suggest that the conformational changes in the IGF1RK residues M1054 and M1079, movement of the ⍺C-helix, and the conformational stabilization of the DFG motif favor the selectivity of the inhibitor toward IGF1RK. Our thermodynamic calculations reveal that the observed selectivity can be rationalized through differences observed in the electrostatic interaction energy of the inhibitor in each inhibitor/kinase complex and the hydrogen bonding interactions of the inhibitor with the residue V1063 in IGF1RK that are not attained with the corresponding residue V1060 in IRK. Overall, our study provides a rationale for the molecular basis of recognition of this allosteric inhibitor by IGF1RK and IRK, which is potentially useful in developing novel inhibitors with improved affinity and selectivity.
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Affiliation(s)
- Jyoti Verma
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, NH 03824
| | - Harish Vashisth
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, NH 03824
- Department of Chemistry, University of New Hampshire, Durham, NH 03824
- Integrated Applied Mathematics Program, University of New Hampshire, Durham, NH 03824
- Molecular and Cellular Biotechnology Program, University of New Hampshire, Durham, NH 03824
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12
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Kugler V, Schwaighofer S, Feichtner A, Enzler F, Fleischmann J, Strich S, Schwarz S, Wilson R, Tschaikner P, Troppmair J, Sexl V, Meier P, Kaserer T, Stefan E. Impact of protein and small molecule interactions on kinase conformations. eLife 2024; 13:RP94755. [PMID: 39088265 PMCID: PMC11293870 DOI: 10.7554/elife.94755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024] Open
Abstract
Protein kinases act as central molecular switches in the control of cellular functions. Alterations in the regulation and function of protein kinases may provoke diseases including cancer. In this study we investigate the conformational states of such disease-associated kinases using the high sensitivity of the kinase conformation (KinCon) reporter system. We first track BRAF kinase activity conformational changes upon melanoma drug binding. Second, we also use the KinCon reporter technology to examine the impact of regulatory protein interactions on LKB1 kinase tumor suppressor functions. Third, we explore the conformational dynamics of RIP kinases in response to TNF pathway activation and small molecule interactions. Finally, we show that CDK4/6 interactions with regulatory proteins alter conformations which remain unaffected in the presence of clinically applied inhibitors. Apart from its predictive value, the KinCon technology helps to identify cellular factors that impact drug efficacies. The understanding of the structural dynamics of full-length protein kinases when interacting with small molecule inhibitors or regulatory proteins is crucial for designing more effective therapeutic strategies.
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Affiliation(s)
- Valentina Kugler
- Institute for Molecular Biology and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckInnsbruckAustria
- Tyrolean Cancer Research Institute (TKFI)InnsbruckAustria
| | - Selina Schwaighofer
- Institute for Molecular Biology and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckInnsbruckAustria
- Tyrolean Cancer Research Institute (TKFI)InnsbruckAustria
| | - Andreas Feichtner
- Institute for Molecular Biology and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckInnsbruckAustria
- Tyrolean Cancer Research Institute (TKFI)InnsbruckAustria
| | - Florian Enzler
- Daniel Swarovski Research Laboratory, Department of Visceral, Transplant and Thoracic Surgery, Medical University of InnsbruckInnsbruckAustria
| | - Jakob Fleischmann
- Institute for Molecular Biology and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckInnsbruckAustria
- Tyrolean Cancer Research Institute (TKFI)InnsbruckAustria
| | - Sophie Strich
- Institute for Molecular Biology and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckInnsbruckAustria
- Tyrolean Cancer Research Institute (TKFI)InnsbruckAustria
| | - Sarah Schwarz
- Tyrolean Cancer Research Institute (TKFI)InnsbruckAustria
| | - Rebecca Wilson
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer ResearchLondonUnited Kingdom
| | - Philipp Tschaikner
- Tyrolean Cancer Research Institute (TKFI)InnsbruckAustria
- KinCon biolabs GmbHInnsbruckAustria
| | - Jakob Troppmair
- Daniel Swarovski Research Laboratory, Department of Visceral, Transplant and Thoracic Surgery, Medical University of InnsbruckInnsbruckAustria
| | | | - Pascal Meier
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer ResearchLondonUnited Kingdom
| | - Teresa Kaserer
- Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckInnsbruckAustria
| | - Eduard Stefan
- Institute for Molecular Biology and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckInnsbruckAustria
- Tyrolean Cancer Research Institute (TKFI)InnsbruckAustria
- KinCon biolabs GmbHInnsbruckAustria
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13
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Choi S, Seo S, Kim BJ, Park C, Park S. PIDiff: Physics informed diffusion model for protein pocket-specific 3D molecular generation. Comput Biol Med 2024; 180:108865. [PMID: 39067153 DOI: 10.1016/j.compbiomed.2024.108865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 07/02/2024] [Accepted: 07/07/2024] [Indexed: 07/30/2024]
Abstract
Designing drugs capable of binding to the structure of target proteins for treating diseases is essential in drug development. Recent remarkable advancements in geometric deep learning have led to unprecedented progress in three-dimensional (3D) generation of ligands that can bind to the protein pocket. However, most existing methods primarily focus on modeling the geometric information of ligands in 3D space. Consequently, these methods fail to consider that the binding of proteins and ligands is a phenomenon driven by intrinsic physicochemical principles. Motivated by this understanding, we propose PIDiff, a model for generating molecules by accounting in the physicochemical principles of protein-ligand binding. Our model learns not only the structural information of proteins and ligands but also to minimize the binding free energy between them. To evaluate the proposed model, we introduce an experimental framework that surpasses traditional assessment methods by encompassing various essential aspects for the practical application of generative models to actual drug development. The results confirm that our model outperforms baseline models on the CrossDocked2020 benchmark dataset, demonstrating its superiority. Through diverse experiments, we have illustrated the promising potential of the proposed model in practical drug development.
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Affiliation(s)
- Seungyeon Choi
- Department of Computer Science, Yonsei University, Seoul, 03722, Republic of Korea
| | - Sangmin Seo
- Department of Computer Science, Yonsei University, Seoul, 03722, Republic of Korea
| | - Byung Ju Kim
- UBLBio Corporation, Suwon, 16679, Republic of Korea
| | - Chihyun Park
- Department of Computer Science and Engineering, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Sanghyun Park
- Department of Computer Science, Yonsei University, Seoul, 03722, Republic of Korea.
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14
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Abdel-Mohsen HT, Syam YM, Abd El-Ghany MS, Abd El-Karim SS. Benzimidazole-oxindole hybrids: A novel class of selective dual CDK2 and GSK-3β inhibitors of potent anticancer activity. Arch Pharm (Weinheim) 2024:e2300721. [PMID: 39041665 DOI: 10.1002/ardp.202300721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 06/25/2024] [Accepted: 07/01/2024] [Indexed: 07/24/2024]
Abstract
A new series of benzimidazole-oxindole hybrids 8a-x was discovered as dual cyclin-dependent kinase (CDK2) and glycogen synthase kinase-3-beta (GSK-3β) inhibitors with potent anticancer activity. The synthesized hits displayed potent anticancer activity against national cancer institute cancer cell lines in single-dose and five-dose assays. Moreover, the derivatives 8k, 8l, 8n, 8o, and 8p demonstrated potent cytotoxic activity against PANC-1 cells with IC50 = 1.88-2.79 µM. In addition, the hybrids 8l, 8n, 8o, and 8p displayed potent antiproliferative activity on the MG-63 cell line (IC50 = 0.99-1.90 µM). Concurrently, the benzimidazole-oxindole hybrid 8v exhibited potent dual CDK2/GSK-3β inhibitory activity with IC50 values of 0.04 and 0.021 µM, respectively. In addition, 8v displayed more than 10-fold higher selectivity toward CDK2 and GSK-3 β over CDK1, CDK5, GSK-3α, vascular endothelial growth factor receptor-2, and B-rapidly accelerated fibrosarcoma. Screening of the effect of 8n and 8v on the cell cycle and apoptosis of PANC-1 and MG-63 cells displayed their ability to arrest their cell cycle at the G2-M phase and to potentiate the apoptosis of both cell lines. In silico docking of the benzimidazole-oxindole hybrid 8v into the catalytic pocket of both CDK2 and GSK-3β revealed its perfect fitting through the formation of hydrogen bonding and hydrophobic interactions with the key amino acids in the binding sites. In addition, in silico absorption, distribution, metabolism, excretion studies proved that 8a-x exhibit satisfactory drug-likeness properties for drug development.
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Affiliation(s)
- Heba T Abdel-Mohsen
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Cairo, Egypt
| | - Yasmin M Syam
- Department of Therapeutic Chemistry, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Cairo, Egypt
| | | | - Somaia S Abd El-Karim
- Department of Therapeutic Chemistry, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Cairo, Egypt
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15
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Frey Y, Lungu C, Meyer F, Hauth F, Hahn D, Kersten C, Heller V, Franz-Wachtel M, Macek B, Barsukov I, Olayioye MA. Regulation of the DLC3 tumor suppressor by a novel phosphoswitch. iScience 2024; 27:110203. [PMID: 39021807 PMCID: PMC11253157 DOI: 10.1016/j.isci.2024.110203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 03/04/2024] [Accepted: 06/04/2024] [Indexed: 07/20/2024] Open
Abstract
Deleted in liver cancer 3 (DLC3) is a Rho GTPase-activating protein (RhoGAP) that plays a crucial role in maintaining adherens junction integrity and coordinating polarized vesicle transport by modulating Rho activity at the plasma membrane and endomembranes. By employing bioinformatical sequence analysis, in vitro experiments, and in cellulo assays we here identified a polybasic region (PBR) in DLC3 that facilitates the association of the protein with cellular membranes. Within the PBR, we mapped two serines whose phosphorylation can alter the electrostatic character of the region. Consequently, phosphomimetic mutations of these sites impaired the membrane association of DLC3. Furthermore, we found a new PBR-dependent localization of DLC3 at the midbody region, where the protein locally controlled Rho activity. Here, the phosphorylation-dependent regulation of DLC3 appeared to be required for proper cytokinesis. Our work thus provides a novel mechanism for spatiotemporal termination of Rho signaling by the RhoGAP protein DLC3.
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Affiliation(s)
- Yannick Frey
- University of Stuttgart, Institute of Cell Biology and Immunology, Stuttgart, Germany
| | - Cristiana Lungu
- University of Stuttgart, Institute of Cell Biology and Immunology, Stuttgart, Germany
- University of Stuttgart, Stuttgart Research Center Systems Biology, Stuttgart, Germany
| | - Florian Meyer
- University of Stuttgart, Institute of Cell Biology and Immunology, Stuttgart, Germany
| | - Franziskus Hauth
- University of Liverpool, Institute of Systems, Molecular and Integrative Biology, Department of Biochemistry, Cell and Systems Biology, Liverpool, UK
| | - Daniel Hahn
- University of Stuttgart, Institute of Cell Biology and Immunology, Stuttgart, Germany
| | - Corinna Kersten
- University of Stuttgart, Institute of Cell Biology and Immunology, Stuttgart, Germany
| | - Vivien Heller
- University of Stuttgart, Institute of Cell Biology and Immunology, Stuttgart, Germany
| | | | - Boris Macek
- Proteome Center Tübingen, University of Tübingen, Tübingen, Germany
| | - Igor Barsukov
- University of Liverpool, Institute of Systems, Molecular and Integrative Biology, Department of Biochemistry, Cell and Systems Biology, Liverpool, UK
| | - Monilola A. Olayioye
- University of Stuttgart, Institute of Cell Biology and Immunology, Stuttgart, Germany
- University of Stuttgart, Stuttgart Research Center Systems Biology, Stuttgart, Germany
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16
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Abdel-Aziz AAM, El-Azab AS, Brogi S, Ayyad RR, Alkahtani HM, Abuelizz HA, Al-Suwaidan IA, Al-Obaid AM. Synthesis, enzyme inhibition assay, and molecular modeling study of novel pyrazolines linked to 4-methylsulfonylphenyl scaffold: antitumor activity and cell cycle analysis. RSC Adv 2024; 14:22132-22146. [PMID: 39005246 PMCID: PMC11240878 DOI: 10.1039/d4ra03902e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 06/20/2024] [Indexed: 07/16/2024] Open
Abstract
Antitumor activity using 59 cancer cell lines and enzyme inhibitory activity of a newly synthesized pyrazoline-linked 4-methylsulfonylphenyl scaffold (compounds 18a-q) were measured and compared with those of standard drugs. Pyrazolines 18b, 18c, 18f, 18g, 18h, and 18n possessed significant antitumor activity, with a positive cytotoxic effect (PCE) of 22/59, 21/59, 21/59, 48/59, 51/59, and 20/59, respectively. The cancer cell lines HL60, MCF-7, and MDA-MB-231 were used to measure the IC50 values of derivatives 18c, 18g, and 18hvia the MTT assay method, and the results were compared with those of reference drugs. Derivatives 18g and 18h showed potent and broad-spectrum antitumor activities against HL60 (IC50 of 10.43, 8.99 μM, respectively), MCF-7 (IC50 of 11.7 and 12.4 μM, respectively), and MDA-MB-231 (IC50 of 4.07 and 7.18 μM, respectively). Compound 18c exhibited strong antitumor activity against HL60 and MDA-MB-231 cell lines with IC50 values of 8.43 and 12.54 μM, respectively, and moderate antitumor activity against MCF-7 cell lines with an IC50 value of 16.20 μM. Compounds 18c, 18g, and 18h remarkably inhibited VEGFR2 kinase (IC50 = 0.218, 0.168, and 0.135 μM, respectively) compared with the reference drug sorafenib (IC50 = 0.041 μM). Compounds 18g and 18h effectively inhibited HER2 kinase (IC50 = 0.496 and 0.253 μM, respectively) compared with erlotinib (IC50 = 0.085 μM). Compound 18h inhibited EGFR kinase (IC50 = 0.574 μM) with a potency comparable with that of the reference drug erlotinib (IC50 = 0.105 μM). Pyrazolines 18c, 18f, and 18h arrested the S/G2 phase of the cell cycle in HL-60 cells. In addition, derivatives 18c, 18f, and 18h revealed lower Bcl-2 protein expression anti-apoptotic levels and higher Bax, caspase-3, and caspase-9 expression levels. Molecular docking studies of derivative 18h into the binding sites of EGFR, HER2, and VEGFR2 kinases explored the interaction mode of these pyrazoline derivatives and their structural requirements for antitumor activity.
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Affiliation(s)
- Alaa A-M Abdel-Aziz
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P. O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Adel S El-Azab
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P. O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Simone Brogi
- Department of Pharmacy, University of Pisa Via Bonanno 6 56126 Pisa Italy
| | - Rezk R Ayyad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-AzharUniversity Cairo Egypt
| | - Hamad M Alkahtani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P. O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Hatem A Abuelizz
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P. O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Ibrahim A Al-Suwaidan
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P. O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Abdulrahman M Al-Obaid
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P. O. Box 2457 Riyadh 11451 Saudi Arabia
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17
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Li J, Zhan X. Mass spectrometry analysis of phosphotyrosine-containing proteins. MASS SPECTROMETRY REVIEWS 2024; 43:857-887. [PMID: 36789499 DOI: 10.1002/mas.21836] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 12/19/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Tyrosine phosphorylation is a crucial posttranslational modification that is involved in various aspects of cell biology and often has functions in cancers. It is necessary not only to identify the specific phosphorylation sites but also to quantify their phosphorylation levels under specific pathophysiological conditions. Because of its high sensitivity and accuracy, mass spectrometry (MS) has been widely used to identify endogenous and synthetic phosphotyrosine proteins/peptides across a range of biological systems. However, phosphotyrosine-containing proteins occur in extremely low abundance and they degrade easily, severely challenging the application of MS. This review highlights the advances in both quantitative analysis procedures and enrichment approaches to tyrosine phosphorylation before MS analysis and reviews the differences among phosphorylation, sulfation, and nitration of tyrosine residues in proteins. In-depth insights into tyrosine phosphorylation in a wide variety of biological systems will offer a deep understanding of how signal transduction regulates cellular physiology and the development of tyrosine phosphorylation-related drugs as cancer therapeutics.
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Affiliation(s)
- Jiajia Li
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, Jinan, People's Republic of China
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Central South University, Changsha, Hunan, People's Republic of China
| | - Xianquan Zhan
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, Jinan, People's Republic of China
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18
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Jeyaprakash K, Kumaran M, Kim U, Santhi R, Muthukkaruppan V, Devarajan B, Vanniarajan A. Investigating druggable kinases for targeted therapy in retinoblastoma. J Hum Genet 2024:10.1038/s10038-024-01267-0. [PMID: 38956221 DOI: 10.1038/s10038-024-01267-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 04/04/2024] [Accepted: 06/14/2024] [Indexed: 07/04/2024]
Abstract
Retinoblastoma (RB) is a childhood retinal neoplasm and commonly treated with cytotoxic chemotherapeutic agents. However, these therapeutic approaches often lead to diverse adverse effects. A precise molecular therapy will alleviate these side effects and offer better treatment outcomes. Over the years, kinases have become potential drug targets in cancer therapy. Hence, we aimed to investigate genetic alterations of putative kinase drug targets in RB. Targeted exome sequencing was performed on 35 RB tumors with paired blood samples using a gene panel consisting of 29 FDA-approved kinase genes. Single nucleotide variants were analyzed for pathogenicity using an in-house pipeline and copy number variations (CNVs) were detected by a depth of coverage and CNVPanelizer. The correlation between genetic changes and clinicopathological features was assessed using GraphPad Prism. Three somatic mutations, two in ERBB4 and one in EGFR were identified. Two of these mutations (ERBB4 c.C3836A & EGFR c.A1196T) were not reported earlier. CNV analysis revealed recurrent gains of ALK, MAP2K2, SRC, STK11, and FGFR3 as well as frequent losses of ATM, PI3KCA and ERBB4. Notably, nonresponsive tumors had a higher incidence of amplifications in clinically actionable genes such as ALK. Moreover, ALK gain and ATM loss were strongly correlated with optic nerve head invasion. In conclusion, our study revealed genetic alterations of druggable kinases in RB, providing preliminary insights for the exploration of kinase-targeted therapy in RB.
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Affiliation(s)
- Kumar Jeyaprakash
- Department of Molecular Genetics, Aravind Medical Research Foundation, Madurai, India
- Department of Molecular Biology, Aravind Medical Research Foundation, Affiliated to Alagappa University, Karaikudi, Tamil Nadu, India
| | - Manojkumar Kumaran
- Department of Bioinformatics, Aravind Medical Research Foundation, Madurai, India
| | - Usha Kim
- Department of Orbit, Oculoplasty and Oncology, Aravind Eye Hospital, Madurai, India
| | | | | | | | - Ayyasamy Vanniarajan
- Department of Molecular Genetics, Aravind Medical Research Foundation, Madurai, India.
- Department of Molecular Biology, Aravind Medical Research Foundation, Affiliated to Alagappa University, Karaikudi, Tamil Nadu, India.
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19
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Herrington NB, Li YC, Stein D, Pandey G, Schlessinger A. A comprehensive exploration of the druggable conformational space of protein kinases using AI-predicted structures. PLoS Comput Biol 2024; 20:e1012302. [PMID: 39046952 PMCID: PMC11268620 DOI: 10.1371/journal.pcbi.1012302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 07/09/2024] [Indexed: 07/27/2024] Open
Abstract
Protein kinase function and interactions with drugs are controlled in part by the movement of the DFG and ɑC-Helix motifs that are related to the catalytic activity of the kinase. Small molecule ligands elicit therapeutic effects with distinct selectivity profiles and residence times that often depend on the active or inactive kinase conformation(s) they bind. Modern AI-based structural modeling methods have the potential to expand upon the limited availability of experimentally determined kinase structures in inactive states. Here, we first explored the conformational space of kinases in the PDB and models generated by AlphaFold2 (AF2) and ESMFold, two prominent AI-based protein structure prediction methods. Our investigation of AF2's ability to explore the conformational diversity of the kinome at various multiple sequence alignment (MSA) depths showed a bias within the predicted structures of kinases in DFG-in conformations, particularly those controlled by the DFG motif, based on their overabundance in the PDB. We demonstrate that predicting kinase structures using AF2 at lower MSA depths explored these alternative conformations more extensively, including identifying previously unobserved conformations for 398 kinases. Ligand enrichment analyses for 23 kinases showed that, on average, docked models distinguished between active molecules and decoys better than random (average AUC (avgAUC) of 64.58), but select models perform well (e.g., avgAUCs for PTK2 and JAK2 were 79.28 and 80.16, respectively). Further analysis explained the ligand enrichment discrepancy between low- and high-performing kinase models as binding site occlusions that would preclude docking. The overall results of our analyses suggested that, although AF2 explored previously uncharted regions of the kinase conformational space and select models exhibited enrichment scores suitable for rational drug discovery, rigorous refinement of AF2 models is likely still necessary for drug discovery campaigns.
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Affiliation(s)
- Noah B. Herrington
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Yan Chak Li
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - David Stein
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Gaurav Pandey
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
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20
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Zhang N, Wu J, Zheng Q. Chemical proteomics approaches for protein post-translational modification studies. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141017. [PMID: 38641087 DOI: 10.1016/j.bbapap.2024.141017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/05/2024] [Accepted: 04/14/2024] [Indexed: 04/21/2024]
Abstract
The diversity and dynamics of proteins play essential roles in maintaining the basic constructions and functions of cells. The abundance of functional proteins is regulated by the transcription and translation processes, while the alternative splicing enables the same gene to generate distinct protein isoforms of different lengths. Beyond the transcriptional and translational regulations, post-translational modifications (PTMs) are able to further expand the diversity and functional scope of proteins. PTMs have been shown to make significant changes in the surface charges, structures, activation states, and interactome of proteins. Due to the functional complexity, highly dynamic nature, and low presence percentage, the study of protein PTMs remains challenging. Here we summarize and discuss the major chemical biology tools and chemical proteomics approaches to enrich and investigate the protein PTM of interest.
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Affiliation(s)
- Nan Zhang
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH 43210, United States; Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, United States
| | - Jinghua Wu
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH 43210, United States; Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, United States
| | - Qingfei Zheng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH 43210, United States; Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, United States; Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH 43210, United States.
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21
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Fuster-Martínez I, Calatayud S. The current landscape of antifibrotic therapy across different organs: A systematic approach. Pharmacol Res 2024; 205:107245. [PMID: 38821150 DOI: 10.1016/j.phrs.2024.107245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
Fibrosis is a common pathological process that can affect virtually all the organs, but there are hardly any effective therapeutic options. This has led to an intense search for antifibrotic therapies over the last decades, with a great number of clinical assays currently underway. We have systematically reviewed all current and recently finished clinical trials involved in the development of new antifibrotic drugs, and the preclinical studies analyzing the relevance of each of these pharmacological strategies in fibrotic processes affecting tissues beyond those being clinically studied. We analyze and discuss this information with the aim of determining the most promising options and the feasibility of extending their therapeutic value as antifibrotic agents to other fibrotic conditions.
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Affiliation(s)
- Isabel Fuster-Martínez
- Departamento de Farmacología, Universitat de València, Valencia 46010, Spain; FISABIO (Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana), Valencia 46020, Spain.
| | - Sara Calatayud
- Departamento de Farmacología, Universitat de València, Valencia 46010, Spain; CIBERehd (Centro de Investigación Biomédica en Red - Enfermedades Hepáticas y Digestivas), Spain.
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22
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Park M, Kim JW. Updates on the mechanisms of toxicities associated with monoclonal antibodies targeting growth factor signaling and immune cells in cancer. Toxicol Res 2024; 40:335-348. [PMID: 38911540 PMCID: PMC11187026 DOI: 10.1007/s43188-024-00233-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 06/25/2024] Open
Abstract
Monoclonal antibody (mAb)-based immunotherapy currently is considered to be an optimal therapeutic approach to cancer treatment, either in combination with surgery, radiation, and/or chemotherapy or alone. Various solid tumors and hematological malignancies have been characterized by distinct molecular targets, which could be utilized as innovative anticancer agents. Notably, receptor tyrosine kinases, including HER2, EGFR, VEGFR, and PDGFR, which act as receptors for growth factors, serve as crucial target proteins, expanding their role in the cancer therapeutic market. In contrast to conventional anticancer agents that directly target cancer cells, the advent of immunotherapy introduces novel approaches, such as immune checkpoint blockers (ICBs) and mAbs targeting surface antigens on immune cells in hematological malignancies and lymphomas. While these immunotherapies have mitigated the acquired resistance observed in traditional targeted therapies, they also exhibit diverse toxicities. Herein, this review focuses on describing the well-established toxicities and newly proposed mechanisms of monoclonal antibody toxicity in recent studies. Understanding these molecular mechanisms is indispensable to overcoming the limitations of mAbs-based therapies, facilitating the development of innovative anticancer agents, and uncovering novel indications for cancer treatment in the future.
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Affiliation(s)
- Miso Park
- College of Pharmacy, Kangwon National University, Chuncheon, Gangwon-do Republic of Korea
| | - Ji Won Kim
- Jeju Research Institute of Pharmaceutical Sciences, College of Pharmacy, Jeju National University, Jeju-do, Republic of Korea
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23
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Wang X, DeFilippis RA, Yan W, Shah NP, Li HY. Overcoming Secondary Mutations of Type II Kinase Inhibitors. J Med Chem 2024; 67:9776-9788. [PMID: 38837951 DOI: 10.1021/acs.jmedchem.3c01629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Type II kinase inhibitors bind in the "DFG-out" kinase conformation and are generally considered to be more potent and selective than type I inhibitors, which target a DFG-in conformation. Nine type II inhibitors are currently clinically approved, with more undergoing clinical development. Resistance-conferring secondary mutations emerged with the first series of type II inhibitors, most commonly at residues within the kinase activation loop and at the "gatekeeper" position. Recently, new inhibitors have been developed to overcome such mutations; however, mutations activating other pathways (and/or other targets) have subsequently emerged on occasion. Here, we systematically summarize the secondary mutations that confer resistance to type II inhibitors, the structural basis for resistance, newer inhibitors designed to overcome resistance, as well as the challenges and opportunities for the development of new inhibitors to overcome secondary kinase domain mutations.
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Affiliation(s)
- Xiuqi Wang
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Rosa Anna DeFilippis
- Division of Hematology/Oncology, University of California, San Francisco, California 94143, United States
| | - Wei Yan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
- Department of Pharmacology, School of Medicine, The University of Texas Health San Antonio, San Antonio, Texas 78229, United States
| | - Neil P Shah
- Division of Hematology/Oncology, University of California, San Francisco, California 94143, United States
| | - Hong-Yu Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
- Department of Pharmacology, School of Medicine, The University of Texas Health San Antonio, San Antonio, Texas 78229, United States
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24
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Mangla B, Mittal P, Kumar P, Aggarwal G. Multifaceted role of erlotinib in various cancer: nanotechnology intervention, patent landscape, and advancements in clinical trials. Med Oncol 2024; 41:173. [PMID: 38864966 DOI: 10.1007/s12032-024-02414-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 05/23/2024] [Indexed: 06/13/2024]
Abstract
Erlotinib (ELB) is a tyrosine kinase inhibitor that targets the activity of Epidermal Growth Factor Receptor (EGFR) protein found in both healthy and cancerous cells. It binds reversibly to the ATP-binding site of the EGFR tyrosine kinase. ELB was approved by the US Food and Drug Administration (FDA) in 2004 for advanced non-small cell lung cancer (NSCLC) treatment in patients who relapsed after at least one other therapy. It was authorized for use with gemcitabine in 2005 for the treatment of advanced pancreatic cancer. In addition to lung cancer, ELB has shown promising results in the treatment of other cancers, including breast, prostate, colon, pancreatic, cervical, ovarian, and head and neck cancers. However, its limited water solubility, as a BCS class II drug, presents biopharmaceutical problems. Nanoformulations have been developed to overcome these issues, including increased solubility, controlled release, enhanced stability, tumor accumulation, reduced toxicity, and overcoming drug resistance. In older patients, ELB management should involve individualized dosing based on age-related changes in drug metabolism and close monitoring for adverse effects. Regular assessments of renal and hepatic functions are essential. This review provides an overview of ELB's role of ELB in treating various cancers, its associated biopharmaceutical issues, and the latest developments in ELB-related nanotechnology interventions. It also covers ELB patents granted in previous years and the ongoing clinical trials.
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Affiliation(s)
- Bharti Mangla
- Centre for Advanced Formulation and Technology, Delhi Pharmaceutical Sciences and Research University, New Delhi, 110017, India
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, New Delhi, 110017, India
| | - Priya Mittal
- Centre for Advanced Formulation and Technology, Delhi Pharmaceutical Sciences and Research University, New Delhi, 110017, India
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, New Delhi, 110017, India
| | - Pankaj Kumar
- Centre for Advanced Formulation and Technology, Delhi Pharmaceutical Sciences and Research University, New Delhi, 110017, India
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, New Delhi, 110017, India
| | - Geeta Aggarwal
- Centre for Advanced Formulation and Technology, Delhi Pharmaceutical Sciences and Research University, New Delhi, 110017, India.
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, New Delhi, 110017, India.
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25
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Lutze RD, Ingersoll MA, Thotam A, Joseph A, Fernandes J, Teitz T. ERK1/2 Inhibition via the Oral Administration of Tizaterkib Alleviates Noise-Induced Hearing Loss While Tempering down the Immune Response. Int J Mol Sci 2024; 25:6305. [PMID: 38928015 PMCID: PMC11204379 DOI: 10.3390/ijms25126305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 06/02/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Noise-induced hearing loss (NIHL) is a major cause of hearing impairment and is linked to dementia and mental health conditions, yet no FDA-approved drugs exist to prevent it. Downregulating the mitogen-activated protein kinase (MAPK) cellular pathway has emerged as a promising approach to attenuate NIHL, but the molecular targets and the mechanism of protection are not fully understood. Here, we tested specifically the role of the kinases ERK1/2 in noise otoprotection using a newly developed, highly specific ERK1/2 inhibitor, tizaterkib, in preclinical animal models. Tizaterkib is currently being tested in phase 1 clinical trials for cancer treatment and has high oral bioavailability and low predicted systemic toxicity in mice and humans. In this study, we performed dose-response measurements of tizaterkib's efficacy against permanent NIHL in adult FVB/NJ mice, and its minimum effective dose (0.5 mg/kg/bw), therapeutic index (>50), and window of opportunity (<48 h) were determined. The drug, administered orally twice daily for 3 days, 24 h after 2 h of 100 dB or 106 dB SPL noise exposure, at a dose equivalent to what is prescribed currently for humans in clinical trials, conferred an average protection of 20-25 dB SPL in both female and male mice. The drug shielded mice from the noise-induced synaptic damage which occurs following loud noise exposure. Equally interesting, tizaterkib was shown to decrease the number of CD45- and CD68-positive immune cells in the mouse cochlea following noise exposure. This study suggests that repurposing tizaterkib and the ERK1/2 kinases' inhibition could be a promising strategy for the treatment of NIHL.
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Affiliation(s)
- Richard D. Lutze
- Department of Pharmacology and Neuroscience, School of Medicine, Creighton University, Omaha, NE 68178, USA; (R.D.L.); (M.A.I.); (A.T.); (A.J.); (J.F.)
| | - Matthew A. Ingersoll
- Department of Pharmacology and Neuroscience, School of Medicine, Creighton University, Omaha, NE 68178, USA; (R.D.L.); (M.A.I.); (A.T.); (A.J.); (J.F.)
| | - Alena Thotam
- Department of Pharmacology and Neuroscience, School of Medicine, Creighton University, Omaha, NE 68178, USA; (R.D.L.); (M.A.I.); (A.T.); (A.J.); (J.F.)
| | - Anjali Joseph
- Department of Pharmacology and Neuroscience, School of Medicine, Creighton University, Omaha, NE 68178, USA; (R.D.L.); (M.A.I.); (A.T.); (A.J.); (J.F.)
| | - Joshua Fernandes
- Department of Pharmacology and Neuroscience, School of Medicine, Creighton University, Omaha, NE 68178, USA; (R.D.L.); (M.A.I.); (A.T.); (A.J.); (J.F.)
| | - Tal Teitz
- Department of Pharmacology and Neuroscience, School of Medicine, Creighton University, Omaha, NE 68178, USA; (R.D.L.); (M.A.I.); (A.T.); (A.J.); (J.F.)
- The Scintillon Research Institute, San Diego, CA 92121, USA
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26
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Lu Y, Elrod J, Herrmann M, Knopf J, Boettcher M. Neutrophil Extracellular Traps: A Crucial Factor in Post-Surgical Abdominal Adhesion Formation. Cells 2024; 13:991. [PMID: 38891123 PMCID: PMC11171752 DOI: 10.3390/cells13110991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/27/2024] [Accepted: 06/05/2024] [Indexed: 06/21/2024] Open
Abstract
Post-surgical abdominal adhesions, although poorly understood, are highly prevalent. The molecular processes underlying their formation remain elusive. This review aims to assess the relationship between neutrophil extracellular traps (NETs) and the generation of postoperative peritoneal adhesions and to discuss methods for mitigating peritoneal adhesions. A keyword or medical subject heading (MeSH) search for all original articles and reviews was performed in PubMed and Google Scholar. It included studies assessing peritoneal adhesion reformation after abdominal surgery from 2003 to 2023. After assessing for eligibility, the selected articles were evaluated using the Critical Appraisal Skills Programme checklist for qualitative research. The search yielded 127 full-text articles for assessment of eligibility, of which 7 studies met our criteria and were subjected to a detailed quality review using the Critical Appraisal Skills Programme (CASP) checklist. The selected studies offer a comprehensive analysis of adhesion pathogenesis with a special focus on the role of neutrophil extracellular traps (NETs) in the development of peritoneal adhesions. Current interventional strategies are examined, including the use of mechanical barriers, advances in regenerative medicine, and targeted molecular therapies. In particular, this review emphasizes the potential of NET-targeted interventions as promising strategies to mitigate postoperative adhesion development. Evidence suggests that in addition to their role in innate defense against infections and autoimmune diseases, NETs also play a crucial role in the formation of peritoneal adhesions after surgery. Therefore, therapeutic strategies that target NETs are emerging as significant considerations for researchers. Continued research is vital to fully elucidate the relationship between NETs and post-surgical adhesion formation to develop effective treatments.
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Affiliation(s)
- Yuqing Lu
- Department of Pediatric Surgery, University Medical Center Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Julia Elrod
- Department of Pediatric Surgery, University Medical Center Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Martin Herrmann
- Department of Pediatric Surgery, University Medical Center Mannheim, University of Heidelberg, 68167 Mannheim, Germany
- Department of Internal Medicine 3—Rheumatology and Immunology, Friedrich Alexander University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich Alexander University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Jasmin Knopf
- Department of Pediatric Surgery, University Medical Center Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Michael Boettcher
- Department of Pediatric Surgery, University Medical Center Mannheim, University of Heidelberg, 68167 Mannheim, Germany
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27
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Laham AJ, El-Awady R, Saber-Ayad M, Wang N, Yan G, Boudreault J, Ali S, Lebrun JJ. Targeting the DYRK1A kinase prevents cancer progression and metastasis and promotes cancer cells response to G1/S targeting chemotherapy drugs. NPJ Precis Oncol 2024; 8:128. [PMID: 38839871 PMCID: PMC11153725 DOI: 10.1038/s41698-024-00614-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 05/17/2024] [Indexed: 06/07/2024] Open
Abstract
Metastatic cancer remains incurable as patients eventually loose sensitivity to targeted therapies and chemotherapies, further leading to poor clinical outcome. Thus, there is a clear medical gap and urgent need to develop efficient and improved targeted therapies for cancer patients. In this study, we investigated the role of DYRK1A kinase in regulating cancer progression and evaluated the therapeutic potential of DYRK1A inhibition in invasive solid tumors, including colon and triple-negative breast cancers. We uncovered new roles played by the DYRK1A kinase. We found that blocking DYRK1A gene expression or pharmacological inhibition of its kinase activity via harmine efficiently blocked primary tumor formation and the metastatic tumor spread in preclinical models of breast and colon cancers. Further assessing the underlying molecular mechanisms, we found that DYRK1A inhibition resulted in increased expression of the G1/S cell cycle regulators while decreasing expression of the G2/M regulators. Combined, these effects release cancer cells from quiescence, leading to their accumulation in G1/S and further delaying/preventing their progression toward G2/M, ultimately leading to growth arrest and tumor growth inhibition. Furthermore, we show that accumulation of cancer cells in G1/S upon DYRK1A inhibition led to significant potentiation of G1/S targeting chemotherapy drug responses in vitro and in vivo. This study underscores the potential for developing novel DYRK1A-targeting therapies in colon and breast cancers and, at the same time, further defines DYRK1A pharmacological inhibition as a viable and powerful combinatorial treatment approach for improving G1/S targeting chemotherapy drugs treatments in solid tumors.
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Affiliation(s)
- Amina Jamal Laham
- Department of Medicine, Cancer Research Program, McGill University Health Center, Montreal, Quebec, H4A 3J1, Canada
- College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Raafat El-Awady
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates.
- College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates.
| | - Maha Saber-Ayad
- College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Ni Wang
- Department of Medicine, Cancer Research Program, McGill University Health Center, Montreal, Quebec, H4A 3J1, Canada
| | - Gang Yan
- Department of Medicine, Cancer Research Program, McGill University Health Center, Montreal, Quebec, H4A 3J1, Canada
| | - Julien Boudreault
- Department of Medicine, Cancer Research Program, McGill University Health Center, Montreal, Quebec, H4A 3J1, Canada
| | - Suhad Ali
- Department of Medicine, Cancer Research Program, McGill University Health Center, Montreal, Quebec, H4A 3J1, Canada
| | - Jean-Jacques Lebrun
- Department of Medicine, Cancer Research Program, McGill University Health Center, Montreal, Quebec, H4A 3J1, Canada.
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28
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Noor S, Choudhury A, Islam KU, Yousuf M, Raza A, Ansari MA, Ashraf A, Hussain A, Hassan MI. Investigating the chemo-preventive role of noscapine in lung carcinoma via therapeutic targeting of human aurora kinase B. Mol Cell Biochem 2024:10.1007/s11010-024-05036-7. [PMID: 38829482 DOI: 10.1007/s11010-024-05036-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/14/2024] [Indexed: 06/05/2024]
Abstract
Lung carcinoma is the major contributor to global cancer incidence and one of the leading causes of cancer-related mortality worldwide. Irregularities in signal transduction events, genetic alterations, and mutated regulatory genes trigger cancer development and progression. Selective targeting of molecular modulators has substantially revolutionized cancer treatment strategies with improvised efficacy. The aurora kinase B (AURKB) is a critical component of the chromosomal passenger complex and is primarily involved in lung cancer pathogenesis. Since AURKB is an important therapeutic target, the design and development of its potential inhibitors are attractive strategies. In this study, noscapine was selected and validated as a possible inhibitor of AURKB using integrated computational, spectroscopic, and cell-based assays. Molecular docking analysis showed noscapine occupies the substrate-binding pocket of AURKB with strong binding affinity. Subsequently, MD simulation studies confirmed the formation of a stable AURKB-noscapine complex with non-significant alteration in various trajectories, including RMSD, RMSF, Rg, and SASA. These findings were further experimentally validated through fluorescence binding studies. In addition, dose-dependent noscapine treatment significantly attenuated recombinant AURKB activity with an IC50 value of 26.6 µM. Cell viability studies conducted on A549 cells and HEK293 cells revealed significant cytotoxic features of noscapine on A549 cells. Furthermore, Annexin-PI staining validated that noscapine triggered apoptosis in lung cancer cells, possibly via an intrinsic pathway. Our findings indicate that noscapine-based AURKB inhibition can be implicated as a potential therapeutic strategy in lung cancer treatment and can also provide a novel scaffold for developing next-generation AURKB-specific inhibitors.
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Affiliation(s)
- Saba Noor
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Arunabh Choudhury
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Khursheed Ul Islam
- Multidisciplinary Centre for Advance Research and Studies, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mohd Yousuf
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Ali Raza
- Department of Medical Biochemistry, Jawahar Lal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, 202002, India
| | - Mohammad Ahmad Ansari
- Multidisciplinary Research Unit, University College of Medical Sciences, New Delhi, 110095, India
| | - Anam Ashraf
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Afzal Hussain
- Department of Pharmacognosy College of Pharmacy, King Saud University, PO Box 2457, Riyadh, 11451, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
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29
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Rout AK, Dehury B, Parida SN, Rout SS, Jena R, Kaushik N, Kaushik NK, Pradhan SK, Sahoo CR, Singh AK, Arya M, Behera BK. A review on structure-function mechanism and signaling pathway of serine/threonine protein PIM kinases as a therapeutic target. Int J Biol Macromol 2024; 270:132030. [PMID: 38704069 DOI: 10.1016/j.ijbiomac.2024.132030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 04/05/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
The proviral integration for the Moloney murine leukemia virus (PIM) kinases, belonging to serine/threonine kinase family, have been found to be overexpressed in various types of cancers, such as prostate, breast, colon, endometrial, gastric, and pancreatic cancer. The three isoforms PIM kinases i.e., PIM1, PIM2, and PIM3 share a high degree of sequence and structural similarity and phosphorylate substrates controlling tumorigenic phenotypes like proliferation and cell survival. Targeting short-lived PIM kinases presents an intriguing strategy as in vivo knock-down studies result in non-lethal phenotypes, indicating that clinical inhibition of PIM might have fewer adverse effects. The ATP binding site (hinge region) possesses distinctive attributes, which led to the development of novel small molecule scaffolds that target either one or all three PIM isoforms. Machine learning and structure-based approaches have been at the forefront of developing novel and effective chemical therapeutics against PIM in preclinical and clinical settings, and none have yet received approval for cancer treatment. The stability of PIM isoforms is maintained by PIM kinase activity, which leads to resistance against PIM inhibitors and chemotherapy; thus, to overcome such effects, PIM proteolysis targeting chimeras (PROTACs) are now being developed that specifically degrade PIM proteins. In this review, we recapitulate an overview of the oncogenic functions of PIM kinases, their structure, function, and crucial signaling network in different types of cancer, and the potential of pharmacological small-molecule inhibitors. Further, our comprehensive review also provides valuable insights for developing novel antitumor drugs that specifically target PIM kinases in the future. In conclusion, we provide insights into the benefits of degrading PIM kinases as opposed to blocking their catalytic activity to address the oncogenic potential of PIM kinases.
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Affiliation(s)
- Ajaya Kumar Rout
- Rani Lakshmi Bai Central Agricultural University, Jhansi-284003, Uttar Pradesh, India
| | - Budheswar Dehury
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal-576104, India
| | - Satya Narayan Parida
- Rani Lakshmi Bai Central Agricultural University, Jhansi-284003, Uttar Pradesh, India
| | - Sushree Swati Rout
- Department of Zoology, Fakir Mohan University, Balasore-756089, Odisha, India
| | - Rajkumar Jena
- Department of Zoology, Fakir Mohan University, Balasore-756089, Odisha, India
| | - Neha Kaushik
- Department of Biotechnology, The University of Suwon, Hwaseong si, South Korea
| | | | - Sukanta Kumar Pradhan
- Department of Bioinformatics, Odisha University of Agriculture and Technology, Bhubaneswar-751003, Odisha, India
| | - Chita Ranjan Sahoo
- ICMR-Regional Medical Research Centre, Department of Health Research, Ministry of Health and Family Welfare, Government of India, Bhubaneswar-751023, India
| | - Ashok Kumar Singh
- Rani Lakshmi Bai Central Agricultural University, Jhansi-284003, Uttar Pradesh, India
| | - Meenakshi Arya
- Rani Lakshmi Bai Central Agricultural University, Jhansi-284003, Uttar Pradesh, India.
| | - Bijay Kumar Behera
- Rani Lakshmi Bai Central Agricultural University, Jhansi-284003, Uttar Pradesh, India.
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30
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Koroleva EV, Ermolinskaya AL, Ignatovich ZV, Kornoushenko YV, Panibrat AV, Potkin VI, Andrianov AM. Design, in silico Evaluation, and Determination of Antitumor Activity of Potential Inhibitors Against Protein Kinases: Application to BCR-ABL Tyrosine Kinase. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:1094-1108. [PMID: 38981703 DOI: 10.1134/s0006297924060099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 05/07/2024] [Accepted: 05/11/2024] [Indexed: 07/11/2024]
Abstract
Despite significant progress made over the past two decades in the treatment of chronic myeloid leukemia (CML), there is still an unmet need for effective and safe agents to treat patients with resistance and intolerance to the drugs used in clinic. In this work, we designed 2-arylaminopyrimidine amides of isoxazole-3-carboxylic acid, assessed in silico their inhibitory potential against Bcr-Abl tyrosine kinase, and determined their antitumor activity in K562 (CML), HL-60 (acute promyelocytic leukemia), and HeLa (cervical cancer) cells. Based on the analysis of computational and experimental data, three compounds with the antitumor activity against K562 and HL-60 cells were identified. The lead compound efficiently suppressed the growth of these cells, as evidenced by the low IC50 values of 2.8 ± 0.8 μM (K562) and 3.5 ± 0.2 μM (HL-60). The obtained compounds represent promising basic structures for the design of novel, effective, and safe anticancer drugs able to inhibit the catalytic activity of Bcr-Abl kinase by blocking the ATP-binding site of the enzyme.
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Affiliation(s)
- Elena V Koroleva
- Institute of Chemistry of New Materials, National Academy of Sciences of Belarus, Minsk, 220141, Republic of Belarus
| | - Anastasiya L Ermolinskaya
- Institute of Chemistry of New Materials, National Academy of Sciences of Belarus, Minsk, 220141, Republic of Belarus
| | - Zhanna V Ignatovich
- Institute of Chemistry of New Materials, National Academy of Sciences of Belarus, Minsk, 220141, Republic of Belarus
| | - Yury V Kornoushenko
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, 220141, Republic of Belarus
| | - Alesia V Panibrat
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, 220141, Republic of Belarus
| | - Vladimir I Potkin
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus, Minsk, 220072, Republic of Belarus
| | - Alexander M Andrianov
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, 220141, Republic of Belarus.
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31
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Wang L, Yilmaz F, Yildirim O, Schölermann B, Bag S, Greiner L, Pahl A, Sievers S, Scheel R, Strohmann C, Squire C, Foley DJ, Ziegler S, Grigalunas M, Waldmann H. Discovery of a Novel Pseudo-Natural Product Aurora Kinase Inhibitor Chemotype through Morphological Profiling. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309202. [PMID: 38569218 DOI: 10.1002/advs.202309202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/20/2024] [Indexed: 04/05/2024]
Abstract
The pseudo-natural product (pseudo-NP) concept aims to combine NP fragments in arrangements that are not accessible through known biosynthetic pathways. The resulting compounds retain the biological relevance of NPs but are not yet linked to bioactivities and may therefore be best evaluated by unbiased screening methods resulting in the identification of unexpected or unprecedented bioactivities. Herein, various NP fragments are combined with a tricyclic core connectivity via interrupted Fischer indole and indole dearomatization reactions to provide a collection of highly three-dimensional pseudo-NPs. Target hypothesis generation by morphological profiling via the cell painting assay guides the identification of an unprecedented chemotype for Aurora kinase inhibition with both its relatively highly 3D structure and its physicochemical properties being very different from known inhibitors. Biochemical and cell biological characterization indicate that the phenotype identified by the cell painting assay corresponds to the inhibition of Aurora kinase B.
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Affiliation(s)
- Lin Wang
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Furkan Yilmaz
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, 44227, Dortmund, Germany
| | - Okan Yildirim
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Beate Schölermann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Sukdev Bag
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Luca Greiner
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Axel Pahl
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
- Compound Management and Screening Center (COMAS), 44227, Dortmund, Germany
| | - Sonja Sievers
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
- Compound Management and Screening Center (COMAS), 44227, Dortmund, Germany
| | - Rebecca Scheel
- Faculty of Chemistry and Inorganic Chemistry, TU Dortmund University, 44227, Dortmund, Germany
| | - Carsten Strohmann
- Faculty of Chemistry and Inorganic Chemistry, TU Dortmund University, 44227, Dortmund, Germany
| | - Christopher Squire
- School of Biological Sciences, University of Auckland, 1142, Auckland, New Zealand
| | - Daniel J Foley
- School of Physical and Chemical Sciences, University of Canterbury, 8041, Christchurch, New Zealand
| | - Slava Ziegler
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Michael Grigalunas
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, 44227, Dortmund, Germany
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32
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Yao CY, Lin CC, Wang YH, Kao CJ, Tsai CH, Hou HA, Tien HF, Hsu CL, Chou WC. Kinome expression profiling improves risk stratification and therapeutic targeting in myelodysplastic syndromes. Blood Adv 2024; 8:2442-2454. [PMID: 38527292 PMCID: PMC11112608 DOI: 10.1182/bloodadvances.2023011512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/31/2024] [Accepted: 02/12/2024] [Indexed: 03/27/2024] Open
Abstract
ABSTRACT The human kinome, which comprises >500 kinases, plays a critical role in regulating numerous essential cellular functions. Although the dysregulation of kinases has been observed in various human cancers, the characterization and clinical implications of kinase expressions in myelodysplastic syndromes (MDS) have not been systematically investigated. In this study, we evaluated the kinome expression profiles of 341 adult patients with primary MDS and identified 7 kinases (PTK7, KIT, MAST4, NTRK1, PAK6, CAMK1D, and PRKCZ) whose expression levels were highly predictive of compromised patient survival. We then constructed the kinase stratification score (KISS) by combining the weighted expressions of the 7 kinases and validated its prognostic significance in 2 external MDS cohorts. A higher KISS was associated with older age, higher peripheral blood and marrow blast percentages, higher Revised International Prognostic Scoring System (IPSS-R) risks, complex karyotype, and mutations in several adverse-risk genes in MDS, such as ASXL1, EZH2, NPM1, RUNX1, STAG2, and TP53. Multivariate analysis confirmed that a higher KISS was an independent unfavorable risk factor in MDS. Mechanistically, the KISS-high patients were enriched for gene sets associated with hematopoietic and leukemic stem cell signatures. By investigating the Genomics of Drug Sensitivity in Cancer database, we identified axitinib and taselisib as candidate compounds that could potentially target the KISS-high myeloblasts. Altogether, our findings suggest that KISS holds the potential to improve the current prognostic scheme of MDS and inform novel therapeutic opportunities.
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Affiliation(s)
- Chi-Yuan Yao
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chien-Chin Lin
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Hung Wang
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
| | - Chein-Jun Kao
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Cheng-Hong Tsai
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Hsin-An Hou
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Hwei-Fang Tien
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chia-Lang Hsu
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Oncology, College of Medicine, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wen-Chien Chou
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
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33
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Bernasconi R, Kuster GM. Non-coding RNAs and their potential exploitation in cancer therapy-related cardiotoxicity. Br J Pharmacol 2024. [PMID: 38802331 DOI: 10.1111/bph.16416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/28/2024] [Accepted: 03/26/2024] [Indexed: 05/29/2024] Open
Abstract
Life expectancy in cancer patients has been extended in recent years, thanks to major breakthroughs in therapeutic developments. However, this also unmasked an increased incidence of cardiovascular diseases in cancer survivors, which is in part attributable to cancer therapy-related cardiovascular toxicity. Non-coding RNAs (ncRNAs) have received much appreciation due to their impact on gene expression. NcRNAs, which include microRNAs, long ncRNAs and circular RNAs, are non-protein-coding transcripts that are involved in the regulation of various biological processes, hence shaping cell identity and behaviour. They have also been implicated in disease development, including cardiovascular diseases, cancer and, more recently, cancer therapy-associated cardiotoxicity. This review outlines key features of cancer therapy-associated cardiotoxicity, what is known about the roles of ncRNAs in these processes and how ncRNAs could be exploited as therapeutic targets for cardioprotection.
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Affiliation(s)
- Riccardo Bernasconi
- Myocardial Research, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Gabriela M Kuster
- Myocardial Research, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
- Department of Cardiology, University Heart Center Basel, University Hospital Basel, Basel, Switzerland
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Ku AF, Sharma KL, Ta HM, Sutton CM, Bohren KM, Wang Y, Chamakuri S, Chen R, Hakenjos JM, Jimmidi R, Kent K, Li F, Li JY, Ma L, Madasu C, Palaniappan M, Palmer SS, Qin X, Robers MB, Sankaran B, Tan Z, Vasquez YM, Wang J, Wilkinson J, Yu Z, Ye Q, Young DW, Teng M, Kim C, Matzuk MM. Reversible male contraception by targeted inhibition of serine/threonine kinase 33. Science 2024; 384:885-890. [PMID: 38781365 DOI: 10.1126/science.adl2688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 04/03/2024] [Indexed: 05/25/2024]
Abstract
Men or mice with homozygous serine/threonine kinase 33 (STK33) mutations are sterile owing to defective sperm morphology and motility. To chemically evaluate STK33 for male contraception with STK33-specific inhibitors, we screened our multibillion-compound collection of DNA-encoded chemical libraries, uncovered potent STK33-specific inhibitors, determined the STK33 kinase domain structure bound with a truncated hit CDD-2211, and generated an optimized hit CDD-2807 that demonstrates nanomolar cellular potency (half-maximal inhibitory concentration = 9.2 nanomolar) and favorable metabolic stability. In mice, CDD-2807 exhibited no toxicity, efficiently crossed the blood-testis barrier, did not accumulate in brain, and induced a reversible contraceptive effect that phenocopied genetic STK33 perturbations without altering testis size. Thus, STK33 is a chemically validated, nonhormonal contraceptive target, and CDD-2807 is an effective tool compound.
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Affiliation(s)
- Angela F Ku
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kiran L Sharma
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hai Minh Ta
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Courtney M Sutton
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kurt M Bohren
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yong Wang
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Srinivas Chamakuri
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ruihong Chen
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - John M Hakenjos
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ravikumar Jimmidi
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Katarzyna Kent
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Feng Li
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jian-Yuan Li
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lang Ma
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chandrashekhar Madasu
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Murugesan Palaniappan
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stephen S Palmer
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xuan Qin
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Zhi Tan
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yasmin M Vasquez
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jian Wang
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Zhifeng Yu
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qiuji Ye
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Damian W Young
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mingxing Teng
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Choel Kim
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Martin M Matzuk
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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Yan Q, Li R, Yang J, Bai X, Guo X, Yang X, Song J. Efficacy and safety evaluation of combined therapies incorporating whole-brain radiotherapy in patients with brain metastases: a systematic review and meta-analysis. Clin Transl Oncol 2024:10.1007/s12094-024-03525-1. [PMID: 38789890 DOI: 10.1007/s12094-024-03525-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 05/12/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND Whole-brain radiotherapy (WBRT) is a standard and effective approach for brain metastases, but it is linked to neurocognitive complications, specifically issues related to the hippocampus. Innovative strategies are being explored to enhance outcomes. However, a consensus is yet to be reached in this field. Our aim is to investigate the efficacy and safety of WBRT combined with simultaneous integrated boost (SIB), memantine, and hippocampal avoidance (HA) techniques in treatment of brain metastases. METHODS In this systematic review and meta-analysis, we comprehensively searched PubMed, MEDLINE, Embase, and Cochrane for studies reporting the efficacy and toxicity of WBRT-based combination therapies from inception to September 19, 2023. Data were pooled using random-effects models. Results were reported as risk ratios (RRs) and risk differences (RDs) for dichotomous outcomes, along with their 95% confidence intervals (CIs). Heterogeneity was evaluated using the I2 statistic. RESULTS Among 2175 articles, 29 studies involving 3460 patients were included. The meta-analysis revealed that compared to WBRT alone, combination therapies significantly mitigated neurocognitive function decline (RD = -0.09, 95% CI [-0.18-0.01]; P = 0.03) and intracranial control failure (RR = 0.86, 95% CI [0.52-1.44]; P = 0.02), without increasing the risk of hippocampal recurrence or high-grade toxicities. Notably, HA-WBRT + SIB/memantine demonstrated improved neurocognitive outcomes and survival benefits. CONCLUSION WBRT-based combination therapies demonstrate improved efficacy and comparable safety to WBRT alone, with specific emphasis on the effectiveness of HA-WBRT + Memantine and HA-WBRT + SIB in optimizing therapeutic outcomes for brain metastases.
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Affiliation(s)
- Qi Yan
- Cancer Center, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences Tongji Shanxi Hospital, Longcheng Street No. 99, Taiyuan, Shanxi, China
| | - Rong Li
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Longcheng Street No. 99, Taiyuan, Shanxi, China
| | - Jiayang Yang
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Longcheng Street No. 99, Taiyuan, Shanxi, China
| | - Xueqi Bai
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Longcheng Street No. 99, Taiyuan, Shanxi, China
| | - Xiudong Guo
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Longcheng Street No. 99, Taiyuan, Shanxi, China
| | - Xin Yang
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Longcheng Street No. 99, Taiyuan, Shanxi, China.
| | - Jianbo Song
- Cancer Center, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences Tongji Shanxi Hospital, Longcheng Street No. 99, Taiyuan, Shanxi, China.
- Shanxi Provincial Key Laboratory for Translational Nuclear Medicine and Precision Protection, Taiyuan, China.
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36
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Halder P, Rai A, Talukdar V, Das P, Lakkaniga NR. Pyrazolopyridine-based kinase inhibitors for anti-cancer targeted therapy. RSC Med Chem 2024; 15:1452-1470. [PMID: 38784451 PMCID: PMC11110789 DOI: 10.1039/d4md00003j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/24/2024] [Indexed: 05/25/2024] Open
Abstract
The need for effective cancer treatments continues to be a challenge for the biomedical research community. In this case, the advent of targeted therapy has significantly improved therapeutic outcomes. Drug discovery and development efforts targeting kinases have resulted in the approval of several small-molecule anti-cancer drugs based on ATP-mimicking heterocyclic cores. Pyrazolopyridines are a group of privileged heterocyclic cores in kinase drug discovery, which are present in several inhibitors that have been developed against various cancers. Notably, selpercatinib, glumetinib, camonsertib and olverembatinib have either received approval or are in late-phase clinical studies. This review presents the success stories employing pyrazolopyridine scaffolds as hinge-binding cores to address various challenges in kinase-targeted drug discovery research.
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Affiliation(s)
- Pallabi Halder
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines) Dhanbad India
| | - Anubhav Rai
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines) Dhanbad India
| | - Vishal Talukdar
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines) Dhanbad India
| | - Parthasarathi Das
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines) Dhanbad India
| | - Naga Rajiv Lakkaniga
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines) Dhanbad India
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Chowdhury MG, Kalmegh V, Kapoor S, Kamble V, Shard A. Imidazopyrimidine: from a relatively exotic scaffold to an evolving structural motif in drug discovery. RSC Med Chem 2024; 15:1488-1507. [PMID: 38784469 PMCID: PMC11110759 DOI: 10.1039/d3md00718a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/10/2024] [Indexed: 05/25/2024] Open
Abstract
Nitrogen-fused heterocycles are of immense importance in modern drug discovery and development. Among them, imidazopyrimidine is a highly versatile scaffold with vast pharmacological utility. These compounds demonstrate a broad spectrum of pharmacological actions, including antiviral, antifungal, anti-inflammatory, and anticancer. Their adaptable structure allows for extensive structural modifications, which can be utilized for optimizing pharmacological effects via structure-activity relationship (SAR) studies. Additionally, imidazopyrimidine derivatives are particularly noteworthy for their ability to target specific molecular entities, such as protein kinases, which are crucial components of various cellular signaling pathways associated with multiple diseases. Despite the evident importance of imidazopyrimidines in drug discovery, there is a notable lack of a comprehensive review that outlines their role in this field. This review highlights the ongoing interest and investment in exploring the therapeutic potential of imidazopyrimidine compounds, underscoring their pivotal role in shaping the future of drug discovery and clinical medicine.
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Affiliation(s)
- Moumita Ghosh Chowdhury
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research Ahmedabad (NIPER-A) Opposite Airforce Station, Palaj Gandhinagar Gujarat-382355 India
| | - Vaishnavi Kalmegh
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research Ahmedabad (NIPER-A) Opposite Airforce Station, Palaj Gandhinagar Gujarat-382355 India
| | - Saumya Kapoor
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research Ahmedabad (NIPER-A) Opposite Airforce Station, Palaj Gandhinagar Gujarat-382355 India
| | - Vaishnavi Kamble
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research Ahmedabad (NIPER-A) Opposite Airforce Station, Palaj Gandhinagar Gujarat-382355 India
| | - Amit Shard
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research Ahmedabad (NIPER-A) Opposite Airforce Station, Palaj Gandhinagar Gujarat-382355 India
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Li J, Gong C, Zhou H, Liu J, Xia X, Ha W, Jiang Y, Liu Q, Xiong H. Kinase Inhibitors and Kinase-Targeted Cancer Therapies: Recent Advances and Future Perspectives. Int J Mol Sci 2024; 25:5489. [PMID: 38791529 PMCID: PMC11122109 DOI: 10.3390/ijms25105489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/09/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Over 120 small-molecule kinase inhibitors (SMKIs) have been approved worldwide for treating various diseases, with nearly 70 FDA approvals specifically for cancer treatment, focusing on targets like the epidermal growth factor receptor (EGFR) family. Kinase-targeted strategies encompass monoclonal antibodies and their derivatives, such as nanobodies and peptides, along with innovative approaches like the use of kinase degraders and protein kinase interaction inhibitors, which have recently demonstrated clinical progress and potential in overcoming resistance. Nevertheless, kinase-targeted strategies encounter significant hurdles, including drug resistance, which greatly impacts the clinical benefits for cancer patients, as well as concerning toxicity when combined with immunotherapy, which restricts the full utilization of current treatment modalities. Despite these challenges, the development of kinase inhibitors remains highly promising. The extensively studied tyrosine kinase family has 70% of its targets in various stages of development, while 30% of the kinase family remains inadequately explored. Computational technologies play a vital role in accelerating the development of novel kinase inhibitors and repurposing existing drugs. Recent FDA-approved SMKIs underscore the importance of blood-brain barrier permeability for long-term patient benefits. This review provides a comprehensive summary of recent FDA-approved SMKIs based on their mechanisms of action and targets. We summarize the latest developments in potential new targets and explore emerging kinase inhibition strategies from a clinical perspective. Lastly, we outline current obstacles and future prospects in kinase inhibition.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Huihua Xiong
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (J.L.)
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Taghizadeh MS, Taherishirazi M, Niazi A, Afsharifar A, Moghadam A. Structure-guided design and cloning of peptide inhibitors targeting CDK9/cyclin T1 protein-protein interaction. Front Pharmacol 2024; 15:1327820. [PMID: 38808256 PMCID: PMC11130503 DOI: 10.3389/fphar.2024.1327820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/18/2024] [Indexed: 05/30/2024] Open
Abstract
CDK9 (cyclin-dependent kinase 9) plays a significant role in numerous pathological conditions, such as HIV-1 infection and cancer. The interaction between CDK9 and cyclin T1 is crucial for maintaining the kinase's active state. Therefore, targeting this protein-protein interaction offers a promising strategy for inhibiting CDK9. In this study, we aimed to design and characterize a library of mutant peptides based on the binding region of cyclin T1 to CDK9. Using Osprey software, a total of 7,776 mutant peptides were generated. After conducting a comprehensive analysis, three peptides, namely, mp3 (RAADVEGQRKRRE), mp20 (RAATVEGQRKRRE), and mp29 (RAADVEGQDKRRE), were identified as promising inhibitors that possess the ability to bind to CDK9 with high affinity and exhibit low free binding energy. These peptides exhibited favorable safety profiles and displayed promising dynamic behaviors. Notably, our findings revealed that the mp3 and mp29 peptides interacted with a conserved sequence in CDK9 (residues 60-66). In addition, by designing the structure of potential peptides in the plasmid vector pET28a (+), we have been able to pave the way for facilitating the process of their recombinant production in an Escherichia coli expression system in future studies. Predictions indicated good solubility upon overexpression, further supporting their potential for downstream applications. While these results demonstrate the promise of the designed peptides as blockers of CDK9 with high affinity, additional experimental studies are required to validate their biological activity and assess their selectivity. Such investigations will provide valuable insights into their therapeutic potential and pave the way for the future development of peptide-based inhibitors targeting the CDK9-cyclin T1 complex.
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Affiliation(s)
| | | | - Ali Niazi
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
| | - Alireza Afsharifar
- Plant Virology Research Center, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Ali Moghadam
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
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40
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Ravichandran A, Araque JC, Lawson JW. Predicting the functional state of protein kinases using interpretable graph neural networks from sequence and structural data. Proteins 2024; 92:623-636. [PMID: 38083830 DOI: 10.1002/prot.26641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 10/13/2023] [Accepted: 11/09/2023] [Indexed: 04/13/2024]
Abstract
Protein kinases are central to cellular activities and are actively pursued as drug targets for several conditions including cancer and autoimmune diseases. Despite the availability of a large structural database for kinases, methodologies to elucidate the structure-function relationship of these proteins (without manual intervention) are lacking. Such techniques are essential in structural biology and to accelerate drug discovery efforts. Here, we implement an interpretable graph neural network (GNN) framework for classifying the functionally active and inactive states of a large set of protein kinases by only using their tertiary structure and amino acid sequence. We show that the GNN models can classify kinase structures with high accuracy (>97%). We implement the Gradient-weighted Class Activation Mapping for graphs (Graph Grad-CAM) to automatically identify structurally important residues and residue-residue contacts of the kinases without any a priori input. We show that the motifs identified through the Graph Grad-CAM methodology are functionally critical, consistent with the existing kinase literature. Notably, the highly conserved DFG and HRD motifs of the well-known hydrophobic spine are identified by the interpretable framework in addition to some of the lesser known motifs. Further, using Grad-CAM maps as the vector embedding of the protein structures, we identify the subtle differences in the crystal structures among different sub-classes of kinases in the Protein Data Bank (PDB). Frameworks such as the one implemented here, for high-throughput identification of protein structure-function relationships are essential in designing targeted small molecules therapies as well as in engineering new proteins for novel applications.
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Affiliation(s)
- Ashwin Ravichandran
- KBR Inc., Intelligent Systems Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Juan C Araque
- KBR Inc., Intelligent Systems Division, NASA Ames Research Center, Moffett Field, California, USA
| | - John W Lawson
- Intelligent Systems Division, NASA Ames Research Center, Moffett Field, California, USA
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41
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Khan MS, Altwaijry N, Al-Bagmi MS, Alafaleq NO, Alokail MS, Shahwan M, Shamsi A. Structure-guided identification of potent inhibitors of ROS1 kinase for therapeutic development against non-small cell lung cancer. J Biomol Struct Dyn 2024; 42:3837-3847. [PMID: 37254309 DOI: 10.1080/07391102.2023.2217450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 05/12/2023] [Indexed: 06/01/2023]
Abstract
Proto-oncogene tyrosine-protein kinase ROS (ROS1) is a member of the sevenless receptor, which affects epithelial cell differentiation and is highly expressed in a variety of tumor cells. The elevated expression and dysfunction of ROS1 have been involved in various malignancies, such as non-small cell lung cancer (NSCLC), stomach cancer, ovarian, breast cancer, cholangiocarcinoma, colorectal cancer, adenosarcoma, oesophageal cancer, etc. ROS1 has been postulated as a potential drug target in anticancer therapeutics. In this study, we carried out a virtual screening of phytochemicals against ROS1 to identify its potential inhibitors. The virtual screening process was performed on the ROS1 structure, where two phytochemicals, Helioscopinolide C and Taiwanin C, were identified. These compounds resulted from filters like Lipinski rule of five, PAINS filter, binding affinities values, and all-atom molecular dynamics (MD) simulations followed by principal component analysis (PCA) and essential dynamics. The findings of this study highlight the role of ROS1 in multiple physiological candidates and its therapeutic targeting using phytochemicals. This study suggests Helioscopinolide C and Taiwanin C as potential compounds for therapeutic development targeting ROS1-associated non-small cell lung cancer for clinical applications. Further in vitro and in vivo experiments are required to validate these findings.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohd Shahnawaz Khan
- Department of Biochemistry, College of Science, King Saud University, KSA, Riyadh, Saudi Arabia
| | - Nojood Altwaijry
- Department of Biochemistry, College of Science, King Saud University, KSA, Riyadh, Saudi Arabia
| | - Moneera Saud Al-Bagmi
- Department of Biochemistry, College of Science, King Saud University, KSA, Riyadh, Saudi Arabia
| | - Nouf Omar Alafaleq
- Department of Biochemistry, College of Science, King Saud University, KSA, Riyadh, Saudi Arabia
| | - Majed S Alokail
- Department of Biochemistry, College of Science, King Saud University, KSA, Riyadh, Saudi Arabia
| | - Moyad Shahwan
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Anas Shamsi
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
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42
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Saini T, Gupta P, Raut R, Nayak V, Bharathnaveen P, Mishra P, Misra A. AR-V7 expression facilitates accelerated G2/M phase transition in castration-resistant prostate cancer. Exp Cell Res 2024; 438:114026. [PMID: 38604522 DOI: 10.1016/j.yexcr.2024.114026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 03/25/2024] [Accepted: 03/28/2024] [Indexed: 04/13/2024]
Abstract
The emergence of AR-V7, a truncated isoform of AR upon androgen deprivation therapy treatment, leads to the development of castration resistant prostate cancer (CRPC). Understanding mechanisms that regulate AR-V7 expression is critical for developing newer therapeutic strategies. In this study, we have investigated the regulation of AR-V7 during cell cycle and identified a distinct pattern of periodic fluctuation, peaking during G2/M phase. This fluctuation correlates with the expression of Cdc-2 like kinase 1 (CLK1) and phosphorylated serine/arginine-rich splicing factor 1 (p-SRSF1) during these phases, pointing towards their role in AR-V7 generation. Functional assays reveal that CLK1 knockdown prolongs the S phase, leading to altered cell cycle distribution and increased accumulation of AR-V7 and pSRSF1 in G1/S phase. Conversely, CLK1 overexpression rescues AR-V7 and p-SRSF1 levels in the G2/M phase, consistent with observed cell cycle alterations upon AR-V7 knockdown and overexpression in CRPC cells. Furthermore, overexpression of kinase-deficient CLK1 mutant leads to diminished AR-V7 levels during G2/M, underlining the essential contribution of CLK1's kinase activity in modulating AR-V7 expression. Collectively, our findings, for the first time, show periodic regulation of AR-V7 expression, its effect on cell cycle progression and the critical role of CLK1-pSRSF1 axis in modulating AR-V7 expression throughout the cell cycle.
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Affiliation(s)
- Taruna Saini
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502284, India
| | - Parth Gupta
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502284, India
| | - Rajnikant Raut
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502284, India
| | - Vinayak Nayak
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502284, India
| | - Pabbithi Bharathnaveen
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502284, India
| | - Parul Mishra
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Ashish Misra
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502284, India.
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McMahon NP, Solanki A, Wang LG, Montaño AR, Jones JA, Samkoe KS, Tichauer KM, Gibbs SL. In situ single-cell therapeutic response imaging facilitated by the TRIPODD fluorescence imaging platform. Theranostics 2024; 14:2816-2834. [PMID: 38773974 PMCID: PMC11103495 DOI: 10.7150/thno.93256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/21/2024] [Indexed: 05/24/2024] Open
Abstract
Purpose: Small molecule drugs such as tyrosine kinase inhibitors (TKIs) targeting tumoral molecular dependencies have become standard of care for numerous cancer types. Notably, epidermal growth factor receptor (EGFR) TKIs (e.g., erlotinib, afatinib, osimertinib) are the current first-line treatment for non-small cell lung cancer (NSCLC) due to their improved therapeutic outcomes for EGFR mutated and overexpressing disease over traditional platinum-based chemotherapy. However, many NSCLC tumors develop resistance to EGFR TKI therapy causing disease progression. Currently, the relationship between in situ drug target availability (DTA), local protein expression and therapeutic response cannot be accurately assessed using existing analytical tools despite being crucial to understanding the mechanism of therapeutic efficacy. Procedure: We have previously reported development of our fluorescence imaging platform termed TRIPODD (Therapeutic Response Imaging through Proteomic and Optical Drug Distribution) that is capable of simultaneous quantification of single-cell DTA and protein expression with preserved spatial context within a tumor. TRIPODD combines two complementary fluorescence imaging techniques: intracellular paired agent imaging (iPAI) to measure DTA and cyclic immunofluorescence (cyCIF), which utilizes oligonucleotide conjugated antibodies (Ab-oligos) for spatial proteomic expression profiling on tissue samples. Herein, TRIPODD was modified and optimized to provide a downstream analysis of therapeutic response through single-cell DTA and proteomic response imaging. Results: We successfully performed sequential imaging of iPAI and cyCIF resulting in high dimensional imaging and biomarker assessment to quantify single-cell DTA and local protein expression on erlotinib treated NSCLC models. Pharmacodynamic and pharmacokinetic studies of the erlotinib iPAI probes revealed that administration of 2.5 mg/kg each of the targeted and untargeted probe 4 h prior to tumor collection enabled calculation of DTA values with high Pearson correlation to EGFR, the erlotinib molecular target, expression in the tumors. Analysis of single-cell biomarker expression revealed that a single erlotinib dose was insufficient to enact a measurable decrease in the EGFR signaling cascade protein expression, where only the DTA metric detected the presence of bound erlotinib. Conclusion: We demonstrated the capability of TRIPODD to evaluate therapeutic response imaging to erlotinib treatment as it relates to signaling inhibition, DTA, proliferation, and apoptosis with preserved spatial context.
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Affiliation(s)
- Nathan P. McMahon
- Biomedical Engineering Department, Oregon Health & Science University, Portland, OR 97201, USA
| | - Allison Solanki
- Biomedical Engineering Department, Oregon Health & Science University, Portland, OR 97201, USA
| | - Lei G. Wang
- Biomedical Engineering Department, Oregon Health & Science University, Portland, OR 97201, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
| | - Antonio R. Montaño
- Biomedical Engineering Department, Oregon Health & Science University, Portland, OR 97201, USA
| | - Jocelyn A. Jones
- Biomedical Engineering Department, Oregon Health & Science University, Portland, OR 97201, USA
| | - Kimberley S. Samkoe
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
- Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Kenneth M. Tichauer
- Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Summer L. Gibbs
- Biomedical Engineering Department, Oregon Health & Science University, Portland, OR 97201, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
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BHUSARE NILAM, KUMAR MAUSHMI. A review on potential heterocycles for the treatment of glioblastoma targeting receptor tyrosine kinases. Oncol Res 2024; 32:849-875. [PMID: 38686058 PMCID: PMC11055995 DOI: 10.32604/or.2024.047042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/10/2024] [Indexed: 05/02/2024] Open
Abstract
Glioblastoma, the most aggressive form of brain tumor, poses significant challenges in terms of treatment success and patient survival. Current treatment modalities for glioblastoma include radiation therapy, surgical intervention, and chemotherapy. Unfortunately, the median survival rate remains dishearteningly low at 12-15 months. One of the major obstacles in treating glioblastoma is the recurrence of tumors, making chemotherapy the primary approach for secondary glioma patients. However, the efficacy of drugs is hampered by the presence of the blood-brain barrier and multidrug resistance mechanisms. Consequently, considerable research efforts have been directed toward understanding the underlying signaling pathways involved in glioma and developing targeted drugs. To tackle glioma, numerous studies have examined kinase-downstream signaling pathways such as RAS-RAF-MEK-ERK-MPAK. By targeting specific signaling pathways, heterocyclic compounds have demonstrated efficacy in glioma therapeutics. Additionally, key kinases including phosphatidylinositol 3-kinase (PI3K), serine/threonine kinase, cytoplasmic tyrosine kinase (CTK), receptor tyrosine kinase (RTK) and lipid kinase (LK) have been considered for investigation. These pathways play crucial roles in drug effectiveness in glioma treatment. Heterocyclic compounds, encompassing pyrimidine, thiazole, quinazoline, imidazole, indole, acridone, triazine, and other derivatives, have shown promising results in targeting these pathways. As part of this review, we propose exploring novel structures with low toxicity and high potency for glioma treatment. The development of these compounds should strive to overcome multidrug resistance mechanisms and efficiently penetrate the blood-brain barrier. By optimizing the chemical properties and designing compounds with enhanced drug-like characteristics, we can maximize their therapeutic value and minimize adverse effects. Considering the complex nature of glioblastoma, these novel structures should be rigorously tested and evaluated for their efficacy and safety profiles.
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Affiliation(s)
- NILAM BHUSARE
- Somaiya Institute for Research & Consultancy, Somaiya Vidyavihar University, Vidyavihar (East), Mumbai, 400077, India
| | - MAUSHMI KUMAR
- Somaiya Institute for Research & Consultancy, Somaiya Vidyavihar University, Vidyavihar (East), Mumbai, 400077, India
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45
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Kim HY, Kim YM, Hong S. CK2α-mediated phosphorylation of GRP94 facilitates the metastatic cascade in triple-negative breast cancer. Cell Death Discov 2024; 10:185. [PMID: 38649679 PMCID: PMC11035675 DOI: 10.1038/s41420-024-01956-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 04/25/2024] Open
Abstract
Distant metastasis is a significant hallmark affecting to the high death rate of patients with triple-negative breast cancer (TNBC). Thus, it is crucial to identify and develop new therapeutic strategies to hinder cancer metastasis. While emerging studies have hinted a pivotal role of glucose-regulated protein 94 (GRP94) in tumorigenesis, the exact biological functions and molecular mechanisms of GRP94 in modulating cancer metastasis remain to be elucidated. Our study demonstrated an increased expression of GRP94 in TNBC correlated with metastatic progression and unfavorable prognosis in patients. Functionally, we identified that GRP94 depletion significantly diminished TNBC tumorigenesis and subsequent lung metastasis. In contrast, GRP94 overexpression exacerbated the invasiveness, migration, and lung metastasis of non-TNBC cells. Mechanistically, we found that casein kinase 2 alpha (CK2α) active in advanced breast cancer phosphorylated GRP94 at a conserved serine 306 (S306) residue. This phosphorylation increased the stability of GRP94 and enhanced its interaction with LRP6, leading to activation of canonical Wnt signaling. From a therapeutic standpoint, we found that benzamidine, a novel CK2α inhibitor, effectively suppressed GRP94 phosphorylation, LRP6 stabilization, and metastasis of TNBC. Our results point to the critical role of CK2α-mediated GRP94 phosphorylation in TNBC metastasis through activation of Wnt signaling, highlighting GRP94 as a therapeutic target to impede TNBC metastasis.
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Affiliation(s)
- Hye-Youn Kim
- Department of Biochemistry, Lee Gil Ya Cancer and Diabetes Institute, Gachon University College of Medicine, Incheon, 21999, Republic of Korea
| | - Young-Mi Kim
- Department of Biochemistry, Lee Gil Ya Cancer and Diabetes Institute, Gachon University College of Medicine, Incheon, 21999, Republic of Korea
| | - Suntaek Hong
- Department of Biochemistry, Lee Gil Ya Cancer and Diabetes Institute, Gachon University College of Medicine, Incheon, 21999, Republic of Korea.
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46
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Du M, Xie X, Luo J, Li J. Meta-learning-based Inductive logistic matrix completion for prediction of kinase inhibitors. J Cheminform 2024; 16:44. [PMID: 38627866 PMCID: PMC11301988 DOI: 10.1186/s13321-024-00838-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 03/31/2024] [Indexed: 08/09/2024] Open
Abstract
Protein kinases become an important source of potential drug targets. Developing new, efficient, and safe small-molecule kinase inhibitors has become an important topic in the field of drug research and development. In contrast with traditional wet experiments which are time-consuming and expensive, machine learning-based approaches for predicting small molecule inhibitors for protein kinases are time-saving and cost-effective, which are highly desired for us. However, the issue of sample scarcity (known active and inactive compounds are usually limited for most kinases) poses a challenge to the research and development of machine learning-based kinase inhibitors' active prediction methods. To alleviate the data scarcity problem in the prediction of kinase inhibitors, in this study, we present a novel Meta-learning-based inductive logistic matrix completion method for the Prediction of Kinase Inhibitors (MetaILMC). MetaILMC adopts a meta-learning framework to learn a well-generalized model from tasks with sufficient samples, which can fast adapt to new tasks with limited samples. As MetaILMC allows the effective transfer of the prior knowledge learned from kinases with sufficient samples to kinases with a small number of samples, the proposed model can produce accurate predictions for kinases with limited data. Experimental results show that MetaILMC has excellent performance for prediction tasks of kinases with few-shot samples and is significantly superior to the state-of-the-art multi-task learning in terms of AUC, AUPR, etc., various performance metrics. Case studies also provided for two drugs to predict Kinase Inhibitory scores, further validating the proposed method's effectiveness and feasibility. SCIENTIFIC CONTRIBUTION: Considering the potential correlation between activity prediction tasks for different kinases, we propose a novel meta learning algorithm MetaILMC, which learns a prior of strong generalization capacity during meta-training from the tasks with sufficient training samples, such that it can be easily and quickly adapted to the new tasks of the kinase with scarce data during meta-testing. Thus, MetaILMC can effectively alleviate the data scarcity problem in the prediction of kinase inhibitors.
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Affiliation(s)
- Ming Du
- School of Software, Yunnan University, Kunming, 650091, China
| | - XingRan Xie
- School of Software, Yunnan University, Kunming, 650091, China
| | - Jing Luo
- State Key Laboratory for Conservation and Utilization of Bio-Resource, School of Ecology and Environment and School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Jin Li
- School of Software, Yunnan University, Kunming, 650091, China.
- The Key Laboratory of Software Engineering of Yunnan Province, Kunming, 650091, China.
- The Cloud Computing Engineering Research Center of Yunnan Province, Kunming, 650091, China.
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47
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Makey DM, Gadkari VV, Kennedy RT, Ruotolo BT. Cyclic Ion Mobility-Mass Spectrometry and Tandem Collision Induced Unfolding for Quantification of Elusive Protein Biomarkers. Anal Chem 2024; 96:6021-6029. [PMID: 38557001 PMCID: PMC11081454 DOI: 10.1021/acs.analchem.4c00477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Sensitive analytical techniques that are capable of detecting and quantifying disease-associated biomolecules are indispensable in our efforts to understand disease mechanisms and guide therapeutic intervention through early detection, accurate diagnosis, and effective monitoring of disease. Parkinson's Disease (PD), for example, is one of the most prominent neurodegenerative disorders in the world, but the diagnosis of PD has primarily been based on the observation of clinical symptoms. The protein α-synuclein (α-syn) has emerged as a promising biomarker candidate for PD, but a lack of analytical methods to measure complex disease-associated variants of α-syn has prevented its widespread use as a biomarker. Antibody-based methods such as immunoassays and mass spectrometry-based approaches have been used to measure a limited number of α-syn forms; however, these methods fail to differentiate variants of α-syn that display subtle differences in only the sequence and structure. In this work, we developed a cyclic ion mobility-mass spectrometry method that combines multiple stages of activation and timed ion selection to quantify α-syn variants using both mass- and structure-based measurements. This method can allow for the quantification of several α-syn variants present at physiological levels in biological fluid. Taken together, this approach can be used to galvanize future efforts aimed at understanding the underlying mechanisms of PD and serves as a starting point for the development of future protein-structure-based diagnostics and therapeutic interventions.
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Affiliation(s)
- Devin M Makey
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Varun V Gadkari
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Robert T Kennedy
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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48
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Aghahasani R, Shiri F, Kamaladiny H, Haddadi F, Pirhadi S. Hit discovery of potential CDK8 inhibitors and analysis of amino acid mutations for cancer therapy through computer-aided drug discovery. BMC Chem 2024; 18:73. [PMID: 38615023 PMCID: PMC11016228 DOI: 10.1186/s13065-024-01175-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 03/28/2024] [Indexed: 04/15/2024] Open
Abstract
Cyclin-dependent kinase 8 (CDK8) has emerged as a promising target for inhibiting cancer cell function, intensifying efforts towards the development of CDK8 inhibitors as potential cancer therapeutics. Mutations in CDK8, a protein kinase, are also implicated as a primary factor associated with tumor formation. In this study, we identified potential inhibitors through virtual screening for CDK8 and single amino acid mutations in CDK8, namely D173A (Aspartate 173 mutate to Alanine), D189N (Aspartate 189 mutate to Asparagine), T196A (Threonine 196 mutate to Alanine) and T196D (Threonine 196 mutate to Aspartate). Four databases (CHEMBEL, ZINC, MCULE, and MolPort) containing 65,209,131 molecules have been searched to identify new inhibitors for CDK8 and its single mutations. In the first step, structure-based pharmacophore modeling in the Pharmit server was used to select the compounds to know the inhibitors. Then molecules with better predicted drug-like molecule properties were selected. The final filter used to select more effective inhibitors among the previously selected molecules was molecular docking. Finally, 13 hits for CDK8, 11 hits for D173A, 11 hits for D189N, 15 hits for T196A, and 12 hits for T196D were considered potential inhibitors. A majority of the virtual screening hits exhibited satisfactorily predict pharmacokinetic characteristics and toxicity properties.
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Affiliation(s)
| | | | | | | | - Somayeh Pirhadi
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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49
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De Silva S, Alli-Shaik A, Gunaratne J. FlexStat: combinatory differentially expressed protein extraction. BIOINFORMATICS ADVANCES 2024; 4:vbae056. [PMID: 38681522 PMCID: PMC11055397 DOI: 10.1093/bioadv/vbae056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/25/2024] [Accepted: 04/10/2024] [Indexed: 05/01/2024]
Abstract
Motivation Mass spectrometry-based system proteomics allows identification of dysregulated protein hubs and associated disease-related features. Obtaining differentially expressed proteins (DEPs) is the most important step of downstream bioinformatics analysis. However, the extraction of statistically significant DEPs from datasets with multiple experimental conditions or disease types through currently available tools remains a laborious task. More often such an analysis requires considerable bioinformatics expertise, making it inaccessible to researchers with limited computational analytics experience. Results To uncover the differences among the many conditions within the data in a user-friendly manner, here we introduce FlexStat, a web-based interface that extracts DEPs through combinatory analysis. This tool accepts a protein expression matrix as input and systematically generates DEP results for every conceivable combination of various experimental conditions or disease types. FlexStat includes a suite of robust statistical tools for data preprocessing, in addition to DEP extraction, and publication-ready visualization, which are built on established R scientific libraries in an automated manner. This analytics suite was validated in diverse public proteomic datasets to showcase its high performance of rapid and simultaneous pairwise comparisons of comprehensive datasets. Availability and implementation FlexStat is implemented in R and is freely available at https://jglab.shinyapps.io/flexstatv1-pipeline-only/. The source code is accessible at https://github.com/kts-desilva/FlexStat/tree/main.
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Affiliation(s)
- Senuri De Silva
- Translational Biomedical Proteomics Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore
| | - Asfa Alli-Shaik
- Translational Biomedical Proteomics Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
| | - Jayantha Gunaratne
- Translational Biomedical Proteomics Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore
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50
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Vani BP, Aranganathan A, Tiwary P. Exploring Kinase Asp-Phe-Gly (DFG) Loop Conformational Stability with AlphaFold2-RAVE. J Chem Inf Model 2024; 64:2789-2797. [PMID: 37981824 PMCID: PMC11001530 DOI: 10.1021/acs.jcim.3c01436] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
Kinases compose one of the largest fractions of the human proteome, and their misfunction is implicated in many diseases, in particular, cancers. The ubiquitousness and structural similarities of kinases make specific and effective drug design difficult. In particular, conformational variability due to the evolutionarily conserved Asp-Phe-Gly (DFG) motif adopting in and out conformations and the relative stabilities thereof are key in structure-based drug design for ATP competitive drugs. These relative conformational stabilities are extremely sensitive to small changes in sequence and provide an important problem for sampling method development. Since the invention of AlphaFold2, the world of structure-based drug design has noticeably changed. In spite of it being limited to crystal-like structure prediction, several methods have also leveraged its underlying architecture to improve dynamics and enhanced sampling of conformational ensembles, including AlphaFold2-RAVE. Here, we extend AlphaFold2-RAVE and apply it to a set of kinases: the wild type DDR1 sequence and three mutants with single point mutations that are known to behave drastically differently. We show that AlphaFold2-RAVE is able to efficiently recover the changes in relative stability using transferable learned order parameters and potentials, thereby supplementing AlphaFold2 as a tool for exploration of Boltzmann-weighted protein conformations (Meller, A.; Bhakat, S.; Solieva, S.; Bowman, G. R. Accelerating Cryptic Pocket Discovery Using AlphaFold. J. Chem. Theory Comput. 2023, 19, 4355-4363).
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Affiliation(s)
- Bodhi P. Vani
- Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA
| | - Akashnathan Aranganathan
- Biophysics Program and Institute for Physical Science and Technology, University of Maryland, College Park 20742, USA
| | - Pratyush Tiwary
- Department of Chemistry and Biochemistry and Institute for Physical Science and Technology, University of Maryland, College Park 20742, USA
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