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Alniss HY, Saber-Ayad MM, Ramadan WS, Manasa Bhamidimarri P, Msallam YA, Al-Jubeh HM, Ravi A, Menon V, Hamoudi R, El-Awady R. Transcriptomic analysis of MCF7 breast cancer cells treated with MGBs reveals a profound inhibition of estrogen receptor genes. Bioorg Chem 2024; 151:107680. [PMID: 39084151 DOI: 10.1016/j.bioorg.2024.107680] [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: 05/16/2024] [Revised: 07/21/2024] [Accepted: 07/26/2024] [Indexed: 08/02/2024]
Abstract
Breast cancer poses a significant health risk worldwide. However, the effectiveness of current chemotherapy is limited due to increasing drug resistance and side effects, making it crucial to develop new compounds with novel mechanism of action that can surpass these limitations. As a consequence of their reversible and targeted mechanism, DNA minor groove binders (MGBs) are considered as a relatively safer and more effective alternative. In this study, transcriptomic analysis was conducted to reveal the dysregulated genes and signaling pathways in MCF7 cancer cells following treatment with novel MGB ligands to gain insights into the mechanism of action of MGBs at the molecular level. The transcriptomic results were validated using real-time PCR. The findings of this study indicate that the investigated MGBs primarily inhibit the genes associated with the estrogen receptor. Remarkably, ligand 5 showed downregulation of 34 out of the 35 genes regulated by estrogen receptor, highlighting its potential as a promising candidate for breast cancer therapy.
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Affiliation(s)
- Hasan Y Alniss
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, Sharjah 27272, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates.
| | - Maha M Saber-Ayad
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Wafaa S Ramadan
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Poorna Manasa Bhamidimarri
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Yousef A Msallam
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, Sharjah 27272, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Hadeel M Al-Jubeh
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Anil Ravi
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Varsha Menon
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Rifat Hamoudi
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates; Center of Excellence for Precision Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates; BIMAI-Lab, Biomedically Informed Artificial Intelligence Laboratory, University of Sharjah, Sharjah 27272, United Arab Emirates; Division of Surgery and Interventional Science, Faculty of Medicine, University College London, London, United Kingdom
| | - Raafat El-Awady
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, Sharjah 27272, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
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2
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Alniss HY, Al-Jubeh HM, Msallam YA, Siddiqui R, Makhlouf Z, Ravi A, Hamdy R, Soliman SSM, Khan NA. Structure-based drug design of DNA minor groove binders and evaluation of their antibacterial and anticancer properties. Eur J Med Chem 2024; 271:116440. [PMID: 38678825 DOI: 10.1016/j.ejmech.2024.116440] [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: 12/07/2023] [Revised: 04/09/2024] [Accepted: 04/18/2024] [Indexed: 05/01/2024]
Abstract
Antimicrobial and chemotherapy resistance are escalating medical problem of paramount importance. Yet, research for novel antimicrobial and anticancer agents remains lagging behind. With their reported medical applications, DNA minor groove binders (MGBs) are worthy of exploration. In this study, the approach of structure-based drug design was implemented to generate 11 MGB compounds including a novel class of bioactive alkyne-linked MGBs. The NCI screening protocol was utilized to evaluate the antitumor activity of the target MGBs. Furthermore, a variety of bactericidal, cytopathogenicity, MIC90, and cytotoxicity assays were carried out using these MGBs against 6 medically relevant bacteria: Salmonella enterica, Escherichia coli, Serratia marcescens, Bacillus cereus, Streptococcus pneumoniae and Streptococcus pyogenes. Moreover, molecular docking, molecular dynamic simulations, DNA melting, and isothermal titration calorimetry (ITC) analyses were utilized to explore the binding mode and interactions between the most potent MGBs and the DNA duplex d(CGACTAGTCG)2. NCI results showed that alkyne-linked MGBs (26 & 28) displayed the most significant growth inhibition among the NCI-60 panel. In addition, compounds MGB3, MGB4, MGB28, and MGB32 showed significant bactericidal effects, inhibited B. cereus and S. enterica-mediated cytopathogenicity, and exhibited low cytotoxicity. MGB28 and MGB32 demonstrated significant inhibition of S. pyogenes, whereas MGB28 notably inhibited S. marcescens and all four minor groove binders significantly inhibited B. cereus. The ability of these compounds to bind with DNA and distort its groove dimensions provides the molecular basis for the allosteric perturbation of proteins-DNA interactions by MGBs. This study shed light on the mechanism of action of MGBs and revealed the important structural features for their antitumor and antibacterial activities, which are important to guide future development of MGB derivatives as novel antibacterial and anticancer agents.
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Affiliation(s)
- Hasan Y Alniss
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, 27272, Sharjah, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates.
| | - Hadeel M Al-Jubeh
- Research Institute for Medical and Health Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Yousef A Msallam
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, 27272, Sharjah, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Ruqaiyyah Siddiqui
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University Edinburgh, EH14 4AS, United Kingdom; Department of Medical Biology, Faculty of Medicine, Istinye University, Istanbul, 34010, Turkey
| | - Zinb Makhlouf
- College of Medicine, Department of Clinical Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Anil Ravi
- Research Institute for Medical and Health Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Rania Hamdy
- Research Institute for Medical and Health Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Sameh S M Soliman
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, 27272, Sharjah, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Naveed A Khan
- Department of Medical Biology, Faculty of Medicine, Istinye University, Istanbul, 34010, Turkey.
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Philips SJ, Danda A, Ansari AZ. Using synthetic genome readers/regulators to interrogate chromatin processes: A brief review. Methods 2024; 225:20-27. [PMID: 38471600 PMCID: PMC11055675 DOI: 10.1016/j.ymeth.2024.03.001] [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: 12/22/2023] [Revised: 03/02/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
Aberrant gene expression underlies numerous human ailments. Hence, developing small molecules to target and remedy dysfunctional gene regulation has been a long-standing goal at the interface of chemistry and medicine. A major challenge for designing small molecule therapeutics aimed at targeting desired genomic loci is the minimization of widescale disruption of genomic functions. To address this challenge, we rationally design polyamide-based multi-functional molecules, i.e., Synthetic Genome Readers/Regulators (SynGRs), which, by design, target distinct sequences in the genome. Herein, we briefly review how SynGRs access chromatin-bound and chromatin-free genomic sites, then highlight the methods for the study of chromatin processes using SynGRs on positioned nucleosomes in vitro or disease-causing repressive genomic loci in vivo.
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Affiliation(s)
- Steven J Philips
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Adithi Danda
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Aseem Z Ansari
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA.
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Chen CY, Li Y, Zeng N, He L, Zhang X, Tu T, Tang Q, Alba M, Mir S, Stiles EX, Hong H, Cadenas E, Stolz AA, Li G, Stiles BL. Inhibition of Estrogen-Related Receptor α Blocks Liver Steatosis and Steatohepatitis and Attenuates Triglyceride Biosynthesis. THE AMERICAN JOURNAL OF PATHOLOGY 2021; 191:1240-1254. [PMID: 33894178 PMCID: PMC8261472 DOI: 10.1016/j.ajpath.2021.04.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/08/2021] [Accepted: 04/12/2021] [Indexed: 01/02/2023]
Abstract
The estrogen-related receptor (ERR) family of orphan nuclear receptors are transcriptional activators for genes involved in mitochondrial bioenergetics and metabolism. The goal of this study was to explore the role of ERRα in lipid metabolism and the potential effect of inhibiting ERRα on the development of nonalcoholic fatty liver disease (NAFLD) and nonalcoholic steatohepatitis (NASH). In the current study, three experimental mouse models: high-fat diet, high-carbohydrate diet, and a genetic model of hepatic insulin resistance where the liver hyperinsulinemia signal is mimicked via hepatic deletion of Pten (phosphatase and tensin homolog deleted on chromosome 10), the negative regulator of the insulin/phosphatidylinositol 3-kinase signaling pathway, were used. A recently developed small-molecule inhibitor for ERRα was used to demonstrate that inhibiting ERRα blocked NAFLD development induced by either high-carbohydrate diet or high-fat diet feeding. ERRα inhibition also diminished lipid accumulation and attenuated NASH development in the Pten null mice. Glycerolipid synthesis was discovered as an additional mechanism for ERRα-regulated NAFLD/NASH development and glycerophosphate acyltransferase 4 was identified as a novel transcriptional target of ERRα. In summary, these results establish ERRα as a major transcriptional regulator of lipid biosynthesis in addition to its characterized primary function as a regulator for mitochondrial function. This study recognizes ERRα as a potential target for NAFLD/NASH treatment and elucidates novel signaling pathways regulated by ERRα.
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Affiliation(s)
- Chien-Yu Chen
- Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California
| | - Yang Li
- Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California
| | - Ni Zeng
- Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California
| | - Lina He
- Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California
| | - Xinwen Zhang
- Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California
| | - Taojian Tu
- Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California
| | - Qi Tang
- Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California
| | - Mario Alba
- Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California
| | - Sabrina Mir
- Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California
| | - Eileen X Stiles
- Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California
| | - Handan Hong
- Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California
| | - Enrique Cadenas
- Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California; Department of Biochemistry, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Andrew A Stolz
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Gang Li
- Faculty of Health Sciences, University of Macau, Macau
| | - Bangyan L Stiles
- Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California.
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5
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Chen J, Debebe A, Zeng N, Kopp J, He L, Sander M, Stiles BL. Transformation of SOX9 + cells by Pten deletion synergizes with steatotic liver injury to drive development of hepatocellular and cholangiocarcinoma. Sci Rep 2021; 11:11823. [PMID: 34083580 PMCID: PMC8175600 DOI: 10.1038/s41598-021-90958-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/19/2021] [Indexed: 01/07/2023] Open
Abstract
SOX9 (Sex-determining region Y Box 9) is a well-characterized transcription factor that is a marker for progenitor cells in various tissues. In the liver, cells delineated by SOX9 are responsible for regenerating liver parenchyma when cell proliferation is impaired following chronic injury. However, whether these SOX9+ cells play a role in liver carcinogenesis has not been fully understood, although high SOX9 expression has been linked to poor survival outcome in liver cancer patients. To address this question, we developed a liver cancer mouse model (PtenloxP/loxP; Sox9-CreERT+; R26RYFP) where tumor suppressor Pten (phosphatase and tensin homolog deleted on chromosome ten) is deleted in SOX9+ cells following tamoxifen injection. In this paper, we employ lineage-tracing to demonstrate the tumorigenicity potential of the Pten-, SOX9+ cells. We show that these cells are capable of giving rise to mixed-lineage tumors that manifest features of both hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (CCA). Our results suggest that PTEN loss induces the transformation of SOX9+ cells. We further show that to activate these transformed SOX9+ cells, the presence of liver injury is crucial. Liver injury, induced by hepatotoxin 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) or high-fat diet (HFD), substantially increases tumor incidence and accelerates liver carcinogenesis from SOX9+ cells in Pten null mice but not in control mice. We further examine the mechanisms underlying tumor formation in this model to show that concurrent with the induction of niche signal (i.e., Wnt signaling), liver injury significantly stimulates the expansion of tumor-initiating cells (TICs). Together, these data show that (1) SOX9+ cells have the potential to become TICs following the primary transformation (i.e. Pten deletion) and that (2) liver injury is necessary for promoting the activation and proliferation of transformed SOX9+ cells, resulting in the genesis of mixed-lineage liver tumors.
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Affiliation(s)
- Jingyu Chen
- Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, 90033, USA
| | - Anketse Debebe
- Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, 90033, USA
| | - Ni Zeng
- Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, 90033, USA
| | - Janel Kopp
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Lina He
- Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, 90033, USA
| | - Maike Sander
- Department of Pediatrics and Cellar and Molecular Medicine, UCSD, La Jolla, CA, 92093, USA
| | - Bangyan L Stiles
- Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, 90033, USA.
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
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