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González-Alemán R, Chevrollier N, Simoes M, Montero-Cabrera L, Leclerc F. MCSS-Based Predictions of Binding Mode and Selectivity of Nucleotide Ligands. J Chem Theory Comput 2021; 17:2599-2618. [PMID: 33764770 DOI: 10.1021/acs.jctc.0c01339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Computational fragment-based approaches are widely used in drug design and discovery. One of their limitations is the lack of performance of docking methods, mainly the scoring functions. With the emergence of fragment-based approaches for single-stranded RNA ligands, we analyze the performance in docking and screening powers of an MCSS-based approach. The performance is evaluated on a benchmark of protein-nucleotide complexes where the four RNA residues are used as fragments. The screening power can be considered the major limiting factor for the fragment-based modeling or design of sequence-selective oligonucleotides. We show that the MCSS sampling is efficient even for such large and flexible fragments. Hybrid solvent models based on some partial explicit representations improve both the docking and screening powers. Clustering of the n best-ranked poses can also contribute to a lesser extent to better performance. A detailed analysis of molecular features suggests various ways to optimize the performance further.
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Affiliation(s)
- Roy González-Alemán
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Saclay, Gif-sur-Yvette F-91198, France.,Laboratorio de Química Computacional y Teórica (LQCT), Facultad de Química, Universidad de La Habana, 10400 La Habana, Cuba
| | - Nicolas Chevrollier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Saclay, Gif-sur-Yvette F-91198, France
| | - Manuel Simoes
- CPC Manufacturing Analytics, 67000 Strasbourg, France
| | - Luis Montero-Cabrera
- Laboratorio de Química Computacional y Teórica (LQCT), Facultad de Química, Universidad de La Habana, 10400 La Habana, Cuba
| | - Fabrice Leclerc
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Saclay, Gif-sur-Yvette F-91198, France
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2
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Computational Prediction of the Epitopes of HA1 Protein of Influenza Viruses to its Neutralizing Antibodies. Antibodies (Basel) 2018; 8:antib8010002. [PMID: 31544808 PMCID: PMC6640696 DOI: 10.3390/antib8010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 12/11/2018] [Accepted: 12/19/2018] [Indexed: 11/17/2022] Open
Abstract
In this work, we have used a new method to predict the epitopes of HA1 protein of influenza virus to several antibodies HC19, CR9114, BH151 and 4F5. While our results reproduced the binding epitopes of H3N2 or H5N1 for the neutralizing antibodies HC19, CR9114, and BH151 as revealed from the available crystal structures, additional epitopes for these antibodies were also suggested. Moreover, the predicted epitopes of H5N1 HA1 for the newly developed antibody 4F5 are located at the receptor binding domain, while previous study identified a region 76-WLLGNP-81 as the epitope. The possibility of antibody recognition of influenza virus via different mechanism by binding to different epitopes of an antigen is also discussed.
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3
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Tan X, Liu N, Legge FS, Yang M, Zeng J. Computational identification of antibody epitopes of human papillomavirus 16 (HPV16) L1 proteins. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2018. [DOI: 10.1142/s0219633618500177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Previously, we developed a method to predict epitopes on a protein recognized by specific antibodies. In this study, we have applied this method to identify the epitopes of the human papillomavirus 16 (HPV16) L1 capsomer that is bound by monoclonal antibodies U4, AE3 and AG7. Initially, the method was validated by the identification of epitopes of HPV16 L1 capsomer that bind to antibody U4. Our predicted epitopes were in agreement with the cryto-electron microscopy (cryto-EM) structure of the complex. The method was then used to predict the epitopes of HPV16 L1 binding of antibodies AE3 and AG7. Our calculations indicated that antibody AE3 binds to the HPV16 L1 capsomer at two different regions. Firstly, the region recognized by antibody U4 and secondly, the region recognized by antibody V5, which have been shown in the cryto-EM structure of the V5 and HPV16 L1 complex. In comparison, the antibody AG7 binds to the capsomer only at the epitopes bound by antibody U4. Therefore, antibody AE3 is predicted to have higher affinity than antibody AG7 and could be used for developing highly efficient anti-HPV monoclonal antibodies in the clinical treatment of HPV infections.
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Affiliation(s)
- Xin Tan
- Department of Obstetrics and Gynecology, West China Second University Hospital, Chengdu 610041, P. R. China
- Key Laboratory of Birth Defects and Related, Diseases of Women and Children, Sichuan University Ministry of Education, Chengdu 610041, P. R. China
| | - Na Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Fiona S. Legge
- MedChemSoft Solutions Wheelers Hill, VIC 3150, Australia
| | - Minghui Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Jun Zeng
- MedChemSoft Solutions Wheelers Hill, VIC 3150, Australia
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4
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Liu LJ, Wang W, Huang SY, Hong Y, Li G, Lin S, Tian J, Cai Z, Wang HMD, Ma DL, Leung CH. Inhibition of the Ras/Raf interaction and repression of renal cancer xenografts in vivo by an enantiomeric iridium(iii) metal-based compound. Chem Sci 2017; 8:4756-4763. [PMID: 28959398 PMCID: PMC5603957 DOI: 10.1039/c7sc00311k] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 05/08/2017] [Indexed: 01/09/2023] Open
Abstract
Targeting protein-protein interactions (PPIs) offers tantalizing opportunities for therapeutic intervention for the treatment of human diseases. Modulating PPI interfaces with organic small molecules has been found to be exceptionally challenging, and few candidates have been successfully developed into clinical drugs. Meanwhile, the striking array of distinctive properties exhibited by metal compounds renders them attractive scaffolds for the development of bioactive leads. Here, we report the identification of iridium(iii) compounds as inhibitors of the H-Ras/Raf-1 PPI. The lead iridium(iii) compound 1 exhibited potent inhibitory activity against the H-Ras/Raf-1 interaction and its signaling pathway in vitro and in vivo, and also directly engaged both H-Ras and Raf-1-RBD in cell lysates. Moreover, 1 repressed tumor growth in a mouse renal xenograft tumor model. Intriguingly, the Δ-enantiomer of 1 showed superior potency in the biological assays compared to Λ-1 or racemic 1. These compounds could potentially be used as starting scaffolds for the development of more potent Ras/Raf PPI inhibitors for the treatment of kidney cancer or other proliferative diseases.
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Affiliation(s)
- Li-Juan Liu
- State Key Laboratory of Quality Research in Chinese Medicine , Institute of Chinese Medical Sciences , University of Macau , Macao , China .
| | - Wanhe Wang
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
| | - Shi-Ying Huang
- College of Oceanology and Food Science , Quanzhou Normal University , Quanzhou 362000 , China
- Key Laboratory for the Development of Bioactive Material from Marine Algae , Quanzhou 362000 , China
| | - Yanjun Hong
- Partner State Key Laboratory of Environmental and Biological Analysis , Department of Chemistry , Hong Kong Baptist University , 224 Waterloo Road , Kowloon Tong , Hong Kong SAR , P. R. China .
| | - Guodong Li
- State Key Laboratory of Quality Research in Chinese Medicine , Institute of Chinese Medical Sciences , University of Macau , Macao , China .
| | - Sheng Lin
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
| | - Jinglin Tian
- Partner State Key Laboratory of Environmental and Biological Analysis , Department of Chemistry , Hong Kong Baptist University , 224 Waterloo Road , Kowloon Tong , Hong Kong SAR , P. R. China .
| | - Zongwei Cai
- Partner State Key Laboratory of Environmental and Biological Analysis , Department of Chemistry , Hong Kong Baptist University , 224 Waterloo Road , Kowloon Tong , Hong Kong SAR , P. R. China .
| | - Hui-Min David Wang
- Graduate Institute of Biomedical Engineering , National Chung Hsing University , Taichung 402 , Taiwan .
| | - Dik-Lung Ma
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine , Institute of Chinese Medical Sciences , University of Macau , Macao , China .
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5
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Levinson AM, McGee JH, Roberts AG, Creech GS, Wang T, Peterson MT, Hendrickson RC, Verdine GL, Danishefsky SJ. Total Chemical Synthesis and Folding of All-l and All-d Variants of Oncogenic KRas(G12V). J Am Chem Soc 2017; 139:7632-7639. [PMID: 28448128 PMCID: PMC5606205 DOI: 10.1021/jacs.7b02988] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The Ras proteins are essential GTPases involved in the regulation of cell proliferation and survival. Mutated oncogenic forms of Ras alter effector binding and innate GTPase activity, leading to deregulation of downstream signal transduction. Mutated forms of Ras are involved in approximately 30% of human cancers. Despite decades of effort to develop direct Ras inhibitors, Ras has long been considered "undruggable" due to its high affinity for GTP and its lack of hydrophobic binding pockets. Herein, we report a total chemical synthesis of all-l- and all-d-amino acid biotinylated variants of oncogenic mutant KRas(G12V). The protein is synthesized using Fmoc-based solid-phase peptide synthesis and assembled using combined native chemical ligation and isonitrile-mediated activation strategies. We demonstrate that both KRas(G12V) enantiomers can successfully fold and bind nucleotide substrates and binding partners with observable enantiodiscrimination. By demonstrating the functional competency of a mirror-image form of KRas bound to its corresponding enantiomeric nucleotide triphosphate, this study sets the stage for further biochemical studies with this material. In particular, this protein will enable mirror-image yeast surface display experiments to identify all-d peptide ligands for oncogenic KRas, providing a useful tool in the search for new therapeutics against this challenging disease target.
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Affiliation(s)
- Adam M. Levinson
- Laboratory for Bio-Organic Chemistry, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States of America
- Chemical Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States of America
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medical College, New York, New York, United States of America
| | - John H. McGee
- Departments of Molecular and Cellular Biology, Stem Cell and Regenerative Biology, and Chemistry and Chemical Biology, Harvard University and Harvard Medical School, Cambridge, MA 02138
| | - Andrew G. Roberts
- Laboratory for Bio-Organic Chemistry, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States of America
- Chemical Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States of America
| | - Gardner S. Creech
- Laboratory for Bio-Organic Chemistry, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States of America
- Chemical Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States of America
| | - Ting Wang
- Laboratory for Bio-Organic Chemistry, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States of America
- Chemical Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States of America
| | - Michael T. Peterson
- Laboratory for Bio-Organic Chemistry, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States of America
- Chemical Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States of America
| | - Ronald C. Hendrickson
- Chemical Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States of America
| | - Gregory L. Verdine
- Departments of Molecular and Cellular Biology, Stem Cell and Regenerative Biology, and Chemistry and Chemical Biology, Harvard University and Harvard Medical School, Cambridge, MA 02138
| | - Samuel J. Danishefsky
- Laboratory for Bio-Organic Chemistry, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States of America
- Chemical Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States of America
- Department of Chemistry, Columbia University, Havemeyer Hall, 3000 Broadway, New York, New York 10027, United States of America
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6
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Tan X, Liu N, Yang M, Duan M, Zeng J. Design of peptide inhibitors of human papillomavirus 16 (HPV16) transcriptional regulator E1–E2 formation. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2017. [DOI: 10.1142/s0219633617500262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Here, we have proposed a new scheme of the computational combinatorial design approach to identify potential inhibitor peptides. It consists of four steps: (i) using “multiple copy simultaneous search” (MCSS) procedure to locate specific functional groups on the protein surface; (ii) the peptide main chain is constructed based on the location of favored N-methylacetamide (NMA) groups; (iii) molecular dynamics simulations of the complex formed between the constructed peptides with the target protein in explicit water molecules are carried to select the peptides with strong binding to the protein and (iv) the sequences of the stable peptides selected from (iii) are aligned and the frequencies of the amino acids at each position of peptide are calculated. Sequence patterns of potential inhibitors are determined based on the frequency of amino acids at each position. It was applied to design peptide inhibitors that bind to the E2 protein of HPV16 so as to disrupt its transcriptional regulator of E1–E2 complex formation. The sequence pattern of these potential inhibitors is in agreement with known inhibitors obtained from phage display, and the MCSS calculations indicate that a hydrophobic pocket on HPV16 E2 plays a significant role in E1–E2 formation and inhibitor-E2 binding.
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Affiliation(s)
- Xin Tan
- Department of Obstetrics and Gynaecology, West China Second University Hospital, No. 20, the Third Part Renmin South Road, Chengdu 610041, P. R. China
- Key Laboratory of Birth Defects and Related Diseases of Woman and Children, Sichuan University, Ministry of Education, No. 20, the Third Part Renmin South Road, Chengdu 610041, P. R. China
| | - Na Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Min Yang
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, Sichuan 610500, P. R. China
| | - Mojie Duan
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Jun Zeng
- School of Medical Sciences, Royal Melbourne Institute of Technology, Plenty Road, Bundoora, VIC 3083, Australia
- MedChemSoft Solutions, Level 3, 2 Brandon Park Drive, Wheelers Hill, VIC 3150, Australia
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7
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Jones ML, Legge FS, Lebani K, Mahler SM, Young PR, Watterson D, Treutlein HR, Zeng J. Computational Identification of Antibody Epitopes on the Dengue Virus NS1 Protein. Molecules 2017; 22:E607. [PMID: 28394300 PMCID: PMC6154621 DOI: 10.3390/molecules22040607] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 04/05/2017] [Accepted: 04/06/2017] [Indexed: 12/04/2022] Open
Abstract
We have previously described a method to predict antigenic epitopes on proteins recognized by specific antibodies. Here we have applied this method to identify epitopes on the NS1 proteins of the four Dengue virus serotypes (DENV1-4) that are bound by a small panel of monoclonal antibodies 1H7.4, 1G5.3 and Gus2. Several epitope regions were predicted for these antibodies and these were found to reflect the experimentally observed reactivities. The known binding epitopes on DENV2 for the antibodies 1H7.4 and 1G5.3 were identified, revealing the reasons for the serotype specificity of 1H7.4 and 1G5.3, and the non-selectivity of Gus2. As DENV NS1 is critical for virus replication and a key vaccine candidate, epitope prediction will be valuable in designing appropriate vaccine control strategies. The ability to predict potential epitopes by computational methods significantly reduces the amount of experimental work required to screen peptide libraries for epitope mapping.
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Affiliation(s)
- Martina L Jones
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD 4072, Australia.
- ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia.
| | - Fiona S Legge
- Computist Bio-Nanotech, 1 Dalmore Drive, Scoresby, VIC 3179, Australia.
| | - Kebaneilwe Lebani
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD 4072, Australia.
| | - Stephen M Mahler
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD 4072, Australia.
- ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia.
| | - Paul R Young
- ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia.
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia.
- Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, QLD 4072, Australia.
| | - Daniel Watterson
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia.
- Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, QLD 4072, Australia.
| | - Herbert R Treutlein
- Computist Bio-Nanotech, 1 Dalmore Drive, Scoresby, VIC 3179, Australia.
- School of Medical Sciences, RMIT University, P.O. Box 71, Bundoora, VIC 3083, Australia.
| | - Jun Zeng
- Computist Bio-Nanotech, 1 Dalmore Drive, Scoresby, VIC 3179, Australia.
- School of Medical Sciences, RMIT University, P.O. Box 71, Bundoora, VIC 3083, Australia.
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8
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Russo A, Scognamiglio PL, Hong Enriquez RP, Santambrogio C, Grandori R, Marasco D, Giordano A, Scoles G, Fortuna S. In Silico Generation of Peptides by Replica Exchange Monte Carlo: Docking-Based Optimization of Maltose-Binding-Protein Ligands. PLoS One 2015; 10:e0133571. [PMID: 26252476 PMCID: PMC4529233 DOI: 10.1371/journal.pone.0133571] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Accepted: 06/27/2015] [Indexed: 12/25/2022] Open
Abstract
Short peptides can be designed in silico and synthesized through automated techniques, making them advantageous and versatile protein binders. A number of docking-based algorithms allow for a computational screening of peptides as binders. Here we developed ex-novo peptides targeting the maltose site of the Maltose Binding Protein, the prototypical system for the study of protein ligand recognition. We used a Monte Carlo based protocol, to computationally evolve a set of octapeptides starting from a polialanine sequence. We screened in silico the candidate peptides and characterized their binding abilities by surface plasmon resonance, fluorescence and electrospray ionization mass spectrometry assays. These experiments showed the designed binders to recognize their target with micromolar affinity. We finally discuss the obtained results in the light of further improvement in the ex-novo optimization of peptide based binders.
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Affiliation(s)
- Anna Russo
- Department of Medical and Biological Sciences, University of Udine, Piazzale Kolbe, Udine, Italy
- Department of Medical Biotechnology, University of Siena, Policlinico Le Scotte, Viale Bracci, Siena, Italy
| | - Pasqualina Liana Scognamiglio
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi- University of Naples “Federico II”, DFM-Scarl, Naples, Italy
| | | | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, Milan, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, Milan, Italy
| | - Daniela Marasco
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi- University of Naples “Federico II”, DFM-Scarl, Naples, Italy
- * E-mail: (SF); (DM)
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine & Center for Biotechnology Temple University Philadelphia, Pennsylvania, United States of America
- Department of Medicine, Surgery & Neuroscience University of Siena, Strada delle Scotte n. 6, Siena, Italy
| | - Giacinto Scoles
- Department of Medical and Biological Sciences, University of Udine, Piazzale Kolbe, Udine, Italy
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Sara Fortuna
- Department of Medical and Biological Sciences, University of Udine, Piazzale Kolbe, Udine, Italy
- * E-mail: (SF); (DM)
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Jiao Y, Legge FS, Zeng X, Treutlein HR, Zeng J. Antibody recognition of Shiga toxins (Stxs): computational identification of the epitopes of Stx2 subunit A to the antibodies 11E10 and S2C4. PLoS One 2014; 9:e88191. [PMID: 24516609 PMCID: PMC3917601 DOI: 10.1371/journal.pone.0088191] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 01/04/2014] [Indexed: 11/18/2022] Open
Abstract
We have recently developed a new method to predict the epitopes of the antigens that are
recognized by a specific antibody. In this work, we applied the method to identify the epitopes of
the Shiga toxin (Stx2 subunit A) that were bound by two specific antibodies 11E10 and S2C4. The
predicted epitopes of Stx2 binding to the antibody 11E10 resembles the recognition surface
constructed by the regions of Stx2 identified experimentally. For the S2C4, our results indicate
that the antibody recognizes the Stx2 at two different regions on the protein surface. The first
region (residues 246-254: ARSVRAVNE) is similar to the recognition region of the 11E10, while the
second region is formed by two epitopes. The second region is particularly significant because it
includes the amino acid sequence region that is diverse between Stx2 and other Stx (residues
176-188: QREFRQALSETAPV). This new recognition region is believed to play an important role in the
experimentally observed selectivity of S2C4 to the Stx2.
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Affiliation(s)
- Yongjun Jiao
- Institute of Pathogenic Microbiology, Jiangsu Provincial
Center for Disease Prevention and Control, Key Laboratory of Enteric Pathogenic Microbiology,
Ministry Health, Nanjing, China
| | - Fiona S. Legge
- Computist Bio-Nanotech, Small Technology Clusters,
Scoresby, Victoria, Australia
| | - Xiaoyan Zeng
- Institute of Pathogenic Microbiology, Jiangsu Provincial
Center for Disease Prevention and Control, Key Laboratory of Enteric Pathogenic Microbiology,
Ministry Health, Nanjing, China
| | - Herbert R. Treutlein
- Monash Institute of Pharmaceutical Sciences, Monash
University, Parkville, Victoria, Australia
- Computist Bio-Nanotech, Small Technology Clusters,
Scoresby, Victoria, Australia
- * E-mail: (HRT); (JZ)
| | - Jun Zeng
- Monash Institute of Pharmaceutical Sciences, Monash
University, Parkville, Victoria, Australia
- Computist Bio-Nanotech, Small Technology Clusters,
Scoresby, Victoria, Australia
- * E-mail: (HRT); (JZ)
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10
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Zhang W, Zeng X, Zhang L, Peng H, Jiao Y, Zeng J, Treutlein HR. Computational identification of epitopes in the glycoproteins of novel bunyavirus (SFTS virus) recognized by a human monoclonal antibody (MAb 4-5). J Comput Aided Mol Des 2013; 27:539-50. [PMID: 23838839 DOI: 10.1007/s10822-013-9661-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 06/24/2013] [Indexed: 12/12/2022]
Abstract
In this work, we have developed a new approach to predict the epitopes of antigens that are recognized by a specific antibody. Our method is based on the "multiple copy simultaneous search" (MCSS) approach which identifies optimal locations of small chemical functional groups on the surfaces of the antibody, and identifying sequence patterns of peptides that can bind to the surface of the antibody. The identified sequence patterns are then used to search the amino-acid sequence of the antigen protein. The approach was validated by reproducing the binding epitope of HIV gp120 envelop glycoprotein for the human neutralizing antibody as revealed in the available crystal structure. Our method was then applied to predict the epitopes of two glycoproteins of a newly discovered bunyavirus recognized by an antibody named MAb 4-5. These predicted epitopes can be verified by experimental methods. We also discuss the involvement of different amino acids in the antigen-antibody recognition based on the distributions of MCSS minima of different functional groups.
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Affiliation(s)
- Wenshuai Zhang
- Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Prevention and Control, Institute of Pathogenic Microbiology, Ministry Health, Nanjing 210009, China
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11
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Schubert CR, Stultz CM. The multi-copy simultaneous search methodology: a fundamental tool for structure-based drug design. J Comput Aided Mol Des 2009; 23:475-89. [PMID: 19506805 DOI: 10.1007/s10822-009-9287-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2009] [Accepted: 05/20/2009] [Indexed: 10/20/2022]
Abstract
Fragment-based ligand design approaches, such as the multi-copy simultaneous search (MCSS) methodology, have proven to be useful tools in the search for novel therapeutic compounds that bind pre-specified targets of known structure. MCSS offers a variety of advantages over more traditional high-throughput screening methods, and has been applied successfully to challenging targets. The methodology is quite general and can be used to construct functionality maps for proteins, DNA, and RNA. In this review, we describe the main aspects of the MCSS method and outline the general use of the methodology as a fundamental tool to guide the design of de novo lead compounds. We focus our discussion on the evaluation of MCSS results and the incorporation of protein flexibility into the methodology. In addition, we demonstrate on several specific examples how the information arising from the MCSS functionality maps has been successfully used to predict ligand binding to protein targets and RNA.
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Affiliation(s)
- Christian R Schubert
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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12
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Nagata T. Automated design of protecting molecules for metal nanoparticles by combinatorial molecular simulations. J Organomet Chem 2007. [DOI: 10.1016/j.jorganchem.2006.05.058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Chen F, Hancock CN, Macias AT, Joh J, Still K, Zhong S, MacKerell AD, Shapiro P. Characterization of ATP-independent ERK inhibitors identified through in silico analysis of the active ERK2 structure. Bioorg Med Chem Lett 2006; 16:6281-7. [PMID: 17000106 PMCID: PMC1857279 DOI: 10.1016/j.bmcl.2006.09.038] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2006] [Revised: 09/04/2006] [Accepted: 09/07/2006] [Indexed: 11/24/2022]
Abstract
The extracellular signal-regulated kinases (ERK1 and ERK2) are important mediators of cell proliferation. Constitutive activation of the ERK proteins plays a critical role in the proliferation of many human cancers. Taking advantage of recently identified substrate docking domains on ERK2, we have used computer-aided drug design (CADD) to identify novel low molecular weight compounds that interact with ERK2 in an ATP-independent manner and disrupt substrate-specific interactions. In the current study, a CADD screen of the 3D structure of active phosphorylated ERK2 protein was used to identify inhibitory compounds. We tested 13 compounds identified by the CADD screen in ERK-specific phosphorylation, cell proliferation, and binding assays. Of the 13 compounds tested, 4 compounds strongly inhibited ERK-mediated phosphorylation of ribosomal S6 kinase-1 (Rsk-1) and/or the transcription factor Elk-1 and inhibited the proliferation of HeLa cervical carcinoma cells with IC(50) values in the 2-10 microM range. These studies demonstrate that CADD can be used to identify lead compounds for development of novel non-ATP-dependent inhibitors selective for active ERK and its interactions with substrates involved in cancer cell proliferation.
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Affiliation(s)
- Fengming Chen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy
| | - Chad N. Hancock
- Molecular and Cell Biology Program, University of Maryland, Baltimore, MD 21201
| | - Alba T. Macias
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy
| | - Joseph Joh
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy
| | - Kimberly Still
- Senior Honors Program, Department of Biological Sciences, Villa Julie College, Stevenson, MD 21153
| | - Shijun Zhong
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy
- *Correspondence: Phone: 410-706-8522 (PS), 410-706-7442 (AM); Fax: 410-706-0346; or
| | - Paul Shapiro
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy
- *Correspondence: Phone: 410-706-8522 (PS), 410-706-7442 (AM); Fax: 410-706-0346; or
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Raines K, Cao GL, Lee E, Rosen G, Shapiro P. Neuronal nitric oxide synthase-induced S-nitrosylation of H-Ras inhibits calcium ionophore-mediated extracellular-signal-regulated kinase activity. Biochem J 2006; 397:329-36. [PMID: 16569214 PMCID: PMC1513287 DOI: 10.1042/bj20052002] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
nNOS (neuronal nitric oxide synthase) is a constitutively expressed enzyme responsible for the production of NO* from L-arginine and O2. NO* acts as both an intra- and an inter-cellular messenger that mediates a variety of signalling pathways. Previous studies from our laboratory have demonstrated that nNOS production of NO* blocks Ca2+-ionophore-induced activation of ERK1/2 (extracellular-signal-regulated kinase 1/2) of the mitogen-activated protein kinases through a mechanism involving Ras G-proteins and Raf-1 kinase. Herein we describe a mechanism by which NO* blocks Ca2+-mediated ERK1/2 activity through direct modification of H-Ras. Ca2+-mediated ERK1/2 activation in NO*-producing cells could be restored by exogenous expression of constitutively active mitogen-activated protein kinase kinase 1. In contrast, exogenous expression of constitutively active mutants of Raf-1 and H-Ras only partially restored ERK1/2 activity, by 50% and 10% respectively. On the basis of these findings, we focused on NO*-mediated mechanisms of H-Ras inhibition. Assays for GTP loading and H-Ras interactions with the Ras-binding domain on Raf-1 demonstrated a decrease in H-Ras activity in the presence of NO*. We demonstrate that S-nitrosylation of H-Ras occurs in nNOS-expressing cells activated with Ca2+ ionophore. Mutation of a putative nitrosylation site at Cys118 inhibited S-nitrosylation and restored ERK1/2 activity by constitutively active H-Ras even in the presence of NO*. These findings indicate that intracellular generation of NO* by nNOS leads to S-nitrosylation of H-Ras, which interferes with Raf-1 activation and propagation of signalling through ERK1/2.
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Affiliation(s)
- Kimberly W. Raines
- *Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, U.S.A
| | - Guan-Liang Cao
- *Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, U.S.A
- †Medical Biotechnology Center, University of Maryland Biotechnology Institute, Baltimore, MD 21201, U.S.A
- ‡Center for EPR Imaging for In Vivo Physiology, University of Maryland Biotechnology Institute, Baltimore, MD 21201, U.S.A
| | - Eun Kyoung Lee
- *Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, U.S.A
| | - Gerald M. Rosen
- *Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, U.S.A
- †Medical Biotechnology Center, University of Maryland Biotechnology Institute, Baltimore, MD 21201, U.S.A
- ‡Center for EPR Imaging for In Vivo Physiology, University of Maryland Biotechnology Institute, Baltimore, MD 21201, U.S.A
| | - Paul Shapiro
- *Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, U.S.A
- To whom correspondence should be addressed (email )
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Hancock CN, Macias A, Lee EK, Yu SY, Mackerell AD, Shapiro P. Identification of novel extracellular signal-regulated kinase docking domain inhibitors. J Med Chem 2005; 48:4586-95. [PMID: 15999996 DOI: 10.1021/jm0501174] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The extracellular signal regulated kinase (ERK1 and ERK2) signal transduction pathways play a critical role in cell proliferation. Hyperactivation of the ERK proteins either through increased expression of membrane-bound growth factor receptors or genetic mutations of upstream proteins is thought to be involved in the pathogenesis of many human cancers. Thus, targeted inhibition of ERK signaling is viewed as a potential approach to prevent cancer cell proliferation. Currently, no specific inhibitors of the ERK proteins exist. Moreover, most kinase inhibitors lack specificity because they target the ATP binding region, which is well conserved among the protein kinase families. Taking advantage of recently identified ERK docking domains, which are reported to facilitate substrate protein interactions, we have used computer-aided drug design (CADD) to identify novel small molecular weight ERK inhibitors. Following a CADD screen of over 800 000 molecules, 80 potential compounds were selected and tested for activity in biological assays. Several compounds inhibited ERK-specific phosphorylation of ribosomal S6 kinase-1 (Rsk-1) or the ternary complex factor Elk-1 (TCF/Elk-1), both of which are involved in promoting cell proliferation. Active compounds showed a dose-dependent reduction in the proliferation of several cancer cell lines as measured by colony survival assays. Direct binding between the active compounds and ERK2 was indicated by fluorescence quenching. These active compounds may serve as lead candidates for development of novel specific inhibitors of ERK-substrate interactions involved in cell proliferation.
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Affiliation(s)
- Chad N Hancock
- Department of Pharmaceutical Sciences, School of Pharmacy, and Molecular and Cell Biology Program, University of Maryland, Baltimore, 21201, USA
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Gohlke H, Kiel C, Case DA. Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. J Mol Biol 2003; 330:891-913. [PMID: 12850155 DOI: 10.1016/s0022-2836(03)00610-7] [Citation(s) in RCA: 976] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Absolute binding free energy calculations and free energy decompositions are presented for the protein-protein complexes H-Ras/C-Raf1 and H-Ras/RalGDS. Ras is a central switch in the regulation of cell proliferation and differentiation. In our study, we investigate the capability of the molecular mechanics (MM)-generalized Born surface area (GBSA) approach to estimate absolute binding free energies for the protein-protein complexes. Averaging gas-phase energies, solvation free energies, and entropic contributions over snapshots extracted from trajectories of the unbound proteins and the complexes, calculated binding free energies (Ras-Raf: -15.0(+/-6.3)kcal mol(-1); Ras-RalGDS: -19.5(+/-5.9)kcal mol(-1)) are in fair agreement with experimentally determined values (-9.6 kcal mol(-1); -8.4 kcal mol(-1)), if appropriate ionic strength is taken into account. Structural determinants of the binding affinity of Ras-Raf and Ras-RalGDS are identified by means of free energy decomposition. For the first time, computationally inexpensive generalized Born (GB) calculations are applied in this context to partition solvation free energies along with gas-phase energies between residues of both binding partners. For selected residues, in addition, entropic contributions are estimated by classical statistical mechanics. Comparison of the decomposition results with experimentally determined binding free energy differences for alanine mutants of interface residues yielded correlations with r(2)=0.55 and 0.46 for Ras-Raf and Ras-RalGDS, respectively. Extension of the decomposition reveals residues as far apart as 25A from the binding epitope that can contribute significantly to binding free energy. These "hotspots" are found to show large atomic fluctuations in the unbound proteins, indicating that they reside in structurally less stable regions. Furthermore, hotspot residues experience a significantly larger-than-average decrease in local fluctuations upon complex formation. Finally, by calculating a pair-wise decomposition of interactions, interaction pathways originating in the binding epitope of Raf are found that protrude through the protein structure towards the loop L1. This explains the finding of a conformational change in this region upon complex formation with Ras, and it may trigger a larger structural change in Raf, which is considered to be necessary for activation of the effector by Ras.
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Affiliation(s)
- Holger Gohlke
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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Brive L, Abagyan R. Computational structural proteomics. ERNST SCHERING RESEARCH FOUNDATION WORKSHOP 2002:149-66. [PMID: 12061000 DOI: 10.1007/978-3-662-04747-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- L Brive
- Department of Molecular Biology, TPC-28, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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Abstract
We have assembled references of 700 articles published in 2001 that describe work performed using commercially available optical biosensors. To illustrate the technology's diversity, the citation list is divided into reviews, methods and specific applications, as well as instrument type. We noted marked improvements in the utilization of biosensors and the presentation of kinetic data over previous years. These advances reflect a maturing of the technology, which has become a standard method for characterizing biomolecular interactions.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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