1
|
Jose J, Varughese JK, Parvez MK, Mathew TV. Probing the inhibition of MAO-B by chalcones: an integrated approach combining molecular docking, ADME analysis, MD simulation, and MM-PBSA calculations. J Mol Model 2024; 30:103. [PMID: 38478122 DOI: 10.1007/s00894-024-05889-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 02/26/2024] [Indexed: 04/06/2024]
Abstract
CONTEXT Monoamine oxidase B (MAO-B), an enzyme of significant relevance in the realm of neurodegenerative disorders, has garnered considerable attention as a potential target for therapeutic intervention. Natural compounds known as chalcones have shown potential as MAO-B inhibitors. In this particular study, we employed a multimodal computational method to evaluate the inhibitory effects of chalcones on MAO-B. METHODS Molecular docking methods were used to study and assess the complicated binding interactions that occur between chalcones and MAO-B. This extensive analysis provided a valuable and deep understanding of possible binding methods as well as the key residues implicated in the inhibition process. Furthermore, the ADME investigation gave valuable insights into the pharmacokinetic properties of chalcones. This allowed them to be assessed in terms of drug-like attributes. The use of MD simulations has benefited in the research of ligand-protein interactions' dynamic behaviour and temporal stability. MM-PBSA calculations were also done to estimate the binding free energies and acquire a better knowledge and understanding of the binding affinity between chalcones and MAO-B. Our thorough method gives a thorough knowledge of chalcones' potential as MAO-B inhibitors, which will be useful for future experimental validation and drug development efforts in the context of neurodegenerative illnesses.
Collapse
Affiliation(s)
- Jisna Jose
- Department of Chemistry, St. Thomas College, Palai, Arunapuram P.O., Kottayam, Kerala, 686574, India
| | - Jibin K Varughese
- Department of Chemistry, St. Thomas College, Palai, Arunapuram P.O., Kottayam, Kerala, 686574, India
| | - Mohammad Khalid Parvez
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Thomas V Mathew
- Department of Chemistry, St. Thomas College, Palai, Arunapuram P.O., Kottayam, Kerala, 686574, India.
| |
Collapse
|
2
|
Moharana M, Pattanayak SK, Khan F. Bioactive compounds from Pandanous fascicularis as potential therapeutic candidate to tackle hepatitis a inhibition: Docking and molecular dynamics simulation study. J Biomol Struct Dyn 2023; 41:10478-10494. [PMID: 36541128 DOI: 10.1080/07391102.2022.2158940] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022]
Abstract
Due to extensive pharmacological research, medicinal plants the underpinning of indigenous herbal serve as a possible source of key compounds for the development of new drugs. Hepatitis A, one of the most widespread infectious diseases associated with global public health issues. The transmission of hepatitis A virus (HAV) occurs, through personal contact, as well as contaminated food/water. The HAV 3C cysteine protease is a non-structural protein, plays pivotal role in proliferation and viral replication. Significant phytochemicals of Pandanous fascicularis include phytosterol, kobusin, epipinoresinol, and ceroptene, which have a wide variety of biological functions. Through ADMET investigation, we have screened fifteen phytochemicals for this study. Additionally, using molecular docking, these phytochemicals were docked with the HAV 3C protease which signifies the phytochemicals phytosterol, kobusin, epipinoresinol, and ceroptene have a significant capability to bind with hepatitis A virus protein.The docking study was further accompanied by analyzes RMSD, RMSF, Rg, SASA, H-bond number, and principal component analysis through 100 ns MD simulations. The molecular dynamics study reveals that, all four phytochemicals possess considerable binding efficacy with hepatitis A virus protein. Based on our computational study and MMGBSA calculations, phytosterol, kobusin and epipinoresinol phytochemicals may be a potential drug candidate for inhibition of hepatitis A. The potential therapeutic characteristics of the phytochemicals against hepatitis A inhibition offer additional support for the in vitro and in vivo studies in future.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Maheswata Moharana
- Department of Chemistry, National Institute of Technology, Raipur, India
| | | | - Fahmida Khan
- Department of Chemistry, National Institute of Technology, Raipur, India
| |
Collapse
|
3
|
Chancellor A, Alan Simmons R, Khanolkar RC, Nosi V, Beshirova A, Berloffa G, Colombo R, Karuppiah V, Pentier JM, Tubb V, Ghadbane H, Suckling RJ, Page K, Crean RM, Vacchini A, De Gregorio C, Schaefer V, Constantin D, Gligoris T, Lloyd A, Hock M, Srikannathasan V, Robinson RA, Besra GS, van der Kamp MW, Mori L, Calogero R, Cole DK, De Libero G, Lepore M. Promiscuous recognition of MR1 drives self-reactive mucosal-associated invariant T cell responses. J Exp Med 2023; 220:e20221939. [PMID: 37382893 PMCID: PMC10309188 DOI: 10.1084/jem.20221939] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 04/02/2023] [Accepted: 05/25/2023] [Indexed: 06/30/2023] Open
Abstract
Mucosal-associated invariant T (MAIT) cells use canonical semi-invariant T cell receptors (TCR) to recognize microbial riboflavin precursors displayed by the antigen-presenting molecule MR1. The extent of MAIT TCR crossreactivity toward physiological, microbially unrelated antigens remains underexplored. We describe MAIT TCRs endowed with MR1-dependent reactivity to tumor and healthy cells in the absence of microbial metabolites. MAIT cells bearing TCRs crossreactive toward self are rare but commonly found within healthy donors and display T-helper-like functions in vitro. Experiments with MR1-tetramers loaded with distinct ligands revealed significant crossreactivity among MAIT TCRs both ex vivo and upon in vitro expansion. A canonical MAIT TCR was selected on the basis of extremely promiscuous MR1 recognition. Structural and molecular dynamic analyses associated promiscuity to unique TCRβ-chain features that were enriched within self-reactive MAIT cells of healthy individuals. Thus, self-reactive recognition of MR1 represents a functionally relevant indication of MAIT TCR crossreactivity, suggesting a potentially broader role of MAIT cells in immune homeostasis and diseases, beyond microbial immunosurveillance.
Collapse
Affiliation(s)
- Andrew Chancellor
- Experimental Immunology, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | | | | | - Vladimir Nosi
- Experimental Immunology, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Aisha Beshirova
- Experimental Immunology, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Giuliano Berloffa
- Experimental Immunology, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Rodrigo Colombo
- Experimental Immunology, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | | | | | | | | | | | | | - Rory M. Crean
- Department of Biology and Biochemistry, University of Bath, Bath, UK
- Doctoral Training Centre in Sustainable Chemical Technologies, University of Bath, Bath, UK
| | - Alessandro Vacchini
- Experimental Immunology, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Corinne De Gregorio
- Experimental Immunology, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Verena Schaefer
- Experimental Immunology, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Daniel Constantin
- Experimental Immunology, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | | | | | | | | | | | - Gurdyal S. Besra
- School of Biosciences, Institute of Microbiology and Infection, University of Birmingham, Edgbaston, UK
| | | | - Lucia Mori
- Experimental Immunology, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Raffaele Calogero
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | | | - Gennaro De Libero
- Experimental Immunology, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | | |
Collapse
|
4
|
Sanchis I, Spinelli R, Dias J, Brazzolotto X, Rietmann Á, Aimaretti F, Siano ÁS. Inhibition of Human Cholinesterases and in vitro β-Amyloid Aggregation by Rationally Designed Peptides. ChemMedChem 2023; 18:e202200691. [PMID: 36995341 DOI: 10.1002/cmdc.202200691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/08/2023] [Accepted: 03/29/2023] [Indexed: 03/31/2023]
Abstract
The multifactorial nature of Alzheimer's disease (AD) is now widely recognized, which has increased the interest in compounds that can address more than one AD-associated targets. Herein, we report the inhibitory activity on the human cholinesterases (acetylcholinesterase, hAChE and butyrylcholinesterase, hBChE) and on the AChE-induced β-amyloid peptide (Aβ) aggregation by a series of peptide derivatives designed by mutating aliphatic residues for aromatic ones. We identified peptide W3 (LGWVSKGKLL-NH2 ) as an interesting scaffold for the development of new anti-AD multitarget-directed drugs. It showed the lowest IC50 value against hAChE reported for a peptide (0.99±0.02 μM) and inhibited 94.2 %±1.2 of AChE-induced Aβ aggregation at 10 μM. Furthermore, it inhibited hBChE (IC50 , 15.44±0.91 μM), showed no in vivo toxicity in brine shrimp and had shown moderated radical scavenging and Fe2+ chelating capabilities in previous studies. The results are in line with multiple reports showing the utility of the indole moiety for the development of cholinesterase inhibitors.
Collapse
Affiliation(s)
- Ivan Sanchis
- Department of Organic Chemistry, Faculty of Biochemistry and Biological Sciences, National University of the Littoral, Ciudad Universitaria UNL, 3000, Santa Fe, Argentina
- National Scientific and Technical Research Council (CONICET), Ministry of Science, Technology and Innovation, Godoy Cruz, 2290, Ciudad de Buenos Aires, Argentina
| | - Roque Spinelli
- Department of Organic Chemistry, Faculty of Biochemistry and Biological Sciences, National University of the Littoral, Ciudad Universitaria UNL, 3000, Santa Fe, Argentina
- National Scientific and Technical Research Council (CONICET), Ministry of Science, Technology and Innovation, Godoy Cruz, 2290, Ciudad de Buenos Aires, Argentina
| | - José Dias
- Département de Toxicologie et Risques Chimiques, Institut de Recherche Biomédicale des Armées (IRBA) 1, Place du Général Valérie André, 91220, Brétigny-sur-Orge, France
| | - Xavier Brazzolotto
- Département de Toxicologie et Risques Chimiques, Institut de Recherche Biomédicale des Armées (IRBA) 1, Place du Général Valérie André, 91220, Brétigny-sur-Orge, France
| | - Álvaro Rietmann
- Department of Organic Chemistry, Faculty of Biochemistry and Biological Sciences, National University of the Littoral, Ciudad Universitaria UNL, 3000, Santa Fe, Argentina
- National Scientific and Technical Research Council (CONICET), Ministry of Science, Technology and Innovation, Godoy Cruz, 2290, Ciudad de Buenos Aires, Argentina
| | - Florencia Aimaretti
- Department of Organic Chemistry, Faculty of Biochemistry and Biological Sciences, National University of the Littoral, Ciudad Universitaria UNL, 3000, Santa Fe, Argentina
- National Scientific and Technical Research Council (CONICET), Ministry of Science, Technology and Innovation, Godoy Cruz, 2290, Ciudad de Buenos Aires, Argentina
| | - Álvaro S Siano
- Department of Organic Chemistry, Faculty of Biochemistry and Biological Sciences, National University of the Littoral, Ciudad Universitaria UNL, 3000, Santa Fe, Argentina
- National Scientific and Technical Research Council (CONICET), Ministry of Science, Technology and Innovation, Godoy Cruz, 2290, Ciudad de Buenos Aires, Argentina
| |
Collapse
|
5
|
Schmidt J, Chiffelle J, Perez MAS, Magnin M, Bobisse S, Arnaud M, Genolet R, Cesbron J, Barras D, Navarro Rodrigo B, Benedetti F, Michel A, Queiroz L, Baumgaertner P, Guillaume P, Hebeisen M, Michielin O, Nguyen-Ngoc T, Huber F, Irving M, Tissot-Renaud S, Stevenson BJ, Rusakiewicz S, Dangaj Laniti D, Bassani-Sternberg M, Rufer N, Gfeller D, Kandalaft LE, Speiser DE, Zoete V, Coukos G, Harari A. Neoantigen-specific CD8 T cells with high structural avidity preferentially reside in and eliminate tumors. Nat Commun 2023; 14:3188. [PMID: 37280206 DOI: 10.1038/s41467-023-38946-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 05/23/2023] [Indexed: 06/08/2023] Open
Abstract
The success of cancer immunotherapy depends in part on the strength of antigen recognition by T cells. Here, we characterize the T cell receptor (TCR) functional (antigen sensitivity) and structural (monomeric pMHC-TCR off-rates) avidities of 371 CD8 T cell clones specific for neoantigens, tumor-associated antigens (TAAs) or viral antigens isolated from tumors or blood of patients and healthy donors. T cells from tumors exhibit stronger functional and structural avidity than their blood counterparts. Relative to TAA, neoantigen-specific T cells are of higher structural avidity and, consistently, are preferentially detected in tumors. Effective tumor infiltration in mice models is associated with high structural avidity and CXCR3 expression. Based on TCR biophysicochemical properties, we derive and apply an in silico model predicting TCR structural avidity and validate the enrichment in high avidity T cells in patients' tumors. These observations indicate a direct relationship between neoantigen recognition, T cell functionality and tumor infiltration. These results delineate a rational approach to identify potent T cells for personalized cancer immunotherapy.
Collapse
Affiliation(s)
- Julien Schmidt
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Johanna Chiffelle
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Marta A S Perez
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Morgane Magnin
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Sara Bobisse
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Marion Arnaud
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Raphael Genolet
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Julien Cesbron
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - David Barras
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Blanca Navarro Rodrigo
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Fabrizio Benedetti
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Alexandra Michel
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Lise Queiroz
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Petra Baumgaertner
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Philippe Guillaume
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Michael Hebeisen
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
| | - Olivier Michielin
- Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Tu Nguyen-Ngoc
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
| | - Florian Huber
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Melita Irving
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
| | - Stéphanie Tissot-Renaud
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Brian J Stevenson
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Sylvie Rusakiewicz
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Denarda Dangaj Laniti
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Nathalie Rufer
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
| | - David Gfeller
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Lana E Kandalaft
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Daniel E Speiser
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
| | - Vincent Zoete
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - George Coukos
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Alexandre Harari
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland.
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland.
| |
Collapse
|
6
|
Shehata MA, Contreras J, Martín-Hurtado A, Froux A, Mohamed HT, El-Sherif AA, Plaza-Menacho I. Structural and dynamic determinants for highly selective RET kinase inhibition reveal cryptic druggability. J Adv Res 2023; 45:87-100. [PMID: 35595215 PMCID: PMC10006619 DOI: 10.1016/j.jare.2022.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 04/05/2022] [Accepted: 05/05/2022] [Indexed: 11/24/2022] Open
Abstract
INTRODUCTION The structural and dynamic determinants that confer highly selective RET kinase inhibition are poorly understood. OBJECTIVES To explore the druggability landscape of the RET active site in order to uncover structural and dynamic vulnerabilities that can be therapeutically exploited. METHODS We apply an integrated structural, computational and biochemical approach in order to explore the druggability landscape of the RET active site. RESULTS We demonstrate that the that the druggability landscape of the RET active site is determined by the conformational setting of the ATP-binding (P-) loop and its coordination with the αC helix. Open and intermediate P-loop structures display additional druggable vulnerabilities within the active site that were not exploited by first generation RET inhibitors. We identify a cryptic pocket adjacent to the catalytic lysine formed by K758, L760, E768 and L772, that we name the post-lysine pocket, with higher druggability potential than the adenine-binding site and with important implications in the regulation of the phospho-tyrosine kinase activity. Crystal structure and simulation data show that the binding mode of highly-selective RET kinase inhibitors LOXO-292 and BLU-667 is controlled by a synchronous open P-loop and αC-in configuration that allows accessibility to the post-lysine pocket. Molecular dynamics simulations show that these inhibitors efficiently occupy the post-lysine pocket with high stability through the simulation time-scale (300 ns), with both inhibitors forming hydrophobic contacts further stabilized by pi-cation interactions with the catalytic K758. Engineered mutants targeting the post-lysine pocket impact on inhibitor binding and sensitivity, as well as RET tyrosine kinase activity. CONCLUSIONS The identification of the post-lysine pocket as a new druggable vulnerability in the RET kinase and its exploitation by second generation RET inhibitors have important implications for future drug design and the development of personalized therapies for patients with RET-driven cancers.
Collapse
Affiliation(s)
- Moustafa A Shehata
- Kinases, Protein Phosphorylation and Cancer Group, Structural Biology Programme, Spanish National Cancer Research Center (CNIO), Madrid 28029, Spain; Chemistry Department, Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Julia Contreras
- Kinases, Protein Phosphorylation and Cancer Group, Structural Biology Programme, Spanish National Cancer Research Center (CNIO), Madrid 28029, Spain
| | - Ana Martín-Hurtado
- Kinases, Protein Phosphorylation and Cancer Group, Structural Biology Programme, Spanish National Cancer Research Center (CNIO), Madrid 28029, Spain
| | - Aurane Froux
- Kinases, Protein Phosphorylation and Cancer Group, Structural Biology Programme, Spanish National Cancer Research Center (CNIO), Madrid 28029, Spain
| | - Hossam Taha Mohamed
- Zoology Department, Faculty of Science, Cairo University, Giza 12613, Egypt; Faculty of Biotechnology, October University for Modern Sciences and Arts, Giza 12451, Egypt
| | - Ahmed A El-Sherif
- Chemistry Department, Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Iván Plaza-Menacho
- Kinases, Protein Phosphorylation and Cancer Group, Structural Biology Programme, Spanish National Cancer Research Center (CNIO), Madrid 28029, Spain.
| |
Collapse
|
7
|
Chang Y, Hawkins BA, Du JJ, Groundwater PW, Hibbs DE, Lai F. A Guide to In Silico Drug Design. Pharmaceutics 2022; 15:pharmaceutics15010049. [PMID: 36678678 PMCID: PMC9867171 DOI: 10.3390/pharmaceutics15010049] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/28/2022] Open
Abstract
The drug discovery process is a rocky path that is full of challenges, with the result that very few candidates progress from hit compound to a commercially available product, often due to factors, such as poor binding affinity, off-target effects, or physicochemical properties, such as solubility or stability. This process is further complicated by high research and development costs and time requirements. It is thus important to optimise every step of the process in order to maximise the chances of success. As a result of the recent advancements in computer power and technology, computer-aided drug design (CADD) has become an integral part of modern drug discovery to guide and accelerate the process. In this review, we present an overview of the important CADD methods and applications, such as in silico structure prediction, refinement, modelling and target validation, that are commonly used in this area.
Collapse
Affiliation(s)
- Yiqun Chang
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Bryson A. Hawkins
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Jonathan J. Du
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Paul W. Groundwater
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - David E. Hibbs
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Felcia Lai
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
- Correspondence:
| |
Collapse
|
8
|
Bram Y, Duan X, Nilsson-Payant BE, Chandar V, Wu H, Shore D, Fajardo A, Sinha S, Hassan N, Weinstein H, TenOever BR, Chen S, Schwartz RE. Dual-Reporter System for Real-Time Monitoring of SARS-CoV-2 Main Protease Activity in Live Cells Enables Identification of an Allosteric Inhibition Path. ACS BIO & MED CHEM AU 2022; 2:627-641. [PMID: 36570071 PMCID: PMC9603010 DOI: 10.1021/acsbiomedchemau.2c00034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 09/21/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022]
Abstract
The SARS-CoV-2 pandemic is an ongoing threat to global health, and the continuing emergence of contagious variants highlights the urgent need for additional antiviral therapy to attenuate COVID-19 disease. The SARS-CoV-2 main protease (3CLpro) presents an attractive target for such therapy due to its high sequence conservation and key role in the viral life cycle. In this study, we designed a fluorescent-luminescent cell-based reporter for the detection and quantification of 3CLpro intracellular activity. Employing this platform, we examined the efficiency of known protease inhibitors against 3CLpro and further identified potent inhibitors through high-throughput chemical screening. Computational analysis confirmed a direct interaction of the lead compounds with the protease catalytic site and identified a prototype for efficient allosteric inhibition. These developments address a pressing need for a convenient sensor and specific targets for both virus detection and rapid discovery of potential inhibitors.
Collapse
Affiliation(s)
- Yaron Bram
- Division
of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Xiaohua Duan
- Department
of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Benjamin E. Nilsson-Payant
- Department
of Microbiology, Icahn School of Medicine
at Mount Sinai, One Gustav L Levy Place, New York, New York 10029, United
States
| | - Vasuretha Chandar
- Division
of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Hao Wu
- Department
of Physiology, Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Derek Shore
- Department
of Physiology, Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Alvaro Fajardo
- Division
of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Saloni Sinha
- Division
of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Nora Hassan
- Division
of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Harel Weinstein
- Department
of Physiology, Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10065, United States,
| | - Benjamin R. TenOever
- Department
of Microbiology, Icahn School of Medicine
at Mount Sinai, One Gustav L Levy Place, New York, New York 10029, United
States,
| | - Shuibing Chen
- Department
of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States,
| | - Robert E. Schwartz
- Division
of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States,Department
of Physiology, Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10065, United States,
| |
Collapse
|
9
|
Li Z, Chan KC, Nickels JD, Cheng X. Electrostatic Contributions to the Binding Free Energy of Nicotine to the Acetylcholine Binding Protein. J Phys Chem B 2022; 126:8669-8679. [PMID: 36260486 PMCID: PMC10056799 DOI: 10.1021/acs.jpcb.2c04641] [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: 01/11/2023]
Abstract
Biomolecular binding relies on specific attractive interactions between two partner molecules, including electrostatics, dispersion, hydrophobicity, and solvation. Assessing the contributions of electrostatic interactions to binding is key to the understanding of ligand binding mechanisms and the design of improved biomolecular binders. For example, nicotine is a well-known agonist of nicotinic acetylcholine receptors (nAChRs), but the molecular mechanisms for the differential action of nicotine on brain and muscle nAChRs remain elusive. In this work, we have chosen the acetylcholine binding protein (AChBP) in complex with nicotine as a model system to interrogate the electrostatic contributions to nicotine binding. Our absolute binding free energy simulations confirm that nicotine binds AChBP predominantly in its protonated (charged) form. By comparing energetic contributions from decomposed interactions for either neutral or charged nicotine, our calculations shed light on the nature of the binding of nicotine to the AChBP. The preferred binding of charged nicotine over neutral nicotine originates from its stronger electrostatic interactions with AChBP, a cation-π interaction to a tryptophan residue and a hydrogen bond between nicotine and the backbone carbonyl of the tryptophan, whereas the major force driving the binding process appears to be van der Waals interactions. The various nonelectrostatic terms can also indirectly modulate the electrostatic interactions through fine-tuning the binding pose of the ligand in the binding site, providing an explanation of why the binding specificity of nicotine to the brain versus muscle nAChRs is driven by electrostatic interaction, given that the immediate binding site residues, including the key tryptophan residue, are identical in the two receptors.
Collapse
Affiliation(s)
- Zoe Li
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy at The Ohio State University, Columbus, Ohio43210, United States
| | - Kevin C Chan
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy at The Ohio State University, Columbus, Ohio43210, United States
| | - Jonathan D Nickels
- Department of Chemical and Environmental Engineering, University of Cincinnati, Cincinnati, Ohio45221, United States
| | - Xiaolin Cheng
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy at The Ohio State University, Columbus, Ohio43210, United States
- Translational Data Analytics Institute (TDAI) at The Ohio State University, Columbus, Ohio43210, United States
| |
Collapse
|
10
|
Jeevana R, Kavitha AP, Abi TG, Sajith PK, Varughese JK, Aravindakshan KK. Targeting COVID-19 pandemic: in silico evaluation of 2-hydroxy-1, 2-diphenylethanone N(4)-methyl-N(4)-phenylthiosemicarbazone as a potential inhibitor of SARS-CoV-2. Struct Chem 2022; 34:1-17. [PMID: 36274924 PMCID: PMC9574830 DOI: 10.1007/s11224-022-02033-8] [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: 05/23/2022] [Accepted: 08/03/2022] [Indexed: 11/25/2022]
Abstract
The global spread of the COVID-19 pandemic caused by the etiological agent, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), triggered researchers to identify and develop novel antiviral therapeutics. Herein, we report a new molecule 2-hydroxy-1,2-diphenylethanone N(4)-methyl-N(4)-phenyl thiosemicarbazone (BMPTSC), as a potential inhibitor of SARS-CoV-2. BMPTSC was synthesized, characterized by IR and NMR studies, and the structural parameters were analyzed computationally by B3LYP/cc-pVDZ method. Molecular docking studies were performed to get insights into the energetics and compatibility of BMPTSC against various SARS-CoV-2 drug targets. The best docking poses of target protein-BMPTSC complex structures were further subjected to molecular dynamics (MD) simulations. Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations on the binding of BMPTSC with the target proteins viz. spike glycoprotein and ACE-2 protein showed energy values of -179.87 and -145.61 kJ/mol, respectively. Moreover, BMPTSC obeys Lipinski's rule, and further in silico assessment of oral bioavailability, bioactivity scores, ADME, drug-likeness, and medicinal chemistry friendliness suggests that this molecule is a promising candidate for the COVID-19 drug discovery process. Supplementary Information The online version contains supplementary material available at 10.1007/s11224-022-02033-8.
Collapse
Affiliation(s)
- Rajan Jeevana
- PG & Research Department of Chemistry, Govt. College, Madappally, Kozhikode, 673102 Kerala India
| | | | - Thoppilan G. Abi
- PG & Research Department of Chemistry, Sacred Heart College (Autonomous), Kochi, 682013 Kerala India
| | - Pookkottu K. Sajith
- PG & Research Department of Chemistry, Farook College (Autonomous), Kozhikode, 673632 Kerala India
| | - Jibin K. Varughese
- PG & Research Department of Chemistry, Sacred Heart College (Autonomous), Kochi, 682013 Kerala India
| | | |
Collapse
|
11
|
Identification of some dietary flavonoids as potential inhibitors of TMPRSS2 through protein–ligand interaction studies and binding free energy calculations. Struct Chem 2022; 33:1489-1502. [PMID: 35645548 PMCID: PMC9130695 DOI: 10.1007/s11224-022-01955-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 04/27/2022] [Indexed: 11/13/2022]
Abstract
The continuing threat of COVID-19 and deaths need an urgent cost-effective pharmacological approach. Here, we examine the inhibitory activity of a group of dietary bioactive flavonoids against the human protease TMPRSS2, which plays a major role in SARS CoV-2 viral entry. After the molecular docking studies of a large number of flavonoids, four compounds with high binding scores were selected and studied in detail. The binding affinities of these four ligands, Amentoflavone, Narirutin, Eriocitrin, and Naringin, at the active site of the TMPRSS2 target, were investigated using MD simulations followed by MM-PBSA binding energy calculations. From the studies, a number of significant hydrophobic and hydrogen bonding interactions between the ligands and binding site amino residues of TMPRSS2 are identified which showcase their excellent inhibitory activity against TMPRSS2. Among these ligands, Amentoflavone and Narirutin showed MM-PBSA binding energy values of −155.57 and −139.71 kJ/mol, respectively. Our previous studies of the inhibitory activity of these compounds against the main protease of SARS-COV2 and the present study on TMPRSS2 strongly highlighted that Amentoflavone and Naringin can exhibit promising multi-target activity against SARS-CoV-2. Moreover, due to their wide availability, no side effects, and low cost, these compounds could be recommended as dietary supplements for COVID patients or for the development of SARS-CoV-2 treatments.
Collapse
|
12
|
Marsan ES, Dreab A, Bayse CA. In silico insights into the dimer structure and deiodinase activity of type III iodothyronine deiodinase from bioinformatics, molecular dynamics simulations, and QM/MM calculations. J Biomol Struct Dyn 2022:1-11. [PMID: 35579922 PMCID: PMC9878935 DOI: 10.1080/07391102.2022.2073271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The homodimeric family of iodothyronine deiodinases (Dios) regioselectively remove iodine from thyroid hormones. Currently, structural data has only been reported for the monomer of the mus type III thioredoxin (Trx) fold catalytic domain (Dio3Trx), but the mode of dimerization has not yet been determined. Various groups have proposed dimer structures that are similar to the A-type and B-type dimerization modes of peroxiredoxins. Computational methods are used to compare the sequence of Dio3Trx to related proteins known to form A-type and B-type dimers. Sequence analysis and in silico protein-protein docking methods suggest that Dio3Trx is more consistent with proteins that adopt B-type dimerization. Molecular dynamics (MD) simulations of the refined Dio3Trx dimer constructed using the SymmDock and GalaxyRefineComplex databases indicate stable dimer formation along the β4α3 interface consistent with other Trx fold B-type dimers. Free energy calculations show that the dimer is stabilized by interdimer interactions between the β-sheets and α-helices. A comparison of MD simulations of the apo and thyroxine-bound dimers suggests that the active site binding pocket is not affected by dimerization. Determination of the transition state for deiodination of thyroxine from the monomer structure using QM/MM methods provides an activation barrier consistent with previous small model DFT studies.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Eric S. Marsan
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA
| | - Ana Dreab
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA
| | - Craig A. Bayse
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA
| |
Collapse
|
13
|
Crean RM, Pudney CR, Cole DK, van der Kamp MW. Reliable In Silico Ranking of Engineered Therapeutic TCR Binding Affinities with MMPB/GBSA. J Chem Inf Model 2022; 62:577-590. [PMID: 35049312 PMCID: PMC9097153 DOI: 10.1021/acs.jcim.1c00765] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Accurate
and efficient in silico ranking of protein–protein
binding affinities is useful for protein design with applications
in biological therapeutics. One popular approach to rank binding affinities
is to apply the molecular mechanics Poisson–Boltzmann/generalized
Born surface area (MMPB/GBSA) method to molecular dynamics (MD) trajectories.
Here, we identify protocols that enable the reliable evaluation of
T-cell receptor (TCR) variants binding to their target, peptide-human
leukocyte antigens (pHLAs). We suggest different protocols for variant
sets with a few (≤4) or many mutations, with entropy corrections
important for the latter. We demonstrate how potential outliers could
be identified in advance and that just 5–10 replicas of short
(4 ns) MD simulations may be sufficient for the reproducible and accurate
ranking of TCR variants. The protocols developed here can be applied
toward in silico screening during the optimization
of therapeutic TCRs, potentially reducing both the cost and time taken
for biologic development.
Collapse
Affiliation(s)
| | | | - David K. Cole
- Immunocore Ltd., Milton Park, Abingdon OX14 4RY, U.K
- Division of Infection & Immunity, Cardiff University, Cardiff CF14 4XN, U.K
| | - Marc W. van der Kamp
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, U.K
| |
Collapse
|
14
|
Lv Z, Guo M, Zhao X, Shao Y, Zhang W, Li C. IL-17/IL-17 Receptor Pathway-Mediated Inflammatory Response in Apostichopus japonicus Supports the Conserved Functions of Cytokines in Invertebrates. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:464-479. [PMID: 34965964 DOI: 10.4049/jimmunol.2100047] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 11/03/2021] [Indexed: 01/29/2023]
Abstract
Inflammation participates in host defenses against infectious agents and contributes to the pathophysiology of many diseases. IL-17 is a well-known proinflammatory cytokine that contributes to various aspects of inflammation in vertebrates. However, the functional role of invertebrate IL-17 in inflammatory regulation is not well understood. In this study, we first established an inflammatory model in the Vibrio splendidus-challenged sea cucumber Apostichopus japonicus (Echinodermata). Typical inflammatory symptoms, such as increased coelomocyte infiltration, tissue vacuoles, and tissue fractures, were observed in the V. splendidus-infected and diseased tissue of the body wall. Interestingly, A. japonicus IL-17 (AjIL-17) expression in the body wall and coelomocytes was positively correlated with the development of inflammation. The administration of purified recombinant AjIL-17 protein also directly promoted inflammation in A. japonicus Through genome searches and ZDOCK prediction, a novel IL-17R counterpart containing FNIII and hypothetical TIR domains was identified in the sea cucumber genome. Coimmunoprecipitation, far-Western blotting, and laser confocal microscopy confirmed that AjIL-17R could bind AjIL-17. A subsequent cross-linking assay revealed that the AjIL-17 dimer mediates the inflammatory response by the specific binding of dimeric AjIL-17R upon pathogen infection. Moreover, silencing AjIL-17R significantly attenuated the LPS- or exogenous AjIL-17-mediated inflammatory response. Functional analysis revealed that AjIL-17/AjIL-17R modulated inflammatory responses by promoting A. japonicus TRAF6 ubiquitination and p65 nuclear translocation and evenly mediated coelomocyte proliferation and migration. Taken together, our results provide functional evidence that IL-17 is a conserved cytokine in invertebrates and vertebrates associated with inflammatory regulation via the IL-17-IL-17R-TRAF6 axis.
Collapse
Affiliation(s)
- Zhimeng Lv
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, People's Republic of China; and
| | - Ming Guo
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, People's Republic of China; and
| | - Xuelin Zhao
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, People's Republic of China; and
| | - Yina Shao
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, People's Republic of China; and
| | - Weiwei Zhang
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, People's Republic of China; and
| | - Chenghua Li
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, People's Republic of China; and .,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, People's Republic of China
| |
Collapse
|
15
|
Rational design and synthesis of modified natural peptides from Boana pulchella (anura) as acetylcholinesterase inhibitors and antioxidants. Amino Acids 2021; 54:181-192. [PMID: 34738177 DOI: 10.1007/s00726-021-03096-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/26/2021] [Indexed: 10/19/2022]
Abstract
The use of acetylcholinesterase (AChE) inhibitors, antioxidants or multitarget compounds are among the main strategies against Alzheimer's disease (AD). Between AChE inhibitors, those targeting the peripheral anionic site (PAS) are of special interest. Here, we describe the rational design and synthesis of peptide analogs of a natural PAS-targeting sequence that we recently discovered, aiming at increasing its activity against AChE. We also tested their radical scavenging and metal chelating properties. Our design strategy was based on the position-specific, computer-aided insertion of aromatic residues. The analog named as W3 showed a 30-fold higher inhibitory activity than the original sequence and an improved antioxidant activity. W3 is the most potent modified natural peptide against Electrophorus electricus AChE ever reported with an IC50 of 10.42 μM (± 1.02). In addition, it showed a radical scavenging activity of 47.00% ± 3.11 at 50 μM and 93.47% ± 1.53 at 400 μM. Since peptides are receiving increasing interest as drugs, we propose the W3 analog as an attractive sequence for the development of new peptide-based multitarget drugs for AD. Besides, this work sheds light on the importance of the aromatic residues in the modulation of AChE activity and their effect on the radical scavenging activity of a peptide.
Collapse
|
16
|
Khelashvili G, Pillai AN, Lee J, Pandey K, Payne AM, Siegel Z, Cuendet MA, Lewis TR, Arshavsky VY, Broichhagen J, Levitz J, Menon AK. Unusual mode of dimerization of retinitis pigmentosa-associated F220C rhodopsin. Sci Rep 2021; 11:10536. [PMID: 34006992 PMCID: PMC8131606 DOI: 10.1038/s41598-021-90039-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/29/2021] [Indexed: 12/30/2022] Open
Abstract
Mutations in the G protein-coupled receptor (GPCR) rhodopsin are a common cause of autosomal dominant retinitis pigmentosa, a blinding disease. Rhodopsin self-associates in the membrane, and the purified monomeric apo-protein opsin dimerizes in vitro as it transitions from detergent micelles to reconstitute into a lipid bilayer. We previously reported that the retinitis pigmentosa-linked F220C opsin mutant fails to dimerize in vitro, reconstituting as a monomer. Using fluorescence-based assays and molecular dynamics simulations we now report that whereas wild-type and F220C opsin display distinct dimerization propensities in vitro as previously shown, they both dimerize in the plasma membrane of HEK293 cells. Unexpectedly, molecular dynamics simulations show that F220C opsin forms an energetically favored dimer in the membrane when compared with the wild-type protein. The conformation of the F220C dimer is unique, with transmembrane helices 5 and 6 splayed apart, promoting widening of the intracellular vestibule of each protomer and influx of water into the protein interior. FRET experiments with SNAP-tagged wild-type and F220C opsin expressed in HEK293 cells are consistent with this conformational difference. We speculate that the unusual mode of dimerization of F220C opsin in the membrane may have physiological consequences.
Collapse
Affiliation(s)
- George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, 10065, USA.
- Institute of Computational Biomedicine, Weill Cornell Medical College, New York, NY, 10065, USA.
| | | | - Joon Lee
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Kalpana Pandey
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Alexander M Payne
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Zarek Siegel
- Neurosciences Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Michel A Cuendet
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, 10065, USA
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, University Hospital of Lausanne, 1009, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Tylor R Lewis
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Vadim Y Arshavsky
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Johannes Broichhagen
- Leibniz-Forschungsinstitut Für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, 10065, USA.
| | - Anant K Menon
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, 10065, USA.
| |
Collapse
|
17
|
Varughese JK, Joseph Libin KL, Sindhu KS, Rosily AV, Abi TG. Investigation of the inhibitory activity of some dietary bioactive flavonoids against SARS-CoV-2 using molecular dynamics simulations and MM-PBSA calculations. J Biomol Struct Dyn 2021; 40:6755-6770. [PMID: 33618628 DOI: 10.1080/07391102.2021.1891139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Eventhough the development of vaccine against COVID-19 pandemic is progressing in different part of the world a well-defined treatment plan is not yet developed. Therefore, we investigate the inhibitory activity of a group of dietary bioactive flavonoids against SARS-CoV-2 main protease (Mpro), which are identified as one of the potential targets in the drug discovery process of COVID-19. After the initial virtual screening of a number of bioactive flavonoids, the binding affinity of three compounds - Naringin, Naringenin and Amentoflavone - at the active site of Mpro was investigated through MD Simulations, MM-PBSA and DFT Binding Energy calculations. From the MD trajectory analysis, Amentoflavone and Naringin showed consistent protein-ligand interactions with the aminoacid residues of the active site domains of Mpro. The excellent inhibitory activity of Amentoflavone and Naringin was established from its MM-PBSA binding energy values of -190.50 and -129.87 kJ/mol respectively. The MET165 residue of Mpro is identified as one of the key residue which contributed significantly to MM-PBSA binding energy through hydrophobic interactions. Furthermore, the DFT binding energy values of Amentoflavone (-182.92 kJ/mol) and Naringin (-160.67 kJ/mol) in active site molecular clusters with hydrogen bonds confirmed their potential inhibitory activity. These compounds are of high interest because of their wide availability, low cost, no side effects, and long history of use. We can prevent the severity of this disease for home care patients using these effective dietary supplements. We are hopeful that our results have implications for the development of prophylaxis of COVID-19.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Jibin K Varughese
- Department of Chemistry, Sacred Heart College, Thevara, Kochi, Kerala, India
| | - K L Joseph Libin
- Department of Chemistry, Sacred Heart College, Thevara, Kochi, Kerala, India
| | - K S Sindhu
- Department of Chemistry, Morning Star Home Science College Angamaly, Kerala, India
| | - A V Rosily
- Department of Chemistry, Morning Star Home Science College Angamaly, Kerala, India
| | - T G Abi
- Department of Chemistry, Sacred Heart College, Thevara, Kochi, Kerala, India
| |
Collapse
|
18
|
Röhrig UF, Majjigapu SR, Reynaud A, Pojer F, Dilek N, Reichenbach P, Ascencao K, Irving M, Coukos G, Vogel P, Michielin O, Zoete V. Azole-Based Indoleamine 2,3-Dioxygenase 1 (IDO1) Inhibitors. J Med Chem 2021; 64:2205-2227. [PMID: 33557523 DOI: 10.1021/acs.jmedchem.0c01968] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The heme enzyme indoleamine 2,3-dioxygenase 1 (IDO1) plays an essential role in immunity, neuronal function, and aging through catalysis of the rate-limiting step in the kynurenine pathway of tryptophan metabolism. Many IDO1 inhibitors with different chemotypes have been developed, mainly targeted for use in anti-cancer immunotherapy. Lead optimization of direct heme iron-binding inhibitors has proven difficult due to the remarkable selectivity and sensitivity of the heme-ligand interactions. Here, we present experimental data for a set of closely related small azole compounds with more than 4 orders of magnitude differences in their inhibitory activities, ranging from millimolar to nanomolar levels. We investigate and rationalize their activities based on structural data, molecular dynamics simulations, and density functional theory calculations. Our results not only expand the presently known four confirmed chemotypes of sub-micromolar heme binding IDO1 inhibitors by two additional scaffolds but also provide a model to predict the activities of novel scaffolds.
Collapse
Affiliation(s)
- Ute F Röhrig
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Somi Reddy Majjigapu
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Laboratory of Glycochemistry and Asymmetric Synthesis, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Aline Reynaud
- Protein Production and Structure Core Facility, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Florence Pojer
- Protein Production and Structure Core Facility, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Nahzli Dilek
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Patrick Reichenbach
- Department of Oncology UNIL-CHUV, Ludwig Lausanne Branch, University of Lausanne, 1066 Epalinges, Switzerland
| | - Kelly Ascencao
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Melita Irving
- Department of Oncology UNIL-CHUV, Ludwig Lausanne Branch, University of Lausanne, 1066 Epalinges, Switzerland
| | - George Coukos
- Department of Oncology UNIL-CHUV, Ludwig Lausanne Branch, University of Lausanne, 1066 Epalinges, Switzerland.,Department of Oncology, Ludwig Cancer Research-Lausanne Branch, University Hospital of Lausanne (CHUV), 1011 Lausanne, Switzerland
| | - Pierre Vogel
- Laboratory of Glycochemistry and Asymmetric Synthesis, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Olivier Michielin
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Department of Oncology, Ludwig Cancer Research-Lausanne Branch, University Hospital of Lausanne (CHUV), 1011 Lausanne, Switzerland
| | - Vincent Zoete
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Department of Oncology UNIL-CHUV, Ludwig Lausanne Branch, University of Lausanne, 1066 Epalinges, Switzerland
| |
Collapse
|
19
|
Selvaraj C, Panwar U, Dinesh DC, Boura E, Singh P, Dubey VK, Singh SK. Microsecond MD Simulation and Multiple-Conformation Virtual Screening to Identify Potential Anti-COVID-19 Inhibitors Against SARS-CoV-2 Main Protease. Front Chem 2021; 8:595273. [PMID: 33585398 PMCID: PMC7873971 DOI: 10.3389/fchem.2020.595273] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 11/19/2020] [Indexed: 12/14/2022] Open
Abstract
The recent pandemic outbreak of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), raised global health and economic concerns. Phylogenetically, SARS-CoV-2 is closely related to SARS-CoV, and both encode the enzyme main protease (Mpro/3CLpro), which can be a potential target inhibiting viral replication. Through this work, we have compiled the structural aspects of Mpro conformational changes, with molecular modeling and 1-μs MD simulations. Long-scale MD simulation resolves the mechanism role of crucial amino acids involved in protein stability, followed by ensemble docking which provides potential compounds from the Traditional Chinese Medicine (TCM) database. These lead compounds directly interact with active site residues (His41, Gly143, and Cys145) of Mpro, which plays a crucial role in the enzymatic activity. Through the binding mode analysis in the S1, S1′, S2, and S4 binding subsites, screened compounds may be functional for the distortion of the oxyanion hole in the reaction mechanism, and it may lead to the inhibition of Mpro in SARS-CoV-2. The hit compounds are naturally occurring compounds; they provide a sustainable and readily available option for medical treatment in humans infected by SARS-CoV-2. Henceforth, extensive analysis through molecular modeling approaches explained that the proposed molecules might be promising SARS-CoV-2 inhibitors for the inhibition of COVID-19, subjected to experimental validation.
Collapse
Affiliation(s)
- Chandrabose Selvaraj
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Umesh Panwar
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Dhurvas Chandrasekaran Dinesh
- Section of Molecular Biology and Biochemistry, Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Prague, Czechia
| | - Evzen Boura
- Section of Molecular Biology and Biochemistry, Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Prague, Czechia
| | - Poonam Singh
- Corrosion and Materials Protection Division, Council of Scientific and Industrial Research (CSIR)-Central Electrochemical Research Institute, Karaikudi, India
| | - Vikash Kumar Dubey
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| |
Collapse
|
20
|
Meena MK, Kumar D, Jayaraj A, Kumar A, Kumari K, Katata-Seru LM, Bahadur I, Kumar V, Sherawat A, Singh P. Designed thiazolidines: an arsenal for the inhibition of nsP3 of CHIKV using molecular docking and MD simulations. J Biomol Struct Dyn 2020; 40:1607-1616. [PMID: 33073705 DOI: 10.1080/07391102.2020.1832918] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Mahendra Kumar Meena
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
- Department of Chemistry, University of Delhi, Delhi, India
- Department of Chemistry, Shivaji College, University of Delhi, New Delhi, India
| | - Durgesh Kumar
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
- Department of Chemistry, University of Delhi, Delhi, India
- Department of Chemistry, Lady Irwin College, University of Delhi, New Delhi, India
| | | | - Ajay Kumar
- Department of Chemistry, Indian Institute of Technology, New Delhi, India
| | - Kamlesh Kumari
- Department of Zoology, Deen Dayal Upadhyaya College, University of Delhi, New Delhi, India
| | - L. M. Katata-Seru
- Department of Chemistry, Faculty of Natural Sciences, North-West University, Mmabatho, South Africa
| | - Indra Bahadur
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Vinod Kumar
- SCNS, Jawaharlal Nehru University, New Delhi, India
| | - Anjali Sherawat
- Department of Chemistry, Lady Irwin College, University of Delhi, New Delhi, India
| | - Prashant Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
| |
Collapse
|
21
|
Crean RM, MacLachlan BJ, Madura F, Whalley T, Rizkallah PJ, Holland CJ, McMurran C, Harper S, Godkin A, Sewell AK, Pudney CR, van der Kamp MW, Cole DK. Molecular Rules Underpinning Enhanced Affinity Binding of Human T Cell Receptors Engineered for Immunotherapy. Mol Ther Oncolytics 2020; 18:443-456. [PMID: 32913893 PMCID: PMC7452143 DOI: 10.1016/j.omto.2020.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 07/27/2020] [Indexed: 10/25/2022] Open
Abstract
Immuno-oncology approaches that utilize T cell receptors (TCRs) are becoming highly attractive because of their potential to target virtually all cellular proteins, including cancer-specific epitopes, via the recognition of peptide-human leukocyte antigen (pHLA) complexes presented at the cell surface. However, because natural TCRs generally recognize cancer-derived pHLAs with very weak affinities, efforts have been made to enhance their binding strength, in some cases by several million-fold. In this study, we investigated the mechanisms underpinning human TCR affinity enhancement by comparing the crystal structures of engineered enhanced affinity TCRs with those of their wild-type progenitors. Additionally, we performed molecular dynamics simulations to better understand the energetic mechanisms driving the affinity enhancements. These data demonstrate that supra-physiological binding affinities can be achieved without altering native TCR-pHLA binding modes via relatively subtle modifications to the interface contacts, often driven through the addition of buried hydrophobic residues. Individual energetic components of the TCR-pHLA interaction governing affinity enhancements were distinct and highly variable for each TCR, often resulting from additive, or knock-on, effects beyond the mutated residues. This comprehensive analysis of affinity-enhanced TCRs has important implications for the future rational design of engineered TCRs as efficacious and safe drugs for cancer treatment.
Collapse
Affiliation(s)
- Rory M. Crean
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
- Doctoral Training Centre in Sustainable Chemical Technologies, University of Bath, Bath, BA2 7AY, UK
| | | | - Florian Madura
- Division of Infection & Immunity, Cardiff University, Cardiff, CF14 4XN, UK
| | - Thomas Whalley
- Division of Infection & Immunity, Cardiff University, Cardiff, CF14 4XN, UK
| | | | | | | | | | - Andrew Godkin
- Division of Infection & Immunity, Cardiff University, Cardiff, CF14 4XN, UK
| | - Andrew K. Sewell
- Division of Infection & Immunity, Cardiff University, Cardiff, CF14 4XN, UK
| | - Christopher R. Pudney
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
- Centre for Therapeutic Innovation, University of Bath, Bath, BA2 7AY, UK
| | - Marc W. van der Kamp
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, BS8 1TD, UK
| | - David K. Cole
- Division of Infection & Immunity, Cardiff University, Cardiff, CF14 4XN, UK
- Immunocore, Ltd., Abingdon, OX14 4RY, UK
| |
Collapse
|
22
|
Farrokhzadeh A, Badichi Akher F, Olotu FA, Van Heerden FR. Impact of HEC72702 chirality on the selective inhibition of hepatitis B virus capsid dimer: A dynamics-structure-energetics perspective. Chem Biol Drug Des 2020; 97:167-183. [PMID: 32757484 DOI: 10.1111/cbdd.13771] [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: 05/29/2020] [Revised: 07/18/2020] [Accepted: 07/25/2020] [Indexed: 12/17/2022]
Abstract
Chirality in drug design has been attracting wide interests and attention over the years based on its innate potentials of enhancing the selectivity and prowess of therapeutic molecules. This approach was fundamental to the recent design of two inhibitors, where (R,R)-HEC72702 exhibited higher potency inhibition against hepatitis B virus capsid (HBVC) than (R,S)-HEC72702. Nevertheless, the detailed molecular mechanism has remained unresolved. Here, we apply multiple computational approaches to explore, validate, and differentiate the binding modes of (R,R) and (R,S)-HEC72702 and to explain the systematic roles mediated by chirality on the distinctive inhibition of HBVC dimer (HBVCd). Our findings revealed that chirality change from R,S to R,R engenders variations in the position of the propanoic acid group of HEC72702 toward the α5' and C-TER' region of HBVCd chain B which could explain the higher inhibitory affinity of (R,R)-HEC72702. Estimated binding free energies revealed a good correlation with bioactivity data. Moreover, analysis of energy decomposition revealed the prominent effects of van der Waals interactions in the binding process of both compounds to HBVCd. Furthermore, hierarchical clustering of residue-based energetic contributions suggested two hot-spot residues W125´ and F156´ play crucial roles in the systematic motions of the propanoic acid group toward chain B.
Collapse
Affiliation(s)
- Abdolkarim Farrokhzadeh
- School of Chemistry and Physics, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Farideh Badichi Akher
- Department of Computer Science, University of Cape Town, Cape Town, South Africa.,Department of Chemistry, University of Cape Town, Cape Town, South Africa
| | - Fisayo A Olotu
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Fanie R Van Heerden
- School of Chemistry and Physics, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| |
Collapse
|
23
|
Wang H, Reinecke BA, Zhang Y. Computational insights into the molecular mechanisms of differentiated allosteric modulation at the mu opioid receptor by structurally similar bitopic modulators. J Comput Aided Mol Des 2020; 34:879-895. [PMID: 32193867 DOI: 10.1007/s10822-020-00309-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 03/14/2020] [Indexed: 11/27/2022]
Abstract
Targeting the mu opioid receptor (MOR) by applying orthosteric ligands is the most frequently employed method to treat opioid use disorder (OUD). Unfortunately, most of MOR orthosteric ligands produce severe side effects, mainly due to their low selectivity over other opioid receptors. In contrast, some G protein-coupled receptor allosteric modulators have been reported to exhibit high subtype selectivity and can effectively modulate the potency and/or efficacy of orthosteric ligands. Recently, NAQ and its analog NCQ were identified as novel MOR bitopic modulators. Interestingly, NAQ and NCQ were similar in structure but exhibited different efficacy profiles to the MOR. NAQ exhibited an antagonism activity to the MOR while NCQ showed a partial agonism activity to the MOR. In the present study, molecular modeling methods were applied to explore the putative molecular mechanisms of their different functional profiles to the MOR. When NAQ binding with the inactive MOR, the 'address' portion of NAQ interacted with the MOR allosteric site but showed no significant allosteric modulation of the efficacy of the 'message' portion of NAQ. However, when NCQ binding with the inactive and active MOR, the 'address' portion of NCQ seemed to be able to positively modulate the efficacy of the 'message' portion of NCQ at varying levels. Evidentially, the substituents at the 1'- and 4'-positions of the isoquinoline ring of NCQ seemed to play a critical role in the modulatory function of the 'address' portion of NCQ. These findings will be invaluable to develop our next generation of MOR bitopic modulators with high affinity and subtype selectivity to potentially treat OUD.
Collapse
Affiliation(s)
- Huiqun Wang
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, 800 E Leigh Street, Richmond, VA, 23298, USA
| | - Bethany A Reinecke
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, 800 E Leigh Street, Richmond, VA, 23298, USA
| | - Yan Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, 800 E Leigh Street, Richmond, VA, 23298, USA.
| |
Collapse
|
24
|
Smalley T, Metcalf R, Patel R, Islam SMA, Bommareddy RR, Acevedo-Duncan M. The Atypical Protein Kinase C Small Molecule Inhibitor ζ-Stat, and Its Effects on Invasion Through Decreases in PKC-ζ Protein Expression. Front Oncol 2020; 10:209. [PMID: 32175276 PMCID: PMC7056911 DOI: 10.3389/fonc.2020.00209] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 02/06/2020] [Indexed: 12/17/2022] Open
Abstract
Ovarian cancer is estimated to reach 22,530 diagnoses and cause 13,980 cancer deaths per year. The most common histology diagnosed of ovarian cancer is epithelial ovarian carcinomas (EOC). An aggressive epithelial subtype is clear cell ovarian carcinoma (CCOC) and is characterized as a non-serous ovarian cancer. Protein kinase C (PKC) is an enzymatic family of proteins that have been found to be a component in cancer progression, tissue invasion, and metastasis. The atypical PKC (aPKC) isoforms, PKC-ι and PKC-ζ, have been suggested to participate in the increased proliferation of ovarian cancers. Previous studies have indicated that novel aPKC inhibitors ICA-1S and ζ-Stat decreased the migratory behaviors of colorectal cancer cells and were selective for PKC-ι/λ and PKC-ζ, respectively. The aims of this investigation were to further determine the binding mechanisms of ζ-Stat, expand on the tissue range of these compounds, investigate the therapeutic potential of ζ-Stat in CCOC, and to illustrate the disruption of invasion via the PKC-ζ signaling cascade. The methods utilized were molecular docking and virtual target screening, Western blot analysis, end-point PCR, GST pull down, cell viability and invasion and migration assays. We discovered that the small molecule inhibitor, ζ-Stat, is a prospective drug candidate to investigate as a novel potential treatment for CCOC. We also found that the PKC-ζ/Ect2/Rac1 activation pathway was decreased by ζ-Stat, which in turn decreased invasive behavior of CCOC.
Collapse
Affiliation(s)
- Tracess Smalley
- Department of Chemistry, University of South Florida, Tampa, FL, United States
| | - Rainer Metcalf
- Department of Chemistry, University of South Florida, Tampa, FL, United States
| | - Rekha Patel
- Department of Chemistry, University of South Florida, Tampa, FL, United States
| | - S M Anisul Islam
- Department of Chemistry, University of South Florida, Tampa, FL, United States
| | | | | |
Collapse
|
25
|
Acetylcholinesterase inhibitory activity of a naturally occurring peptide isolated from Boana pulchella (Anura: Hylidae) and its analogs. Amino Acids 2020; 52:387-396. [DOI: 10.1007/s00726-019-02815-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 12/22/2019] [Indexed: 02/07/2023]
|
26
|
Tavares D, Reimer A, Roy S, Joublin A, Sentchilo V, van der Meer JR. Computational redesign of the Escherichia coli ribose-binding protein ligand binding pocket for 1,3-cyclohexanediol and cyclohexanol. Sci Rep 2019; 9:16940. [PMID: 31729460 PMCID: PMC6858440 DOI: 10.1038/s41598-019-53507-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 10/31/2019] [Indexed: 01/24/2023] Open
Abstract
Bacterial periplasmic-binding proteins have been acclaimed as general biosensing platform, but their range of natural ligands is too limited for optimal development of chemical compound detection. Computational redesign of the ligand-binding pocket of periplasmic-binding proteins may yield variants with new properties, but, despite earlier claims, genuine changes of specificity to non-natural ligands have so far not been achieved. In order to better understand the reasons of such limited success, we revisited here the Escherichia coli RbsB ribose-binding protein, aiming to achieve perceptible transition from ribose to structurally related chemical ligands 1,3-cyclohexanediol and cyclohexanol. Combinations of mutations were computationally predicted for nine residues in the RbsB binding pocket, then synthesized and tested in an E. coli reporter chassis. Two million variants were screened in a microcolony-in-bead fluorescence-assisted sorting procedure, which yielded six mutants no longer responsive to ribose but with 1.2-1.5 times induction in presence of 1 mM 1,3-cyclohexanediol, one of which responded to cyclohexanol as well. Isothermal microcalorimetry confirmed 1,3-cyclohexanediol binding, although only two mutant proteins were sufficiently stable upon purification. Circular dichroism spectroscopy indicated discernable structural differences between these two mutant proteins and wild-type RbsB. This and further quantification of periplasmic-space abundance suggested most mutants to be prone to misfolding and/or with defects in translocation compared to wild-type. Our results thus affirm that computational design and library screening can yield RbsB mutants with recognition of non-natural but structurally similar ligands. The inherent arisal of protein instability or misfolding concomitant with designed altered ligand-binding pockets should be overcome by new experimental strategies or by improved future protein design algorithms.
Collapse
Affiliation(s)
- Diogo Tavares
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Artur Reimer
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
- Novartis, 4056, Basel, Switzerland
| | - Shantanu Roy
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Aurélie Joublin
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Vladimir Sentchilo
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Jan Roelof van der Meer
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland.
| |
Collapse
|
27
|
Wang E, Sun H, Wang J, Wang Z, Liu H, Zhang JZH, Hou T. End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design. Chem Rev 2019; 119:9478-9508. [DOI: 10.1021/acs.chemrev.9b00055] [Citation(s) in RCA: 578] [Impact Index Per Article: 115.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ercheng Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huiyong Sun
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Junmei Wang
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Zhe Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Liu
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - John Z. H. Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- NYU−ECNU Center for Computational Chemistry, NYU Shanghai, Shanghai 200122, China
- Department of Chemistry, New York University, New York, New York 10003, United States
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Tingjun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| |
Collapse
|
28
|
Allard M, Hebeisen M, Rufer N. Assessing T Cell Receptor Affinity and Avidity Against Tumor Antigens. Oncoimmunology 2018. [DOI: 10.1007/978-3-319-62431-0_40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
|
29
|
Chen Y, Wang J, Zhang J, Wang W. Binding modes of Bcl-2 homology 3 (BH3) peptides with anti-apoptotic protein A1 and redesign of peptide inhibitors: a computational study. J Biomol Struct Dyn 2017; 36:3967-3977. [DOI: 10.1080/07391102.2017.1404933] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yantao Chen
- Shenzhen Key Laboratory of Environmental Chemistry and Ecological Remediation, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Jun Wang
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Jian Zhang
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Wei Wang
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| |
Collapse
|
30
|
Presotto D, Erdes E, Duong MN, Allard M, Regamey PO, Quadroni M, Doucey MA, Rufer N, Hebeisen M. Fine-Tuning of Optimal TCR Signaling in Tumor-Redirected CD8 T Cells by Distinct TCR Affinity-Mediated Mechanisms. Front Immunol 2017; 8:1564. [PMID: 29187853 PMCID: PMC5694758 DOI: 10.3389/fimmu.2017.01564] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 10/31/2017] [Indexed: 11/23/2022] Open
Abstract
Redirecting CD8 T cell immunity with self/tumor-specific affinity-matured T cell receptors (TCRs) is a promising approach for clinical adoptive T cell therapy, with the aim to improve treatment efficacy. Despite numerous functional-based studies, little is known about the characteristics of TCR signaling (i.e., intensity, duration, and amplification) and the regulatory mechanisms underlying optimal therapeutic T cell responses. Using a panel of human SUP-T1 and primary CD8 T cells engineered with incremental affinity TCRs against the cancer-testis antigen NY-ESO-1, we found that upon activation, T cells with optimal-affinity TCRs generated intense and sustained proximal (CD3ζ, LCK) signals associated with distal (ERK1/2) amplification-gain and increased function. In contrast, in T cells with very high affinity TCRs, signal initiation was rapid and strong yet only transient, resulting in poor MAPK activation and low proliferation potential even at high antigen stimulation dose. Under resting conditions, the levels of surface TCR/CD3ε, CD8β, and CD28 expression and of CD3ζ phosphorylation were significantly reduced in those hyporesponsive cells, suggesting the presence of TCR affinity-related activation thresholds. We also show that SHP phosphatases were involved along the TCR affinity gradient, but displayed spatially distinct regulatory roles. While PTPN6/SHP-1 phosphatase activity controlled TCR signaling initiation and subsequent amplification by counteracting CD3ζ and ERK1/2 phosphorylation, PTPN11/SHP-2 augmented MAPK activation without affecting proximal TCR signaling. Together, our findings indicate that optimal TCR signaling can be finely tuned by TCR affinity-dependent SHP-1 and SHP-2 activity, and this may readily be determined at the TCR/CD3 complex level. We propose that these TCR affinity-associated regulations represent potential protective mechanisms preventing high affinity TCR-mediated autoimmune diseases.
Collapse
Affiliation(s)
- Danilo Presotto
- Department of Oncology, Lausanne University Hospital Center, University of Lausanne, Lausanne, Switzerland
| | - Efe Erdes
- Department of Oncology, Lausanne University Hospital Center, University of Lausanne, Lausanne, Switzerland
| | - Minh Ngoc Duong
- Department of Oncology, Lausanne University Hospital Center, University of Lausanne, Lausanne, Switzerland
| | - Mathilde Allard
- Department of Oncology, Lausanne University Hospital Center, University of Lausanne, Lausanne, Switzerland
| | - Pierre-Olivier Regamey
- Protein Analysis Facility, Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Manfredo Quadroni
- Protein Analysis Facility, Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Marie-Agnès Doucey
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Nathalie Rufer
- Department of Oncology, Lausanne University Hospital Center, University of Lausanne, Lausanne, Switzerland
| | - Michael Hebeisen
- Department of Oncology, Lausanne University Hospital Center, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
31
|
Zarei O, Hamzeh-Mivehroud M, Benvenuti S, Ustun-Alkan F, Dastmalchi S. Characterizing the Hot Spots Involved in RON-MSPβ Complex Formation Using In Silico Alanine Scanning Mutagenesis and Molecular Dynamics Simulation. Adv Pharm Bull 2017; 7:141-150. [PMID: 28507948 PMCID: PMC5426727 DOI: 10.15171/apb.2017.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 03/18/2017] [Accepted: 03/20/2017] [Indexed: 12/30/2022] Open
Abstract
Purpose: Implication of protein-protein interactions (PPIs) in development of many diseases such as cancer makes them attractive for therapeutic intervention and rational drug design. RON (Recepteur d'Origine Nantais) tyrosine kinase receptor has gained considerable attention as promising target in cancer therapy. The activation of RON via its ligand, macrophage stimulation protein (MSP) is the most common mechanism of activation for this receptor. The aim of the current study was to perform in silico alanine scanning mutagenesis and to calculate binding energy for prediction of hot spots in protein-protein interface between RON and MSPβ chain (MSPβ). Methods: In this work the residues at the interface of RON-MSPβ complex were mutated to alanine and then molecular dynamics simulation was used to calculate binding free energy. Results: The results revealed that Gln193, Arg220, Glu287, Pro288, Glu289, and His424 residues from RON and Arg521, His528, Ser565, Glu658, and Arg683 from MSPβ may play important roles in protein-protein interaction between RON and MSP. Conclusion: Identification of these RON hot spots is important in designing anti-RON drugs when the aim is to disrupt RON-MSP interaction. In the same way, the acquired information regarding the critical amino acids of MSPβ can be used in the process of rational drug design for developing MSP antagonizing agents, the development of novel MSP mimicking peptides where inhibition of RON activation is required, and the design of experimental site directed mutagenesis studies.
Collapse
Affiliation(s)
- Omid Zarei
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.,Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Students Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Hamzeh-Mivehroud
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medicinal Chemistry, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Silvia Benvenuti
- Molecular Therapeutics and Exploratory Research Laboratory, Candiolo Cancer Institute-FPO-IRCCS, Candiolo, Turin, Italy
| | - Fulya Ustun-Alkan
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Istanbul University, Istanbul, Turkey
| | - Siavoush Dastmalchi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medicinal Chemistry, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|
32
|
Priya P, Kesheri M, Sinha RP, Kanchan S. Molecular Dynamics Simulations for Biological Systems. PHARMACEUTICAL SCIENCES 2017. [DOI: 10.4018/978-1-5225-1762-7.ch040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Molecular dynamics simulation is an important tool to capture the dynamicity of biological molecule and the atomistic insights. These insights are helpful to explore biological functions. Molecular dynamics simulation from femto seconds to milli seconds scale give a large ensemble of conformations that can reveal many biological mysteries. The main focus of the chapter is to throw light on theories, requirement of molecular dynamics for biological studies and application of molecular dynamics simulations. Molecular dynamics simulations are widely used to study protein-protein interaction, protein-ligand docking, effects of mutation on interactions, protein folding and flexibility of the biological molecules. This chapter also deals with various methods/algorithms of protein tertiary structure prediction, their strengths and weaknesses.
Collapse
|
33
|
Xiao X, He QH, Yu LY, Wang SQ, Li Y, Yang H, Zhang AH, Ma XH, Peng YJ, Chen B. Structure-based optimization of salt-bridge network across the complex interface of PTPN4 PDZ domain with its peptide ligands in neuroglioma. Comput Biol Chem 2016; 66:63-68. [PMID: 27923202 DOI: 10.1016/j.compbiolchem.2016.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 11/08/2016] [Accepted: 11/28/2016] [Indexed: 11/28/2022]
Abstract
The PTP non-receptor type 4 (PTPN4) is an important regulator protein in learning, spatial memory and cerebellar synaptic plasticity; targeting the PDZ domain of PTPN4 has become as attractive therapeutic strategy for human neuroglioma. Here, we systematically examined the complex crystal structures of PTPN4 PDZ domain with its known peptide ligands; a number of charged amino acid residues were identified in these ligands and in the peptide-binding pocket of PDZ domain, which can constitute a complicated salt-bridge network across the complex interface. Molecular dynamics (MD) simulations, binding free energy calculations and continuum model analysis revealed that the electrostatic effect plays a predominant role in domain-peptide binding, while other noncovalent interactions such as hydrogen bonds and hydrophobic forces are also responsible for the binding. The computational findings were then used to guide structure-based optimization of the interfacial salt-bridge network. Consequently, five peptides were rationally designed using the high-affinity binder Cyto8-RETEV (RETEV-COOH) as template, including four single-point mutants (i.e. Cyto8-mtxe0: RETEE-COOH, Cyto8-mtxd-1: RETDV-COOH, Cyto8-mtxd-3: RDTEV-COOH and Cyto8-mtxk-4: KETEV-COOH) and one double-point mutant (i.e. Cyto8-mtxd-1k-4: KETDV-COOH). Binding assays confirmed that three (Cyto8-mtxd-1, Cyto8-mtxk-4 and Cyto8-mtxd-1k-4) out of the five designed peptides exhibit moderately or considerably increased affinity as compared to the native peptide Cyto8-RETEV.
Collapse
Affiliation(s)
- Xian Xiao
- Department of Neurosurgery, No. 422 Hospital of PLA, Zhanjiang 524005, PR China
| | - Qiang-Hua He
- Department of Neurosurgery, No. 422 Hospital of PLA, Zhanjiang 524005, PR China
| | - Li-Yan Yu
- Department of Vascular, Thyroid, and Breast Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, PR China
| | - Song-Qing Wang
- Department of Neurosurgery, No. 422 Hospital of PLA, Zhanjiang 524005, PR China
| | - Yang Li
- Department of Neurosurgery, No. 422 Hospital of PLA, Zhanjiang 524005, PR China
| | - Hua Yang
- Department of Neurosurgery, No. 422 Hospital of PLA, Zhanjiang 524005, PR China
| | - Ai-Hua Zhang
- Department of Neurosurgery, No. 422 Hospital of PLA, Zhanjiang 524005, PR China
| | - Xiao-Hong Ma
- Department of Neurosurgery, No. 422 Hospital of PLA, Zhanjiang 524005, PR China
| | - Yu-Jie Peng
- Department of Neurosurgery, No. 422 Hospital of PLA, Zhanjiang 524005, PR China
| | - Bing Chen
- Department of Neurosurgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, PR China.
| |
Collapse
|
34
|
Li J, Zhou N, Liu W, Li J, Feng Y, Wang X, Wu C, Bao J. Discover natural compounds as potential phosphodiesterase-4B inhibitors via computational approaches. J Biomol Struct Dyn 2016; 34:1101-12. [PMID: 26159554 DOI: 10.1080/07391102.2015.1070749] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
cAMP, intracellular cyclic adenosine monophosphate, is a ubiquitous second messenger that plays a key role in many physiological processes. PDE4B which can reduce the cAMP level by hydrolyzing cAMP to 5'-AMP has become a therapeutic target for the treatment of human diseases such as respiratory disorders, inflammation diseases, neurological and psychiatric disorders. However, the use of currently available PDE4B inhibitors is restricted due to serious side effects caused by targeting PDE4D. Hence, we are attempting to find out subfamily-selective PDE4B inhibitors from natural products, using computer-aided approaches such as virtual screening, docking, and molecular dynamics simulation. Finally, four potential PDE4B-selective inhibitors (ZINC67912770, ZINC67912780, ZINC72320169, and ZINC28882432) were found. Compared to the reference drug (roflumilast), they scored better during the virtual screening process. Binding free energy for them was -317.51, -239.44, -215.52, and -165.77 kJ/mol, better than -129.05 kJ/mol of roflumilast. The pharmacophore model of the four candidate inhibitors comprised six features, including one hydrogen bond donor, four hydrogen bond acceptors, and one aromatic ring feature. It is expected that our study will pave the way for the design of potent PDE4B-selective inhibitors of new drugs to treat a wide variety of diseases such as asthma, COPD, psoriasis, depression, etc.
Collapse
Affiliation(s)
- Jing Li
- a College of Life Sciences & Key Laboratory for Bio-resources of Ministry of Education , Sichuan University , Chengdu 610064 , China
| | - Nan Zhou
- a College of Life Sciences & Key Laboratory for Bio-resources of Ministry of Education , Sichuan University , Chengdu 610064 , China
| | - Wen Liu
- a College of Life Sciences & Key Laboratory for Bio-resources of Ministry of Education , Sichuan University , Chengdu 610064 , China
| | - Jianzong Li
- a College of Life Sciences & Key Laboratory for Bio-resources of Ministry of Education , Sichuan University , Chengdu 610064 , China
| | - Yu Feng
- a College of Life Sciences & Key Laboratory for Bio-resources of Ministry of Education , Sichuan University , Chengdu 610064 , China
| | - Xiaoyun Wang
- a College of Life Sciences & Key Laboratory for Bio-resources of Ministry of Education , Sichuan University , Chengdu 610064 , China
| | - Chuanfang Wu
- a College of Life Sciences & Key Laboratory for Bio-resources of Ministry of Education , Sichuan University , Chengdu 610064 , China
| | - Jinku Bao
- a College of Life Sciences & Key Laboratory for Bio-resources of Ministry of Education , Sichuan University , Chengdu 610064 , China.,b State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital , Sichuan University , Chengdu 610041 , China.,c State Key Laboratory of Oral Diseases , West China College of Stomatology, Sichuan University , Chengdu 610041 , China
| |
Collapse
|
35
|
Niu Y, Li S, Pan D, Liu H, Yao X. Computational study on the unbinding pathways of B-RAF inhibitors and its implication for the difference of residence time: insight from random acceleration and steered molecular dynamics simulations. Phys Chem Chem Phys 2016; 18:5622-9. [DOI: 10.1039/c5cp06257h] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Random acceleration and steered molecular dynamics simulations reveal the unbinding pathway of B-RAF inhibitors and the difference in the residence time.
Collapse
Affiliation(s)
- Yuzhen Niu
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry
- Lanzhou University
- Lanzhou 730000
- China
| | - Shuyan Li
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry
- Lanzhou University
- Lanzhou 730000
- China
| | - Dabo Pan
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry
- Lanzhou University
- Lanzhou 730000
- China
| | | | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry
- Lanzhou University
- Lanzhou 730000
- China
- Key Lab of Preclinical Study for New Drugs of Gansu Province
| |
Collapse
|
36
|
Hebeisen M, Allard M, Gannon PO, Schmidt J, Speiser DE, Rufer N. Identifying Individual T Cell Receptors of Optimal Avidity for Tumor Antigens. Front Immunol 2015; 6:582. [PMID: 26635796 PMCID: PMC4649060 DOI: 10.3389/fimmu.2015.00582] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 10/30/2015] [Indexed: 02/02/2023] Open
Abstract
Cytotoxic T cells recognize, via their T cell receptors (TCRs), small antigenic peptides presented by the major histocompatibility complex (pMHC) on the surface of professional antigen-presenting cells and infected or malignant cells. The efficiency of T cell triggering critically depends on TCR binding to cognate pMHC, i.e., the TCR–pMHC structural avidity. The binding and kinetic attributes of this interaction are key parameters for protective T cell-mediated immunity, with stronger TCR–pMHC interactions conferring superior T cell activation and responsiveness than weaker ones. However, high-avidity TCRs are not always available, particularly among self/tumor antigen-specific T cells, most of which are eliminated by central and peripheral deletion mechanisms. Consequently, systematic assessment of T cell avidity can greatly help distinguishing protective from non-protective T cells. Here, we review novel strategies to assess TCR–pMHC interaction kinetics, enabling the identification of the functionally most-relevant T cells. We also discuss the significance of these technologies in determining which cells within a naturally occurring polyclonal tumor-specific T cell response would offer the best clinical benefit for use in adoptive therapies, with or without T cell engineering.
Collapse
Affiliation(s)
- Michael Hebeisen
- Department of Oncology, Lausanne University Hospital Center (CHUV), University of Lausanne , Epalinges , Switzerland
| | - Mathilde Allard
- Department of Oncology, Lausanne University Hospital Center (CHUV), University of Lausanne , Epalinges , Switzerland
| | - Philippe O Gannon
- Department of Oncology, Lausanne University Hospital Center (CHUV), University of Lausanne , Epalinges , Switzerland
| | - Julien Schmidt
- Ludwig Center for Cancer Research, University of Lausanne , Epalinges , Switzerland ; TCMetrix Sàrl , Epalinges , Switzerland
| | - Daniel E Speiser
- Department of Oncology, Lausanne University Hospital Center (CHUV), University of Lausanne , Epalinges , Switzerland ; Ludwig Center for Cancer Research, University of Lausanne , Epalinges , Switzerland
| | - Nathalie Rufer
- Department of Oncology, Lausanne University Hospital Center (CHUV), University of Lausanne , Epalinges , Switzerland ; Ludwig Center for Cancer Research, University of Lausanne , Epalinges , Switzerland
| |
Collapse
|
37
|
Druart K, Palmai Z, Omarjee E, Simonson T. Protein:Ligand binding free energies: A stringent test for computational protein design. J Comput Chem 2015; 37:404-15. [PMID: 26503829 DOI: 10.1002/jcc.24230] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 10/01/2015] [Accepted: 10/02/2015] [Indexed: 01/29/2023]
Abstract
A computational protein design method is extended to allow Monte Carlo simulations where two ligands are titrated into a protein binding pocket, yielding binding free energy differences. These provide a stringent test of the physical model, including the energy surface and sidechain rotamer definition. As a test, we consider tyrosyl-tRNA synthetase (TyrRS), which has been extensively redesigned experimentally. We consider its specificity for its substrate l-tyrosine (l-Tyr), compared to the analogs d-Tyr, p-acetyl-, and p-azido-phenylalanine (ac-Phe, az-Phe). We simulate l- and d-Tyr binding to TyrRS and six mutants, and compare the structures and binding free energies to a more rigorous "MD/GBSA" procedure: molecular dynamics with explicit solvent for structures and a Generalized Born + Surface Area model for binding free energies. Next, we consider l-Tyr, ac- and az-Phe binding to six other TyrRS variants. The titration results are sensitive to the precise rotamer definition, which involves a short energy minimization for each sidechain pair to help relax bad contacts induced by the discrete rotamer set. However, when designed mutant structures are rescored with a standard GBSA energy model, results agree well with the more rigorous MD/GBSA. As a third test, we redesign three amino acid positions in the substrate coordination sphere, with either l-Tyr or d-Tyr as the ligand. For two, we obtain good agreement with experiment, recovering the wildtype residue when l-Tyr is the ligand and a d-Tyr specific mutant when d-Tyr is the ligand. For the third, we recover His with either ligand, instead of wildtype Gln.
Collapse
Affiliation(s)
- Karen Druart
- Laboratoire De Biochimie (UMR CNRS 7654), Department of Biology, Ecole Polytechnique, Palaiseau, France
| | - Zoltan Palmai
- Laboratoire De Biochimie (UMR CNRS 7654), Department of Biology, Ecole Polytechnique, Palaiseau, France
| | - Eyaz Omarjee
- Laboratoire De Biochimie (UMR CNRS 7654), Department of Biology, Ecole Polytechnique, Palaiseau, France
| | - Thomas Simonson
- Laboratoire De Biochimie (UMR CNRS 7654), Department of Biology, Ecole Polytechnique, Palaiseau, France
| |
Collapse
|
38
|
Babula JJ, Liu JY. Integrate Omics Data and Molecular Dynamics Simulations toward Better Understanding of Human 14-3-3 Interactomes and Better Drugs for Cancer Therapy. J Genet Genomics 2015; 42:531-547. [PMID: 26554908 DOI: 10.1016/j.jgg.2015.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/03/2015] [Accepted: 09/03/2015] [Indexed: 12/13/2022]
Abstract
The 14-3-3 protein family is among the most extensively studied, yet still largely mysterious protein families in mammals to date. As they are well recognized for their roles in apoptosis, cell cycle regulation, and proliferation in healthy cells, aberrant 14-3-3 expression has unsurprisingly emerged as instrumental in the development of many cancers and in prognosis. Interestingly, while the seven known 14-3-3 isoforms in humans have many similar functions across cell types, evidence of isoform-specific functions and localization has been observed in both healthy and diseased cells. The strikingly high similarity among 14-3-3 isoforms has made it difficult to delineate isoform-specific functions and for isoform-specific targeting. Here, we review our knowledge of 14-3-3 interactome(s) generated by high-throughput techniques, bioinformatics, structural genomics and chemical genomics and point out that integrating the information with molecular dynamics (MD) simulations may bring us new opportunity to the design of isoform-specific inhibitors, which can not only be used as powerful research tools for delineating distinct interactomes of individual 14-3-3 isoforms, but also can serve as potential new anti-cancer drugs that selectively target aberrant 14-3-3 isoform.
Collapse
Affiliation(s)
- JoAnne J Babula
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 980 W. Walnut Street, Indianapolis, IN 46202, USA
| | - Jing-Yuan Liu
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 980 W. Walnut Street, Indianapolis, IN 46202, USA; Department of Computer and Information Science, Indiana University Purdue University Indianapolis, 723 W. Michigan St., Indianapolis, IN 46202, USA.
| |
Collapse
|
39
|
Hoffmann T, Krackhardt AM, Antes I. Quantitative Analysis of the Association Angle between T-cell Receptor Vα/Vβ Domains Reveals Important Features for Epitope Recognition. PLoS Comput Biol 2015; 11:e1004244. [PMID: 26185983 PMCID: PMC4505886 DOI: 10.1371/journal.pcbi.1004244] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 03/17/2015] [Indexed: 02/01/2023] Open
Abstract
T-cell receptors (TCR) play an important role in the adaptive immune system as they recognize pathogen- or cancer-based epitopes and thus initiate the cell-mediated immune response. Therefore there exists a growing interest in the optimization of TCRs for medical purposes like adoptive T-cell therapy. However, the molecular mechanisms behind T-cell signaling are still predominantly unknown. For small sets of TCRs it was observed that the angle between their Vα- and Vβ-domains, which bind the epitope, can vary and might be important for epitope recognition. Here we present a comprehensive, quantitative study of the variation in the Vα/Vβ interdomain-angle and its influence on epitope recognition, performing a systematic bioinformatics analysis based on a representative set of experimental TCR structures. For this purpose we developed a new, cuboid-based superpositioning method, which allows a unique, quantitative analysis of the Vα/Vβ-angles. Angle-based clustering led to six significantly different clusters. Analysis of these clusters revealed the unexpected result that the angle is predominantly influenced by the TCR-clonotype, whereas the bound epitope has only a minor influence. Furthermore we could identify a previously unknown center of rotation (CoR), which is shared by all TCRs. All TCR geometries can be obtained by rotation around this center, rendering it a new, common TCR feature with the potential of improving the accuracy of TCR structure prediction considerably. The importance of Vα/Vβ rotation for signaling was confirmed as we observed larger variances in the Vα/Vβ-angles in unbound TCRs compared to epitope-bound TCRs. Our results strongly support a two-step mechanism for TCR-epitope: First, preformation of a flexible TCR geometry in the unbound state and second, locking of the Vα/Vβ-angle in a TCR-type specific geometry upon epitope-MHC association, the latter being driven by rotation around the unique center of rotation. The recognition of antigenic peptides by cytotoxic T-cells is one of the crucial steps during the adaptive immune response. Thus a detailed understanding of this process is not only important for elucidating the mechanism behind T-cell signaling, but also for various emerging new medical applications like T-cell based immunotherapies and designed bio-therapeutics. However, despite the fast growing interest in this field, the mechanistic basis of the immune response is still largely unknown. Previous qualitative studies suggested that the T-cell receptor (TCR) Vα/Vβ-interdomain angle plays a crucial role in epitope recognition as it predetermines the relative position of its antigen-recognizing CDR1-3 loops and thus TCR specificity. In the manuscript we present a systematic bioinformatic analysis of the structural characteristics of bound and unbound TCR molecules focusing on the Vα/Vβ-angle. Our results demonstrate the importance of this angle for signaling, as several distinct Vα/Vβ-angle based structural clusters could be observed and larger angle flexibilities exist for unbound TCRs than for bound TCRs, providing quantitative proof for a two-step locking mechanism upon epitope recognition. In this context, we could identify a unique rotational point, which allows a quantitative, yet intuitive description of all observed angle variations and the structural changes upon epitope binding.
Collapse
MESH Headings
- Binding Sites
- Computer Simulation
- Epitope Mapping/methods
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/ultrastructure
- Models, Chemical
- Models, Immunological
- Models, Molecular
- Protein Binding
- Protein Conformation
- Protein Structure, Tertiary
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, alpha-beta/ultrastructure
Collapse
Affiliation(s)
- Thomas Hoffmann
- Department of Biosciences and Center for Integrated Protein Science Munich,Technische Universität München, Freising-Weihenstephan, Germany
| | - Angela M. Krackhardt
- Medizinische Klinik III, Innere Medizin mit Schwerpunkt Hämatologie und Onkologie, Technische Universität München, Munich, Germany
- Clinical Cooperation Group, Antigen specific T cell therapy, Helmholtz Zentrum München (GmbH), German Center for Environmental Health, Munich, Germany
- German Cancer Consortium (DKTK), Munich, Germany
| | - Iris Antes
- Department of Biosciences and Center for Integrated Protein Science Munich,Technische Universität München, Freising-Weihenstephan, Germany
- * E-mail:
| |
Collapse
|
40
|
Interactions between Bcl-xl and its inhibitors: Insights into ligand design from molecular dynamics simulation. J Mol Graph Model 2015; 59:1-13. [DOI: 10.1016/j.jmgm.2015.02.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 02/24/2015] [Accepted: 02/25/2015] [Indexed: 11/21/2022]
|
41
|
Nakatsugawa M, Yamashita Y, Ochi T, Tanaka S, Chamoto K, Guo T, Butler MO, Hirano N. Specific roles of each TCR hemichain in generating functional chain-centric TCR. THE JOURNAL OF IMMUNOLOGY 2015; 194:3487-500. [PMID: 25710913 DOI: 10.4049/jimmunol.1401717] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
TCRα- and β-chains cooperatively recognize peptide-MHC complexes. It has been shown that a "chain-centric" TCR hemichain can, by itself, dictate MHC-restricted Ag specificity without requiring major contributions from the paired TCR counterchain. Little is known, however, regarding the relative contributions and roles of chain-centric and its counter, non-chain-centric, hemichains in determining T cell avidity. We comprehensively analyzed a thymically unselected T cell repertoire generated by transducing the α-chain-centric HLA-A*02:01(A2)/MART127-35 TCRα, clone SIG35α, into A2-matched and unmatched postthymic T cells. Regardless of their HLA-A2 positivity, a substantial subset of peripheral T cells transduced with SIG35α gained reactivity for A2/MART127-35. Although the generated A2/MART127-35-specific T cells used various TRBV genes, TRBV27 predominated with >10(2) highly diverse and unique clonotypic CDR3β sequences. T cells individually reconstituted with various A2/MART127-35 TRBV27 TCRβ genes along with SIG35α possessed a wide range (>2 log orders) of avidity. Approximately half possessed avidity higher than T cells expressing clone DMF5, a naturally occurring A2/MART127-35 TCR with one of the highest affinities. Importantly, similar findings were recapitulated with other self-Ags. Our results indicate that, although a chain-centric TCR hemichain determines Ag specificity, the paired counterchain can regulate avidity over a broad range (>2 log orders) without compromising Ag specificity. TCR chain centricity can be exploited to generate a thymically unselected Ag-specific T cell repertoire, which can be used to isolate high-avidity antitumor T cells and their uniquely encoded TCRs rarely found in the periphery because of tolerance.
Collapse
Affiliation(s)
- Munehide Nakatsugawa
- Immune Therapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada
| | - Yuki Yamashita
- Immune Therapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada
| | - Toshiki Ochi
- Immune Therapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada
| | - Shinya Tanaka
- Immune Therapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Takara Bio, Inc., Otsu, Shiga 520-2193, Japan
| | - Kenji Chamoto
- Immune Therapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada
| | - Tingxi Guo
- Immune Therapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Department of Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada; and
| | - Marcus O Butler
- Immune Therapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Department of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Naoto Hirano
- Immune Therapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Department of Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada; and
| |
Collapse
|
42
|
He JY, Li C, Wu G. Discovery of potential drugs for human-infecting H7N9 virus containing R294K mutation. DRUG DESIGN DEVELOPMENT AND THERAPY 2014; 8:2377-90. [PMID: 25489236 PMCID: PMC4257025 DOI: 10.2147/dddt.s74061] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Background After the first epidemic wave from February through May 2013, the influenza A (H7N9) virus emerged and has followed a second epidemic wave since June 2013. As of June 27, 2014, the outbreak of H7N9 had caused 450 confirmed cases of human infection, with 165 deaths included. The case-fatality rate of all confirmed cases is about 36%, making the H7N9 virus a significant threat to people’s health. At present, neuraminidase inhibitors are the only licensed antiviral medications available to treat H7N9 infections in humans. Oseltamivir is the most commonly used inhibitor, and it is also a front-line drug for the threatening H7N9. Unfortunately, it has been reported that patients treated with oseltamivir can induce R294K (Arg294Lys) substitution in the H7N9 virus, which is a rare mutation and can reduce the antiviral efficacy of inhibitors. Even worse, deaths caused by such mutation after oseltamivir treatment have already been reported, indicating that the need to find substitutive neuraminidase inhibitors for currently available drugs to treat drug-resistant H7N9 is really pressing. Materials and methods First, the structure of H7N9 containing the R294K substitution was downloaded from the Protein Data Bank, and structural information of approved drugs was downloaded from the ZINC (ZINC Is Not Commercial) database. Taking oseltamivir carboxylate as a reference drug, we then filtered these molecules through virtual screening to find out potential inhibitors targeting the mutated H7N9 virus. For further evaluation, we carried out a 14 ns molecular dynamic simulation for each H7N9–drug complex and calculated the binding energy for each candidate drug. Results We found five inhibitors that could be candidate drugs for treating the mutated H7N9 virus. Docking poses showed these drugs could bind to the virus effectively, with the contribution of hydrogen bonds and hydrophobic interactions. With regard to the molecular dynamic simulations, receptor–ligand complexes formed by these candidate drugs were more stable than the one formed by oseltamivir carboxylate. The binding energy of oseltamivir carboxylate was −122.4 kJ/mol, while those for these potential inhibitors were −417.5, −404.7, −372.2, −304.3, and −289.9 kJ/mol, much better than the reference drug. Conclusion Given the current and future threat of the mutated H7N9 virus, it is urgent that potent drugs and effective antiviral therapeutics be found. Our study therefore is able to complement currently available drugs for influenza A infectors and helps to prevent the ongoing threat of H7N9 virus.
Collapse
Affiliation(s)
- Jiao-Yu He
- College of Life Sciences and Key Laboratory for Bio-resources of Ministry of Education, Sichuan University, Chengdu, People's Republic of China
| | - Cheng Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, People's Republic of China
| | - Guo Wu
- College of Life Sciences, Sichuan Normal University, Chengdu, People's Republic of China
| |
Collapse
|
43
|
Molecular insight into γ–γ tubulin lateral interactions within the γ-tubulin ring complex (γ-TuRC). J Comput Aided Mol Des 2014; 28:961-72. [DOI: 10.1007/s10822-014-9779-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 07/09/2014] [Indexed: 10/25/2022]
|
44
|
Molecular recognition of CXCR4 by a dual tropic HIV-1 gp120 V3 loop. Biophys J 2014; 105:1502-14. [PMID: 24048002 DOI: 10.1016/j.bpj.2013.07.049] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 07/16/2013] [Accepted: 07/29/2013] [Indexed: 01/01/2023] Open
Abstract
HIV-1 cell entry is initiated by the interaction of the viral envelope glycoprotein gp120 with CD4, and chemokine coreceptors CXCR4 and CCR5. The molecular recognition of CXCR4 or CCR5 by the HIV-1 gp120 is mediated through the V3 loop, a fragment of gp120. The binding of the V3 loop to CXCR4 or CCR5 determines the cell tropism of HIV-1 and constitutes a key step before HIV-1 cell entry. Thus, elucidating the molecular recognition of CXCR4 by the V3 loop is important for understanding HIV-1 viral infectivity and tropism, and for the design of HIV-1 inhibitors. We employed a comprehensive set of computational tools, predominantly based on free energy calculations and molecular-dynamics simulations, to investigate the molecular recognition of CXCR4 by a dual tropic V3 loop. We report what is, to our knowledge, the first HIV-1 gp120 V3 loop:CXCR4 complex structure. The computationally derived structure reveals an abundance of polar and nonpolar intermolecular interactions contributing to the HIV-1 gp120:CXCR4 binding. Our results are in remarkable agreement with previous experimental findings. Therefore, this work sheds light on the functional role of HIV-1 gp120 V3 loop and CXCR4 residues associated with HIV-1 coreceptor activity.
Collapse
|
45
|
Lee S, Lee HC, Kwon YW, Lee SE, Cho Y, Kim J, Lee S, Kim JY, Lee J, Yang HM, Mook-Jung I, Nam KY, Chung J, Lazar MA, Kim HS. Adenylyl cyclase-associated protein 1 is a receptor for human resistin and mediates inflammatory actions of human monocytes. Cell Metab 2014; 19:484-97. [PMID: 24606903 PMCID: PMC3969988 DOI: 10.1016/j.cmet.2014.01.013] [Citation(s) in RCA: 179] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 10/31/2013] [Accepted: 01/03/2014] [Indexed: 01/15/2023]
Abstract
Human resistin is a cytokine that induces low-grade inflammation by stimulating monocytes. Resistin-mediated chronic inflammation can lead to obesity, atherosclerosis, and other cardiometabolic diseases. Nevertheless, the receptor for human resistin has not been clarified. Here, we identified adenylyl cyclase-associated protein 1 (CAP1) as a functional receptor for human resistin and clarified its intracellular signaling pathway to modulate inflammatory action of monocytes. We found that human resistin directly binds to CAP1 in monocytes and upregulates cyclic AMP (cAMP) concentration, protein kinase A (PKA) activity, and NF-κB-related transcription of inflammatory cytokines. Overexpression of CAP1 in monocytes enhanced the resistin-induced increased activity of the cAMP-dependent signaling. Moreover, CAP1-overexpressed monocytes aggravated adipose tissue inflammation in transgenic mice that express human resistin from their monocytes. In contrast, suppression of CAP1 expression abrogated the resistin-mediated inflammatory activity both in vitro and in vivo. Therefore, CAP1 is the bona fide receptor for resistin leading to inflammation in humans.
Collapse
Affiliation(s)
- Sahmin Lee
- Department of Internal Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul 110-744, Korea; Department of Molecular Medicine & Biopharmaceutical Science, Graduate School of Convergence Science and Technology and College of Medicine, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Korea
| | - Hyun-Chae Lee
- Biomedical Research Institute, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 110-744, Korea
| | - Yoo-Wook Kwon
- Biomedical Research Institute, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 110-744, Korea
| | - Sang Eun Lee
- Department of Internal Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul 110-744, Korea
| | - Youngjin Cho
- Department of Internal Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul 110-744, Korea
| | - Joonoh Kim
- Biomedical Research Institute, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 110-744, Korea
| | - Soobeom Lee
- Biomedical Research Institute, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 110-744, Korea
| | - Ju-Young Kim
- Biomedical Research Institute, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 110-744, Korea
| | - Jaewon Lee
- Biomedical Research Institute, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 110-744, Korea
| | - Han-Mo Yang
- Department of Internal Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul 110-744, Korea
| | - Inhee Mook-Jung
- Department of Biochemistry and Biomedical Sciences, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul 110-744, Korea
| | - Ky-Youb Nam
- Bioinformatics & Molecular Design Research Center, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Korea; Gachon Institute of Pharmaceutical Sciences, Gachon University, 191 Hambakmoi-ro, Yonsu-gu, Incheon 406-813, Korea
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul 110-744, Korea
| | - Mitchell A Lazar
- Division of Endocrinology, Diabetes, and Metabolism, and Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania School of Medicine, 12-102 Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Hyo-Soo Kim
- Department of Internal Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul 110-744, Korea; Department of Molecular Medicine & Biopharmaceutical Science, Graduate School of Convergence Science and Technology and College of Medicine, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Korea; Biomedical Research Institute, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 110-744, Korea.
| |
Collapse
|
46
|
Pierce BG, Hellman LM, Hossain M, Singh NK, Vander Kooi CW, Weng Z, Baker BM. Computational design of the affinity and specificity of a therapeutic T cell receptor. PLoS Comput Biol 2014; 10:e1003478. [PMID: 24550723 PMCID: PMC3923660 DOI: 10.1371/journal.pcbi.1003478] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 01/02/2014] [Indexed: 01/15/2023] Open
Abstract
T cell receptors (TCRs) are key to antigen-specific immunity and are increasingly being explored as therapeutics, most visibly in cancer immunotherapy. As TCRs typically possess only low-to-moderate affinity for their peptide/MHC (pMHC) ligands, there is a recognized need to develop affinity-enhanced TCR variants. Previous in vitro engineering efforts have yielded remarkable improvements in TCR affinity, yet concerns exist about the maintenance of peptide specificity and the biological impacts of ultra-high affinity. As opposed to in vitro engineering, computational design can directly address these issues, in theory permitting the rational control of peptide specificity together with relatively controlled increments in affinity. Here we explored the efficacy of computational design with the clinically relevant TCR DMF5, which recognizes nonameric and decameric epitopes from the melanoma-associated Melan-A/MART-1 protein presented by the class I MHC HLA-A2. We tested multiple mutations selected by flexible and rigid modeling protocols, assessed impacts on affinity and specificity, and utilized the data to examine and improve algorithmic performance. We identified multiple mutations that improved binding affinity, and characterized the structure, affinity, and binding kinetics of a previously reported double mutant that exhibits an impressive 400-fold affinity improvement for the decameric pMHC ligand without detectable binding to non-cognate ligands. The structure of this high affinity mutant indicated very little conformational consequences and emphasized the high fidelity of our modeling procedure. Overall, our work showcases the capability of computational design to generate TCRs with improved pMHC affinities while explicitly accounting for peptide specificity, as well as its potential for generating TCRs with customized antigen targeting capabilities.
Collapse
Affiliation(s)
- Brian G. Pierce
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Lance M. Hellman
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Moushumi Hossain
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Nishant K. Singh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Craig W. Vander Kooi
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Brian M. Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, United States of America
| |
Collapse
|
47
|
Estiu G, Khatri N, Wiest O. Computational Studies of the Cholesterol Transport between NPC2 and the N-Terminal Domain of NPC1 (NPC1(NTD)). Biochemistry 2013; 52:6879-91. [DOI: 10.1021/bi4005478] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Guillermina Estiu
- Department
of Chemistry and Biochemistry and the Center for Rare and Neglected
Diseases, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Nazir Khatri
- Department
of Chemistry and Biochemistry and the Center for Rare and Neglected
Diseases, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Department
of Chemistry, Franklin College, Franklin, Indiana 46131, United States
| | - Olaf Wiest
- Department
of Chemistry and Biochemistry and the Center for Rare and Neglected
Diseases, University of Notre Dame, Notre Dame, Indiana 46556, United States
- The
Lab of Computational Chemistry and Drug Design, Laboratory of Chemical
Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, P.R. China
| |
Collapse
|
48
|
Zoete V, Irving M, Ferber M, Cuendet MA, Michielin O. Structure-Based, Rational Design of T Cell Receptors. Front Immunol 2013; 4:268. [PMID: 24062738 PMCID: PMC3770923 DOI: 10.3389/fimmu.2013.00268] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 08/19/2013] [Indexed: 11/13/2022] Open
Abstract
Adoptive cell transfer using engineered T cells is emerging as a promising treatment for metastatic melanoma. Such an approach allows one to introduce T cell receptor (TCR) modifications that, while maintaining the specificity for the targeted antigen, can enhance the binding and kinetic parameters for the interaction with peptides (p) bound to major histocompatibility complexes (MHC). Using the well-characterized 2C TCR/SIYR/H-2K(b) structure as a model system, we demonstrated that a binding free energy decomposition based on the MM-GBSA approach provides a detailed and reliable description of the TCR/pMHC interactions at the structural and thermodynamic levels. Starting from this result, we developed a new structure-based approach, to rationally design new TCR sequences, and applied it to the BC1 TCR targeting the HLA-A2 restricted NY-ESO-1157–165 cancer-testis epitope. Fifty-four percent of the designed sequence replacements exhibited improved pMHC binding as compared to the native TCR, with up to 150-fold increase in affinity, while preserving specificity. Genetically engineered CD8+ T cells expressing these modified TCRs showed an improved functional activity compared to those expressing BC1 TCR. We measured maximum levels of activities for TCRs within the upper limit of natural affinity, KD = ∼1 − 5 μM. Beyond the affinity threshold at KD < 1 μM we observed an attenuation in cellular function, in line with the “half-life” model of T cell activation. Our computer-aided protein-engineering approach requires the 3D-structure of the TCR-pMHC complex of interest, which can be obtained from X-ray crystallography. We have also developed a homology modeling-based approach, TCRep 3D, to obtain accurate structural models of any TCR-pMHC complexes when experimental data is not available. Since the accuracy of the models depends on the prediction of the TCR orientation over pMHC, we have complemented the approach with a simplified rigid method to predict this orientation and successfully assessed it using all non-redundant TCR-pMHC crystal structures available. These methods potentially extend the use of our TCR engineering method to entire TCR repertoires for which no X-ray structure is available. We have also performed a steered molecular dynamics study of the unbinding of the TCR-pMHC complex to get a better understanding of how TCRs interact with pMHCs. This entire rational TCR design pipeline is now being used to produce rationally optimized TCRs for adoptive cell therapies of stage IV melanoma.
Collapse
Affiliation(s)
- V Zoete
- Molecular Modeling Group, Swiss Institute of Bioinformatics , Lausanne , Switzerland
| | | | | | | | | |
Collapse
|
49
|
Stone JD, Kranz DM. Role of T cell receptor affinity in the efficacy and specificity of adoptive T cell therapies. Front Immunol 2013; 4:244. [PMID: 23970885 PMCID: PMC3748443 DOI: 10.3389/fimmu.2013.00244] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 08/05/2013] [Indexed: 01/09/2023] Open
Abstract
Over the last several years, there has been considerable progress in the treatment of cancer using gene modified adoptive T cell therapies. Two approaches have been used, one involving the introduction of a conventional αβ T cell receptor (TCR) against a pepMHC cancer antigen, and the second involving introduction of a chimeric antigen receptor (CAR) consisting of a single-chain antibody as an Fv fragment linked to transmembrane and signaling domains. In this review, we focus on one aspect of TCR-mediated adoptive T cell therapies, the impact of the affinity of the αβ TCR for the pepMHC cancer antigen on both efficacy and specificity. We discuss the advantages of higher-affinity TCRs in mediating potent activity of CD4 T cells. This is balanced with the potential disadvantage of higher-affinity TCRs in mediating greater self-reactivity against a wider range of structurally similar antigenic peptides, especially in synergy with the CD8 co-receptor. Both TCR affinity and target selection will influence potential safety issues. We suggest pre-clinical strategies that might be used to examine each TCR for possible on-target and off-target side effects due to self-reactivities, and to adjust TCR affinities accordingly.
Collapse
Affiliation(s)
- Jennifer D Stone
- Department of Biochemistry, University of Illinois , Urbana, IL , USA
| | | |
Collapse
|
50
|
Chen S, Gfeller D, Buth SA, Michielin O, Leiman PG, Heinis C. Improving binding affinity and stability of peptide ligands by substituting glycines with D-amino acids. Chembiochem 2013; 14:1316-22. [PMID: 23828687 DOI: 10.1002/cbic.201300228] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Indexed: 11/07/2022]
Abstract
Improving the binding affinity and/or stability of peptide ligands often requires testing of large numbers of variants to identify beneficial mutations. Herein we propose a type of mutation that promises a high success rate. In a bicyclic peptide inhibitor of the cancer-related protease urokinase-type plasminogen activator (uPA), we observed a glycine residue that has a positive ϕ dihedral angle when bound to the target. We hypothesized that replacing it with a D-amino acid, which favors positive ϕ angles, could enhance the binding affinity and/or proteolytic resistance. Mutation of this specific glycine to D-serine in the bicyclic peptide indeed improved inhibitory activity (1.75-fold) and stability (fourfold). X-ray-structure analysis of the inhibitors in complex with uPA showed that the peptide backbone conformation was conserved. Analysis of known cyclic peptide ligands showed that glycine is one of the most frequent amino acids, and that glycines with positive ϕ angles are found in many protein-bound peptides. These results suggest that the glycine-to-D-amino acid mutagenesis strategy could be broadly applied.
Collapse
Affiliation(s)
- Shiyu Chen
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, BCH 5305 (Batochime), Avenue Forel 2, 1015 Lausanne, Switzerland
| | | | | | | | | | | |
Collapse
|