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Wu D, Salsbury FR. Unraveling the Role of Hydrogen Bonds in Thrombin via Two Machine Learning Methods. J Chem Inf Model 2023. [PMID: 37285464 DOI: 10.1021/acs.jcim.3c00153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Hydrogen bonds play a critical role in the folding and stability of proteins, such as proteins and nucleic acids, by providing strong and directional interactions. They help to maintain the secondary and 3D structure of proteins, and structural changes in these molecules often result from the formation or breaking of hydrogen bonds. To gain insights into these hydrogen bonding networks, we applied two machine learning models - a logistic regression model and a decision tree model - to study four variants of thrombin: wild-type, ΔK9, E8K, and R4A. Our results showed that both models have their unique advantages. The logistic regression model highlighted potential key residues (GLU295) in thrombin's allosteric pathways, while the decision tree model identified important hydrogen bonding motifs. This information can aid in understanding the mechanisms of folding in proteins and has potential applications in drug design and other therapies. The use of these two models highlights their usefulness in studying hydrogen bonding networks in proteins.
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Affiliation(s)
- Dizhou Wu
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27106, United States
| | - Freddie R Salsbury
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27106, United States
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Sharma T, Siddiqi MI. In silico identification and design of potent peptide inhibitors against PDZ-3 domain of Postsynaptic Density Protein (PSD-95). J Biomol Struct Dyn 2018; 37:1241-1253. [PMID: 29557723 DOI: 10.1080/07391102.2018.1454851] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Unique intrinsic properties of peptides like low toxicity, high biological activity, and specificity make them attractive therapeutic agents. PDZ-binding peptide inhibitors have been demonstrated for curing of Alzheimer, Parkinson, Dementia, and other central nervous system ailments. In this article, we report the successful use of an integrated computational protocol to analyze the structural basis of how peptides bind to the shallow groove of the third PDZ domain (PDZ-3) from the postsynaptic density (PSD-95) protein. This protocol employs careful and precise computational techniques for design of new strategy for predicting novel and potent peptides against PDZ protein. We attempted to generate a pharmacophore model using crystal structure of peptide inhibitor bound to the PDZ-3. A highly specific and sensitive generated pharmacophore model was used for screening virtual database generated using different combination of amino acid substitutions as well as decoy peptide database for its sensitivity and specificity. Identified hit peptides were further analyzed by docking studies, and their stability analyzed using solvated molecular dynamics. Quantum Mechanics/Molecular Mechanics (QM/MM) interaction energy and GMX-PBSA scoring schemes were used for ranking of stable peptides. Computational approach applied here generated encouraging results for identifying peptides against PDZ interaction model. The workflow can be further exercised as a virtual screening technique for reducing the search space for candidate target peptides against PDZ domains.
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Affiliation(s)
- Tanuj Sharma
- a Laboratory of Computational Biology and Bioinformatics, Division of Molecular and Structural Biology , CSIR-Central Drug Research Institute , Lucknow 226031 , India
| | - Mohammad Imran Siddiqi
- a Laboratory of Computational Biology and Bioinformatics, Division of Molecular and Structural Biology , CSIR-Central Drug Research Institute , Lucknow 226031 , India.,b Academy of Scientific and Innovative Research (AcSIR) , CSIR-Central Drug Research Institute , Campus, Lucknow 226031 , India
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Ding J, Wang K, Tang WJ, Li D, Wei YZ, Lu Y, Li ZH, Liang XF. Construction of Epidermal Growth Factor Receptor Peptide Magnetic Nanovesicles with Lipid Bilayers for Enhanced Capture of Liver Cancer Circulating Tumor Cells. Anal Chem 2016; 88:8997-9003. [PMID: 27558867 DOI: 10.1021/acs.analchem.6b01443] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Highly effective targeted tumor recognition via vectors is crucial for cancer detection. In contrast to antibodies and proteins, peptides are direct targeting ligands with a low molecular weight. In the present study, a peptide magnetic nanovector platform containing a lipid bilayer was designed using a peptide amphiphile (PA) as a skeleton material in a controlled manner without surface modification. Fluorescein isothiocyanate-labeled epidermal growth factor receptor (EGFR) peptide nanoparticles (NPs) could specifically bind to EGFR-positive liver tumor cells. EGFR peptide magnetic vesicles (EPMVs) could efficiently recognize and separate hepatoma carcinoma cells from cell solutions and treated blood samples (ratio of magnetic EPMVs versus anti-EpCAM NPs: 3.5 ± 0.29). Analysis of the circulating tumor cell (CTC) count in blood samples from 32 patients with liver cancer showed that EPMVs could be effectively applied for CTC capture. Thus, this nanoscale, targeted cargo-packaging technology may be useful for designing cancer diagnostic systems.
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Affiliation(s)
- Jian Ding
- Digestive Department, The First Affiliated Hospital of Fujian Medical University , 20 Chazhong Road, Fuzhou 350005, China
| | - Kai Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine , No.25/Ln2200 Xie Tu Road, Shanghai 200032, China
| | - Wen-Jie Tang
- Research Centre for Translational Medicine, East Hospital, Tongji University School of Medicine , 150 Jimo Road, Shanghai 200120, China
| | - Dan Li
- Digestive Department, Union Hospital of Fujian Medical University , Fuzhou 350001, China
| | - You-Zhen Wei
- Research Centre for Translational Medicine, East Hospital, Tongji University School of Medicine , 150 Jimo Road, Shanghai 200120, China
| | - Ying Lu
- Research Centre for Translational Medicine, East Hospital, Tongji University School of Medicine , 150 Jimo Road, Shanghai 200120, China
| | - Zong-Hai Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine , No.25/Ln2200 Xie Tu Road, Shanghai 200032, China
| | - Xiao-Fei Liang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine , No.25/Ln2200 Xie Tu Road, Shanghai 200032, China
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Joshi BP, Zhou J, Pant A, Duan X, Zhou Q, Kuick R, Owens SR, Appelman H, Wang TD. Design and Synthesis of Near-Infrared Peptide for in Vivo Molecular Imaging of HER2. Bioconjug Chem 2015; 27:481-94. [PMID: 26709709 DOI: 10.1021/acs.bioconjchem.5b00565] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We report the development, characterization, and validation of a peptide specific for the extracellular domain of HER2. This probe chemistry was developed for molecular imaging by using a structural model to select an optimal combination of amino acids that maximize the likelihood for unique hydrophobic and hydrophilic interactions with HER2 domain 3. The sequence KSPNPRF was identified and conjugated with either FITC or Cy5.5 via a GGGSK linker using Fmoc-mediated solid-phase synthesis to demonstrate flexibility for this chemical structure to be labeled with different fluorophores. A scrambled sequence was developed for control by altering the conformationally rigid spacer and moving both hydrophobic and hydrophilic amino acids on the C-terminus. We validated peptide specificity for HER2 in knockdown and competition experiments using human colorectal cancer cells in vitro, and measured a binding affinity of kd = 21 nM and time constant of k = 0.14 min(-1) (7.14 min). We used this peptide with either topical or intravenous administration in a preclinical model of colorectal cancer to demonstrate specific uptake in spontaneous adenomas and to show feasibility for real time in vivo imaging with near-infrared fluorescence. We used this peptide in immunofluorescence studies of human proximal colon specimens to evaluate specificity for sessile serrated and sporadic adenomas. Improved visualization can be used endoscopically to guide tissue biopsy and detect premalignant lesions that would otherwise be missed. Our peptide design for specificity to HER2 is promising for clinical translation in molecular imaging methods for early cancer detection.
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Affiliation(s)
- Bishnu P Joshi
- Department of Medicine, Division of Gastroenterology, ‡Department of Biomedical Engineering, §Department of Biostatistics, ∥Department of Pathology, and ⊥Department of Mechanical Engineering, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Juan Zhou
- Department of Medicine, Division of Gastroenterology, ‡Department of Biomedical Engineering, §Department of Biostatistics, ∥Department of Pathology, and ⊥Department of Mechanical Engineering, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Asha Pant
- Department of Medicine, Division of Gastroenterology, ‡Department of Biomedical Engineering, §Department of Biostatistics, ∥Department of Pathology, and ⊥Department of Mechanical Engineering, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Xiyu Duan
- Department of Medicine, Division of Gastroenterology, ‡Department of Biomedical Engineering, §Department of Biostatistics, ∥Department of Pathology, and ⊥Department of Mechanical Engineering, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Quan Zhou
- Department of Medicine, Division of Gastroenterology, ‡Department of Biomedical Engineering, §Department of Biostatistics, ∥Department of Pathology, and ⊥Department of Mechanical Engineering, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Rork Kuick
- Department of Medicine, Division of Gastroenterology, ‡Department of Biomedical Engineering, §Department of Biostatistics, ∥Department of Pathology, and ⊥Department of Mechanical Engineering, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Scott R Owens
- Department of Medicine, Division of Gastroenterology, ‡Department of Biomedical Engineering, §Department of Biostatistics, ∥Department of Pathology, and ⊥Department of Mechanical Engineering, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Henry Appelman
- Department of Medicine, Division of Gastroenterology, ‡Department of Biomedical Engineering, §Department of Biostatistics, ∥Department of Pathology, and ⊥Department of Mechanical Engineering, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Thomas D Wang
- Department of Medicine, Division of Gastroenterology, ‡Department of Biomedical Engineering, §Department of Biostatistics, ∥Department of Pathology, and ⊥Department of Mechanical Engineering, University of Michigan , Ann Arbor, Michigan 48109, United States
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Zalloum H, Tayyem R, Irmaileh BA, Bustanji Y, Zihlif M, Mohammad M, Rjai TA, Mubarak MS. Discovery of new human epidermal growth factor receptor-2 (HER2) inhibitors for potential use as anticancer agents via ligand-based pharmacophore modeling. J Mol Graph Model 2015; 61:61-84. [DOI: 10.1016/j.jmgm.2015.06.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Revised: 05/18/2015] [Accepted: 06/20/2015] [Indexed: 12/23/2022]
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Pappalardo M, Shachaf N, Basile L, Milardi D, Zeidan M, Raiyn J, Guccione S, Rayan A. Sequential application of ligand and structure based modeling approaches to index chemicals for their hH4R antagonism. PLoS One 2014; 9:e109340. [PMID: 25330207 PMCID: PMC4199621 DOI: 10.1371/journal.pone.0109340] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 09/10/2014] [Indexed: 02/03/2023] Open
Abstract
The human histamine H4 receptor (hH4R), a member of the G-protein coupled receptors (GPCR) family, is an increasingly attractive drug target. It plays a key role in many cell pathways and many hH4R ligands are studied for the treatment of several inflammatory, allergic and autoimmune disorders, as well as for analgesic activity. Due to the challenging difficulties in the experimental elucidation of hH4R structure, virtual screening campaigns are normally run on homology based models. However, a wealth of information about the chemical properties of GPCR ligands has also accumulated over the last few years and an appropriate combination of these ligand-based knowledge with structure-based molecular modeling studies emerges as a promising strategy for computer-assisted drug design. Here, two chemoinformatics techniques, the Intelligent Learning Engine (ILE) and Iterative Stochastic Elimination (ISE) approach, were used to index chemicals for their hH4R bioactivity. An application of the prediction model on external test set composed of more than 160 hH4R antagonists picked from the chEMBL database gave enrichment factor of 16.4. A virtual high throughput screening on ZINC database was carried out, picking ∼ 4000 chemicals highly indexed as H4R antagonists' candidates. Next, a series of 3D models of hH4R were generated by molecular modeling and molecular dynamics simulations performed in fully atomistic lipid membranes. The efficacy of the hH4R 3D models in discrimination between actives and non-actives were checked and the 3D model with the best performance was chosen for further docking studies performed on the focused library. The output of these docking studies was a consensus library of 11 highly active scored drug candidates. Our findings suggest that a sequential combination of ligand-based chemoinformatics approaches with structure-based ones has the potential to improve the success rate in discovering new biologically active GPCR drugs and increase the enrichment factors in a synergistic manner.
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Affiliation(s)
- Matteo Pappalardo
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - Nir Shachaf
- Drug Discovery Informatics Lab, QRC-Qasemi Research Center, Al-Qasemi Academic College, Baka El-Garbiah, Israel
| | - Livia Basile
- Etnalead s.r.l., Scuola Superiore di Catania, University of Catania, Catania, Italy
| | - Danilo Milardi
- National Research Council, Institute of Biostructures and Bioimaging, Catania, Italy
| | - Mouhammed Zeidan
- Drug Discovery Informatics Lab, QRC-Qasemi Research Center, Al-Qasemi Academic College, Baka El-Garbiah, Israel
| | - Jamal Raiyn
- Drug Discovery Informatics Lab, QRC-Qasemi Research Center, Al-Qasemi Academic College, Baka El-Garbiah, Israel
| | - Salvatore Guccione
- Etnalead s.r.l., Scuola Superiore di Catania, University of Catania, Catania, Italy
- Department of Pharmaceutical Sciences, University of Catania, Catania, Italy
| | - Anwar Rayan
- Drug Discovery Informatics Lab, QRC-Qasemi Research Center, Al-Qasemi Academic College, Baka El-Garbiah, Israel
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