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Pereira WA, Nascimento ÉCM, Martins JBL. Electronic and structural study of T315I mutated form in DFG-out conformation of BCR-ABL inhibitors. J Biomol Struct Dyn 2022; 40:9774-9788. [PMID: 34121617 DOI: 10.1080/07391102.2021.1935320] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In this work, the four main drugs for the treatment of chronic myeloid leukemia were analyzed, being imatinib, dasatinib, nilotinib and ponatinib followed by four derivative molecules of nilotinib and ponatinib. For these derivative molecules, the fluorine atoms were replaced by hydrogen and chlorine atoms in order to shade light to the structural effects on this set of inhibitors. Electronic studies were performed at density functional theory level with the B3LYP functional and 6-311+G(d,p) basis set. The frontier molecular orbitals, gap HOMO-LUMO, and NBO were analyzed and compared to docking studies for mutant T315I tyrosine kinase protein structure code 3IK3, in the DFG-out conformation. Structural similarities were pointed out, such as the presence of groups common to all inhibitors and modifications raised up on new generations of imatinib-based inhibitors. One of them is the trifluoromethyl group present in nilotinib and later included in ponatinib, in addition to the 1-methylpiperazin-1-ium group that is present in imatinib and ponatinib. The frontier molecular orbitals of imatinib and ponatinib are contributing to the same amino acid residues, and the ineffectiveness of imatinib against the T315I mutation was discussed.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Washington A Pereira
- Institute of Chemistry, Laboratory of Computational Chemistry, University of Brasília, Brasília, Federal District, Brazil
| | - Érica C M Nascimento
- Institute of Chemistry, Laboratory of Computational Chemistry, University of Brasília, Brasília, Federal District, Brazil
| | - João B L Martins
- Institute of Chemistry, Laboratory of Computational Chemistry, University of Brasília, Brasília, Federal District, Brazil
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Uliassi E, de Oliveira AS, de Camargo Nascente L, Romeiro LAS, Bolognesi ML. Cashew Nut Shell Liquid (CNSL) as a Source of Drugs for Alzheimer's Disease. Molecules 2021; 26:molecules26185441. [PMID: 34576912 PMCID: PMC8466601 DOI: 10.3390/molecules26185441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/24/2021] [Accepted: 08/30/2021] [Indexed: 12/18/2022] Open
Abstract
Alzheimer’s disease (AD) is a complex neurodegenerative disorder with a multifaceted pathogenesis. This fact has long halted the development of effective anti-AD drugs. Recently, a therapeutic strategy based on the exploitation of Brazilian biodiversity was set with the aim of discovering new disease-modifying and safe drugs for AD. In this review, we will illustrate our efforts in developing new molecules derived from Brazilian cashew nut shell liquid (CNSL), a natural oil and a byproduct of cashew nut food processing, with a high content of phenolic lipids. The rational modification of their structures has emerged as a successful medicinal chemistry approach to the development of novel anti-AD lead candidates. The biological profile of the newly developed CNSL derivatives towards validated AD targets will be discussed together with the role of these molecular targets in the context of AD pathogenesis.
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Affiliation(s)
- Elisa Uliassi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum—University of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy;
| | - Andressa Souza de Oliveira
- Department of Pharmacy, Health Sciences Faculty, Campus Universitário Darcy Ribeiro, University of Brasília, Brasília 70910-900, DF, Brazil; (A.S.d.O.); (L.d.C.N.)
| | - Luciana de Camargo Nascente
- Department of Pharmacy, Health Sciences Faculty, Campus Universitário Darcy Ribeiro, University of Brasília, Brasília 70910-900, DF, Brazil; (A.S.d.O.); (L.d.C.N.)
| | - Luiz Antonio Soares Romeiro
- Department of Pharmacy, Health Sciences Faculty, Campus Universitário Darcy Ribeiro, University of Brasília, Brasília 70910-900, DF, Brazil; (A.S.d.O.); (L.d.C.N.)
- Correspondence: (L.A.S.R.); (M.L.B.)
| | - Maria Laura Bolognesi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum—University of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy;
- Correspondence: (L.A.S.R.); (M.L.B.)
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Borges NM, Sartori GR, Ribeiro JFR, Rocha JR, Martins JBL, Montanari CA, Gargano R. Similarity search combined with docking and molecular dynamics for novel hAChE inhibitor scaffolds. J Mol Model 2018; 24:41. [PMID: 29332299 DOI: 10.1007/s00894-017-3548-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 11/27/2017] [Indexed: 12/31/2022]
Abstract
The main purpose of this study was to address the performance of virtual screening methods based on ligands and the protein structure of acetylcholinesterase (AChE) in order to retrieve novel human AChE (hAChE) inhibitors. In addition, a protocol was developed to identify novel hit compounds and propose new promising AChE inhibitors from the ZINC database with 10 million commercially available compounds. In this sense, 3D similarity searches using rapid overlay of chemical structures and similarity analysis through comparison of electrostatic overlay of docked hits were used to retrieve AChE inhibitors from collected databases. Molecular dynamics simulation of 100 ns was carried out to study the best docked compounds from similarity searches. Some key residues were identified as crucial for the dual binding mode of inhibitor with the interaction site. All results indicated the relevant use of EON and docking strategy for identifying novel hit compounds as promising potential anticholinesterase candidates, and seven new structures were selected as potential hAChE inhibitors. Graphical abstract Compound N01 in the 4M0E hAChE crystallography structure from docking results. Yellow dashed lines Hydrogen bonds, blue dashed lines π-stacking interactions, green dashed lines cation-π interactions.
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Affiliation(s)
| | | | - Jean F R Ribeiro
- Institute of Chemistry of São Carlos, University of São Paulo, São Carlos, SP, Brazil
| | - Josmar R Rocha
- Institute of Chemistry of São Carlos, University of São Paulo, São Carlos, SP, Brazil
| | - João B L Martins
- Institute of Chemistry, University of Brasilia, Brasilia, DF, Brazil
| | - Carlos A Montanari
- Institute of Chemistry of São Carlos, University of São Paulo, São Carlos, SP, Brazil
| | - Ricardo Gargano
- Institute of Physics, University of Brasilia, Brasilia, DF, Brazil
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Kiametis AS, Silva MA, Romeiro LAS, Martins JBL, Gargano R. Potential acetylcholinesterase inhibitors: molecular docking, molecular dynamics, and in silico prediction. J Mol Model 2017; 23:67. [PMID: 28185116 DOI: 10.1007/s00894-017-3228-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 01/12/2017] [Indexed: 01/23/2023]
Abstract
This paper deals with molecular modeling of new therapeutic agents for treating the Alzheimer's disease. The therapeutic line adopted for this study is the cholinergic hypothesis. To modulate positively the cholinergic function through the inhibition of the acetylcholinesterase, a set of candidates was designed from a natural compound extracted from the cashew nutshell liquid, anacardic acid. In silico screening of this chemical library revealed a ligand that is more promising once it is correlated with an active drug through specific topological and electronic descriptors. The protein-ligand docking showed stable binding modes and the binding free energy computed for the active site of the receptor suggests that our ligand presents a potential biological response. Graphical Abstract Representation of the three dimensional structure of the AChE, showing the important binding sites of the Gorge and the conformation of the ligand.
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Affiliation(s)
| | - Mônica A Silva
- Institute of Physics, University of Brasilia, Brasilia, Brazil.
| | - Luiz A S Romeiro
- Departament of Tropical Medicine, University of Brasilia, Brasilia, Brazil
| | - João B L Martins
- Institute of Chemistry, University of Brasilia, Brasilia, Brazil
| | - Ricardo Gargano
- Institute of Physics, University of Brasilia, Brasilia, Brazil
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Rahman A, Ali MT, Shawan MMAK, Sarwar MG, Khan MAK, Halim MA. Halogen-directed drug design for Alzheimer's disease: a combined density functional and molecular docking study. SPRINGERPLUS 2016; 5:1346. [PMID: 27588239 PMCID: PMC4987752 DOI: 10.1186/s40064-016-2996-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/03/2016] [Indexed: 11/10/2022]
Abstract
A series of halogen-directed donepezil drugs has been designed to inhibit acetyl cholinesterase (AChE). Density Functional theory (DFT) has been employed to optimize the chair as well as boat conformers of the parent drug and modified ligands at B3LYP/MidiX and B3LYP/6-311G + (d,p) level of theories. Charge distribution, dipole moment, enthalpy, free energy and molecular orbitals of these ligands are also investigated to understand how the halogen-directed modifications impact the ligand structure and govern the non-bonding interactions with the receptors. Molecular docking calculation has been performed to understand the similarities and differences between the binding modes of unmodified and halogenated chair-formed ligands. Molecular docking indicated donepezil and modified ligands had non-covalent interactions with hydrophobic gorges and anionic subsites of AChE. The -CF3-directed ligand possessed the most negative binding affinity. Non-covalent interactions within the ligand-receptor systems were found to be mostly hydrophobic and π- stacking type. F, Cl and -CF3 containing ligands emerge as effective and selective AChE inhibitors, which can strongly interact with the two active sites of AChE. In addition, we have also investigated selected pharmacokinetic parameters of the parent and modified ligands.
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Affiliation(s)
- Adhip Rahman
- Division of Computer Aided Drug Design, Green Research Centre, BICCB, 38 Green Road West, Dhaka, 1205 Bangladesh
| | - Mohammad Tuhin Ali
- Division of Computer Aided Drug Design, Green Research Centre, BICCB, 38 Green Road West, Dhaka, 1205 Bangladesh
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000 Bangladesh
| | - Mohammad Mahfuz Ali Khan Shawan
- Division of Computer Aided Drug Design, Green Research Centre, BICCB, 38 Green Road West, Dhaka, 1205 Bangladesh
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Dhaka, 1342 Bangladesh
| | - Mohammed Golam Sarwar
- Fakultät für Chemie und Biochemie, Organische Chemie I, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Mohammad A. K. Khan
- Department of General Studies, Jubail University College, Jubail Industrial City, 31961 The Kingdom of Saudi Arabia
| | - Mohammad A. Halim
- Division of Computer Aided Drug Design, Green Research Centre, BICCB, 38 Green Road West, Dhaka, 1205 Bangladesh
- Institut Lumière Matière, Université Lyon 1 – CNRS, Université de Lyon, 69622 Villeurbanne Cedex, France
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Nascimento ECM, Martins JBL. Electronic structure and PCA analysis of covalent and non-covalent acetylcholinesterase inhibitors. J Mol Model 2010; 17:1371-9. [PMID: 20839017 DOI: 10.1007/s00894-010-0838-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Accepted: 08/25/2010] [Indexed: 11/25/2022]
Abstract
Hartree-Fock and density functional methods were used to analyze electronic and structural properties of known drugs to evaluate the influence of these data on acetylcholinesterase inhibition. The energies of the frontier orbitals and the distances between the more acidic hydrogen species were investigated to determine their contributions to the activity of a group of acetylcholinesterase inhibitors. Electrostatic potential maps indicated suitable sites for drugs-enzyme interactions. In this study, the structural, electronic and spatial properties of nine drugs with known inhibitory effects on acetylcholinesterase were examined. The data were obtained based on calculations at the B3LYP/6-31 + G(d,p) level. Multivariate principal components analysis was applied to 18 parameters to determine the pharmacophoric profile of acetylcholinesterase inhibitors. Desirable features for acetylcholinesterase inhibitor molecules include aromatic systems or groups that simulate the surface electrostatic potential of aromatic systems and the presence of a sufficient number of hydrogen acceptors and few hydrogen donors. PCA showed that electronic properties, including the HOMO-1 orbital energy, logP and aromatic system quantity, as well as structural data, such as volume, size and H-H distance, are the most significant properties.
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Stasiuk M, Kozubek A. Biological activity of phenolic lipids. Cell Mol Life Sci 2010; 67:841-60. [PMID: 20213924 PMCID: PMC11115636 DOI: 10.1007/s00018-009-0193-1] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Revised: 10/21/2009] [Accepted: 10/23/2009] [Indexed: 12/15/2022]
Abstract
Phenolic lipids are a very diversified group of compounds derived from mono and dihydroxyphenols, i.e., phenol, catechol, resorcinol, and hydroquinone. Due to their strong amphiphilic character, these compounds can incorporate into erythrocytes and liposomal membranes. In this review, the antioxidant, antigenotoxic, and cytostatic activities of resorcinolic and other phenolic lipids are described. The ability of these compounds to inhibit bacterial, fungal, protozoan and parasite growth seems to depend on their interaction with proteins and/or on their membrane-disturbing properties.
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Affiliation(s)
- Maria Stasiuk
- Department of Lipids and Liposomes, University of Wroclaw, Poland.
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de Paula A, Martins J, dos Santos M, Nascente LDC, Romeiro L, Areas T, Vieira K, Gambôa N, Castro N, Gargano R. New potential AChE inhibitor candidates. Eur J Med Chem 2009; 44:3754-9. [DOI: 10.1016/j.ejmech.2009.03.045] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2008] [Revised: 01/19/2009] [Accepted: 03/24/2009] [Indexed: 10/20/2022]
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Nascimento ÉC, Martins JB, dos Santos ML, Gargano R. Theoretical study of classical acetylcholinesterase inhibitors. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.05.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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