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Kongkaew N, Hengphasatporn K, Injongkol Y, Mee-Udorn P, Shi L, Mahalapbutr P, Maitarad P, Harada R, Shigeta Y, Rungrotmongkol T, Vangnai AS. Design of electron-donating group substituted 2-PAM analogs as antidotes for organophosphate insecticide poisoning. RSC Adv 2023; 13:32266-32275. [PMID: 37928857 PMCID: PMC10620644 DOI: 10.1039/d3ra03087c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/27/2023] [Indexed: 11/07/2023] Open
Abstract
The use of organophosphate (OPs) pesticides is widespread in agriculture and horticulture, but these chemicals can be lethal to humans, causing fatalities and deaths each year. The inhibition of acetylcholinesterase (AChE) by OPs leads to the overstimulation of cholinergic receptors, ultimately resulting in respiratory arrest, seizures, and death. Although 2-pralidoxime (2-PAM) is the FDA-approved drug for treating OP poisoning, there is difficulty in blood-brain barrier permeation. To address this issue, we designed and evaluated a series of 2-PAM analogs by substituting electron-donating groups on the para and/or ortho positions of the pyridinium core using in silico techniques. Our PCM-ONIOM2 (MP2/6-31G*:PM7//B3LYP/6-31G*:UFF) binding energy results demonstrated that 13 compounds exhibited higher binding energy than 2-PAM. The analog with phenyl and methyl groups substituted on the para and ortho positions, respectively, showed the most favorable binding characteristics, with aromatic residues in the active site (Y124, W286, F297, W338, and Y341) and the catalytic residue S203 covalently bonding with paraoxon. The results of DS-MD simulation revealed a highly favorable apical conformation of the potent analog, which has the potential to enhance reactivation of AChE. Importantly, newly designed compound demonstrated appropriate drug-likeness properties and blood-brain barrier penetration. These results provide a rational guide for developing new antidotes to treat organophosphate insecticide toxicity.
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Affiliation(s)
- Nalinee Kongkaew
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University Bangkok 10330 Thailand
| | - Kowit Hengphasatporn
- Center for Computational Sciences, University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305-8577 Japan
| | - Yuwanda Injongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University Bangkok 10330 Thailand
| | - Pitchayathida Mee-Udorn
- National Center for Genetic Engineering and Biotechnology 113 Thailand Science Park Pathumthani 12120 Thailand
| | - Liyi Shi
- Research Center of Nano Science and Technology, Department of Chemistry, College of Science, Shanghai University Shanghai 200444 China
- Department of Chemistry, College of Sciences, State Key Laboratory of Advanced Special Steel, Research Center of Nano Science and Technology, School of Materials Science and Engineering, Shanghai University Shanghai 200444 China
| | - Panupong Mahalapbutr
- Department of Biochemistry, Center for Translational Medicine, Faculty of Medicine, Khon Kaen University Khon Kaen 40002 Thailand
| | - Phornphimon Maitarad
- Research Center of Nano Science and Technology, Department of Chemistry, College of Science, Shanghai University Shanghai 200444 China
- Department of Chemistry, College of Sciences, State Key Laboratory of Advanced Special Steel, Research Center of Nano Science and Technology, School of Materials Science and Engineering, Shanghai University Shanghai 200444 China
| | - Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305-8577 Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305-8577 Japan
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University Bangkok 10330 Thailand
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University Bangkok 10330 Thailand
| | - Alisa S Vangnai
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University Bangkok 10330 Thailand
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2
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Šinko G. Modeling of a near-attack conformation of oxime in phosphorylated acetylcholinesterase via a reactivation product, a phosphorylated oxime. Chem Biol Interact 2023; 383:110656. [PMID: 37579936 DOI: 10.1016/j.cbi.2023.110656] [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: 02/09/2023] [Revised: 07/26/2023] [Accepted: 08/09/2023] [Indexed: 08/16/2023]
Abstract
At the present, only four antidotes are in use in therapy for poisoning by organophosphorus compounds: 2-PAM, HI-6, obidoxime and trimedoxime. Numerous compounds have been designed and synthetized to be more effective reactivators than those currently in use. Many of those new compounds fail at the enzyme level because interactions formed within the AChE active site are not favourable ones that lead to a successful reactivation. The approach in which the modeling of a phosphorylated oxime (POX), a product of successful reactivation in the AChE active site, may be a way to better understand the role of active site residues during the process of formation of the Michaelis type of complex between an enzyme and oxime. After reactivation, a change in phosphorus stereochemistry occurs leading to a different spatial arrangement of attached substituents, now including an oxime. To study interactions between the AChE oxyanion hole and a phosphorylated oxime, an S203G mutant was used to avoid the steric hindrance caused by the catalytic serine. In this way, the POX could be positioned close to the oxyanion hole. In the final step, the oxime without a phosphoester moiety was transferred into the phosphorylated AChE and molecular dynamics was used to test the stability of the near-attack conformation of the oxime near the phosphorylated serine.
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Affiliation(s)
- Goran Šinko
- Institute for Medical Research and Occupational Health, Ksaverska cesta 2, HR-10 000, Zagreb, Croatia.
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3
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França TCC, Valle da Silva JA, Dos Santos MC, Cavalcante SFDA, Kuca K. Applications of the Near Attack Conformation (NAC) approach in the search for Acetylcholinesterase reactivators. Chem Biol Interact 2023; 382:110619. [PMID: 37406983 DOI: 10.1016/j.cbi.2023.110619] [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: 04/27/2023] [Revised: 06/25/2023] [Accepted: 06/30/2023] [Indexed: 07/07/2023]
Abstract
The Near Attack Conformation (NAC) approach states that the efficiency of an enzyme-catalyzed reaction depends on the prior attainment of optimal conditions for substrate atom organization and positioning for bond formation. These conditions are prerequisites for the transition state (TS) in which the involved atoms are within the van der Waals range of contact and positioned at an angle similar to that achieved after bond formation. The successful application of this approach to investigate the reactivation mechanism of acetylcholinesterase inhibited by nerve agents has contributed to a better understanding of this mechanism and demonstrated consistent corroboration with experimental data. In this article, we summarize the accomplishments achieved thus far and outline future perspectives.
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Affiliation(s)
- Tanos Celmar Costa França
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro, Brazil; Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 50003, Hradec Kralove, Czech Republic.
| | - Jorge Alberto Valle da Silva
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro, Brazil
| | - Marcelo Carneiro Dos Santos
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro, Brazil
| | - Samir Frontino de Almeida Cavalcante
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 50003, Hradec Kralove, Czech Republic; Institute of Chemical, Biological, Radiological and Nuclear Defense (IDQBRN), Brazilian Army Technological Center (CTEx), Rio de Janeiro, RJ, Brazil
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 50003, Hradec Kralove, Czech Republic
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4
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The Structural Basis of African Swine Fever Virus pS273R Protease Binding to E64 through Molecular Dynamics Simulations. Molecules 2023; 28:molecules28031435. [PMID: 36771101 PMCID: PMC9920524 DOI: 10.3390/molecules28031435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/21/2023] [Accepted: 01/22/2023] [Indexed: 02/05/2023] Open
Abstract
Identification of novel drugs for anti-African swine fever (ASF) applications is of utmost urgency, as it negatively affects pig farming and no effective vaccine or treatment is currently available. African swine fever virus (ASFV) encoded pS273R is a cysteine protease that plays an important role in virus replication. E64, acting as an inhibitor of cysteine protease, has been established as exerting an inhibitory effect on pS273R. In order to obtain a better understanding of the interaction between E64 and pS273R, common docking, restriction docking, and covalent docking were employed to analyze the optimal bonding position between pS273R-E64 and its bonding strength. Additionally, three sets of 100 ns molecular dynamics simulations were conducted to examine the conformational dynamics of pS273R and the dynamic interaction of pS273R-E64, based on a variety of analytical methods including root mean square deviation (RMSD), root mean square fluctuation (RMSF), free energy of ligand (FEL), principal component analysis (PCA), and molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) analysis. The results show that E64 and pS273R exhibited close binding degrees at the activity center of ASFV pS273R protease. The data of these simulations indicate that binding of E64 to pS273R results in a reduction in flexibility, particularly in the ARM region, and a change in the conformational space of pS273R. Additionally, the ability of E64 to interact with polar amino acids such as ASN158, SER192, and GLN229, as well as charged amino acids such as LYS167 and HIS168, seems to be an important factor in its inhibitory effect. Finally, Octet biostratigraphy confirmed the binding of E64 and pS273R with a KD value of 903 uM. Overall, these findings could potentially be utilized in the development of novel inhibitors of pS273R to address the challenges posed by ASFV.
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5
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N-substituted arylhydroxamic acids as acetylcholinesterase reactivators. Chem Biol Interact 2022; 365:110078. [DOI: 10.1016/j.cbi.2022.110078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/23/2022] [Accepted: 07/26/2022] [Indexed: 11/03/2022]
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Santos MC, Botelho FD, Gonçalves AS, Kitagawa DAS, Borges CVN, Carvalho-Silva T, Bernardo LB, Ferreira CN, Rodrigues RB, Ferreira Neto DC, Nepovimova E, Kuča K, LaPlante SR, Lima ALS, França TCC, Cavalcante SFA. Are the current commercially available oximes capable of reactivating acetylcholinesterase inhibited by the nerve agents of the A-series? Arch Toxicol 2022; 96:2559-2572. [PMID: 35666269 DOI: 10.1007/s00204-022-03316-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 05/11/2022] [Indexed: 12/20/2022]
Abstract
The misuse of novichok agents in assassination attempts has been reported in the international media since 2018. These relatively new class of neurotoxic agents is claimed to be more toxic than the agents of the G and V series and so far, there is no report yet in literature about potential antidotes against them. To shed some light into this issue, we report here the design and synthesis of NTMGMP, a surrogate of A-242 and also the first surrogate of a novichok agent useful for experimental evaluation of antidotes. Furthermore, the efficiency of the current commercial oximes to reactivate NTMGMP-inhibited acetylcholinesterase (AChE) was evaluated. The Ellman test was used to confirm the complete inhibition of AChE, and to compare the subsequent rates of reactivation in vitro as well as to evaluate aging. In parallel, molecular docking, molecular dynamics and MM-PBSA studies were performed on a computational model of the human AChE (HssAChE)/NTMGMP complex to assess the reactivation performances of the commercial oximes in silico. Experimental and theoretical studies matched the exact hierarchy of efficiency and pointed to trimedoxime as the most promising commercial oxime for reactivation of AChE inhibited by A-242.
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Affiliation(s)
- Marcelo C Santos
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro, Brazil
| | - Fernanda D Botelho
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro, Brazil
| | - Arlan S Gonçalves
- Federal Institute of Education, Science and Technology of Espírito Santo - Units Vila Velha and Vitória, Vitória, ES, Brazil.,Federal University of Espírito Santo, Unit Goiabeiras, Vitória, ES, Brazil
| | - Daniel A S Kitagawa
- Institute of Chemical, Biological, Radiological and Nuclear Defense (IDQBRN), Brazilian Army Technological Center (CTEx), Rio de Janeiro, Brazil
| | - Caio V N Borges
- Institute of Chemical, Biological, Radiological and Nuclear Defense (IDQBRN), Brazilian Army Technological Center (CTEx), Rio de Janeiro, Brazil.,Chemical Engineering Department, Military Institute of Engineering, Rio de Janeiro, Brazil
| | - Taynara Carvalho-Silva
- Institute of Chemical, Biological, Radiological and Nuclear Defense (IDQBRN), Brazilian Army Technological Center (CTEx), Rio de Janeiro, Brazil.,Chemical Engineering Department, Military Institute of Engineering, Rio de Janeiro, Brazil
| | - Leandro B Bernardo
- Institute of Chemical, Biological, Radiological and Nuclear Defense (IDQBRN), Brazilian Army Technological Center (CTEx), Rio de Janeiro, Brazil.,Chemical Engineering Department, Military Institute of Engineering, Rio de Janeiro, Brazil
| | - Cíntia N Ferreira
- Institute of Chemical, Biological, Radiological and Nuclear Defense (IDQBRN), Brazilian Army Technological Center (CTEx), Rio de Janeiro, Brazil
| | - Rafael B Rodrigues
- Institute of Chemical, Biological, Radiological and Nuclear Defense (IDQBRN), Brazilian Army Technological Center (CTEx), Rio de Janeiro, Brazil
| | - Denise C Ferreira Neto
- Chemical Engineering Department, Military Institute of Engineering, Rio de Janeiro, Brazil
| | - Eugenie Nepovimova
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Kamil Kuča
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Steven R LaPlante
- Université de Québec, INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, H7V 1B7, Canada
| | - Antonio L S Lima
- Chemical Engineering Department, Military Institute of Engineering, Rio de Janeiro, Brazil
| | - Tanos C C França
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro, Brazil. .,Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic. .,Université de Québec, INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, H7V 1B7, Canada.
| | - Samir F A Cavalcante
- Institute of Chemical, Biological, Radiological and Nuclear Defense (IDQBRN), Brazilian Army Technological Center (CTEx), Rio de Janeiro, Brazil. .,Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic.
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7
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Theoretical assessment of the performances of commercial oximes on the reactivation of acetylcholinesterase inhibited by the nerve agent A-242 (novichok). Food Chem Toxicol 2022; 165:113084. [PMID: 35489467 DOI: 10.1016/j.fct.2022.113084] [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] [Received: 03/13/2022] [Revised: 04/04/2022] [Accepted: 04/24/2022] [Indexed: 01/19/2023]
Abstract
The nerve agents of the A-series are relatively recent chemical weapons with no antidote available yet. Once inside the human body, those chemicals act similarly to the classic nerve agents, by binding to the catalytic residue Serine 203 (Ser203) of human acetylcholinesterase (HssAChE) and thus preventing the proper function of this enzyme. However, there is no experimental evidence yet if the current antidotes for intoxication by nerve agents are also capable of restoring AChE inhibited by the nerve agents of the A-series. In order to launch some light on this issue, we used computational techniques (molecular docking, molecular dynamics and MM-PBSA interaction energy calculations) to assess the performances of the four currently available commercial oximes (2-PAM, HI-6, obidoxime and trimedoxime) when in contact with HssAChE inhibited by the agent A-242. Based on the near-attack conformation (NAC) criterion, our results suggest that the commercial oximes would have limited efficacy to reactivate the enzyme since they are not able to properly approach the adduct Ser203-A-242. Among those oximes, trimedoxime seems to be the most promising, since it showed lower values of energy in the MM-PBSA calculations, a higher stability inside the catalytic anionic center (CAS) of HssAChE, and was able to adopt a position closer to the NAC that could enable the reactivation mechanism.
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8
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Diharce J, Bignon E, Fiorucci S, Antonczak S. Exploring Dihydroflavonol-4-Reductase Reactivity and Selectivity by QM/MM-MD Simulations. Chembiochem 2021; 23:e202100553. [PMID: 34859558 DOI: 10.1002/cbic.202100553] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/29/2021] [Indexed: 11/12/2022]
Abstract
Flavonoids are secondary metabolites ubiquitously found in plants. Their antioxidant properties make them highly interesting natural compounds for use in pharmacology. Therefore, unravelling the mechanisms of flavonoid biosynthesis is an important challenge. Among all the enzymes involved in this biosynthetic pathway, dihydroflavonol-4-reductase (DFR) plays a key role in the production of anthocyanins and proanthocyanidins. Here, we provide new information on the mechanism of action of this enzyme by using QM/MM-MD simulations applied to both dihydroquercetin (DHQ) and dihydrokaempferol (DHK) substrates. The consideration of these very similar compounds shed light on the major role played by the enzyme on the stabilization of the transition state but also on the activation of the substrate before the reaction through near-attack conformer effects.
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Affiliation(s)
- Julien Diharce
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice, 06108, France.,Université de Paris, INSERM, Biologie Intégrée du Globule Rouge, UMR_S1134, 75015, Paris, France.,Laboratoire d'Excellence GR-Ex, 75015, Paris, France
| | - Emmanuelle Bignon
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice, 06108, France
| | - Sébastien Fiorucci
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice, 06108, France
| | - Serge Antonczak
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice, 06108, France
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9
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In silico studies of semi-synthetic benzo[a]phenazines as inhibitors of dihydrofolate reductase from Plasmodium falciparum. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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10
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Figueroa-Villar JD, Petronilho EC, Kuca K, Franca TCC. Review about Structure and Evaluation of Reactivators of Acetylcholinesterase Inhibited with Neurotoxic Organophosphorus Compounds. Curr Med Chem 2021; 28:1422-1442. [PMID: 32334495 DOI: 10.2174/0929867327666200425213215] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 03/08/2020] [Accepted: 04/01/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Neurotoxic chemical warfare agents can be classified as some of the most dangerous chemicals for humanity. The most effective of those agents are the Organophosphates (OPs) capable of restricting the enzyme Acetylcholinesterase (AChE), which in turn, controls the nerve impulse transmission. When AChE is inhibited by OPs, its reactivation can be usually performed through cationic oximes. However, until today, it has not been developed one universal defense agent, with complete effective reactivation activity for AChE inhibited by any of the many types of existing neurotoxic OPs. For this reason, before treating people intoxicated by an OP, it is necessary to determine the neurotoxic compound that was used for contamination, in order to select the most effective oxime. Unfortunately, this task usually requires a relatively long time, raising the possibility of death. Cationic oximes also display a limited capacity of permeating the Blood-Brain Barrier (BBB). This fact compromises their capacity to reactivating AChE inside the nervous system. METHODS We performed a comprehensive search on the data about OPs available on the scientific literature today in order to cover all the main drawbacks still faced in the research for the development of effective antidotes against those compounds. RESULTS Therefore, this review about neurotoxic OPs and the reactivation of AChE, provides insights for the new agents' development. The most expected defense agent is a molecule without toxicity and effective to reactivate AChE inhibited by all neurotoxic OPs. CONCLUSION To develop these new agents, the application of diverse scientific areas of research, especially theoretical procedures as computational science (computer simulation, docking and dynamics), organic synthesis, spectroscopic methodologies, biology, biochemical and biophysical information, medicinal chemistry, pharmacology and toxicology, is necessary.
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Affiliation(s)
- José Daniel Figueroa-Villar
- Medicinal Chemistry Group, Department of Chemical Engineering, Military Institute of Engineering, 22270- 090, Rio de Janeiro, Brazil
| | - Elaine C Petronilho
- Medicinal Chemistry Group, Department of Chemical Engineering, Military Institute of Engineering, 22270- 090, Rio de Janeiro, Brazil
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Králové 50003, Czech Republic
| | - Tanos C C Franca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Králové 50003, Czech Republic
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11
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Molecular Modeling Studies on the Multistep Reactivation Process of Organophosphate-Inhibited Acetylcholinesterase and Butyrylcholinesterase. Biomolecules 2021; 11:biom11020169. [PMID: 33513955 PMCID: PMC7912477 DOI: 10.3390/biom11020169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/17/2022] Open
Abstract
Poisoning with organophosphorus compounds used as pesticides or misused as chemical weapons remains a serious threat to human health and life. Their toxic effects result from irreversible blockade of the enzymes acetylcholinesterase and butyrylcholinesterase, which causes overstimulation of the cholinergic system and often leads to serious injury or death. Treatment of organophosphorus poisoning involves, among other strategies, the administration of oxime compounds. Oximes reactivate cholinesterases by breaking the covalent bond between the serine residue from the enzyme active site and the phosphorus atom of the organophosphorus compound. Although the general mechanism of reactivation has been known for years, the exact molecular aspects determining the efficiency and selectivity of individual oximes are still not clear. This hinders the development of new active compounds. In our research, using relatively simple and widely available molecular docking methods, we investigated the reactivation of acetyl- and butyrylcholinesterase blocked by sarin and tabun. For the selected oximes, their binding modes at each step of the reactivation process were identified. Amino acids essential for effective reactivation and those responsible for the selectivity of individual oximes against inhibited acetyl- and butyrylcholinesterase were identified. This research broadens the knowledge about cholinesterase reactivation and demonstrates the usefulness of molecular docking in the study of this process. The presented observations and methods can be used in the future to support the search for new effective reactivators.
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12
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Almeida JSFD, Botelho FD, de Souza FR, Dos Santos MC, Goncalves ADS, Rodrigues RLB, Cardozo M, Kitagawa DAS, Vieira LA, Silva RSF, Cavalcante SFA, Bastos LDC, Nogueira MDOT, de Santana PIR, Brum JDOC, Nepovimova E, Kuca K, LaPlante SR, Galante EBF, Franca TCC. Searching for potential drugs against SARS-CoV-2 through virtual screening on several molecular targets. J Biomol Struct Dyn 2021; 40:5229-5242. [PMID: 33416020 PMCID: PMC7876915 DOI: 10.1080/07391102.2020.1869096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2022]
Abstract
The acute respiratory syndrome caused by the SARS-CoV-2, known as COVID-19, has been ruthlessly tormenting the world population for more than six months. However, so far no effective drug or vaccine against this plague have emerged yet, despite the huge effort in course by researchers and pharmaceutical companies worldwide. Willing to contribute with this fight to defeat COVID-19, we performed a virtual screening study on a library containing Food and Drug Administration (FDA) approved drugs, in a search for molecules capable of hitting three main molecular targets of SARS-CoV-2 currently available in the Protein Data Bank (PDB). Our results were refined with further molecular dynamics (MD) simulations and MM-PBSA calculations and pointed to 7 multi-target hits which we propose here for experimental evaluation and repurposing as potential drugs against COVID-19. Additional rounds of docking, MD simulations and MM-PBSA calculations with remdesivir suggested that this compound can also work as a multi-target drug against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Joyce S F D Almeida
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro/RJ, Brazil
| | - Fernanda D Botelho
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro/RJ, Brazil
| | - Felipe R de Souza
- Department of Chemistry, Pontifical Catholic University of Rio de Janeiro, Rio de Janeiro/RJ, Brazil
| | - Marcelo C Dos Santos
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro/RJ, Brazil
| | - Arlan da Silva Goncalves
- Department of Chemistry, Federal Institute of Espírito Santo - Unit Vila Velha, Vila Velha/ES, Brazil.,PPGQUI (Graduate Program in Chemistry), Federal University of Espirito Santo, Vitoria/ES, Brazil
| | - Rodrigo L B Rodrigues
- Department of Chemical Engineering, Instituto Militar de Engenharia, Rio de Janeiro/RJ, Brazil
| | - Monique Cardozo
- Institute of Chemical, Biological, Radiological and Nuclear Defense (IDQBRN), Brazilian Army Technological Center (CTEx), Rio de Janeiro/RJ, Brazil
| | - Daniel A S Kitagawa
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro/RJ, Brazil
| | - Leandro A Vieira
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro/RJ, Brazil
| | - Raphael S F Silva
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro/RJ, Brazil.,Coordination of Chemistry, Federal Institute of Education Science and Technology of Rio de Janeiro, Rio de Janeiro/RJ, Brazil
| | - Samir F A Cavalcante
- Institute of Chemical, Biological, Radiological and Nuclear Defense (IDQBRN), Brazilian Army Technological Center (CTEx), Rio de Janeiro/RJ, Brazil
| | - Leonardo da C Bastos
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro/RJ, Brazil
| | - Mariana de O T Nogueira
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro/RJ, Brazil
| | - Priscila I R de Santana
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro/RJ, Brazil
| | - Juliana de O C Brum
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro/RJ, Brazil
| | - Eugenie Nepovimova
- Faculty of Science, Department of Chemistry, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Kamil Kuca
- Faculty of Science, Department of Chemistry, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Steven R LaPlante
- INRS, Centre Armand-Frappier Santé Biotechnologie 531, Boulevard des Prairies, Laval, QC, Canada
| | - Erick B F Galante
- Department of Chemical Engineering, Instituto Militar de Engenharia, Rio de Janeiro/RJ, Brazil
| | - Tanos C C Franca
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro/RJ, Brazil.,Faculty of Science, Department of Chemistry, University of Hradec Kralove, Hradec Kralove, Czech Republic.,INRS, Centre Armand-Frappier Santé Biotechnologie 531, Boulevard des Prairies, Laval, QC, Canada
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13
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Rubim de Santana PI, Ferreira Neto DC, Goncalves ADS, Almeida JSFDD, França TCC, Figueroa-Villar JD. Complete chemical shift assignment and molecular modeling studies of two chromene derivatives as potential leads for new anticancer drugs. J Biomol Struct Dyn 2020; 39:5498-5508. [PMID: 32657645 DOI: 10.1080/07391102.2020.1790419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The compounds 7-chloro-9-(2-hydroxy-4,4-dimethyl-6-oxocyclohex-1-en-1-yl)-3,3-dimethyl-2,3,4,9-tetrahydro-1H-xanthen-1-one (5) and 5-[-7-chloro-2,4-dioxo-1H, 2H, 3H, 4H, 5H-chromeno[2,3-d]pyrimidin-5-yl)]-1,3-diazinane-2,4,6-trione (7), were synthesized from dimedone and barbituric acid and had their three-dimensional structures and precise chemical shifts assignments obtained by Nuclear Magnetic Resonance (NMR) from 1H, 13C, APT, COSY, HSQC, and HMBC spectra. Additional HOMO-LUMO DFT calculations corroborated the NMR results and pointed to the most stable stereoisomers of each compound. Besides, further docking and molecular dynamic studies suggest that the stereoisomers (9S)-7-chloro-9-(2-hydroxy-4,4-dimethyl-6-oxocyclohex-1-en-1-yl)-3,3-dimethyl-2,3,4,9-tetrahydro-1H-xanthen-1-one, and 5-[(5S)-7-chloro-2,4-dioxo-1H, 2H, 3H, 4H, 5H-chromeno[2,3-d]pyrimidin-5-yl)]-1,3-diazinane-2,4,6-trione of these compounds may act as DNA intercalators and qualify as potential leads for the development of new anticancer drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Priscila Ivo Rubim de Santana
- Medicinal Chemistry Group, Chemical Engineering Department, Military Institute of Engineering, Rio de Janeiro, Brazil
| | - Denise Cristian Ferreira Neto
- Medicinal Chemistry Group, Chemical Engineering Department, Military Institute of Engineering, Rio de Janeiro, Brazil
| | - Arlan da Silva Goncalves
- Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, Brazil.,Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | | | - Tanos Celmar Costa França
- Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, Brazil.,Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - José Daniel Figueroa-Villar
- Medicinal Chemistry Group, Chemical Engineering Department, Military Institute of Engineering, Rio de Janeiro, Brazil
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14
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Cuya T, França TCC. A molecular modeling study of components of the ginger ( Zingiber officinale) extract inside human butyrylcholinesterase: implications for Alzheimer disease. J Biomol Struct Dyn 2020; 38:2809-2815. [PMID: 31304886 DOI: 10.1080/07391102.2019.1644198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 01/10/2023]
Affiliation(s)
- Teobaldo Cuya
- Department of Mathematics, Physics and Computation, Faculty of Technology, University of the State of Rio de Janeiro, Resende, Brazil
| | - Tanos Celmar Costa França
- Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, Brazil
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralové, Czech Republic
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15
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Reactivation of VX-Inhibited Human Acetylcholinesterase by Deprotonated Pralidoxime. A Complementary Quantum Mechanical Study. Biomolecules 2020; 10:biom10020192. [PMID: 32012780 PMCID: PMC7072650 DOI: 10.3390/biom10020192] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/22/2020] [Accepted: 01/23/2020] [Indexed: 01/25/2023] Open
Abstract
In the present work, we performed a complementary quantum mechanical (QM) study to describe the mechanism by which deprotonated pralidoxime (2-PAM) could reactivate human (Homo sapiens sapiens) acetylcholinesterase (HssAChE) inhibited by the nerve agent VX. Such a reaction is proposed to occur in subsequent addition-elimination steps, starting with a nucleophile bimolecular substitution (SN2) mechanism through the formation of a trigonal bipyramidal transition state (TS). A near attack conformation (NAC), obtained in a former study using molecular mechanics (MM) calculations, was taken as a starting point for this project, where we described the possible formation of the TS. Together, this combined QM/MM study on AChE reactivation shows the feasibility of the reactivation occurring via attack of the deprotonated form of 2-PAM against the Ser203-VX adduct of HssAChE.
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16
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Teixeira JP, de Castro AA, Soares FV, da Cunha EFF, Ramalho TC. Future Therapeutic Perspectives into the Alzheimer's Disease Targeting the Oxidative Stress Hypothesis. Molecules 2019; 24:E4410. [PMID: 31816853 PMCID: PMC6930470 DOI: 10.3390/molecules24234410] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 11/27/2019] [Accepted: 11/30/2019] [Indexed: 01/12/2023] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease that is usually accompanied by aging, increasingly being the most common cause of dementia in the elderly. This disorder is characterized by the accumulation of beta amyloid plaques (Aβ) resulting from impaired amyloid precursor protein (APP) metabolism, together with the formation of neurofibrillary tangles and tau protein hyperphosphorylation. The exacerbated production of reactive oxygen species (ROS) triggers the process called oxidative stress, which increases neuronal cell abnormalities, most often followed by apoptosis, leading to cognitive dysfunction and dementia. In this context, the development of new therapies for the AD treatment is necessary. Antioxidants, for instance, are promising species for prevention and treatment because they are capable of disrupting the radical chain reaction, reducing the production of ROS. These species have also proven to be adjunctive to conventional treatments making them more effective. In this sense, several recently published works have focused their attention on oxidative stress and antioxidant species. Therefore, this review seeks to show the most relevant findings of these studies.
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Affiliation(s)
- Jéssika P. Teixeira
- Department of Chemistry, Federal University of Lavras, 37200-000 Lavras, Minas Gerais, Brazil; (J.P.T.); (A.A.d.C.); (F.V.S.); (E.F.F.d.C.)
| | - Alexandre A. de Castro
- Department of Chemistry, Federal University of Lavras, 37200-000 Lavras, Minas Gerais, Brazil; (J.P.T.); (A.A.d.C.); (F.V.S.); (E.F.F.d.C.)
| | - Flávia V. Soares
- Department of Chemistry, Federal University of Lavras, 37200-000 Lavras, Minas Gerais, Brazil; (J.P.T.); (A.A.d.C.); (F.V.S.); (E.F.F.d.C.)
| | - Elaine F. F. da Cunha
- Department of Chemistry, Federal University of Lavras, 37200-000 Lavras, Minas Gerais, Brazil; (J.P.T.); (A.A.d.C.); (F.V.S.); (E.F.F.d.C.)
| | - Teodorico C. Ramalho
- Department of Chemistry, Federal University of Lavras, 37200-000 Lavras, Minas Gerais, Brazil; (J.P.T.); (A.A.d.C.); (F.V.S.); (E.F.F.d.C.)
- Center for Basic and Applied Research, Faculty of Informatics and Management, University of Hradec Kralove, 500 03 Hradec Kralove, Czech Republic
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