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Kaur R, Narang SS, Singh P, Goyal B. Structural and molecular insights into tacrine-benzofuran hybrid induced inhibition of amyloid-β peptide aggregation and BACE1 activity. J Biomol Struct Dyn 2023; 41:13211-13227. [PMID: 37013977 DOI: 10.1080/07391102.2023.2191722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 01/16/2023] [Indexed: 04/05/2023]
Abstract
Amyloid-β (Aβ) aggregation and β-amyloid precursor protein cleaving enzyme 1 (BACE1) are the potential therapeutic drug targets for Alzheimer's disease (AD). A recent study highlighted that tacrine-benzofuran hybrid C1 displayed anti-aggregation activity against Aβ42 peptide and inhibit BACE1 activity. However, the inhibition mechanism of C1 against Aβ42 aggregation and BACE1 activity remains unclear. Thus, molecular dynamics (MD) simulations of Aβ42 monomer and BACE1 with and without C1 were performed to inspect the inhibitory mechanism of C1 against Aβ42 aggregation and BACE1 activity. In addition, a ligand-based virtual screening followed by MD simulations was employed to explore potent new small-molecule dual inhibitors of Aβ42 aggregation and BACE1 activity. MD simulations highlighted that C1 promotes the non aggregating helical conformation in Aβ42 and destabilizes D23-K28 salt bridge that plays a vital role in the self-aggregation of Aβ42. C1 displays a favourable binding free energy (-50.7 ± 7.3 kcal/mol) with Aβ42 monomer and preferentially binds to the central hydrophobic core (CHC) residues. MD simulations highlighted that C1 strongly interacted with the BACE1 active site (Asp32 and Asp228) and active pockets. The scrutiny of interatomic distances among key residues of BACE1 highlighted the close flap (non-active) position in BACE1 on the incorporation of C1. The MD simulations explain the observed high inhibitory activity of C1 against Aβ aggregation and BACE1 in the in vitro studies. The ligand-based virtual screening followed by MD simulations identified CHEMBL2019027 (C2) as a promising dual inhibitor of Aβ42 aggregation and BACE1 activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rajdeep Kaur
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Simranjeet Singh Narang
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Pritpal Singh
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
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2
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Kaur G, Goyal B. Deciphering the Molecular Mechanism of Inhibition of β‐Secretase (BACE1) Activity by a 2‐Amino‐imidazol‐4‐one Derivative. ChemistrySelect 2022. [DOI: 10.1002/slct.202202561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Gurmeet Kaur
- School of Chemistry & Biochemistry Thapar Institute of Engineering & Technology Patiala 147004 Punjab India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry Thapar Institute of Engineering & Technology Patiala 147004 Punjab India
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3
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Molecular insights into the inhibitory mechanism of bi-functional bis-tryptoline triazole against β-secretase (BACE1) enzyme. Amino Acids 2019; 51:1593-1607. [PMID: 31654211 DOI: 10.1007/s00726-019-02797-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 10/04/2019] [Indexed: 02/07/2023]
Abstract
The β-site amyloid precursor protein-cleaving enzyme 1 (β-secretase, BACE1) is involved in the formation of amyloid-β (Aβ) peptide that aggregates into soluble oligomers, amyloid fibrils, and plaques responsible for the neurodegeneration in Alzheimer disease (AD). BACE1 is one of the prime therapeutic targets for the design of inhibitors against AD as BACE1 participate in the rate-limiting step in Aβ production. Jiaranaikulwanitch et al. reported bis-tryptoline triazole (BTT) compound as a potent inhibitor against BACE1, Aβ aggregation as well as possessing metal chelation and antioxidant activity. However, the molecular mechanism of BACE1 inhibition by BTT remains unclear. Thus, molecular docking and molecular dynamics (MD) simulations were performed to elucidate the inhibitory mechanism of BTT against BACE1. MD simulations highlight that BTT interact with catalytic aspartic dyad residues (Asp32 and Asp228) and active pocket residues of BACE1. The hydrogen-bond interactions, hydrophobic contacts, and π-π stacking interactions of BTT with flap residues (Val67-Asp77) of BACE1 confine the movement of the flap and help to achieve closed (non-active) conformation. The PCA analysis highlights lower conformational fluctuations for BACE1-BTT complex, which suggests enhanced conformational stability in comparison to apo-BACE1. The results of the present study provide key insights into the underlying inhibitory mechanism of BTT against BACE1 and will be helpful for the rational design of novel inhibitors with enhanced potency against BACE1.
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Efremov IV, Vajdos FF, Borzilleri KA, Capetta S, Chen H, Dorff PH, Dutra JK, Goldstein SW, Mansour M, McColl A, Noell S, Oborski CE, O’Connell TN, O’Sullivan TJ, Pandit J, Wang H, Wei B, Withka JM. Discovery and Optimization of a Novel Spiropyrrolidine Inhibitor of β-Secretase (BACE1) through Fragment-Based Drug Design. J Med Chem 2012; 55:9069-88. [DOI: 10.1021/jm201715d] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ivan V. Efremov
- Pfizer Worldwide Research, Groton Laboratories, Eastern Point Road,
Groton, Connecticut 06340, United States
| | - Felix F. Vajdos
- Pfizer Worldwide Research, Groton Laboratories, Eastern Point Road,
Groton, Connecticut 06340, United States
| | - Kris A. Borzilleri
- Pfizer Worldwide Research, Groton Laboratories, Eastern Point Road,
Groton, Connecticut 06340, United States
| | - Steven Capetta
- Pfizer Worldwide Research, Groton Laboratories, Eastern Point Road,
Groton, Connecticut 06340, United States
| | - Hou Chen
- Pfizer Worldwide Research, Groton Laboratories, Eastern Point Road,
Groton, Connecticut 06340, United States
| | - Peter H. Dorff
- Pfizer Worldwide Research, Groton Laboratories, Eastern Point Road,
Groton, Connecticut 06340, United States
| | - Jason K. Dutra
- Pfizer Worldwide Research, Groton Laboratories, Eastern Point Road,
Groton, Connecticut 06340, United States
| | - Steven W. Goldstein
- Pfizer Worldwide Research, Groton Laboratories, Eastern Point Road,
Groton, Connecticut 06340, United States
| | - Mahmoud Mansour
- Pfizer Worldwide Research, Groton Laboratories, Eastern Point Road,
Groton, Connecticut 06340, United States
| | - Alexander McColl
- Pfizer Worldwide Research, Groton Laboratories, Eastern Point Road,
Groton, Connecticut 06340, United States
| | - Stephen Noell
- Pfizer Worldwide Research, Groton Laboratories, Eastern Point Road,
Groton, Connecticut 06340, United States
| | - Christine E. Oborski
- Pfizer Worldwide Research, Groton Laboratories, Eastern Point Road,
Groton, Connecticut 06340, United States
| | - Thomas N. O’Connell
- Pfizer Worldwide Research, Groton Laboratories, Eastern Point Road,
Groton, Connecticut 06340, United States
| | - Theresa J. O’Sullivan
- Pfizer Worldwide Research, Groton Laboratories, Eastern Point Road,
Groton, Connecticut 06340, United States
| | - Jayvardhan Pandit
- Pfizer Worldwide Research, Groton Laboratories, Eastern Point Road,
Groton, Connecticut 06340, United States
| | - Hong Wang
- Pfizer Worldwide Research, Groton Laboratories, Eastern Point Road,
Groton, Connecticut 06340, United States
| | - BinQing Wei
- Pfizer Worldwide Research, Groton Laboratories, Eastern Point Road,
Groton, Connecticut 06340, United States
| | - Jane M. Withka
- Pfizer Worldwide Research, Groton Laboratories, Eastern Point Road,
Groton, Connecticut 06340, United States
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Wang YS, Strickland C, Voigt JH, Kennedy ME, Beyer BM, Senior MM, Smith EM, Nechuta TL, Madison VS, Czarniecki M, McKittrick BA, Stamford AW, Parker EM, Hunter JC, Greenlee WJ, Wyss DF. Application of Fragment-Based NMR Screening, X-ray Crystallography, Structure-Based Design, and Focused Chemical Library Design to Identify Novel μM Leads for the Development of nM BACE-1 (β-Site APP Cleaving Enzyme 1) Inhibitors. J Med Chem 2009; 53:942-50. [DOI: 10.1021/jm901472u] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu-Sen Wang
- Schering-Plough Research Institute, 320 Bent Street, Cambridge, Massachusetts 02141
| | - Corey Strickland
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Johannes H. Voigt
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Matthew E. Kennedy
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Brian M. Beyer
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Mary M. Senior
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Elizabeth M. Smith
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Terry L. Nechuta
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Vincent S. Madison
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Michael Czarniecki
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Brian A. McKittrick
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Andrew W. Stamford
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Eric M. Parker
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - John C. Hunter
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - William J. Greenlee
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Daniel F. Wyss
- Schering-Plough Research Institute, 320 Bent Street, Cambridge, Massachusetts 02141
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Abstract
BACKGROUND: Drug discovery is a complex and unpredictable endeavor with a high failure rate. Current trends in the pharmaceutical industry have exasperated these challenges and are contributing to the dramatic decline in productivity observed over the last decade. The industrialization of science by forcing the drug discovery process to adhere to assembly-line protocols is imposing unnecessary restrictions, such as short project time-lines. Recent advances in nuclear magnetic resonance are responding to these self-imposed limitations and are providing opportunities to increase the success rate of drug discovery. OBJECTIVE/METHOD: A review of recent advancements in NMR technology that have the potential of significantly impacting and benefiting the drug discovery process will be presented. These include fast NMR data collection protocols and high-throughput protein structure determination, rapid protein-ligand co-structure determination, lead discovery using fragment-based NMR affinity screens, NMR metabolomics to monitor in vivo efficacy and toxicity for lead compounds, and the identification of new therapeutic targets through the functional annotation of proteins by FAST-NMR. CONCLUSION: NMR is a critical component of the drug discovery process, where the versatility of the technique enables it to continually expand and evolve its role. NMR is expected to maintain this growth over the next decade with advancements in automation, speed of structure calculation, in-cell imaging techniques, and the expansion of NMR amenable targets.
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Affiliation(s)
- Robert Powers
- Department of Chemistry, University of Nebraska Lincoln, Lincoln, NE 68588
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Powers R, Mercier KA, Copeland JC. The application of FAST-NMR for the identification of novel drug discovery targets. Drug Discov Today 2008; 13:172-9. [PMID: 18275915 DOI: 10.1016/j.drudis.2007.11.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2007] [Revised: 10/30/2007] [Accepted: 11/01/2007] [Indexed: 10/22/2022]
Abstract
The continued success of genome sequencing projects has resulted in a wealth of information, but 40-50% of identified genes correspond to hypothetical proteins or proteins of unknown function. The functional annotation screening technology by NMR (FAST-NMR) screen was developed to assign a biological function for these unannotated proteins with a structure solved by the protein structure initiative. FAST-NMR is based on the premise that a biological function can be described by a similarity in binding sites and ligand interactions with proteins of known function. The resulting co-structure and functional assignment may provide a starting point for a drug discovery effort.
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Affiliation(s)
- Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68522, USA.
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