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Workman AS. Comparative analyses and molecular videography of MD simulations on WT human SOD1. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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2
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Sivakumar M, Saravanan K, Saravanan V, Sugarthi S, kumar SM, Alhaji Isa M, Rajakumar P, Aravindhan S. Discovery of new potential triplet acting inhibitor for Alzheimer’s disease via X-ray crystallography, molecular docking and molecular dynamics. J Biomol Struct Dyn 2019; 38:1903-1917. [DOI: 10.1080/07391102.2019.1620128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
| | - Kandasamy Saravanan
- X-Ray Crystallography and Computational Molecular Biology Lab, Department of Physics, Periyar University, Salem, India
| | | | - Srinivasan Sugarthi
- Department of Physics and Nanotechnology, SRM Institute of Science and Technology, Kattankulathur, Kancheepuram, Tamil Nadu, India
| | | | - Mustafa Alhaji Isa
- Bioinformatics and Computational Biology Lab, Department of Microbiology, Faculty of Sciences, University of Maiduguri, Maiduguri, Nigeria
| | - Perumal Rajakumar
- Department of Organic Chemistry, University of Madras, Chennai, India
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3
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Acylguanidine-BACE1 complex: Insights of intermolecular interactions and dynamics. J Theor Biol 2019; 464:33-49. [DOI: 10.1016/j.jtbi.2018.12.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 12/09/2018] [Accepted: 12/15/2018] [Indexed: 12/14/2022]
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Mermelstein DJ, McCammon JA, Walker RC. pH-dependent conformational dynamics of beta-secretase 1: A molecular dynamics study. J Mol Recognit 2019; 32:e2765. [PMID: 30264484 PMCID: PMC6476308 DOI: 10.1002/jmr.2765] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/25/2018] [Accepted: 08/26/2018] [Indexed: 01/19/2023]
Abstract
Beta-secretase 1 (BACE-1) is an aspartyl protease implicated in the overproduction of β-amyloid fibrils responsible for Alzheimer disease. The process of β-amyloid genesis is known to be pH dependent, with an activity peak between solution pH of 3.5 and 5.5. We have studied the pH-dependent dynamics of BACE-1 to better understand the pH dependent mechanism. We have implemented support for graphics processor unit (GPU) accelerated constant pH molecular dynamics within the AMBER molecular dynamics software package and employed this to determine the relative population of different aspartyl dyad protonation states in the pH range of greatest β-amyloid production, followed by conventional molecular dynamics to explore the differences among the various aspartyl dyad protonation states. We observed a difference in dynamics between double-protonated, mono-protonated, and double-deprotonated states over the known pH range of higher activity. These differences include Tyr 71-aspartyl dyad proximity and active water lifetime. This work indicates that Tyr 71 stabilizes catalytic water in the aspartyl dyad active site, enabling BACE-1 activity.
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Affiliation(s)
- Daniel J. Mermelstein
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - J. Andrew McCammon
- Department of Chemistry & Biochemistry, Center for Theoretical Biological Physics, Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Ross C. Walker
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- GlaxoSmithKline PLC, 1250 S. Collegeville Rd, Collegeville, PA, 19426, USA
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Saravanan K, Sivanandam M, Hunday G, Mathiyalagan L, Kumaradhas P. Investigation of intermolecular interactions and stability of verubecestat in the active site of BACE1: Development of first model from QM/MM-based charge density and MD analysis. J Biomol Struct Dyn 2018; 37:2339-2354. [DOI: 10.1080/07391102.2018.1479661] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Kandasamy Saravanan
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, Tamil Nadu, India
| | - Magudeeswaran Sivanandam
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, Tamil Nadu, India
| | - Govindasamy Hunday
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, Tamil Nadu, India
| | - Lakshmanan Mathiyalagan
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, Tamil Nadu, India
| | - Poomani Kumaradhas
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, Tamil Nadu, India
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Gueto-Tettay C, Martinez-Consuegra A, Pelaez-Bedoya L, Drosos-Ramirez JC. G-score: A function to solve the puzzle of modeling the protonation states of β-secretase binding pocket. J Mol Graph Model 2018; 85:1-12. [PMID: 30053756 DOI: 10.1016/j.jmgm.2018.07.008] [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: 05/17/2018] [Revised: 07/13/2018] [Accepted: 07/16/2018] [Indexed: 10/28/2022]
Abstract
The population density concept has emerged as a proposal for the analysis of molecular dynamics results, the key characteristic of population density is the evaluation of the simultaneous occurrence of a set of relevant parameters for a system. However, despite its statistical strength, selection of the tolerance level for the comparison of different models may appear as arbitrary. This work introduces the G-score, a function which summarizes and categorizes the results of population density analysis. Additionally, it incorporates parameters based on rmsd and dihedral angles, besides the protein-protein and protein-ligand interatomic distances conventionally used, which complement each other to provide a better description of the behavior of the system. These newly-proposed tools were applied to determine the most probable protonation state of the aspartic dyad of BACE1, Asp93 and Asp289, in the presence of three types of transition state inhibitors namely: reduced amides, tertiary carbinamines and hydroxyethylamines. The results show a full agreement between G-score values and population density charts, with the advantage of allowing a quick and direct comparison among all the considered models. We anticipate that the simplicity of calculating the parameters employed in this study will permit the extensive use of population density and the G-score for other molecular systems.
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Affiliation(s)
- Carlos Gueto-Tettay
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Campus San Pablo, 130015, Colombia; Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Division of Infection Medicine, Lund, Sweden.
| | - Alejandro Martinez-Consuegra
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Campus San Pablo, 130015, Colombia
| | - Luis Pelaez-Bedoya
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Campus San Pablo, 130015, Colombia
| | - Juan Carlos Drosos-Ramirez
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Campus San Pablo, 130015, Colombia.
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7
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Recent Advances in Computational Approaches for Designing Potential Anti-Alzheimer’s Agents. NEUROMETHODS 2018. [DOI: 10.1007/978-1-4939-7404-7_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Kumar A, Tiwari A, Sharma A. Changing Paradigm from one Target one Ligand Towards Multi-target Directed Ligand Design for Key Drug Targets of Alzheimer Disease: An Important Role of In Silico Methods in Multi-target Directed Ligands Design. Curr Neuropharmacol 2018; 16:726-739. [PMID: 29542413 PMCID: PMC6080096 DOI: 10.2174/1570159x16666180315141643] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 04/01/2017] [Accepted: 05/01/2017] [Indexed: 12/14/2022] Open
Abstract
Alzheimer disease (AD) is now considered as a multifactorial neurodegenerative disorder and rapidly increasing to an alarming situation and causing higher death rate. One target one ligand hypothesis does not provide complete solution of AD due to multifactorial nature of the disease and one target one drug fails to provide better treatment against AD. Moreover, currently available treatments are limited and most of the upcoming treatments under clinical trials are based on modulating single target. So, the current AD drug discovery research is shifting towards a new approach for a better solution that simultaneously modulates more than one targets in the neurodegenerative cascade. This can be achieved by network pharmacology, multi-modal therapies, multifaceted, and/or the more recently proposed term "multi-targeted designed drugs". Drug discovery project is a tedious, costly and long-term project. Moreover, multi-target AD drug discovery added extra challenges such as the good binding affinity of ligands for multiple targets, optimal ADME/T properties, no/less off-target side effect and crossing of the blood-brain barrier. These hurdles may be addressed by insilico methods for an efficient solution in less time and cost as computational methods successfully applied to single target drug discovery project. Here, we are summarizing some of the most prominent and computationally explored single targets against AD and further, we discussed a successful example of dual or multiple inhibitors for same targets. Moreover, we focused on ligand and structure-based computational approach to design MTDL against AD. However, it is not an easy task to balance dual activity in a single molecule but computational approach such as virtual screening docking, QSAR, simulation and free energy is useful in future MTDLs drug discovery alone or in combination with a fragment-based method. However, rational and logical implementations of computational drug designing methods are capable of assisting AD drug discovery and play an important role in optimizing multi-target drug discovery.
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Affiliation(s)
- Akhil Kumar
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow-226015, (U.P.), India
| | - Ashish Tiwari
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow-226015, (U.P.), India
| | - Ashok Sharma
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow-226015, (U.P.), India
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Gueto-Tettay C, Pelaez-Bedoya L, Drosos-Ramirez JC. Population density analysis for determining the protonation state of the catalytic dyad in BACE1-tertiary carbinamine-based inhibitor complex. J Biomol Struct Dyn 2017; 36:3557-3574. [DOI: 10.1080/07391102.2017.1393461] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Carlos Gueto-Tettay
- Grupo de Química Bioorgánica, Universidad de Cartagena, Cartagena de Indias, Colombia
| | - Luis Pelaez-Bedoya
- Grupo de Química Bioorgánica, Universidad de Cartagena, Cartagena de Indias, Colombia
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Gueto-Tettay C, Martinez-Consuegra A, Zuchniarz J, Gueto-Tettay LR, Drosos-Ramírez JC. A PM7 dynamic residue-ligand interactions energy landscape of the BACE1 inhibitory pathway by hydroxyethylamine compounds. Part I: The flap closure process. J Mol Graph Model 2017; 76:274-288. [PMID: 28746905 DOI: 10.1016/j.jmgm.2017.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 07/10/2017] [Accepted: 07/11/2017] [Indexed: 01/08/2023]
Abstract
BACE1 is an enzyme of scientific interest because it participates in the progression of Alzheimer's disease. Hydroxyethylamines (HEAs) are a family of compounds which exhibit inhibitory activity toward BACE1 at a nanomolar level, favorable pharmacokinetic properties and oral bioavailability. The first step in the inhibition of BACE1 by HEAs consists of their entrance into the protease active site and the resultant conformational change in the protein, from Apo to closed form. These two conformations differ in the position of an antiparallel loop (called the flap) which covers the entrance to the catalytic site. For BACE1, closure of this flap is vital to its catalytic activity and to inhibition of the enzyme due to the new interactions thereby formed with the ligand. In the present study a dynamic energy landscape of residue-ligand interaction energies (ReLIE) measured for 112 amino acids in the BACE1 active site and its immediate vicinity during the closure of the flap induced by 8 HEAs of different inhibitory power is presented. A total of 6.272 million ReLIE calculations, based on the PM7 semiempirical method, provided a deep and quantitative view of the first step in the inhibition of the aspartyl protease. The information suggests that residues Asp93, Asp289, Thr292, Thr293, Asn294 and Arg296 are anchor points for the ligand, accounting for approximately 45% of the total protein-ligand interaction. Additionally, flap closure improved the BACE1-HEA interaction by around 25%. Furthermore, the inhibitory activity of HEAs could be related to the capacity of these ligands to form said anchor point interactions and maintain them over time: the lack of some of these anchor interactions delayed flap closure or impeded it completely, or even caused the flap to reopen. The methodology employed here could be used as a tool to evaluate future structural modifications which lead to improvements in the favorability and stability of BACE1-HEA ReLIEs, aiding in the design of better inhibitors.
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Affiliation(s)
- Carlos Gueto-Tettay
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena, Colombia.
| | - Alejandro Martinez-Consuegra
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena, Colombia
| | - Joshua Zuchniarz
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena, Colombia
| | - Luis Roberto Gueto-Tettay
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena, Colombia
| | - Juan Carlos Drosos-Ramírez
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena, Colombia.
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