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Mukherjee RP, Yow GY, Sarakbi S, Menegatti S, Gurgel PV, Carbonell RG, Bobay BG. Integrated in silico and experimental discovery of trimeric peptide ligands targeting Butyrylcholinesterase. Comput Biol Chem 2023; 102:107797. [PMID: 36463785 DOI: 10.1016/j.compbiolchem.2022.107797] [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: 08/11/2022] [Revised: 11/09/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022]
Abstract
Butyrylcholinesterase (BChE) is recognized as a high value biotherapeutic in the treatment of Alzheimer's disease and drug addiction. This study presents the rational design and screening of an in-silico library of trimeric peptides against BChE and the experimental characterization of peptide ligands for purification. The selected peptides consistently afforded high BChE recovery (> 90 %) and purity, yielding up to a 1000-fold purification factor. This study revealed a marked anti-correlated conformational movement governed by the ionic strength and pH of the aqueous environment, which ultimately controls BChE binding and release during chromatographic purification; and highlighted the role of residues within and allosteric to the catalytic triad of BChE in determining biorecognition, thus providing useful guidance for ligand design and affinity maturation.
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Affiliation(s)
- Rudra Palash Mukherjee
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27606, USA; Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27606, USA
| | | | | | - Stefano Menegatti
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27606, USA; Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27606, USA
| | - Patrick V Gurgel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27606, USA; Prometic Bioseparations Ltd, Cambridge CB23 7AJ, UK
| | - Ruben G Carbonell
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27606, USA; Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27606, USA; William R. Kenan, Jr. Institute for Engineering, Technology and Science North Carolina State University, Raleigh, NC 27606, USA.
| | - Benjamin G Bobay
- Duke University NMR Center, Duke University Medical Center, Durham, NC 27710, USA; Department of Biochemistry, Duke University, Durham, NC 27710, USA; Department of Radiology, Duke University, Durham, NC 27710, USA.
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Metabolomics Profiling, Biological Activities, and Molecular Docking Studies of Elephant Garlic (Allium ampeloprasum L.). Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Wajid S, Khatoon A, Khan MA, Zafar H, Kanwal S, Atta-ur-Rahman, Choudhary MI, Basha FZ. Microwave-Assisted Organic Synthesis, structure–activity relationship, kinetics and molecular docking studies of non-cytotoxic benzamide derivatives as selective butyrylcholinesterase inhibitors. Bioorg Med Chem 2019; 27:4030-4040. [DOI: 10.1016/j.bmc.2019.07.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/05/2019] [Accepted: 07/09/2019] [Indexed: 12/16/2022]
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Vistoli G, Mazzolari A, Testa B, Pedretti A. Binding Space Concept: A New Approach To Enhance the Reliability of Docking Scores and Its Application to Predicting Butyrylcholinesterase Hydrolytic Activity. J Chem Inf Model 2017. [PMID: 28633528 DOI: 10.1021/acs.jcim.7b00121] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Docking simulations are very popular approaches able to assess the capacity of a given ligand to interact with a target. Docking simulations are usually focused on a single best complex even though many studies showed that ligands retain a significant mobility within a binding pocket by assuming different binding modes all of which may contribute to the monitored ligand affinity. The present study describes an innovative concept, the binding space, which allows an exploration of the ligand mobility within the binding pocket by simultaneously considering several ligand poses as generated by docking simulations. The multiple poses and the relative docking scores can then be analyzed by taking advantage of the same concepts already used in the property space analysis; hence the binding space can be parametrized by (a) mean scores, (b) score ranges, and (c) score sensitivity values. The first parameter represents a very simple procedure to account for the contribution of the often neglected alternative binding modes, while the last two descriptors encode the degree of mobility which a given ligand retains within the binding cavity (score range) as well as the ease with which a ligand explores such a mobility (score sensitivity). Here, the binding space concept is applied to the prediction of the hydrolytic activity of BChE by synergistically considering multiple poses and multiple protein structures. The obtained results shed light on the remarkable potential of the binding space concept, whose parameters allow a significant increase of the predictive power of the docking results as revealed by extended correlative analyses. Mean scores are the parameters affording the largest statistical improvement, and all the here proposed docking-based descriptors show enhancing effects in developing predictive models. Finally, the study describes a new score function (Contacts score) simply based on the number of surrounding residues which appears to be particularly productive in the framework of the binding space.
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Affiliation(s)
- Giulio Vistoli
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano , Via Mangiagalli, 25, I-20133 Milano, Italy
| | - Angelica Mazzolari
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano , Via Mangiagalli, 25, I-20133 Milano, Italy
| | - Bernard Testa
- Department of Pharmacy, University Hospital Centre (CHUV) , Rue du Bugnon, CH-1011 Lausanne, Switzerland
| | - Alessandro Pedretti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano , Via Mangiagalli, 25, I-20133 Milano, Italy
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