1
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Khalid Zia M, Siddiqui T, Ansari S, Muaz M, Ahsan H, Halim Khan F. Insight into the molecular interaction between the anticancer drug, enzalutamide and human alpha-2-macroglobulin: Biochemical and biophysical approach. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 311:123957. [PMID: 38310741 DOI: 10.1016/j.saa.2024.123957] [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: 10/19/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/06/2024]
Abstract
The drug pharmacokinetics is affected upon binding with proteins, thus making drug-protein interactions crucial. This study investigated the interaction between enzalutamide and human major antiproteinase alpha-2-macroglobulin (α2M) by using multi spectroscopic and calorimetric techniques. The spectroscopic techniques such as circular dichroism (CD), intrinsic fluorescence, and UV-visible absorption were used to determine the mechanism of enzalutamide-α2M interaction. Studies on the quenching of fluorescence at three different temperatures showed that the enzalutamide-α2M complex is formed through static quenching mechanism. The change in microenvironment around tyrosine residues in protein was detected through synchronised fluorescence. The secondary structure of α2M was slightly altered by enzalutamide according to far UV-CD spectral analysis. Changes in position of amide I band in FTIR spectra further confirm the secondary structural alteration in α2M. According to thermodynamic characteristics such as fluorescence quenching and isothermal titration calorimetry (ITC), hydrogen bonds and hydrophobic interactions were involved in the interaction machanism. The ITC reiterated the exothermic and spontaneous nature of the interaction. The lower proteinase inhibitory activity of the α2M-enzalutamide conjugate as reflects the disruption of the native α2M structure upon interaction with enzalutamide.
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Affiliation(s)
- Mohammad Khalid Zia
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Tooba Siddiqui
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Sana Ansari
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Mohammad Muaz
- Interdisciplinary Nanotechnology Centre, Aligarh Muslim University, Aligarh 202002, India
| | - Haseeb Ahsan
- Department of Biochemistry, Faculty of Dentistry, Jamia Millia Islamia, New Delhi 110025, India
| | - Fahim Halim Khan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India.
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2
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Jain A, Kishore N. Glycation and drug binding by serum albumin. VITAMINS AND HORMONES 2024; 125:89-115. [PMID: 38997173 DOI: 10.1016/bs.vh.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
Accumulation of glycation products in patients with hyperglycaemic conditions can lead to their reaction with the proteins in the human system such as serum albumin, haemoglobin, insulin, plasma lipoproteins, lens proteins and collagen among others which have important biological functions. Therefore, it is important to understand if glycation of these proteins affects their normal action not only qualitatively, but also importantly quantitatively. Glycation of human serum albumin can easily be carried out over period of weeks and its drug transportability may be examined, in addition to characterisation of the amadori products. A combination of ultrasensitive isothermal titration calorimetry, differential scanning calorimetry, spectroscopy and chromatography provides structure-property-energetics correlations which are important to obtain mechanistic aspects of drug recognition, conformation of the protein, and role of amadori products under conditions of glycation. The role of advance glycation end products is important in recognition of antidiabetic drugs. Further, the extent of glycation of the protein and its implication on drug transportability investigated by direct calorimetric methods enables unravelling mechanistic insights into role of functionality on drug molecules in the binding process, and hinderance in the recognition process, if any, as a result of glycation. It is possible that the drug binding ability of the protein under glycation conditions may not be adversely affected, or may even lead to strengthened ability. Rigorous studies on such systems with diverse functionality on the drug molecules is required which is essential in deriving guidelines for improvements in the existing drugs or in the synthesis of new molecular entities directed towards addressing diabetic conditions.
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Affiliation(s)
- Anu Jain
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
| | - Nand Kishore
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India.
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3
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Zang J, Peters F, Cambet Y, Cifuentes-Pagano E, Hissabu MMS, Dustin CM, Svensson LH, Olesen MM, Poulsen MFL, Jacobsen S, Tuelung PS, Narayanan D, Langkilde AE, Gajhede M, Pagano PJ, Jaquet V, Vilhardt F, Bach A. Targeting NOX2 with Bivalent Small-Molecule p47phox-p22phox Inhibitors. J Med Chem 2023; 66:14963-15005. [PMID: 37857466 DOI: 10.1021/acs.jmedchem.3c01548] [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: 10/21/2023]
Abstract
Nicotinamide adenine dinucleotide phosphate oxidase isoform 2 (NOX2) is an enzymatic complex whose function is the regulated generation of reactive oxygen species (ROS). NOX2 activity is central to redox signaling events and antibacterial response, but excessive ROS production by NOX2 leads to oxidative stress and inflammation in a range of diseases. The protein-protein interaction between the NOX2 subunits p47phox and p22phox is essential for NOX2 activation, thus p47phox is a potential drug target. Previously, we identified 2-aminoquinoline as a fragment hit toward p47phoxSH3A-B and converted it to a bivalent small-molecule p47phox-p22phox inhibitor (Ki = 20 μM). Here, we systematically optimized the bivalent compounds by exploring linker types and positioning as well as substituents on the 2-aminoquinoline part and characterized the bivalent binding mode with biophysical methods. We identified several compounds with submicromolar binding affinities and cellular activity and thereby demonstrated that p47phox can be targeted by potent small molecules.
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Affiliation(s)
- Jie Zang
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Felix Peters
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Yves Cambet
- READS unit, Centre Médical Universitaire, University of Geneva, Geneva CH-1211, Switzerland
| | - Eugenia Cifuentes-Pagano
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Department of Pharmacology and ChemicalBiology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Munira Mohamed Shishay Hissabu
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Christopher M Dustin
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Department of Pharmacology and ChemicalBiology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Lars Henrik Svensson
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Martin Mariboe Olesen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Mathias Feldt Lomholt Poulsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Stig Jacobsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Pernille Sønderby Tuelung
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Dilip Narayanan
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Annette Eva Langkilde
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Michael Gajhede
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Patrick J Pagano
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Department of Pharmacology and ChemicalBiology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Vincent Jaquet
- READS unit, Centre Médical Universitaire, University of Geneva, Geneva CH-1211, Switzerland
- Department of Pathology and Immunology, Centre Médical Universitaire, University of Geneva, Geneva CH-1211, Switzerland
| | - Frederik Vilhardt
- Institute of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Anders Bach
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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Cavalieri G, Cilurzo G, Pettorosso L, Mansueto A, Laurini E, Pricl S. Biophysical and docking study on the interaction of anticancer drugs encorafenib and binimetinib with human serum albumin. Eur J Pharm Sci 2023; 189:106550. [PMID: 37527692 DOI: 10.1016/j.ejps.2023.106550] [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: 06/26/2023] [Revised: 07/21/2023] [Accepted: 07/28/2023] [Indexed: 08/03/2023]
Abstract
The utilization of BRAF and MEK inhibitors in combination therapy has demonstrated superior outcomes in the treatment of melanoma as compared to monotherapy. In the present scenario, the combination therapy of Encorafenib (ENC), a BRAF inhibitor, and Binimetinib (BINI), a MEK inhibitor, has been identified as one of the most efficacious treatment modalities for this malignancy. Investigations of protein binding, particularly with human serum albumin (HSA), are essential to understand drug performance and enhance therapeutic outcomes. The investigation of the interplay between small molecule drugs and HSA is of paramount importance, given that such interactions can exert a substantial influence on the pharmacokinetics of these therapeutic agents. The present study aims to bridge these lacunae by implementing a comprehensive approach that integrates fluorescence spectroscopy (FS), isothermal titration calorimetry (ITC), far-ultraviolet circular dichroism (far-UV CD), and molecular simulations. Through analysis of the fluorescence quenching of HSA at three distinct temperatures, it was ascertained that the association constants for the complexes formed between drugs and HSA were of the magnitude of 104 M-1. This suggests that the interactions between the compounds and albumin were moderate and comparable. Simultaneously, the investigation of fluorescence indicated a contrasting binding mechanism for the two inhibitors: ENC predominantly binds to HSA through enthalpic interaction, while BINI/HSA is stabilized by entropic contributions. The data obtained was confirmed through experimental procedures conducted using the ITC method. The results of ligand-competitive displacement experiments indicate that ENC and BINI can bind to HSA within subdomain IIA, specifically Sudlow site I. However, far-UV CD studies show that there are no notable alterations in the structure of HSA upon binding with either of the two inhibitors. Ultimately, the results were supported by computational molecular analysis, which identified the key interactions that contribute to the stabilization of the two ligand/HSA complexes.
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Affiliation(s)
- Gabriele Cavalieri
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy
| | - Giulia Cilurzo
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy
| | - Lorenzo Pettorosso
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy
| | - Andrea Mansueto
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy
| | - Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy.
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy; Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, ul. Pomorska 141/143, 90-236 Łódź, Poland
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5
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Wang G, Moitessier N, Mittermaier AK. Computational and biophysical methods for the discovery and optimization of covalent drugs. Chem Commun (Camb) 2023; 59:10866-10882. [PMID: 37609777 DOI: 10.1039/d3cc03285j] [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: 08/24/2023]
Abstract
Drugs that act by covalently attaching to their targets have been used to treat human diseases for over a hundred years. However, the deliberate design of covalent drugs was discouraged due to concerns of toxicity and off-target effects. Recent successes in covalent drug discovery have sparked fresh interest in this field. New screening and testing methods aimed at covalent inhibitors can play pivotal roles in facilitating the discovery process. This feature article focuses on computational and biophysical advances originating from our labs over the past decade and how these approaches have contributed to the design of prolyl oligopeptidase (POP) and SARS-CoV-2 3CLpro covalent inhibitors.
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Affiliation(s)
- Guanyu Wang
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.
| | - Nicolas Moitessier
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.
| | - Anthony K Mittermaier
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.
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6
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Arar S, Haque MA, Kayed R. Protein aggregation and neurodegenerative disease: Structural outlook for the novel therapeutics. Proteins 2023:10.1002/prot.26561. [PMID: 37530227 PMCID: PMC10834863 DOI: 10.1002/prot.26561] [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: 06/08/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 08/03/2023]
Abstract
Before the controversial approval of humanized monoclonal antibody lecanemab, which binds to the soluble amyloid-β protofibrils, all the treatments available earlier, for Alzheimer's disease (AD) were symptomatic. The researchers are still struggling to find a breakthrough in AD therapeutic medicine, which is partially attributable to lack in understanding of the structural information associated with the intrinsically disordered proteins and amyloids. One of the major challenges in this area of research is to understand the structural diversity of intrinsically disordered proteins under in vitro conditions. Therefore, in this review, we have summarized the in vitro applications of biophysical methods, which are aimed to shed some light on the heterogeneity, pathogenicity, structures and mechanisms of the intrinsically disordered protein aggregates associated with proteinopathies including AD. This review will also rationalize some of the strategies in modulating disease-relevant pathogenic protein entities by small molecules using structural biology approaches and biophysical characterization. We have also highlighted tools and techniques to simulate the in vivo conditions for native and cytotoxic tau/amyloids assemblies, urge new chemical approaches to replicate tau/amyloids assemblies similar to those in vivo conditions, in addition to designing novel potential drugs.
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Affiliation(s)
- Sharif Arar
- Mitchell Center for Neurodegenerative Diseases
- Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, 77555, USA
- Department of Chemistry, School of Science, The University of Jordan, Amman 11942, Jordan
| | - Md Anzarul Haque
- Mitchell Center for Neurodegenerative Diseases
- Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, 77555, USA
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases
- Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, 77555, USA
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7
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Asano W, Yamanaka K, Ohara Y, Uhara T, Doi S, Orita T, Iwanaga T, Adachi T, Fujioka S, Akaki T, Ikegashira K, Hantani Y. Fragment-Based Discovery of Novel VE-PTP Inhibitors Using Orthogonal Biophysical Techniques. Biochemistry 2023. [PMID: 37414577 DOI: 10.1021/acs.biochem.3c00079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Tyrosine phosphorylation is an essential post-translational modification that regulates various biological events and is implicated in many diseases including cancer and atherosclerosis. Vascular endothelial protein tyrosine phosphatase (VE-PTP), which plays an important role in vascular homeostasis and angiogenesis, is therefore an attractive drug target for these diseases. However, there are still no drugs targeting PTP including VE-PTP. In this paper, we report the discovery of a novel VE-PTP inhibitor, Cpd-2, by fragment-based screening combining various biophysical techniques. Cpd-2 is the first VE-PTP inhibitor with a weakly acidic structure and high selectivity, unlike known strongly acidic inhibitors. We believe that this compound represents a new possibility for the development of bioavailable VE-PTP inhibitors.
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Affiliation(s)
- Wataru Asano
- Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Kenji Yamanaka
- Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Yasunori Ohara
- Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Toru Uhara
- Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Satoki Doi
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Takuya Orita
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Tomoko Iwanaga
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Tsuyoshi Adachi
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Shingo Fujioka
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Tatsuo Akaki
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Kazutaka Ikegashira
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Yoshiji Hantani
- Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
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8
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Nirgude S, Ravindran F, Kumar S, Sharma S, Mahadeva R, Mhatre A, Karki SS, Choudhary B. A Coumarin-Imidazothiadiazole Derivative, SP11 Abrogates Tumor Growth by Targeting HSP90 and Its Client Proteins. Molecules 2023; 28:5226. [PMID: 37446888 DOI: 10.3390/molecules28135226] [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: 05/30/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Despite several treatment options for blood cancer, mortality remains high due to relapse and the disease's aggressive nature. Elevated levels of HSP90, a molecular chaperone essential for protein folding, are associated with poor prognosis in leukemia and lymphoma. HSP90 as a target for chemotherapy has been met with limited success due to toxicity and induction of heat shock. This study tested the activity of an HSP90 inhibitor, SP11, against leukemic cells, mouse lymphoma allograft, and xenograft models. SP11 induced cytotoxicity in vitro in leukemic cell lines and induced cell death via apoptosis, with minimal effect on normal cells. SP11 induced cell death by altering the status of HSP90 client proteins both in vitro and in vivo. SP11 reduced the tumor burden in allograft and xenograft mouse models without apparent toxicity. The half-life of SP11 in the plasma was approximately 2 h. SP11 binding was observed at both the N-terminal and C-terminal domains of HSP90. C-terminal binding was more potent than N-terminal binding of HSP90 in silico and in vitro using isothermal calorimetry. SP11 bioavailability and minimal toxicity in vivo make it a potential candidate to be developed as a novel anticancer agent.
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Affiliation(s)
- Snehal Nirgude
- Institute of Bioinformatics and Applied Biotechnology, Electronic City Phase 1, Bangalore 560100, Karnataka, India
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Febina Ravindran
- Institute of Bioinformatics and Applied Biotechnology, Electronic City Phase 1, Bangalore 560100, Karnataka, India
| | - Sujeet Kumar
- Dr. Prabhakar B. Kore Basic Science Research Laboratory Center (Off-Campus), Department of Pharmaceutical Chemistry, KLE College of Pharmacy, Rajajinagar, (A Constituent Unit of KLE Academy of Higher Education; Research, Belagavi), Bangalore 560010, Karnataka, India
| | - Shivangi Sharma
- Institute of Bioinformatics and Applied Biotechnology, Electronic City Phase 1, Bangalore 560100, Karnataka, India
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Raghunandan Mahadeva
- Institute of Bioinformatics and Applied Biotechnology, Electronic City Phase 1, Bangalore 560100, Karnataka, India
| | - Anisha Mhatre
- Institute of Bioinformatics and Applied Biotechnology, Electronic City Phase 1, Bangalore 560100, Karnataka, India
| | - Subhas S Karki
- Dr. Prabhakar B. Kore Basic Science Research Laboratory Center (Off-Campus), Department of Pharmaceutical Chemistry, KLE College of Pharmacy, Rajajinagar, (A Constituent Unit of KLE Academy of Higher Education; Research, Belagavi), Bangalore 560010, Karnataka, India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Electronic City Phase 1, Bangalore 560100, Karnataka, India
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Wang C, Shivcharan S, Tian T, Wright S, Ma D, Chang J, Li K, Song K, Xu C, Rathinam VA, Ruan J. Structural basis for GSDMB pore formation and its targeting by IpaH7.8. Nature 2023; 616:590-597. [PMID: 36991122 PMCID: PMC10115629 DOI: 10.1038/s41586-023-05832-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 02/13/2023] [Indexed: 03/31/2023]
Abstract
Gasdermins (GSDMs) are pore-forming proteins that play critical roles in host defence through pyroptosis1,2. Among GSDMs, GSDMB is unique owing to its distinct lipid-binding profile and a lack of consensus on its pyroptotic potential3-7. Recently, GSDMB was shown to exhibit direct bactericidal activity through its pore-forming activity4. Shigella, an intracellular, human-adapted enteropathogen, evades this GSDMB-mediated host defence by secreting IpaH7.8, a virulence effector that triggers ubiquitination-dependent proteasomal degradation of GSDMB4. Here, we report the cryogenic electron microscopy structures of human GSDMB in complex with Shigella IpaH7.8 and the GSDMB pore. The structure of the GSDMB-IpaH7.8 complex identifies a motif of three negatively charged residues in GSDMB as the structural determinant recognized by IpaH7.8. Human, but not mouse, GSDMD contains this conserved motif, explaining the species specificity of IpaH7.8. The GSDMB pore structure shows the alternative splicing-regulated interdomain linker in GSDMB as a regulator of GSDMB pore formation. GSDMB isoforms with a canonical interdomain linker exhibit normal pyroptotic activity whereas other isoforms exhibit attenuated or no pyroptotic activity. Overall, this work sheds light on the molecular mechanisms of Shigella IpaH7.8 recognition and targeting of GSDMs and shows a structural determinant in GSDMB critical for its pyroptotic activity.
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Affiliation(s)
- Chengliang Wang
- Department of Immunology, School of Medicine, University of Connecticut Health Center, Farmington, CT, USA
| | - Sonia Shivcharan
- Department of Immunology, School of Medicine, University of Connecticut Health Center, Farmington, CT, USA
| | - Tian Tian
- Department of Immunology, School of Medicine, University of Connecticut Health Center, Farmington, CT, USA
| | - Skylar Wright
- Department of Immunology, School of Medicine, University of Connecticut Health Center, Farmington, CT, USA
| | - Danyang Ma
- Department of Immunology, School of Medicine, University of Connecticut Health Center, Farmington, CT, USA
| | - JengYih Chang
- Department of Biochemistry & Molecular Biotechnology and Cryo-Electron Microscopy Core Facility, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kunpeng Li
- Cryo-Electron Microscopy Core, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Kangkang Song
- Department of Biochemistry & Molecular Biotechnology and Cryo-Electron Microscopy Core Facility, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Chen Xu
- Department of Biochemistry & Molecular Biotechnology and Cryo-Electron Microscopy Core Facility, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Vijay A Rathinam
- Department of Immunology, School of Medicine, University of Connecticut Health Center, Farmington, CT, USA
| | - Jianbin Ruan
- Department of Immunology, School of Medicine, University of Connecticut Health Center, Farmington, CT, USA.
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10
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Fiorentino F, Rotili D, Mai A. Native mass spectrometry-directed drug discovery: Recent advances in investigating protein function and modulation. Drug Discov Today 2023; 28:103548. [PMID: 36871843 DOI: 10.1016/j.drudis.2023.103548] [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: 12/18/2022] [Revised: 02/15/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023]
Abstract
Native mass spectrometry (nMS) is a biophysical method for studying protein complexes and can provide insights into subunit stoichiometry and composition, protein-ligand, and protein-protein interactions (PPIs). These analyses are made possible by preserving non-covalent interactions in the gas phase, thereby allowing the analysis of proteins in their native state. Consequently, nMS has been increasingly applied in early drug discovery campaigns for the characterization of protein-drug interactions and the evaluation of PPI modulators. Here, we discuss recent developments in nMS-directed drug discovery and provide a timely perspective on the possible applications of this technology in drug discovery.
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Affiliation(s)
- Francesco Fiorentino
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; Pasteur Institute, Cenci-Bolognetti Foundation, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
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11
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Mazumder S, Sinha A, Ghosh S, Sharma GC, Prusty BM, Manna D, Pal D, Pal C, Dasgupta S. Leishmania LPG interacts with LRR5/LRR6 of macrophage TLR4 for parasite invasion and impairs the macrophage functions. Pathog Dis 2023; 81:ftad019. [PMID: 37604789 DOI: 10.1093/femspd/ftad019] [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: 03/24/2023] [Revised: 08/14/2023] [Accepted: 08/18/2023] [Indexed: 08/23/2023] Open
Abstract
Visceral leishmaniasis (VL) is a severe form of leishmaniasis, primarily affecting the poor in developing countries. Although several studies have highlighted the importance of toll-like receptors (TLRs) in the pathophysiology of leishmaniasis, the role of specific TLRs and their binding partners involved in Leishmania donovani uptake are still elusive. To investigate the mechanism of L. donovani entry inside the macrophages, we found that the parasite lipophosphoglycan (LPG) interacted with the macrophage TLR4, leading to parasite uptake without any significant alteration of macrophage cell viability. Increased parasite numbers within macrophages markedly inhibited lipopolysachharide-induced pro-inflammatory cytokines gene expression. Silencing of macrophage-TLR4, or inhibition of parasite-LPG, significantly stemmed parasite infection in macrophages. Interestingly, we observed a significant enhancement of macrophage migration, and generation of reactive oxygen species (ROS) in the parasite-infected TLR4-silenced macrophages, whereas parasite infection in TLR4-overexpressed macrophages exhibited a notable reduction of macrophage migration and ROS generation. Moreover, mutations in the leucine-rich repeats (LRRs), particularly LRR5 and LRR6, significantly prevented TLR4 interaction with LPG, thus inhibiting cellular parasite entry. All these results suggest that parasite LPG recognition by the LRR5 and LRR6 of macrophage-TLR4 facilitated parasite entry, and impaired macrophage functions. Therefore, targeting LRR5/LRR6 interactions with LPG could provide a novel option to prevent VL.
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Affiliation(s)
- Sayani Mazumder
- Metabolic Disease Biology Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
| | - Archana Sinha
- Metabolic Disease Biology Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
| | - Sanhita Ghosh
- Cellular Immunology and Vector Molecular Biology Laboratory, Department of Zoology, West Bengal State University, Barasat 700126, West Bengal, India
| | - Gurumayum Chourajit Sharma
- Metabolic Disease Biology Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
| | - Biswa Mohan Prusty
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Debasis Manna
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Durba Pal
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar 140001, Punjab, India
| | - Chiranjib Pal
- Cellular Immunology and Vector Molecular Biology Laboratory, Department of Zoology, West Bengal State University, Barasat 700126, West Bengal, India
| | - Suman Dasgupta
- Metabolic Disease Biology Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
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12
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Non-ionic surfactants in drug delivery vehicles: Physicochemical insights with systems of drugs, Igepal CA-630, bovine serum albumin and hen egg-white lysozyme. Colloids Surf A Physicochem Eng Asp 2023. [DOI: 10.1016/j.colsurfa.2022.130433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Analytical Perspectives in the Study of Polyvalent Interactions of Free and Surface-Bound Oligonucleotides and Their Implications in Affinity Biosensing. Int J Mol Sci 2022; 24:ijms24010175. [PMID: 36613616 PMCID: PMC9820729 DOI: 10.3390/ijms24010175] [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: 12/01/2022] [Revised: 12/17/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
The high affinity and/or selectivity of oligonucleotide-mediated binding offers a myriad of therapeutical and analytical applications, whose rational design implies an accurate knowledge of the involved molecular mechanisms, concurring equilibrium processes and key affinity parameters. Oligonucleotide-functionalized gold surfaces or nanostructures are regularly employed analytical platforms for the development of label-free optical or electrochemical biosensors, and recently, novel detection platform designs have been increasingly considering the synergistic effect of polyvalent binding, involving the simultaneous interaction of two or several oligonucleotide strands. Considering the general lack of studies involving ternary single-stranded DNA (ssDNA) interactions, a complementary analytical workflow involving capillary gel electrophoretic (CGE) mobility shift assay, microcalorimetry and computational modeling has been deployed for the characterization of a series of free and surface-bound binary and ternary oligonucleotide interactions. As a proof of concept, the DNA analogue of MicroRNA 21 (miR21), a well-known oncogenic short MicroRNA (miRNA) sequence, has been chosen as a target molecule, simulating limiting-case scenarios involved in dual molecular recognition models exploited in affinity (bio)sensing. Novel data for the characterization of oligonucleotide interacting modules is revealed, offering a fast and complete mapping of the specific or non-specific, often competing, binary and ternary order interactions in dynamic equilibria, occurring between various free and metal surface-bound oligonucleotides.
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14
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Nguyen TH, La VNT, Burke K, Minh DDL. Bayesian regression and model selection for isothermal titration calorimetry with enantiomeric mixtures. PLoS One 2022; 17:e0273656. [PMID: 36173969 PMCID: PMC9521810 DOI: 10.1371/journal.pone.0273656] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 08/13/2022] [Indexed: 11/26/2022] Open
Abstract
Bayesian regression is performed to infer parameters of thermodynamic binding models from isothermal titration calorimetry measurements in which the titrant is an enantiomeric mixture. For some measurements the posterior density is multimodal, indicating that additional data with a different protocol are required to uniquely determine the parameters. Models of increasing complexity-two-component binding, racemic mixture, and enantiomeric mixture-are compared using model selection criteria. To precisely estimate one of these criteria, the Bayes factor, a variation of bridge sampling is developed.
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Affiliation(s)
- Trung Hai Nguyen
- Laboratory of Theoretical and Computational Biophysics, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Van N. T. La
- Department of Biology, Illinois Institute of Technology, Chicago, IL, United States of America
| | - Kyle Burke
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, United States of America
| | - David D. L. Minh
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, United States of America
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15
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Minetti CA, Remeta DP. Forces Driving a Magic Bullet to Its Target: Revisiting the Role of Thermodynamics in Drug Design, Development, and Optimization. Life (Basel) 2022; 12:1438. [PMID: 36143474 PMCID: PMC9504344 DOI: 10.3390/life12091438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/02/2022] [Accepted: 09/03/2022] [Indexed: 11/27/2022] Open
Abstract
Drug discovery strategies have advanced significantly towards prioritizing target selectivity to achieve the longstanding goal of identifying "magic bullets" amongst thousands of chemical molecules screened for therapeutic efficacy. A myriad of emerging and existing health threats, including the SARS-CoV-2 pandemic, alarming increase in bacterial resistance, and potentially fatal chronic ailments, such as cancer, cardiovascular disease, and neurodegeneration, have incentivized the discovery of novel therapeutics in treatment regimens. The design, development, and optimization of lead compounds represent an arduous and time-consuming process that necessitates the assessment of specific criteria and metrics derived via multidisciplinary approaches incorporating functional, structural, and energetic properties. The present review focuses on specific methodologies and technologies aimed at advancing drug development with particular emphasis on the role of thermodynamics in elucidating the underlying forces governing ligand-target interaction selectivity and specificity. In the pursuit of novel therapeutics, isothermal titration calorimetry (ITC) has been utilized extensively over the past two decades to bolster drug discovery efforts, yielding information-rich thermodynamic binding signatures. A wealth of studies recognizes the need for mining thermodynamic databases to critically examine and evaluate prospective drug candidates on the basis of available metrics. The ultimate power and utility of thermodynamics within drug discovery strategies reside in the characterization and comparison of intrinsic binding signatures that facilitate the elucidation of structural-energetic correlations which assist in lead compound identification and optimization to improve overall therapeutic efficacy.
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Affiliation(s)
- Conceição A. Minetti
- Department of Chemistry and Chemical Biology, Rutgers—The State University of New Jersey, Piscataway, NJ 08854, USA
| | - David P. Remeta
- Department of Chemistry and Chemical Biology, Rutgers—The State University of New Jersey, Piscataway, NJ 08854, USA
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16
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Bui D, Li Z, Kitov PI, Han L, Kitova EN, Fortier M, Fuselier C, Granger Joly de Boissel P, Chatenet D, Doucet N, Tompkins SM, St-Pierre Y, Mahal LK, Klassen JS. Quantifying Biomolecular Interactions Using Slow Mixing Mode (SLOMO) Nanoflow ESI-MS. ACS CENTRAL SCIENCE 2022; 8:963-974. [PMID: 35912341 PMCID: PMC9335916 DOI: 10.1021/acscentsci.2c00215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) is a powerful label-free assay for detecting noncovalent biomolecular complexes in vitro and is increasingly used to quantify binding thermochemistry. A common assumption made in ESI-MS affinity measurements is that the relative ion signals of free and bound species quantitatively reflect their relative concentrations in solution. However, this is valid only when the interacting species and their complexes have similar ESI-MS response factors (RFs). For many biomolecular complexes, such as protein-protein interactions, this condition is not satisfied. Existing strategies to correct for nonuniform RFs are generally incompatible with static nanoflow ESI (nanoESI) sources, which are typically used for biomolecular interaction studies, thereby significantly limiting the utility of ESI-MS. Here, we introduce slow mixing mode (SLOMO) nanoESI-MS, a direct technique that allows both the RF and affinity (K d) for a biomolecular interaction to be determined from a single measurement using static nanoESI. The approach relies on the continuous monitoring of interacting species and their complexes under nonhomogeneous solution conditions. Changes in ion signals of free and bound species as the system approaches or moves away from a steady-state condition allow the relative RFs of the free and bound species to be determined. Combining the relative RF and the relative abundances measured under equilibrium conditions enables the K d to be calculated. The reliability of SLOMO and its ease of use is demonstrated through affinity measurements performed on peptide-antibiotic, protease-protein inhibitor, and protein oligomerization systems. Finally, affinities measured for the binding of human and bacterial lectins to a nanobody, a viral glycoprotein, and glycolipids displayed within a model membrane highlight the tremendous power and versatility of SLOMO for accurately quantifying a wide range of biomolecular interactions important to human health and disease.
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Affiliation(s)
- Duong
T. Bui
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Zhixiong Li
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Pavel I. Kitov
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Ling Han
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Elena N. Kitova
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Marlène Fortier
- Centre
Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université
du Québec, Laval, Québec H7V 1B7, Canada
| | - Camille Fuselier
- Centre
Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université
du Québec, Laval, Québec H7V 1B7, Canada
| | - Philippine Granger Joly de Boissel
- Centre
Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université
du Québec, Laval, Québec H7V 1B7, Canada
| | - David Chatenet
- Centre
Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université
du Québec, Laval, Québec H7V 1B7, Canada
| | - Nicolas Doucet
- Centre
Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université
du Québec, Laval, Québec H7V 1B7, Canada
| | - Stephen M. Tompkins
- Center
for Vaccines and Immunology, University
of Georgia, Athens, Georgia 30605, United States
- Emory-UGA
Centers of Excellence for Influenza Research and Surveillance (CEIRS), Emory University School of Medicine, Athens, Georgia 30322, United States
| | - Yves St-Pierre
- Centre
Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université
du Québec, Laval, Québec H7V 1B7, Canada
| | - Lara K. Mahal
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - John S. Klassen
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
- . Telephone: (780) 492-3501. Fax: (780) 492-8231
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17
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Application of In Silico Filtering and Isothermal Titration Calorimetry for the Discovery of Small Molecule Inhibitors of MDM2. Pharmaceuticals (Basel) 2022; 15:ph15060752. [PMID: 35745671 PMCID: PMC9230431 DOI: 10.3390/ph15060752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 02/01/2023] Open
Abstract
The initial discovery phase of protein modulators, which consists of filtering molecular libraries and in vitro direct binding validation, is central in drug discovery. Thus, virtual screening of large molecular libraries, together with the evaluation of binding affinity by isothermal calorimetry, generates an efficient experimental setup. Herein, we applied virtual screening for discovering small molecule inhibitors of MDM2, a major negative regulator of the tumor suppressor p53, and thus a promising therapeutic target. A library of 20 million small molecules was screened against an averaged model derived from multiple structural conformations of MDM2 based on published structures. Selected molecules originating from the computational filtering were tested in vitro for their direct binding to MDM2 via isothermal titration calorimetry. Three new molecules, representing distinct chemical scaffolds, showed binding to MDM2. These were further evaluated by exploring structure-similar chemical analogues. Two scaffolds were further evaluated by de novo synthesis of molecules derived from the initial molecules that bound MDM2, one with a central oxoazetidine acetamide and one with benzene sulfonamide. Several molecules derived from these scaffolds increased wild-type p53 activity in MCF7 cancer cells. These set a basis for further chemical optimization and the development of new chemical entities as anticancer drugs.
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18
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Duarte LG, Alencar WM, Iacuzio R, Silva NC, Picone CS. Synthesis, characterization and application of antibacterial lactoferrin nanoparticles. Curr Res Food Sci 2022; 5:642-652. [PMID: 35373146 PMCID: PMC8971344 DOI: 10.1016/j.crfs.2022.03.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 12/24/2022] Open
Abstract
Lactoferrin (L) and gellan gum (G) nanoparticles were produced in different biopolymer proportions through electrostatic complexation to enhance the antimicrobial properties of lactoferrin. The nanoparticles were characterized according to size, charge density, morphology and antimicrobial activity against S. aureus and E. coli, in two different broths to show the effect of the broth composition on the nanoparticle activity. The 9L:1G particles showed the highest positive zeta potential (+21.20 mV) and reduced diameter (92.03 nm) which resulted in a minimum inhibitory concentration six times smaller (0.3 mg/ml) than pure lactoferrin (2 mg/ml). However, the bacteriostatic action of nanoparticles was inhibited in the presence of divalent cations. When applied to strawberries as a coating, lactoferrin nanoparticles extended fruit shelf-life up to 6 days in the presence of carboxymethylcellulose (CMC). Therefore, lactoferrin-gellan gum complexation was proved to be a promising tool to enhance lactoferrin antimicrobial action and broaden its application as a food preserver.
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Affiliation(s)
- Larissa G.R. Duarte
- School of Food Engineering, University of Campinas (UNICAMP), 13083-862 Campinas, SP, Brazil
| | - William M.P. Alencar
- School of Food Engineering, University of Campinas (UNICAMP), 13083-862 Campinas, SP, Brazil
| | - Raiza Iacuzio
- School of Food Engineering, University of Campinas (UNICAMP), 13083-862 Campinas, SP, Brazil
| | - Nathália C.C. Silva
- School of Food Engineering, University of Campinas (UNICAMP), 13083-862 Campinas, SP, Brazil
| | - Carolina S.F. Picone
- School of Food Engineering, University of Campinas (UNICAMP), 13083-862 Campinas, SP, Brazil
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19
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Maity S, Gridnev A, Misra JR. Assays Used for Discovering Small Molecule Inhibitors of YAP Activity in Cancers. Cancers (Basel) 2022; 14:cancers14041029. [PMID: 35205777 PMCID: PMC8869775 DOI: 10.3390/cancers14041029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/29/2022] [Accepted: 02/13/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Cancer is a disease in which cells grow in an uncontrolled manner. This can be due to excessive cell proliferation or reduced cell death or a combination of the two. The Hippo signaling pathway, when misregulated, promotes excessive growth and cancer development by inducing uncontrolled cell proliferation and inhibiting cell death. This is achieved due to unregulated activity of the oncogenic effector of this pathway, YAP/TAZ. Therefore, it is critical to develop inhibitors to disrupt YAP activity in cancers. This article reviews the different types of assays that are used in development of small molecule inhibitors for YAP activity in cancers. Abstract YAP/TAZ are transcriptional coactivators that function as the key downstream effectors of Hippo signaling. They are commonly misregulated in most human cancers, which exhibit a higher level of expression and nuclear localization of YAP/TAZ, and display addiction to YAP-dependent transcription. In the nucleus, these coactivators associate with TEA domain transcription factors (TEAD1-4) to regulate the expression of genes that promote cell proliferation and inhibit cell death. Together, this results in an excessive growth of the cancerous tissue. Further, YAP/TAZ play a critical role in tumor metastasis and chemotherapy resistance by promoting cancer stem cell fate. Furthermore, they affect tumor immunity by promoting the expression of PD-L1. Thus, YAP plays an important role in multiple aspects of cancer biology and thus, provides a critical target for cancer therapy. Here we discuss various assays that are used for conducting high-throughput screens of small molecule libraries for hit identification, and subsequent hit validation for successful discovery of potent inhibitors of YAP-transcriptional activity. Furthermore, we describe the advantages and limitations of these assays.
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20
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KRAS(G12D) can be targeted by potent inhibitors via formation of salt bridge. Cell Discov 2022; 8:5. [PMID: 35075146 PMCID: PMC8786924 DOI: 10.1038/s41421-021-00368-w] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 12/23/2021] [Indexed: 12/11/2022] Open
Abstract
KRAS mutation occurs in nearly 30% of human cancers, yet the most prevalent and oncogenic KRAS(G12D) variant still lacks inhibitors. Herein, we designed a series of potent inhibitors that can form a salt bridge with KRAS’s Asp12 residue. Our ITC results show that these inhibitors have similar binding affinity with both GDP-bound and GTP-bound KRAS(G12D), and our crystallographic studies reveal the structural basis of inhibitor binding-induced switch-II pocket in KRAS(G12D), experimentally confirming the formation of a salt bridge between the piperazine moiety of the inhibitors and the Asp12 residue of the mutant protein. Among KRAS family proteins and mutants, both ITC and enzymatic assays demonstrate the selectivity of the inhibitors for KRAS(G12D); and the inhibitors disrupt the KRAS–CRAF interaction. We also observed the inhibition of cancer cell proliferation as well as MAPK signaling by a representative inhibitor (TH-Z835). However, since the inhibition was not fully dependent on KRAS mutation status, it is possible that our inhibitors may have off-target effects via targeting non-KRAS small GTPases. Experiments with mouse xenograft models of pancreatic cancer showed that TH-Z835 significantly reduced tumor volume and synergized with an anti-PD-1 antibody. Collectively, our study demonstrates proof-of-concept for a strategy based on salt-bridge and induced-fit pocket formation for KRAS(G12D) targeting, which warrants future medicinal chemistry efforts for optimal efficacy and minimized off-target effects.
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21
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Pessoa JC, Santos MF, Correia I, Sanna D, Sciortino G, Garribba E. Binding of vanadium ions and complexes to proteins and enzymes in aqueous solution. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214192] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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22
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Nasreddine R, Nehmé R. Microscale thermophoresis for studying protein-small molecule affinity: Application to hyaluronidase. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106763] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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23
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Sullivan JR, Lupien A, Kalthoff E, Hamela C, Taylor L, Munro KA, Schmeing TM, Kremer L, Behr MA. Efficacy of epetraborole against Mycobacterium abscessus is increased with norvaline. PLoS Pathog 2021; 17:e1009965. [PMID: 34637487 PMCID: PMC8535176 DOI: 10.1371/journal.ppat.1009965] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/22/2021] [Accepted: 09/23/2021] [Indexed: 12/16/2022] Open
Abstract
Mycobacterium abscessus is the most common rapidly growing non-tuberculous mycobacteria to cause pulmonary disease in patients with impaired lung function such as cystic fibrosis. M. abscessus displays high intrinsic resistance to common antibiotics and inducible resistance to macrolides like clarithromycin. As such, M. abscessus is clinically resistant to the entire regimen of front-line M. tuberculosis drugs, and treatment with antibiotics that do inhibit M. abscessus in the lab results in cure rates of 50% or less. Here, we identified epetraborole (EPT) from the MMV pandemic response box as an inhibitor against the essential protein leucyl-tRNA synthetase (LeuRS) in M. abscessus. EPT protected zebrafish from lethal M. abscessus infection and did not induce self-resistance nor against clarithromycin. Contrary to most antimycobacterials, the whole-cell activity of EPT was greater against M. abscessus than M. tuberculosis, but crystallographic and equilibrium binding data showed that EPT binds LeuRSMabs and LeuRSMtb with similar residues and dissociation constants. Since EPT-resistant M. abscessus mutants lost LeuRS editing activity, these mutants became susceptible to misaminoacylation with leucine mimics like the non-proteinogenic amino acid norvaline. Proteomic analysis revealed that when M. abscessus LeuRS mutants were fed norvaline, leucine residues in proteins were replaced by norvaline, inducing the unfolded protein response with temporal changes in expression of GroEL chaperonins and Clp proteases. This supports our in vitro data that supplementation of media with norvaline reduced the emergence of EPT mutants in both M. abscessus and M. tuberculosis. Furthermore, the combination of EPT and norvaline had improved in vivo efficacy compared to EPT in a murine model of M. abscessus infection. Our results emphasize the effectiveness of EPT against the clinically relevant cystic fibrosis pathogen M. abscessus, and these findings also suggest norvaline adjunct therapy with EPT could be beneficial for M. abscessus and other mycobacterial infections like tuberculosis. Current antimycobacterial drugs are inadequate to handle the increasing number of non-tuberculous mycobacteria infections that eclipse tuberculosis infections in many developed countries. Of particular importance for cystic fibrosis patients, Mycobacterium abscessus is notoriously difficult to treat where patients spend extended time on antibiotics with cure rates comparable to extreme drug resistant M. tuberculosis. Here, we identified epetraborole (EPT) with in vitro and in vivo activities against M. abscessus. We showed that EPT targets the editing domain of the leucyl-tRNA synthetase (LeuRS) and that escape mutants lost LeuRS editing activity, making these mutants susceptible to misaminoacylation with leucine mimics. Most importantly, combination therapy of EPT and norvaline limited the rate of EPT resistance in both M. abscessus and M. tuberculosis, and this was the first study to demonstrate improved in vivo efficacy of EPT and norvaline compared to EPT in a murine model of M. abscessus pulmonary infection. The demonstration of norvaline adjunct therapy with EPT for M. abscessus infections is promising for cystic fibrosis patients and could translate to other mycobacterial infections, such as tuberculosis.
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Affiliation(s)
- Jaryd R. Sullivan
- Department of Microbiology & Immunology, McGill University, Montréal, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
- McGill International TB Centre, Montréal, Canada
| | - Andréanne Lupien
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
- McGill International TB Centre, Montréal, Canada
| | - Elias Kalthoff
- Department of Biochemistry, McGill University, Montréal, Canada
- Centre de Recherche en Biologie Structural, McGill University, Montréal, Canada
| | - Claire Hamela
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
| | - Lorne Taylor
- Clinical Proteomics Platform, Research Institute of the McGill University Health Centre, Montréal, Canada
| | - Kim A. Munro
- Department of Biochemistry, McGill University, Montréal, Canada
- Centre de Recherche en Biologie Structural, McGill University, Montréal, Canada
| | - T. Martin Schmeing
- Department of Biochemistry, McGill University, Montréal, Canada
- Centre de Recherche en Biologie Structural, McGill University, Montréal, Canada
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
- INSERM, IRIM, Montpellier, France
| | - Marcel A. Behr
- Department of Microbiology & Immunology, McGill University, Montréal, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
- McGill International TB Centre, Montréal, Canada
- Department of Medicine, McGill University Health Centre, Montréal, Canada
- * E-mail:
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24
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Evolution of biophysical tools for quantitative protein interactions and drug discovery. Emerg Top Life Sci 2021; 5:1-12. [PMID: 33739398 DOI: 10.1042/etls20200258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/23/2021] [Accepted: 02/25/2021] [Indexed: 12/13/2022]
Abstract
With millions of signalling events occurring simultaneously, cells process a continuous flux of information. The genesis, processing, and regulation of information are dictated by a huge network of protein interactions. This is proven by the fact that alterations in the levels of proteins, single amino acid changes, post-translational modifications, protein products arising out of gene fusions alter the interaction landscape leading to diseases such as congenital disorders, deleterious syndromes like cancer, and crippling diseases like the neurodegenerative disorders which are often fatal. Needless to say, there is an immense effort to understand the biophysical basis of such direct interactions between any two proteins, the structure, domains, and sequence motifs involved in tethering them, their spatio-temporal regulation in cells, the structure of the network, and their eventual manipulation for intervention in diseases. In this chapter, we will deliberate on a few techniques that allow us to dissect the thermodynamic and kinetic aspects of protein interaction, how innovation has rendered some of the traditional techniques applicable for rapid analysis of multiple samples using small amounts of material. These advances coupled with automation are catching up with the genome-wide or proteome-wide studies aimed at identifying new therapeutic targets. The chapter will also summarize how some of these techniques are suited either in the standalone mode or in combination with other biophysical techniques for the drug discovery process.
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Bhakat S. Pepsin-like aspartic proteases (PAPs) as model systems for combining biomolecular simulation with biophysical experiments. RSC Adv 2021; 11:11026-11047. [PMID: 35423571 PMCID: PMC8695779 DOI: 10.1039/d0ra10359d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/21/2021] [Indexed: 01/26/2023] Open
Abstract
Pepsin-like aspartic proteases (PAPs) are a class of aspartic proteases which shares tremendous structural similarity with human pepsin. One of the key structural features of PAPs is the presence of a β-hairpin motif otherwise known as flap. The biological function of the PAPs is highly dependent on the conformational dynamics of the flap region. In apo PAPs, the conformational dynamics of the flap is dominated by the rotational degrees of freedom associated with χ1 and χ2 angles of conserved Tyr (or Phe in some cases). However it is plausible that dihedral order parameters associated with several other residues might play crucial roles in the conformational dynamics of apo PAPs. Due to their size, complexities associated with conformational dynamics and clinical significance (drug targets for malaria, Alzheimer's disease etc.), PAPs provide a challenging testing ground for computational and experimental methods focusing on understanding conformational dynamics and molecular recognition in biomolecules. The opening of the flap region is necessary to accommodate substrate/ligand in the active site of the PAPs. The BIG challenge is to gain atomistic details into how reversible ligand binding/unbinding (molecular recognition) affects the conformational dynamics. Recent reports of kinetics (K i, K d) and thermodynamic parameters (ΔH, TΔS, and ΔG) associated with macro-cyclic ligands bound to BACE1 (belongs to PAP family) provide a perfect challenge (how to deal with big ligands with multiple torsional angles and select optimum order parameters to study reversible ligand binding/unbinding) for computational methods to predict binding free energies and kinetics beyond typical test systems e.g. benzamide-trypsin. In this work, i reviewed several order parameters which were proposed to capture the conformational dynamics and molecular recognition in PAPs. I further highlighted how machine learning methods can be used as order parameters in the context of PAPs. I then proposed some open ideas and challenges in the context of molecular simulation and put forward my case on how biophysical experiments e.g. NMR, time-resolved FRET etc. can be used in conjunction with biomolecular simulation to gain complete atomistic insights into the conformational dynamics of PAPs.
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Affiliation(s)
- Soumendranath Bhakat
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University P. O. Box 124 SE-22100 Lund Sweden +46-769608418
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Leitner NS, Schroffenegger M, Reimhult E. Polymer Brush-Grafted Nanoparticles Preferentially Interact with Opsonins and Albumin. ACS APPLIED BIO MATERIALS 2020; 4:795-806. [PMID: 33490885 PMCID: PMC7818653 DOI: 10.1021/acsabm.0c01355] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/13/2020] [Indexed: 12/18/2022]
Abstract
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Nanoparticles
find increasing applications in life science and
biomedicine. The fate of nanoparticles in a biological system is determined
by their protein corona, as remodeling of their surface properties
through protein adsorption triggers specific recognition such as cell
uptake and immune system clearance and nonspecific processes such
as aggregation and precipitation. The corona is a result of nanoparticle–protein
and protein–protein interactions and is influenced by particle
design. The state-of-the-art design of biomedical nanoparticles is
the core–shell structure exemplified by superparamagnetic iron
oxide nanoparticles (SPIONs) grafted with dense, well-hydrated polymer
shells used for biomedical magnetic imaging and therapy. Densely grafted
polymer chains form a polymer brush, yielding a highly repulsive barrier
to the formation of a protein corona via nonspecific
particle–protein interactions. However, recent studies showed
that the abundant blood serum protein albumin interacts with dense
polymer brush-grafted SPIONs. Herein, we use isothermal titration
calorimetry to characterize the nonspecific interactions between human
serum albumin, human serum immunoglobulin G, human transferrin, and
hen egg lysozyme with monodisperse poly(2-alkyl-2-oxazoline)-grafted
SPIONs with different grafting densities and core sizes. These particles
show similar protein interactions despite their different “stealth”
capabilities in cell culture. The SPIONs resist attractive interactions
with lysozymes and transferrins, but they both show a significant
exothermic enthalpic and low exothermic entropic interaction with
low stoichiometry for albumin and immunoglobulin G. Our results highlight
that protein size, flexibility, and charge are important to predict
protein corona formation on polymer brush-stabilized nanoparticles.
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Affiliation(s)
- Nikolaus Simon Leitner
- Institute for Biologically Inspired Materials, Department of Nanobiotechnology, University of Natural Resources and Life Sciences, Vienna A-1190, Vienna, Austria
| | - Martina Schroffenegger
- Institute for Biologically Inspired Materials, Department of Nanobiotechnology, University of Natural Resources and Life Sciences, Vienna A-1190, Vienna, Austria
| | - Erik Reimhult
- Institute for Biologically Inspired Materials, Department of Nanobiotechnology, University of Natural Resources and Life Sciences, Vienna A-1190, Vienna, Austria
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Makrecka-Kuka M, Dimitrijevs P, Domracheva I, Jaudzems K, Dambrova M, Arsenyan P. Fused isoselenazolium salts suppress breast cancer cell growth by dramatic increase in pyruvate-dependent mitochondrial ROS production. Sci Rep 2020; 10:21595. [PMID: 33299068 PMCID: PMC7725824 DOI: 10.1038/s41598-020-78620-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 11/26/2020] [Indexed: 12/12/2022] Open
Abstract
The development of targeted drugs for the treatment of cancer remains an unmet medical need. This study was designed to investigate the mechanism underlying breast cancer cell growth suppression caused by fused isoselenazolium salts. The ability to suppress the proliferation of malignant and normal cells in vitro as well as the effect on NAD homeostasis (NAD+, NADH, and NMN levels), NAMPT inhibition and mitochondrial functionality were studied. The interactions of positively charged isoselenazolium salts with the negatively charged mitochondrial membrane model were assessed. Depending on the molecular structure, fused isoselenazolium salts display nanomolar to high micromolar cytotoxicities against MCF-7 and 4T1 breast tumor cell lines. The studied compounds altered NMN, NAD+, and NADH levels and the NAD+/NADH ratio. Mitochondrial functionality experiments showed that fused isoselenazolium salts inhibit pyruvate-dependent respiration but do not directly affect complex I of the electron transfer system. Moreover, the tested compounds induce an immediate dramatic increase in the production of reactive oxygen species. In addition, the isoselenazolothiazolium derivative selectively binds to cardiolipin in a liposomal model. Isoselenazolium salts may be a promising platform for the development of potent drug candidates for anticancer therapy that impact mitochondrial pyruvate-dependent metabolism in breast cancer cells.
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Affiliation(s)
| | - Pavels Dimitrijevs
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, 1006, Latvia.,Riga Stradins University, Dzirciema 16, Riga, 1007, Latvia
| | - Ilona Domracheva
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, 1006, Latvia
| | - Kristaps Jaudzems
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, 1006, Latvia
| | - Maija Dambrova
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, 1006, Latvia.,Riga Stradins University, Dzirciema 16, Riga, 1007, Latvia
| | - Pavel Arsenyan
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, 1006, Latvia.
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Decherchi S, Cavalli A. Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation. Chem Rev 2020; 120:12788-12833. [PMID: 33006893 PMCID: PMC8011912 DOI: 10.1021/acs.chemrev.0c00534] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Indexed: 12/19/2022]
Abstract
Computational studies play an increasingly important role in chemistry and biophysics, mainly thanks to improvements in hardware and algorithms. In drug discovery and development, computational studies can reduce the costs and risks of bringing a new medicine to market. Computational simulations are mainly used to optimize promising new compounds by estimating their binding affinity to proteins. This is challenging due to the complexity of the simulated system. To assess the present and future value of simulation for drug discovery, we review key applications of advanced methods for sampling complex free-energy landscapes at near nonergodicity conditions and for estimating the rate coefficients of very slow processes of pharmacological interest. We outline the statistical mechanics and computational background behind this research, including methods such as steered molecular dynamics and metadynamics. We review recent applications to pharmacology and drug discovery and discuss possible guidelines for the practitioner. Recent trends in machine learning are also briefly discussed. Thanks to the rapid development of methods for characterizing and quantifying rare events, simulation's role in drug discovery is likely to expand, making it a valuable complement to experimental and clinical approaches.
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Affiliation(s)
- Sergio Decherchi
- Computational
and Chemical Biology, Fondazione Istituto
Italiano di Tecnologia, 16163 Genoa, Italy
| | - Andrea Cavalli
- Computational
and Chemical Biology, Fondazione Istituto
Italiano di Tecnologia, 16163 Genoa, Italy
- Department
of Pharmacy and Biotechnology, University
of Bologna, 40126 Bologna, Italy
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29
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Wang Y, Wang G, Moitessier N, Mittermaier AK. Enzyme Kinetics by Isothermal Titration Calorimetry: Allostery, Inhibition, and Dynamics. Front Mol Biosci 2020; 7:583826. [PMID: 33195429 PMCID: PMC7604385 DOI: 10.3389/fmolb.2020.583826] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/11/2020] [Indexed: 12/14/2022] Open
Abstract
Isothermal titration calorimetry (ITC) involves accurately measuring the heat that is released or absorbed in real time when one solution is titrated into another. This technique is usually used to measure the thermodynamics of binding reactions. However, there is mounting interest in using it to measure reaction kinetics, particularly enzymatic catalysis. This application of ITC has been steadily growing for the past two decades, and the method is proving to be sensitive, generally applicable, and capable of providing information on enzyme activity that is difficult to obtain using traditional biochemical assays. This review aims to give a broad overview of the use of ITC to measure enzyme kinetics. It describes several different classes of ITC experiment, their strengths and weaknesses, and recent methodological advancements. A summary of applications in the literature is given and several examples where ITC has been used to investigate challenging aspects of enzyme behavior are presented in more detail. These include examples of allostery, where small-molecule binding outside the active site modulates activity. We describe the use of ITC to measure the strength, mode (i.e., competitive, uncompetitive, or mixed), and association and dissociation kinetics of enzyme inhibitors. Further, we provide examples of ITC applied to complex, heterogeneous mixtures, such as insoluble substrates and live cells. These studies exemplify the wide range of problems where ITC can provide answers, and illustrate the versatility of the technique and potential for future development and applications.
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Affiliation(s)
- Yun Wang
- Department of Chemistry, McGill University, Montreal, QC, Canada
| | - Guanyu Wang
- Department of Chemistry, McGill University, Montreal, QC, Canada
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30
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Ding Y, Ball KA, Webb KJ, Gao Y, D'Alessandro A, Old WM, Stowell MHB, Ding X. On-Chip Acousto Thermal Shift Assay for Rapid and Sensitive Assessment of Protein Thermodynamic Stability. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2003506. [PMID: 32893496 DOI: 10.1002/smll.202003506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/12/2020] [Indexed: 06/11/2023]
Abstract
Thermal shift assays (TSAs) have been extensively used to study thermodynamics of proteins and provide an efficient means to assess protein-ligand binding or protein-protein interactions. However, existing TSAs have limitations, such as being time consuming, labor intensive, or having low sensitivity. Herein, an acousto thermal shift assay (ATSA), the first ultrasound enabled TSA, is reported for real-time analysis of protein thermodynamic stability. It capitalizes the coupling of unique acoustic mechanisms to achieve protein unfolding, concentration, and measurement on a single microfluidic chip within minutes. Compared to conventional TSA methods, the ATSA technique enables ultrafast (at least 30 times faster), highly sensitive (7-34 folds higher), and label-free monitoring of protein-ligand interactions and protein stability. ATSA paves new avenues for protein analysis in biology, medicine, and fast diagnosis.
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Affiliation(s)
- Yonghui Ding
- Paul M. Rady Department of Mechanical Engineering, University of Colorado, Boulder, CO, 80309, USA
| | - Kerri A Ball
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Kristofor J Webb
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Yu Gao
- Paul M. Rady Department of Mechanical Engineering, University of Colorado, Boulder, CO, 80309, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - William M Old
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Michael H B Stowell
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Xiaoyun Ding
- Paul M. Rady Department of Mechanical Engineering, University of Colorado, Boulder, CO, 80309, USA
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31
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Ghorbani F, Fathi F, Aghebati-Maleki L, Abolhasan R, Rikhtegar R, Dolatabadi JEN, Babaloo Z, Khalilzadeh B, Ebrahimi-Warkiani M, Sharifzadeh Z, Rashidi MR, Yousefi M. Kinetic and thermodynamic study of c-Met interaction with single chain fragment variable (scFv) antibodies using phage based surface plasmon resonance. Eur J Pharm Sci 2020; 150:105362. [PMID: 32416255 DOI: 10.1016/j.ejps.2020.105362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 03/19/2020] [Accepted: 04/23/2020] [Indexed: 11/17/2022]
Abstract
Mesenchymal epithelial transition factor (c-Met) has been recently regarded as an attractive target for the treatment of cancer. Our previous study showed that c-Met-specific single chain fragment variables (scFvs) can be considered as a promising therapy for cancer, however, their molecular interaction with c-Met protein have not been assessed. Accordingly, in the current study we aim to evaluate the kinetic and thermodynamic properties of c-Met interaction with these scFvs as anticancer agents by means of surface plasmon resonance (SPR) technique. Phage-scFvs were immobilized on the 11-mercaptoundecanoic acid gold chips after carboxylic groups activation by N-ethyl-N-(3-diethylaminopropyl) carbodiimide/N-hydroxysuccinimide and, then the c-Met binding to each scFvs (ES1, ES2, and ES3) at different concentrations (ranging from 20 to 665 μM) was explored. Kinetic studies revealed that ES1 has the highest affinity (KD = 3.36 × 10-8) toward its target at 25°C. Calculation of thermodynamic parameters also showed positive values for enthalpy and entropy changes, which was representative of hydrophobic forces between c-Met and ES1. Furthermore, the positive value of Gibbs free energy indicated that c-Met binding to ES1 was enthalpy-driven. Taken together, we concluded that produced ES1 can be applied as promising scFv-based therapy for diagnosis or targeting of c-Met in various cancers.
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Affiliation(s)
- Farzaneh Ghorbani
- Stem Cell and Regenerative Medicine Institute (SCARM), Tabriz University of Medical Sciences, Tabriz, Iran; Student research committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farzaneh Fathi
- Pharmaceutical Sciences Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | | | - Rozita Abolhasan
- Stem Cell and Regenerative Medicine Institute (SCARM), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Rikhtegar
- Aging Research Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Zohreh Babaloo
- Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Balal Khalilzadeh
- Stem Cell and Regenerative Medicine Institute (SCARM), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Majid Ebrahimi-Warkiani
- School of Biomedical Engineering, University Technology of Sydney, Sydney, New South Wales, 2007, Australia
| | - Zahra Sharifzadeh
- Department of Immunology, Hybridoma Lab, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad-Reza Rashidi
- Stem Cell and Regenerative Medicine Institute (SCARM), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Yousefi
- Stem Cell and Regenerative Medicine Institute (SCARM), Tabriz University of Medical Sciences, Tabriz, Iran; Aging Research Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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32
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Huang XH, Yan X, Zhang QH, Hong P, Zhang WX, Liu YP, Xu WW, Li B, He QY. Direct targeting of HSP90 with daurisoline destabilizes β-catenin to suppress lung cancer tumorigenesis. Cancer Lett 2020; 489:66-78. [PMID: 32544514 DOI: 10.1016/j.canlet.2020.05.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 05/12/2020] [Accepted: 05/20/2020] [Indexed: 12/24/2022]
Abstract
Lung cancer is the most frequent cancer worldwide with a poor prognosis. Identification of novel cancer targets and useful therapeutic strategies without toxicity are urgently needed. In this study, we screened natural products for anticancer bioactivity in a library consisting of 429 small molecules. We demonstrated for the first time that daurisoline, a constituent of Rhizoma Menispermi, repressed lung cancer cell proliferation by inducing cell cycle arrest at the G1 phase. Furthermore, daurisoline was found not only to suppress the growth of lung tumor xenografts in animals without obvious side effects, but also to inhibit cell migration and invasion. Mechanistically, quantitative proteomics and bioinformatics analyses, Western blotting and qRT-PCR confirmed that daurisoline exerted its anticancer effects by inhibiting the expression levels of β-catenin and its downstream targets c-myc and cyclin D1. Furthermore, our data from Drug Affinity Responsive Target Stability (DARTS), isothermal titration calorimetry (ITC) and a series of functional assays demonstrated that daurisoline could target HSP90 directly and disrupt its interaction with β-catenin, therefore increasing the ubiquitin-mediated proteasomal degradation of β-catenin. This study reveals that daurisoline could be a promising therapeutic strategy for the treatment of lung cancer.
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Affiliation(s)
- Xiao-Hui Huang
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Xin Yan
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Qi-Hua Zhang
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Pan Hong
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Wei-Xia Zhang
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Ya-Ping Liu
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Wen Wen Xu
- MOE Key Laboratory of Tumor Molecular Biology and Guangdong Provincial Key Laboratory of Bioengineering Medicine, National Engineering Research Center of Genetic Medicine, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Bin Li
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China.
| | - Qing-Yu He
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China.
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33
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Gauglitz G. Critical assessment of relevant methods in the field of biosensors with direct optical detection based on fibers and waveguides using plasmonic, resonance, and interference effects. Anal Bioanal Chem 2020; 412:3317-3349. [PMID: 32313998 PMCID: PMC7214504 DOI: 10.1007/s00216-020-02581-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/28/2020] [Accepted: 03/04/2020] [Indexed: 12/16/2022]
Abstract
Direct optical detection has proven to be a highly interesting tool in biomolecular interaction analysis to be used in drug discovery, ligand/receptor interactions, environmental analysis, clinical diagnostics, screening of large data volumes in immunology, cancer therapy, or personalized medicine. In this review, the fundamental optical principles and applications are reviewed. Devices are based on concepts such as refractometry, evanescent field, waveguides modes, reflectometry, resonance and/or interference. They are realized in ring resonators; prism couplers; surface plasmon resonance; resonant mirror; Bragg grating; grating couplers; photonic crystals, Mach-Zehnder, Young, Hartman interferometers; backscattering; ellipsometry; or reflectance interferometry. The physical theories of various optical principles have already been reviewed in detail elsewhere and are therefore only cited. This review provides an overall survey on the application of these methods in direct optical biosensing. The "historical" development of the main principles is given to understand the various, and sometimes only slightly modified variations published as "new" methods or the use of a new acronym and commercialization by different companies. Improvement of optics is only one way to increase the quality of biosensors. Additional essential aspects are the surface modification of transducers, immobilization strategies, selection of recognition elements, the influence of non-specific interaction, selectivity, and sensitivity. Furthermore, papers use for reporting minimal amounts of detectable analyte terms such as value of mass, moles, grams, or mol/L which are difficult to compare. Both these essential aspects (i.e., biochemistry and the presentation of LOD values) can be discussed only in brief (but references are provided) in order to prevent the paper from becoming too long. The review will concentrate on a comparison of the optical methods, their application, and the resulting bioanalytical quality.
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Affiliation(s)
- Günter Gauglitz
- Institute of Physical and Theoretical Chemistry, Eberhard Karls Universität, Auf der Morgenstelle 18, 72076, Tübingen, Germany.
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Characteristic of interaction mechanism between β-lactoglobulin and nobiletin: A multi-spectroscopic, thermodynamics methods and docking study. Food Res Int 2019; 120:255-263. [DOI: 10.1016/j.foodres.2019.01.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 01/03/2019] [Accepted: 01/04/2019] [Indexed: 12/11/2022]
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