1
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Foster EG, Palermo NY, Liu Y, Edagwa B, Gendelman HE, Bade AN. Inhibition of matrix metalloproteinases by HIV-1 integrase strand transfer inhibitors. Front Toxicol 2023; 5:1113032. [PMID: 36896351 PMCID: PMC9988942 DOI: 10.3389/ftox.2023.1113032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/03/2023] [Indexed: 02/25/2023] Open
Abstract
More than fifteen million women with the human immunodeficiency virus type-1 (HIV-1) infection are of childbearing age world-wide. Due to improved and affordable access to antiretroviral therapy (ART), the number of in utero antiretroviral drug (ARV)-exposed children has exceeded a million and continues to grow. While most recommended ART taken during pregnancy suppresses mother to child viral transmission, the knowledge of drug safety linked to fetal neurodevelopment remains an area of active investigation. For example, few studies have suggested that ARV use can be associated with neural tube defects (NTDs) and most notably with the integrase strand transfer inhibitor (INSTI) dolutegravir (DTG). After risk benefit assessments, the World Health Organization (WHO) made recommendations for DTG usage as a first and second-line preferred treatment for infected populations including pregnant women and those of childbearing age. Nonetheless, long-term safety concerns remain for fetal health. This has led to a number of recent studies underscoring the need for biomarkers to elucidate potential mechanisms underlying long-term neurodevelopmental adverse events. With this goal in mind, we now report the inhibition of matrix metalloproteinases (MMPs) activities by INSTIs as an ARV class effect. Balanced MMPs activities play a crucial role in fetal neurodevelopment. Inhibition of MMPs activities by INSTIs during neurodevelopment could be a potential mechanism for adverse events. Thus, comprehensive molecular docking testing of the INSTIs, DTG, bictegravir (BIC), and cabotegravir (CAB), against twenty-three human MMPs showed broad-spectrum inhibition. With a metal chelating chemical property, each of the INSTI were shown to bind Zn++ at the MMP's catalytic domain leading to MMP inhibition but to variable binding energies. These results were validated in myeloid cell culture experiments demonstrating MMP-2 and 9 inhibitions by DTG, BIC and CAB and even at higher degree than doxycycline (DOX). Altogether, these data provide a potential mechanism for how INSTIs could affect fetal neurodevelopment.
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Affiliation(s)
- Emma G. Foster
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, United States
| | - Nicholas Y. Palermo
- Computational Chemistry Core, University of Nebraska Medical Center, Omaha, NE, United States
| | - Yutong Liu
- Department of Radiology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Benson Edagwa
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, United States
| | - Howard E. Gendelman
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, United States
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NeE, United States
| | - Aditya N. Bade
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, United States
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2
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Alomar FA, Tian C, Bidasee SR, Venn ZL, Schroder E, Palermo NY, AlShabeeb M, Edagwa BJ, Payne JJ, Bidasee KR. HIV-Tat Exacerbates the Actions of Atazanavir, Efavirenz, and Ritonavir on Cardiac Ryanodine Receptor (RyR2). Int J Mol Sci 2022; 24:ijms24010274. [PMID: 36613717 PMCID: PMC9820108 DOI: 10.3390/ijms24010274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/05/2022] [Accepted: 12/19/2022] [Indexed: 12/28/2022] Open
Abstract
The incidence of sudden cardiac death (SCD) in people living with HIV infection (PLWH), especially those with inadequate viral suppression, is high and the reasons for this remain incompletely characterized. The timely opening and closing of type 2 ryanodine receptor (RyR2) is critical for ensuring rhythmic cardiac contraction-relaxation cycles, and the disruption of these processes can elicit Ca2+ waves, ventricular arrhythmias, and SCD. Herein, we show that the HIV protein Tat (HIV-Tat: 0-52 ng/mL) and therapeutic levels of the antiretroviral drugs atazanavir (ATV: 0-25,344 ng/mL), efavirenz (EFV: 0-11,376 ng/mL), and ritonavir (RTV: 0-25,956 ng/mL) bind to and modulate the opening and closing of RyR2. Abacavir (0-14,315 ng/mL), bictegravir (0-22,469 ng/mL), Rilpivirine (0-14,360 ng/mL), and tenofovir disoproxil fumarate (0-18,321 ng/mL) did not alter [3H]ryanodine binding to RyR2. Pretreating RyR2 with low HIV-Tat (14 ng/mL) potentiated the abilities of ATV and RTV to bind to open RyR2 and enhanced their ability to bind to EFV to close RyR2. In silico molecular docking using a Schrodinger Prime protein-protein docking algorithm identified three thermodynamically favored interacting sites for HIV-Tat on RyR2. The most favored site resides between amino acids (AA) 1702-1963; the second favored site resides between AA 467-1465, and the third site resides between AA 201-1816. Collectively, these new data show that HIV-Tat, ATV, EFV, and RTV can bind to and modulate the activity of RyR2 and that HIV-Tat can exacerbate the actions of ATV, EFV, and RTV on RyR2. Whether the modulation of RyR2 by these agents increases the risk of arrhythmias and SCD remains to be explored.
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Affiliation(s)
- Fadhel A. Alomar
- Department of Pharmacology and Toxicology, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Chengju Tian
- Departments of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Sean R. Bidasee
- Departments of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Zachary L. Venn
- Departments of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Evan Schroder
- Departments of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Nicholas Y. Palermo
- Vice Chancellor for Research Cores, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Mohammad AlShabeeb
- Population Health Research Section, King Abdullah International Medical Research Center, King Saudi bin Abdulaziz University for Health Sciences, Riyadh 11426, Saudi Arabia
| | - Benson J. Edagwa
- Departments of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Jason J. Payne
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Keshore R. Bidasee
- Departments of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Department of Environment and Occupational Health, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Nebraska Redox Biology Center, Lincoln, NE 68588, USA
- Correspondence: ; Tel.: +402-559-9018; Fax: +402-559-7495
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3
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de Campos L, Palermo NY, Conda-Sheridan M. Targeting SARS-CoV-2 Receptor Binding Domain with Stapled Peptides: An In Silico Study. J Phys Chem B 2021; 125:6572-6586. [PMID: 34114829 PMCID: PMC8230963 DOI: 10.1021/acs.jpcb.1c02398] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/26/2021] [Indexed: 02/06/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved into a pandemic of unprecedented scale. This coronavirus enters cells by the interaction of the receptor binding domain (RBD) with the human angiotensin-converting enzyme 2 receptor (hACE2). In this study, we employed a rational structure-based design to propose 22-mer stapled peptides using the structure of the hACE2 α1 helix as a template. These peptides were designed to retain the α-helical character of the natural structure, to enhance binding affinity, and to display a better solubility profile compared to other designed peptides available in the literature. We employed different docking strategies (PATCHDOCK and ZDOCK) followed by a double-step refinement process (FIBERDOCK) to rank our peptides, followed by stability analysis/evaluation of the interaction profile of the best docking predictions using a 500 ns molecular dynamics (MD) simulation, and a further binding affinity analysis by molecular mechanics with generalized Born and surface area (MM/GBSA) method. Our most promising stapled peptides presented a stable profile and could retain important interactions with the RBD in the presence of the E484K RBD mutation. We predict that these peptides can bind to the viral RBD with similar potency to the control NYBSP-4 (a 30-mer experimentally proven peptide inhibitor). Furthermore, our study provides valuable information for the rational design of double-stapled peptide as inhibitors of SARS-CoV-2 infection.
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Affiliation(s)
- Luana
Janaína de Campos
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Nicholas Y. Palermo
- Computational
Chemistry Core Facility, Vice Chancellor for Research Cores, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Martin Conda-Sheridan
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
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4
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Napoleon JV, Singh S, Rana S, Bendjennat M, Kumar V, Kizhake S, Palermo NY, Ouellette MM, Huxford T, Natarajan A. Small molecule binding to inhibitor of nuclear factor kappa-B kinase subunit beta in an ATP non-competitive manner. Chem Commun (Camb) 2021; 57:4678-4681. [PMID: 33977973 PMCID: PMC8162871 DOI: 10.1039/d1cc01245b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Inhibitor of nuclear factor kappa-B kinase subunit beta (IKKβ) is a key regulator of the cannonical NF-κB pathway. IKKβ has been validated as a drug target for pathological conditions, which include chronic inflammatory diseases and cancer. Pharmacological studies revealed that chronic administration of ATP-competitive IKKβ inhibitors resulted in unexpected toxicity. We previously reported the discovery of 13-197 as a non-toxic IKKβ inhibitor that reduced tumor growth. Here, we show that 13-197 inhibits IKKβ in a ATP non-competitive manner and an allosteric pocket at the interface of the kinase and ubiquitin like domains was identified as the potential binding site.
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Affiliation(s)
- John V Napoleon
- Eppley Institute for Research in Cancer and Allied Diseases, UNMC, USA.
| | - Sarbjit Singh
- Eppley Institute for Research in Cancer and Allied Diseases, UNMC, USA.
| | - Sandeep Rana
- Eppley Institute for Research in Cancer and Allied Diseases, UNMC, USA.
| | - Mourad Bendjennat
- Eppley Institute for Research in Cancer and Allied Diseases, UNMC, USA.
| | - Vikas Kumar
- Mass Spectrometry and Proteomics Core Facility, UNMC, USA
| | - Smitha Kizhake
- Eppley Institute for Research in Cancer and Allied Diseases, UNMC, USA.
| | - Nicholas Y Palermo
- Mass Spectrometry and Proteomics Core Facility, UNMC, USA and Computational Chemistry Core Facility, UNMC, USA
| | - Michel M Ouellette
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, UNMC, USA and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68022, USA
| | - Tom Huxford
- Structural Biochemistry Laboratory, Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA 92182, USA
| | - Amarnath Natarajan
- Eppley Institute for Research in Cancer and Allied Diseases, UNMC, USA. and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68022, USA and Department of Pharmaceutical Sciences and Department of Genetics, Cell Biology and Anatomy, UNMC, USA
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5
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Holmes TR, Al Matouq J, Holmes M, Sioda N, Rudd JC, Bloom C, Nicola L, Palermo NY, Madson JG, Lovas S, Hansen LA. Targeting 14-3-3ε activates apoptotic signaling to prevent cutaneous squamous cell carcinoma. Carcinogenesis 2021; 42:232-242. [PMID: 32816038 PMCID: PMC7905839 DOI: 10.1093/carcin/bgaa091] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 08/06/2020] [Accepted: 08/13/2020] [Indexed: 12/12/2022] Open
Abstract
More than a million cases of cutaneous squamous cell carcinoma are diagnosed in the USA each year, and its incidence is increasing. Most of these malignancies arise from premalignant lesions, providing an opportunity for intervention before malignant progression. We previously documented how cytoplasmic mislocalization of CDC25A in premalignant and malignant skin cancers confers resistance to apoptotic cell death via a mechanism that depends on its interaction with 14-3-3ε. From these data, we hypothesized that 14-3-3ε overexpression drives skin tumor development and progression, such that targeting 14-3-3ε may be a useful strategy for skin cancer treatment. Like CDC25A, 14-3-3ε was overexpressed and mislocalized to the cytoplasm of both benign and malignant human skin cancer. Skin-targeted deletion of the 14-3-3ε gene reduced skin tumor development by 75% and blocked malignant progression. 14-3-3ε suppressed apoptosis through activation of Akt, leading to inhibition of BCL2 associated agonist of cell death and upregulation of Survivin. Using virtual tetrapeptide libraries, we developed a novel peptide that specifically blocked 14-3-3ε heterodimerization and thereby prevented its interaction with CDC25A. The peptide reduced prosurvival signaling, killed skin cancer cells and reduced skin tumor growth in xenograft. Normal skin keratinocytes were unaffected by inhibition or deletion of 14-3-3ε. Thus, targeting of 14-3-3ε dimerization is a promising strategy for the treatment of premalignant skin lesions.
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MESH Headings
- 14-3-3 Proteins/antagonists & inhibitors
- 14-3-3 Proteins/genetics
- 14-3-3 Proteins/metabolism
- 9,10-Dimethyl-1,2-benzanthracene/administration & dosage
- 9,10-Dimethyl-1,2-benzanthracene/toxicity
- Animals
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/therapeutic use
- Apoptosis/drug effects
- Carcinogens/administration & dosage
- Carcinogens/toxicity
- Carcinoma, Squamous Cell/drug therapy
- Carcinoma, Squamous Cell/pathology
- Cell Line, Tumor
- Cytoplasm/drug effects
- Cytoplasm/metabolism
- Female
- Humans
- Keratinocytes
- Male
- Mice
- Mice, Knockout
- Neoplasms, Experimental/chemically induced
- Neoplasms, Experimental/drug therapy
- Neoplasms, Experimental/pathology
- Protein Multimerization/drug effects
- Skin Neoplasms/drug therapy
- Skin Neoplasms/pathology
- Tetradecanoylphorbol Acetate/administration & dosage
- Tetradecanoylphorbol Acetate/analogs & derivatives
- Tetradecanoylphorbol Acetate/toxicity
- Xenograft Model Antitumor Assays
- cdc25 Phosphatases/metabolism
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Affiliation(s)
- Thomas R Holmes
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - Jenan Al Matouq
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - Matti Holmes
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - Natasha Sioda
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - Justin C Rudd
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - Celia Bloom
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - Lauren Nicola
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - Nicholas Y Palermo
- Holland Computing Center, University of Nebraska–Lincoln, Lincoln, NE, USA
| | | | - Sándor Lovas
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - Laura A Hansen
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
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6
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Sagar S, Rathinavel AK, Lutz WE, Struble LR, Khurana S, Schnaubelt AT, Mishra NK, Guda C, Palermo NY, Broadhurst MJ, Hoffmann T, Bayles KW, Reid SPM, Borgstahl GEO, Radhakrishnan P. Bromelain inhibits SARS-CoV-2 infection via targeting ACE-2, TMPRSS2, and spike protein. Clin Transl Med 2021; 11:e281. [PMID: 33635001 PMCID: PMC7811777 DOI: 10.1002/ctm2.281] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/23/2020] [Accepted: 12/28/2020] [Indexed: 12/16/2022] Open
Affiliation(s)
- Satish Sagar
- Eppley Institute for Research in Cancer and Allied DiseasesUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Ashok Kumar Rathinavel
- Eppley Institute for Research in Cancer and Allied DiseasesUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - William E. Lutz
- Eppley Institute for Research in Cancer and Allied DiseasesUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Lucas R. Struble
- Eppley Institute for Research in Cancer and Allied DiseasesUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Surender Khurana
- Division of Viral ProductsCenter for Biologics Evaluation and Research (CBER)FDASilver SpringMarylandUSA
| | - Andy T. Schnaubelt
- Department of Pathology and MicrobiologyUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Nitish Kumar Mishra
- Department of GeneticsCell Biology and AnatomyUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Chittibabu Guda
- Department of GeneticsCell Biology and AnatomyUniversity of Nebraska Medical CenterOmahaNebraskaUSA
- Fred & Pamela Buffett Cancer CenterUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Nicholas Y. Palermo
- Computational Chemistry CoreUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Mara J. Broadhurst
- Department of Pathology and MicrobiologyUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Tobias Hoffmann
- Advanced Light and Electron MicroscopyCentre for Biological Threats and Special Pathogens 4 (ZBS 4)Robert Koch InstituteBerlinGermany
| | - Kenneth W. Bayles
- Department of Pathology and MicrobiologyUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - St. Patrick M. Reid
- Department of Pathology and MicrobiologyUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Gloria E. O. Borgstahl
- Eppley Institute for Research in Cancer and Allied DiseasesUniversity of Nebraska Medical CenterOmahaNebraskaUSA
- Fred & Pamela Buffett Cancer CenterUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Prakash Radhakrishnan
- Eppley Institute for Research in Cancer and Allied DiseasesUniversity of Nebraska Medical CenterOmahaNebraskaUSA
- Department of Pathology and MicrobiologyUniversity of Nebraska Medical CenterOmahaNebraskaUSA
- Department of GeneticsCell Biology and AnatomyUniversity of Nebraska Medical CenterOmahaNebraskaUSA
- Fred & Pamela Buffett Cancer CenterUniversity of Nebraska Medical CenterOmahaNebraskaUSA
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7
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Kumar EA, Yuan Z, Palermo NY, Dong L, Ahmad G, Lokesh GL, Kolar C, Kizhake S, Borgstahl GEO, Band H, Natarajan A. Peptide truncation leads to a twist and an unusual increase in affinity for casitas B-lineage lymphoma tyrosine kinase binding domain. J Med Chem 2012; 55:3583-7. [PMID: 22394513 DOI: 10.1021/jm300078z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We describe truncation and SAR studies to identify a pentapeptide that binds Cbl tyrosine kinase binding domain with a higher affinity than the parental peptide. The pentapeptide has an alternative binding mode that allows occupancy of a previously uncharacterized groove. A peptide library was used to map the binding site and define the interface landscape. Our results suggest that the pentapeptide is an ideal starting point for the development of inhibitors against Cbl driven diseases.
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Affiliation(s)
- Eric A Kumar
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68022, USA
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8
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Palermo NY, Thomas P, Murphy RF, Lovas S. Hexapeptide fragment of carcinoembryonic antigen which acts as an agonist of heterogeneous ribonucleoprotein M. J Pept Sci 2012; 18:252-60. [PMID: 22392880 DOI: 10.1002/psc.2393] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 12/08/2011] [Accepted: 12/12/2011] [Indexed: 12/15/2022]
Abstract
Colorectal cancers with metastatic potential secrete the glycoprotein carcinoembryonic antigen (CEA). CEA has been implicated in colorectal cancer metastasis by inducing Kupffer cells to produce inflammatory cytokines which, in turn, make the hepatic micro-environment ideal for tumor cell implantation. CEA binds to the heterogeneous ribonucleoprotein M (hnRNP M) which acts as a cell surface receptor in Kupffer cells. The amino acid sequence in CEA, which binds the hnRNP M receptor, is Tyr-Pro-Glu-Leu-Pro-Lys. In this study, the structure of Ac-Tyr-Pro-Glu-Leu-Pro-Lys-NH₂ (YPELPK) was investigated using electronic circular dichroism, vibrational circular dichroism, and molecular dynamics simulations. The binding of the peptide to hnRNP M was also investigated using molecular docking calculations. The biological activity of YPELPK was studied using differentiated human THP-1 cells, which express hnRNP M on their surface and secrete IL-6 when stimulated by CEA. YPELPK forms a stable polyproline-II helix and stimulates IL-6 production of THP-1 cells at micromolar concentrations.
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Affiliation(s)
- Nicholas Y Palermo
- Departments of Biomedical Sciences, Creighton University, Omaha, NE 68178, USA
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9
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Yuan Z, Kumar EA, Campbell SJ, Palermo NY, Kizhake S, Glover JNM, Natarajan A. Exploiting the P-1 pocket of BRCT domains toward a structure guided inhibitor design. ACS Med Chem Lett 2011; 2:764-767. [PMID: 22046493 DOI: 10.1021/ml200147a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Breast cancer gene 1 carboxy terminus (BRCT) domains are found in a number of proteins that are important for DNA damage response (DDR). The BRCT domains bind phosphorylated proteins and these protein-protein interactions are essential for DDR and DNA repair. High affinity domain specific inhibitors are needed to facilitate the dissection of the protein-protein interactions in the DDR signaling. The BRCT domains of BRCA1 bind phosphorylated protein through a pSXXF consensus recognition motif. We identified a hydrophobic pocket at the P-1 position of the pSXXF binding site. Here we conducted a structure-guided synthesis of peptide analogs with hydrophobic functional groups at the P-1 position. Evaluation of these led to the identification of a peptide mimic 15 with a inhibitory constant (K(i)) of 40 nM for BRCT(BRCA1). Analysis of the TopBP1 and MDC1 BRCT domains suggests a similar approach is viable to design high affinity inhibitors.
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Affiliation(s)
| | | | - Stephen J. Campbell
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | | | | | - J. N. Mark Glover
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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10
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Palermo NY, Natarajan A. Beyond the frog: the evolution of homology models of human IKKβ. Bioorg Med Chem Lett 2011; 21:6081-4. [PMID: 21911292 DOI: 10.1016/j.bmcl.2011.08.051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 08/10/2011] [Accepted: 08/11/2011] [Indexed: 01/02/2023]
Abstract
Nuclear Factor κ B is implicated in tumor progression and chronic inflammatory diseases and is regulated by IκB kinase β (IKKβ). The crystal structure of IKKβ has been recently solved for Xenopus laevis. Homology models of human IKKβ have been developed prior to and after the crystal structure was solved. Here, we compare four models of human IKKβ and evaluate their performance in both broad and focused library docking studies.
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Affiliation(s)
- Nicholas Y Palermo
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE 68198, USA
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11
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Kim BH, Palermo NY, Lovas S, Zaikova T, Keana JFW, Lyubchenko YL. Single-molecule atomic force microscopy force spectroscopy study of Aβ-40 interactions. Biochemistry 2011; 50:5154-62. [PMID: 21553928 DOI: 10.1021/bi200147a] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Misfolding and aggregation of amyloid β-40 (Aβ-40) peptide play key roles in the development of Alzheimer's disease (AD). However, very little is known about the molecular mechanisms underlying these molecular processes. We developed a novel experimental approach that can directly probe aggregation-prone states of proteins and their interactions. In this approach, the proteins are anchored to the surface of the atomic force microscopy substrate (mica) and the probe, and the interaction between anchored molecules is measured in the approach-retraction cycles. We used dynamic force spectroscopy (DFS) to measure the stability of transiently formed dimers. One of the major findings from DFS analysis of α-synuclein (α-Syn) is that dimeric complexes formed by misfolded α-Syn protein are very stable and dissociate over a range of seconds. This differs markedly from the dynamics of monomers, which occurs on a microsecond to nanosecond time scale. Here we applied the same approach to quantitatively characterize interactions of Aβ-40 peptides over a broad range of pH values. These studies showed that misfolded dimers are characterized by lifetimes in the range of seconds. This value depends on pH and varies between 2.7 s for pH 2.7 and 0.1 s for pH 7, indicating that the aggregation properties of Aβ-40 are modulated by the environmental conditions. The analysis of the contour lengths revealed the existence of various pathways for dimer dissociation, suggesting that dimers with different conformations are formed. These structural variations result in different aggregation pathways, leading to different types of oligomers and higher-order aggregates, including fibrils.
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Affiliation(s)
- Bo-Hyun Kim
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, NE, USA
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12
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Csontos J, Palermo NY, Murphy RF, Lovas S. Calculation of weakly polar interaction energies in polypeptides using density functional and local Møller-Plesset perturbation theory. J Comput Chem 2008; 29:1344-52. [PMID: 18172837 DOI: 10.1002/jcc.20898] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The interaction energies of ubiquitous weakly polar interactions in proteins are comparable with those of hydrogen bonds, consequently, they stabilize local, secondary, and tertiary structures. However, the most widely-used density functionals fail to describe the weakly polar interactions. Thus, it is important to find and test functionals which adequately describe and quantify the energetics of such interactions. For this purpose, interaction energies in the hydrophobic core of rubredoxin (PDB id: 1rb9) and in the S22 subset of the JSCH-2005 benchmark database were computed with the BHandHLYP and PWPW91 functionals and with the pseudospectral implementation of the local MP2 (PS-LMP2) method. The cc-pVDZ, cc-pVTZ(-f), cc-pVTZ, cc-pVQZ(-g), aug-cc-pVDZ, aug-cc-VTZ(-f), and aug-cc-pVTZ basis sets were used for the calculations. In the S22 subset the PS-LMP2 results were extrapolated to the complete basis set limit. Furthermore, the a posteriori counterpoise method of Boys and Bernardi was used to correct the basis set superposition errors in the calculation of interaction energies. Calculations using the BHandHLYP functional, both for the various weakly polar interactions in rubredoxin and for the dispersion interactions in the S22 subset, were in good agreement with those using the coupled cluster (CCSD(T)) and the resolution of identity MP2 (RIMP2) methods and clearly outperformed both the PWPW91 functional and the PS-LMP2 method. The results for the S22 hydrogen bonded subset, obtained with PWPW91 calculations, were closest to those of the reference high level calculations. For the "mixed" (hydrogen bonded and dispersive) interactions in the S22 subset, results obtained with the BHandHLYP and PS-LMP2 calculations agreed well with the reference calculations.
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Affiliation(s)
- József Csontos
- Department of Biomedical Sciences, Creighton University Medical Center, 2500 California Plaza, Omaha, Nebraska 68178, USA
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Hatfield MPD, Palermo NY, Csontos J, Murphy RF, Lovas S. Quantum chemical quantification of weakly polar interaction energies in the TC5b miniprotein. J Phys Chem B 2008; 112:3503-8. [PMID: 18303883 DOI: 10.1021/jp077674h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The tertiary structure of the TC5b miniprotein is stabilized by inter-residue interactions of the Trp-cage, which is composed of a Tyr and several Pro residues surrounding a central Trp residue. The interactions include Ar-Ar (aromatic side-chain-aromatic side-chain), Ar-NH (aromatic side-chain-backbone amide), and CH-pi (aromatic side-chain-aliphatic hydrogen) interactions. In the present work, the strength of the weakly polar interactions found in the TC5b miniprotein was quantified using all of the available 38 NMR structures (1L2Y) from the Protein Data Bank with DFT quantum chemical calculations at the BHandHLYP/cc-pVTZ level of theory and molecular fragmentation with capping of the partial structures. The energies of interaction between the individual residues of the Trp-cage range between -5.85+/-1.41 and -21.30+/-0.88 kcal mol(-1), leading to a significant total structural stabilization energy of -52.13+/-2.56 kcal mol(-1) of which about 50% is from the weakly polar interactions. Furthermore, the strengths of the individual weakly polar interactions are between -2.32+/-0.17 and -2.93+/-0.12 kcal mol(-1) for the CH-pi interactions, between -2.48+/-0.97 and -3.09+/-1.02 kcal mol(-1) for the Ar-NH interaction and -2.74+/-1.06 kcal mol(-1) for the Ar-Ar interaction.
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Hatfield MPD, Palermo NY, Csontos J, Murphy RF, Lovas S. Evaluation of methods to cap molecular fragments in calculating energies of interaction in avian pancreatic polypeptide. Int J Quantum Chem 2008; 108:1017-1021. [PMID: 18985167 PMCID: PMC2577377 DOI: 10.1002/qua.21553] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The accuracy of the determination of the energy of interaction between Phe20 and the Pro5-Thr6-Tyr7-Pro8 complex inside the hydrophobic core of avian pancreatic polypeptide was investigated using three capping strategies for molecular fractionation with conjugated caps and DFT quantum chemical calculations at the BHandHLYP/cc-pVTZ level of theory. The most accurate determination resulted from acetylation of the alpha-amino group combined with methyl amidation of the alpha-carbonyl group with relative deviations less than 10%. Combinations of hydrogenation of the alpha-amino group with the replacement of the alpha-carbonyl group with a hydrogen and the hydrogenation of the alpha-amino group with methylation of the alpha-carbonyl group were less accurate, leading to relative deviations up to 35%. Choice of capping methods depends on the structural features of the polypeptide system, the desired accuracy and the available computational resources.
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Affiliation(s)
- Marcus P. D. Hatfield
- Nebraska Wesleyan University, Lincoln, NE 68504, U.S.A
- Department of Biomedical Sciences, Creighton University, Omaha, NE 68178, U.S.A
| | - Nicholas Y. Palermo
- Department of Biomedical Sciences, Creighton University, Omaha, NE 68178, U.S.A
| | - József Csontos
- Department of Biomedical Sciences, Creighton University, Omaha, NE 68178, U.S.A
| | - Richard F. Murphy
- Department of Biomedical Sciences, Creighton University, Omaha, NE 68178, U.S.A
| | - Sándor Lovas
- Department of Biomedical Sciences, Creighton University, Omaha, NE 68178, U.S.A
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Palermo NY, Csontos J, Murphy RF, Lovas S. The Role of Aromatic Residues in Stabilizing the Secondary and Tertiary Structure of Avian Pancreatic Polypeptide. Int J Quantum Chem 2008; 108:814-819. [PMID: 18985166 PMCID: PMC2577375 DOI: 10.1002/qua.21521] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Avian Pancreatic Polypeptide is a 36 residue protein that exhibits a tertiary fold. Results of previous experimental and computational studies indicate that the structure of aPP is stabilized more by non-bonded interactions than by the hydrophobic effect. Aromatic residues are known to participate in a variety of long range non-bonded interactions, with both backbone atoms and the atoms of other side-chains, which could be responsible, in part, for the stability of both the local secondary structure and the tertiary fold. The effect of these aromatic interactions on the stability of aPP was calculated using BHandHLYP/cc-pVTZ. Aromatic residues were shown to participate in multiple hydrogen bonded and weakly polar interactions in the secondary structure. The energies of the weakly polar interactions are comparable with those of hydrogen bonds. Aromatic residues were also shown to participate in multiple weakly polar interactions across the tertiary fold, again with energies similar to those of hydrogen bonds.
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Affiliation(s)
- Nicholas Y Palermo
- Department of Biomedical Sciences, Creighton University, Omaha, NE 68178, USA
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Abstract
The effects on helical stability of weak polar interactions between aromatic side-chains and the peptide backbone were examined. alpha-Helical model peptides, hexa-Ala, with sequential Tyr replacement, were investigated computationally to obtain the geometries and energetics of the interactions. Geometries were obtained with the B3LYP/6-31G* level of theory. Interaction energies were calculated using BHandHLYP/cc-pVTZ and an improved method to correct for basis set superposition error when fragmentation caused steric clashes. Both i, i + 1 and i, i - 4 interactions were observed when Tyr was in position i = 5. The position of the aromatic residue in the amino acid sequence was crucial in facilitating aromatic-backbone interactions. The distance between the center of the aromatic ring of Tyr and the individual interacting backbone atoms ranged from 3.65 to 5.50 A. The interactions have energies of the same order as hydrogen bonds and, thus, could have a significant impact on the stability of the helix.
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Affiliation(s)
- Nicholas Y Palermo
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, Nebraska, USA
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Csontos J, Palermo NY, Murphy RF, Lovas S. Reply to “Comment on Aromatic-Backbone Interactions in Model α-Helical Peptides”. J Comput Chem 2007. [DOI: 10.1002/jcc.20868] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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