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Chen EV, Nicoludis JM, Powell BM, Li KS, Yatsunyk LA. Crystal structure of a three-tetrad, parallel, K +-stabilized human telomeric G-quadruplex at 1.35 Å resolution. Acta Crystallogr F Struct Biol Commun 2023; 79:144-150. [PMID: 37223975 PMCID: PMC10231262 DOI: 10.1107/s2053230x23003977] [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: 02/04/2023] [Accepted: 05/03/2023] [Indexed: 05/25/2023] Open
Abstract
The crystal structure of the G-rich human telomeric DNA Tel22 has been determined at 1.35 Å resolution in space group P6. Tel22 forms a non-canonical DNA structure called the G-quadruplex. The space group and unit-cell parameters are comparable to those in the crystal structures with PDB codes 6ip3 (1.40 Å resolution) and 1kf1 (2.15 Å resolution). The G-quadruplexes are highly similar in all of the structures. However, this structure of Tel22 displays clear density for polyethylene glycol and two potassium ions, which are located outside the ion channel in the G-quadruplex and play an important role in stabilizing the crystal contacts. In addition, 111 water molecules were identified (compared with 79 and 68 in PDB entries 6ip3 and 1kf1, respectively) that participate in intricate and extensive networks providing high stability to the G-quadruplex.
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Affiliation(s)
- E. V. Chen
- Chemistry and Biochemistry, Swarthmore College, 500 College Avenue, Swarthmore, PA 19081, USA
| | - J. M. Nicoludis
- Chemistry and Biochemistry, Swarthmore College, 500 College Avenue, Swarthmore, PA 19081, USA
| | - B. M. Powell
- Chemistry and Biochemistry, Swarthmore College, 500 College Avenue, Swarthmore, PA 19081, USA
| | - K. S. Li
- Chemistry and Biochemistry, Swarthmore College, 500 College Avenue, Swarthmore, PA 19081, USA
| | - L. A. Yatsunyk
- Chemistry and Biochemistry, Swarthmore College, 500 College Avenue, Swarthmore, PA 19081, USA
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2
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Pandey B, Dev A, Chakravorty D, Bhandare VV, Polley S, Roy S, Basu G. Insights on the disruption of the complex between human positive coactivator 4 and p53 by small molecules. Biochem Biophys Res Commun 2021; 578:15-20. [PMID: 34534740 DOI: 10.1016/j.bbrc.2021.09.020] [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: 08/07/2021] [Revised: 08/29/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
Interaction between human positive coactivator 4 (PC4), an abundant nuclear protein, and the tumor suppressor protein p53 plays a crucial role in initiating apoptosis. In certain neurodegenerative diseases PC4 assisted-p53-dependent apoptosis may play a central role. Thus, disruption of p53-PC4 interaction may be a good drug target for certain disease pathologies. A p53-derived short peptide (AcPep) that binds the C-terminal domain of PC4 (C-PC4) is known to disrupt PC4-p53 interaction. To fully characterize its binding mode and binding site on PC4, we co-crystallized C-PC4 with the peptide and determined its structure. The crystal, despite exhibiting mass spectrometric signature of the peptide, lacked peptide electron density and showed a novel crystal lattice, when compared to C-PC4 crystals without the peptide. Using peptide-docked models of crystal lattices, corresponding to our structure and the peptide-devoid structure we show the origin of the novel crystal lattice to be dynamically bound peptide at the previously identified putative binding site. The weak binding is proposed to be due to the lack of the N-terminal domain of PC4 (N-PC4), which we experimentally show to be disordered with no effect on PC4 stability. Taking cue from the structure, virtual screening of ∼18.6 million small molecules from the ZINC15 database was performed, followed by toxicity and binding free energy filtering. The novel crystal lattice of C-PC4 in presence of the peptide, the role of the disordered N-PC4 and the high throughput identification of potent small molecules will allow a better understanding and control of p53-PC4 interaction.
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Affiliation(s)
- Bhawna Pandey
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Aditya Dev
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Debamitra Chakravorty
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | | | - Smarajit Polley
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Siddhartha Roy
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Gautam Basu
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India.
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Mala John GS, Takeuchi S, Venkatraman G, Rayala SK. Nordihydroguaiaretic Acid in Therapeutics: Beneficial to Toxicity Profiles and the Search for its Analogs. Curr Cancer Drug Targets 2021; 20:86-103. [PMID: 31642411 DOI: 10.2174/1568009619666191022141547] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/26/2019] [Accepted: 08/22/2019] [Indexed: 12/16/2022]
Abstract
Nordihydroguaiaretic acid (NDGA) is a plant lignan obtained from creosote bush, Larrea tridentata and is known to possess antioxidant, anticancer activities and is used in traditional medicine in North America and Mexico. However, its prolonged consumption leads to liver damage and kidney dysfunction. Despite its toxicity and side effects, there is little awareness to forbid its consumption and its use in the treatment of medical ailments has continued over the years. Several reports discuss its therapeutic efficiency and its medical applications have tremendously been on the rise to date. There has been a recent surge of interest in the chemical synthesis of NDGA derivatives for therapeutic applications. NDGA derivatives have been developed as better alternatives to NDGA. Although several NDGA derivatives have been chemically synthesized as evidenced by recent literature, there is a paucity of information on their therapeutic efficacies. This review is to highlight the medicinal applications of NDGA, its toxicity evaluations and discuss the chemical derivatives of NDGA synthesized and studied so far and suggest to continue research interests in the development of NDGA analogs for therapeutic applications. We suggest that NDGA derivatives should be investigated more in terms of chemical synthesis with preferred conformational structures and exploit their biological potentials with future insights to explore in this direction to design and develop structurally modified NDGA derivatives for potential pharmacological properties.
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Affiliation(s)
| | - Satoru Takeuchi
- Factory of Takeuchi Nenshi, TAKENEN, 85NE Takamatsu, Kahoku Ishikawa 929-1215, Japan
| | - Ganesh Venkatraman
- Sri Ramachandra Center for Biomedical Nanotechnology, Sri Ramachandra Institute of Higher Education & Research, Chennai-600116, India
| | - Suresh Kumar Rayala
- Department of Biotechnology, Indian Institute of Technology (IIT), Madras, Chennai-600036, India
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In vivo amelioration of endogenous antitumor autoantibodies via low-dose P4N through the LTA4H/activin A/BAFF pathway. Proc Natl Acad Sci U S A 2016; 113:E7798-E7807. [PMID: 27856749 DOI: 10.1073/pnas.1604752113] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cancer progression is associated with the development of antitumor autoantibodies in patients' sera. Although passive treatment with antitumor antibodies has exhibited remarkable therapeutic efficacy, inhibitory effects on tumor progression by endogenous antitumor autoantibodies (EAAs) have been limited. In this study, we show that P4N, a derivative of the plant lignan nordihydroguaiaretic acid (NDGA), enhanced the production of EAAs and inhibited tumor growth at low noncytotoxic concentrations via its immunoregulatory activity. Intratumoral injection of P4N improved the quantity and quality of EAAs, and passive transfer of P4N-induced EAAs dramatically suppressed lung metastasis formation and prolonged the survival of mice inoculated with metastatic CT26 tumor cells. P4N-induced EAAs specifically recognized two surface antigens, 78-kDa glucose-regulated protein (GRP78) and F1F0 ATP synthase, on the plasma membrane of cancer cells. Additionally, P4N treatment led to B-cell proliferation, differentiation to plasma cells, and high titers of autoantibody production. By serial induction of autocrine and paracrine signals in monocytes, P4N increased B-cell proliferation and antibody production via the leukotriene A4 hydrolase (LTA4H)/activin A/B-cell activating factor (BAFF) pathway. This mechanism provides a useful platform for studying and seeking a novel immunomodulator that can be applied in targeting therapy by improving the quantity and quality of the EAAs.
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Gnabre J, Bates R, Huang RC. Creosote bush lignans for human disease treatment and prevention: Perspectives on combination therapy. J Tradit Complement Med 2015; 5:119-26. [PMID: 26151022 PMCID: PMC4488564 DOI: 10.1016/j.jtcme.2014.11.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 10/02/2014] [Accepted: 11/13/2014] [Indexed: 12/31/2022] Open
Abstract
The medicinal properties of the most successful plant in the deserts of the western hemisphere, the creosote bush (Larrea tridentata), are evidenced by the long traditional usage of the plants by the Native Americans Indian tribes in Southwestern North America and the Amerindians from South America. The plant is rich in simple bisphenyl lignans and tricyclic lignans known as cyclolignans. These compounds are responsible for many of the pharmacological activities of extracts of the plants. Some of these activities, namely antiherpes, antioxidant, antifungal, and anti-inflammatory, were known a century ago. Only recently have further studies revealed other crucial activities of the same plant molecules as powerful agents against human immunodeficiency virus, human papillomavirus, cancer, neurodegenerative diseases, and symptoms of aging. Molecular mechanisms underlying the antiviral and anticancer activities have been elucidated and involve the inhibition of SP1 dependent gene transcription. This review summarizes the recent findings on creosote bush lignans. We introduce the concept of a cocktail of safe well-characterized natural products from the creosote bush that would represent a bridge between oriental herbal medicines and Western drug-based therapies.
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Affiliation(s)
- John Gnabre
- Mal-4 Research Institute, Baltimore, MD, USA
| | - Robert Bates
- Department of Chemistry, University of Arizona, Tucson, AZ, USA
| | - Ru Chih Huang
- Department of Biology, Johns Hopkins University, Mudd Hall, Baltimore, MD, USA
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Ferreira CMH, Pinto ISS, Soares EV, Soares HMVM. (Un)suitability of the use of pH buffers in biological, biochemical and environmental studies and their interaction with metal ions – a review. RSC Adv 2015. [DOI: 10.1039/c4ra15453c] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The present work reviews, discusses and update the metal complexation characteristics of thirty one buffers commercially available. Additionally, their impact on the biological systems is also presented and discussed.
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Affiliation(s)
- Carlos M. H. Ferreira
- REQUIMTE/LAQV
- Department of Chemical Engineering
- Faculty of Engineering
- University of Porto
- Porto
| | - Isabel S. S. Pinto
- REQUIMTE/LAQV
- Department of Chemical Engineering
- Faculty of Engineering
- University of Porto
- Porto
| | - Eduardo V. Soares
- Bioengineering Laboratory
- Chemical Engineering Department
- ISEP-School of Engineering of Polytechnic Institute of Porto
- Porto
- Portugal
| | - Helena M. V. M. Soares
- REQUIMTE/LAQV
- Department of Chemical Engineering
- Faculty of Engineering
- University of Porto
- Porto
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Sheng J, Gan J, Huang Z. Structure-based DNA-targeting strategies with small molecule ligands for drug discovery. Med Res Rev 2013; 33:1119-73. [PMID: 23633219 DOI: 10.1002/med.21278] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nucleic acids are the molecular targets of many clinical anticancer drugs. However, compared with proteins, nucleic acids have traditionally attracted much less attention as drug targets in structure-based drug design, partially because limited structural information of nucleic acids complexed with potential drugs is available. Over the past several years, enormous progresses in nucleic acid crystallization, heavy-atom derivatization, phasing, and structural biology have been made. Many complicated nucleic acid structures have been determined, providing new insights into the molecular functions and interactions of nucleic acids, especially DNAs complexed with small molecule ligands. Thus, opportunities have been created to further discover nucleic acid-targeting drugs for disease treatments. This review focuses on the structure studies of DNAs complexed with small molecule ligands for discovering lead compounds, drug candidates, and/or therapeutics.
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Affiliation(s)
- Jia Sheng
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
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Fulciniti M, Amin S, Nanjappa P, Rodig S, Prabhala R, Li C, Minvielle S, Tai YT, Tassone P, Avet-Loiseau H, Hideshima T, Anderson KC, Munshi NC. Significant biological role of sp1 transactivation in multiple myeloma. Clin Cancer Res 2011; 17:6500-9. [PMID: 21856768 DOI: 10.1158/1078-0432.ccr-11-1036] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
PURPOSE The transcription factor specificity protein 1 (Sp1) controls number of cellular processes by regulating the expression of critical cell cycle, differentiation, and apoptosis-related genes containing proximal GC/GT-rich promoter elements. We here provide experimental and clinical evidence that Sp1 plays an important regulatory role in multiple myeloma (MM) cell growth and survival. EXPERIMENTAL DESIGN We have investigated the functional Sp1 activity in MM cells using a plasmid with Firefly luciferase reporter gene driven by Sp1-responsive promoter. We have also used both siRNA- and short hairpin RNA-mediated Sp1 knockdown to investigate the growth and survival effects of Sp1 on MM cells and further investigated the anti-MM activity of terameprocol (TMP), a small molecule that specifically competes with Sp1-DNA binding in vitro and in vivo. RESULTS We have confirmed high Sp1 activity in MM cells that is further induced by adhesion to bone marrow stromal cells (BMSC). Sp1 knockdown decreases MM cell proliferation and induces apoptosis. Sp1-DNA binding inhibition by TMP inhibits MM cell growth both in vitro and in vivo, inducing caspase-9-dependent apoptosis and overcoming the protective effects of BMSCs. CONCLUSIONS Our results show Sp1 as an important transcription factor in myeloma that can be therapeutically targeted for clinical application by TMP.
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Affiliation(s)
- Mariateresa Fulciniti
- Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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Hwu JR, Hsu CI, Hsu MH, Liang YC, Huang RCC, Lee YC. Glycosylated nordihydroguaiaretic acids as anti-cancer agents. Bioorg Med Chem Lett 2010; 21:380-2. [PMID: 21123067 DOI: 10.1016/j.bmcl.2010.10.137] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 10/23/2010] [Accepted: 10/28/2010] [Indexed: 11/18/2022]
Abstract
Three perglycosylated nordihydroguaiaretic acids (NDGA) were synthesized through the Huiseng 1,3-dipolar cycloaddition reaction. These sugar-NDGA conjugates containing triazole-linkages possessed good solubility in water. NDGA-(triazol-galactose)(4) (12b) and NDGA-(triazol-glucose)(4) (12c) were found to act as inhibitors against human hepatocellular carcinoma Hep3B cells in culture.
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Affiliation(s)
- Jih Ru Hwu
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC.
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Boer DR, Canals A, Coll M. DNA-binding drugs caught in action: the latest 3D pictures of drug-DNA complexes. Dalton Trans 2008:399-414. [PMID: 19122895 DOI: 10.1039/b809873p] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this paper, we review recent DNA-binding agents that are expected to influence the field of DNA-targeting. We restrict ourselves to binders for which the three-dimensional structure in complex with DNA or RNA has been determined by X-ray crystallography or NMR. Furthermore, we primarily focus on unprecedented ways of targeting peculiar DNA structures, such as junctions, quadruplexes, and duplex DNAs different from the B-form. Classical binding modes of small molecular weight compounds to DNA, i.e. groove binding, intercalation and covalent addition are discussed in those cases where the structures represent a novelty. In addition, we review 3D structures of triple-stranded DNA, of the so-called Peptide Nucleic Acids (PNAs), which are oligonucleotide bases linked by a polypeptide backbone, and of aptamers, which are DNA or RNA receptors that are designed combinatorially. A discussion on perspectives in the field of DNA-targeting and on sequence recognition is also provided.
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Affiliation(s)
- D Roeland Boer
- Institute for Research in Biomedicine and Institut de Biologia Molecular de Barcelona (CSIC), Barcelona Science Park, Barcelona, Spain
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Phase I Clinical Trial of Repeat Dose Terameprocol Vaginal Ointment in Healthy Female Volunteers. Sex Transm Dis 2008; 35:577-82. [DOI: 10.1097/olq.0b013e31816766af] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Khanna N, Dalby R, Tan M, Arnold S, Stern J, Frazer N. Phase I/II clinical safety studies of terameprocol vaginal ointment. Gynecol Oncol 2007; 107:554-62. [PMID: 17905420 DOI: 10.1016/j.ygyno.2007.08.074] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2007] [Revised: 08/14/2007] [Accepted: 08/15/2007] [Indexed: 11/22/2022]
Abstract
OBJECTIVES Terameprocol (M4N, EM-1421) is a novel transcription inhibitor that selectively interferes with HPV viral genes E6/E7 with Sp1-dependent promoters, and induces apoptosis by inactivation of the CDC2/cyclin B complex (maturation promoting factor) and production and phosphorylation of survivin. This trial was designed to define the maximum tolerated dose (MTD), dose-limiting toxicity and determine the pharmacokinetic profiles of intravaginal terameprocol in women with HPV-linked cervical squamous intraepithelial neoplasia. METHODS An open label, dose escalation Phase I/II clinical trial enrolled women with biopsy confirmed CIN 1, 2 or 3. Terameprocol (45 or 90 mg) was physician-administered directly to the cervix uteri in 3 once weekly applications. The pharmacokinetics after administration were examined on Day 1 of dosing. Patients underwent colposcopic examinations, HPV testing, biomarker assessments, cytology and cervical punch biopsy. RESULTS Recruitment ended March 30, 2006 and 7 patients were enrolled. Median age was 24 years. There were no serious adverse events (SAEs) and possible treatment-related Adverse Events (AEs) reported were mild and self-limiting. There was no detectable absorption of terameprocol from the vaginal ointment application. CONCLUSIONS Terameprocol in 1% and 2% vaginal ointment use in Phase I/II trials with women with HPV-linked cervical intraepithelial neoplasia has an excellent safety profile, no SAEs reported and mild, self-limiting treatment-related AEs. There was no detectable absorption of terameprocol. These data support the continued evaluation of terameprocol in in vitro and animal efficacy models followed by definitive human Phase II clinical trials in CIN.
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Affiliation(s)
- Niharika Khanna
- Department of Family and Community Medicine, and Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
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Yeh HC, Puleo CM, Lim TC, Ho YP, Giza PE, Huang RCC, Wang TH. A microfluidic-FCS platform for investigation on the dissociation of Sp1-DNA complex by doxorubicin. Nucleic Acids Res 2006; 34:e144. [PMID: 17108358 PMCID: PMC1669725 DOI: 10.1093/nar/gkl787] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The transcription factor (TF) Sp1 is a well-known RNA polymerase II transcription activator that binds to GC-rich recognition sites in a number of essential cellular and viral promoters. In addition, direct interference of Sp1 binding to DNA cognate sites using DNA-interacting compounds may provide promising therapies for suppression of cancer progression and viral replication. In this study, we present a rapid, sensitive and cost-effective evaluation of a GC intercalative drug, doxorubicin (DOX), in dissociating the Sp1–DNA complex using fluorescence correlation spectroscopy (FCS) in a microfluidic system. FCS allows assay miniaturization without compromising sensitivity, making it an ideal analytical method for integration of binding assays into high-throughput, microfluidic platforms. A polydimethylsiloxane (PDMS)-based microfluidic chip with a mixing network is used to achieve specific drug concentrations for drug titration experiments. Using FCS measurements, the IC50 of DOX on the dissociation of Sp1–DNA complex is estimated to be 0.55 μM, which is comparable to that measured by the electrophoretic mobility shift assay (EMSA). However, completion of one drug titration experiment on the proposed microfluidic-FCS platform is accomplished using only picograms of protein and DNA samples and less than 1 h total assay time, demonstrating vast improvements over traditional ensemble techniques.
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Affiliation(s)
- Hsin-Chih Yeh
- Department of Mechanical Engineering, The Johns Hopkins UniversityBaltimore, MD 21218, USA
| | - Christopher M. Puleo
- Department of Biomedical Engineering, The Johns Hopkins UniversityBaltimore, MD 21218, USA
| | - Teck Chuan Lim
- Department of Biomedical Engineering, The Johns Hopkins UniversityBaltimore, MD 21218, USA
| | - Yi-Ping Ho
- Department of Mechanical Engineering, The Johns Hopkins UniversityBaltimore, MD 21218, USA
| | - Paul E. Giza
- Department of Biology, The Johns Hopkins UniversityBaltimore, MD 21218, USA
| | - Ru Chih C. Huang
- Department of Biology, The Johns Hopkins UniversityBaltimore, MD 21218, USA
| | - Tza-Huei Wang
- Department of Mechanical Engineering, The Johns Hopkins UniversityBaltimore, MD 21218, USA
- Department of Biomedical Engineering, The Johns Hopkins UniversityBaltimore, MD 21218, USA
- Whitaker Biomedical Engineering Institute, The Johns Hopkins UniversityBaltimore, MD 21218, USA
- To whom correspondence should be addressed. Tel: +1 410 516 7086; Fax: +1 410 516 7254;
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