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Govindan R, Gnanasekaran C, Govindan R, Muthuchamy M, Quero F, Jothi A, Chelliah CK, Arunachalam A, Viswanathan MR, Natesan M, Kadaikunnan S, Li WJ. Anti-quorum Sensing and Anti-biofilm Effect of Nocardiopsis synnemataformans RMN 4 (MN061002) Compound 2,6-Di-tert-butyl, 1,4-Benzoquinone Against Biofilm-Producing Bacteria. Appl Biochem Biotechnol 2024; 196:3914-3948. [PMID: 37792174 DOI: 10.1007/s12010-023-04738-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2023] [Indexed: 10/05/2023]
Abstract
In this study, the anti-biofilm compound of 2,6-Di-tert-butyl, 1,4-benzoquinone was purified from Nocardiopsis synnemataformans (N. synnemataformans) RMN 4 (MN061002). To confirm the compound, various spectroscopy analyses were done including ultraviolet (UV) spectrometer, Fourier transform infrared spectroscopy (FTIR), analytical high-performance liquid chromatography (HPLC), preparative HPLC, gas chromatography-mass spectroscopy (GC-MS), liquid chromatography-mass spectroscopy (LC-MS), and 2D nuclear magnetic resonance (NMR). Furthermore, the purified compound was shown 94% inhibition against biofilm-producing Proteus mirabilis (P. mirabilis) (MN396686) at 70 µg/mL concentrations. Furthermore, the metabolic activity, exopolysaccharide damage, and hydrophobicity degradation results of identified compound exhibited excellent inhibition at 100 µg/mL concentration. Furthermore, the confocal laser scanning electron microscope (CLSM) and scanning electron microscope (SEM) results were shown with intracellular damages and architectural changes in bacteria. Consecutively, the in vivo toxicity effect of the compound against Artemia franciscana (A. franciscana) was shown to have a low mortality rate at 100 µg/mL. Finally, the molecular docking interaction between the quorum sensing (QS) genes and identified compound clearly suggested that the identified compound 2,6-Di-tert-butyl, 1,4-benzoquinone has anti-quorum sensing and anti-biofilm activities against P. mirabilis (MN396686).
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Affiliation(s)
- Rajivgandhi Govindan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
- Marine Pharmacology & Toxicology Lab, Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India
- Laboratorio de Nanocelulosa y Biomateriales, Departamento de Ingeniería Química, Facultad de CienciasFísicas y Matemáticas, Universidad de Chile, Biotecnología y MaterialesAvenida Beauchef 851, 8370456, Santiago, Chile
| | - Chackaravarthi Gnanasekaran
- Marine Pharmacology & Toxicology Lab, Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India
| | - Ramachandran Govindan
- Marine Pharmacology & Toxicology Lab, Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India.
| | - Maruthupandy Muthuchamy
- Laboratorio de Nanocelulosa y Biomateriales, Departamento de Ingeniería Química, Facultad de CienciasFísicas y Matemáticas, Universidad de Chile, Biotecnología y MaterialesAvenida Beauchef 851, 8370456, Santiago, Chile
- Lab of Toxicology, Department of Health Sciences, The Graduate School of Dong-A University, 37, Nakdong-Dearo 550 Beon-Gil, Saha-Gu, Busan, 49315, South Korea
| | - Franck Quero
- Laboratorio de Nanocelulosa y Biomateriales, Departamento de Ingeniería Química, Facultad de CienciasFísicas y Matemáticas, Universidad de Chile, Biotecnología y MaterialesAvenida Beauchef 851, 8370456, Santiago, Chile
| | - Arunachalam Jothi
- School of Chemical & Biotechnology, SASTRA Deemed University, Tamil Nadu, Tanjore, India, 401
| | - Chenthis Knaisha Chelliah
- Department of Nanotechnology, Noorul Islam Centre for Higher Education, Tamil Nadu, Kumaracoil, Kanyakumari, 629180, India
| | - Arulraj Arunachalam
- Departamento de Electricidad, Facultad de Ingeniería, Universidad Tecnológica Metropolitana (UTEM), Macul, Santiago, Chile
| | - Mangalaraja Ramalinga Viswanathan
- Faculty of Engineering and Sciences, Universidad Adolfo Ibáñez, Región Metropolitana, Diag. Las Torres 2640, 7941169, Peñalolén, Santiago, Chile
| | - Manoharan Natesan
- Marine Pharmacology & Toxicology Lab, Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India
| | - Shine Kadaikunnan
- Department of Botany and Microbiology, College of Science, King Saud University, P. O. Box 2455, 11451, Riyadh, Saudi Arabia
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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Wang Z, Wang S, Wang H, Hu B, Qi Z, Zhang Y, Song P, Cai Q, Yang H, Wang J. Uncovering the selectivity mechanism of phosphodiesterase 7A/8A inhibitors through computational studies. Phys Chem Chem Phys 2024; 26:11770-11781. [PMID: 38566586 DOI: 10.1039/d3cp03913g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The expression of phosphodiesterase 7A (PDE7A) and phosphodiesterase 8A (PDE8) genes is integral to human signaling pathways, and the inhibition of PDE7A has been associated with the onset of various diseases, including effects on the immune system and nervous system. The development of PDE7 selective inhibitors can promote research on immune and nervous system diseases, such as multiple sclerosis, chronic inflammation, and autoimmune responses. PDE8A is expressed alongside PDE8B, and its inhibitory mechanism is still unclear. Studying the mechanisms of selective inhibitors against different PDE subtypes is crucial to prevent potential side effects, such as nausea and cardiac toxicity, and the sequence similarity of the two protein subtypes was 55.9%. Therefore, it is necessary to investigate the differences of both subtypes' ligand binding sites. Selective inhibitors of two proteins were chosen to summarize the reason for their selectivity through molecular docking, molecular dynamics simulation, alanine scanning mutagenesis, and MM-GBSA calculation. We found that Phe384PDE7A, Leu401PDE7A, Gln413PDE7A, Tyr419PDE7A, and Phe416PDE7A in the active site positively contribute to the selectivity towards PDE7A. Additionally, Asn729PDE8A, Phe767PDE8A, Gln778PDE8A, and Phe781PDE8A positively contribute to the selectivity towards PDE8A.
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Affiliation(s)
- Zhijian Wang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Shizun Wang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Hanxun Wang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Baichun Hu
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Zhuo Qi
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Yaming Zhang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Pengfei Song
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Qingkui Cai
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Huali Yang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Jian Wang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China
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Chen Y, Liang W, Huang M, Li C, Song Z, Zheng Y, Yi Z. Exploring the mechanism of interaction between TBG and halogenated thiophenols: Insights from fluorescence analysis and molecular simulation. Int J Biol Macromol 2024; 261:129645. [PMID: 38296143 DOI: 10.1016/j.ijbiomac.2024.129645] [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: 08/29/2023] [Revised: 01/07/2024] [Accepted: 01/18/2024] [Indexed: 02/03/2024]
Abstract
Thyroxine-binding globulin (TBG) plays a vital role in regulating metabolism, growth, organ differentiation, and energy homeostasis, exerting significant effects in various key metabolic pathways. Halogenated thiophenols (HTPs) exhibit high toxicity and harmfulness to organisms, and numerous studies have demonstrated their thyroid-disrupting effects. To understand the mechanism of action of HTPs on TBG, a combination of competitive binding experiments, multiple fluorescence spectroscopy techniques, molecular docking, and molecular simulations was employed to investigate the binding mechanism and identify the binding site. The competition binding assay between HTPs and ANS confirmed the competition of HTPs with thyroid hormone T4 for the active site of TBG, resulting in changes in the TBG microenvironment upon the binding of HTPs to the active site. Key amino acid residues involved in the binding process of HTPs and TBG were further investigated through residue energy decomposition. The distribution of high-energy contributing residues was determined. Analysis of root-mean-square deviation (RMSD) demonstrated the stability of the HTPs-TBG complex. These findings confirm the toxic mechanism of HTPs in thyroid disruption, providing a fundamental reference for accurately assessing the ecological risk of pollutants and human health. Providing mechanistic insights into how HTPS causes thyroid diseases.
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Affiliation(s)
- Yanting Chen
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Wenhui Liang
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Muwei Huang
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Cancan Li
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Zeyu Song
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Yanhong Zheng
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Zhongsheng Yi
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China.
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Zamani M, Mokarram P, Jamshidi M, Siri M, Ghasemi H. Molecular Modelling of Resveratrol Derivatives with SIRT1 for the Stimulation of Deacetylase Activity. Curr Comput Aided Drug Des 2024; 20:943-954. [PMID: 37842901 DOI: 10.2174/0115734099258321231003161602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 07/27/2023] [Accepted: 08/15/2023] [Indexed: 10/17/2023]
Abstract
BACKGROUND Resveratrol is a polyphenol that is found in plants and has been proposed to have a potential therapeutic effect through the activation of SIRT1, which is a crucial member of the mammalian NAD+ -dependent deacetylases. However, how its activity is enhanced toward specific substrates by resveratrol derivatives has not been studied. This study aimed to evaluate the types of interaction of resveratrol and its derivatives with SIRT1 as the target protein, as well as to find out the best ligand with the strangest interaction with SIRT1. MATERIALS AND METHODS In this study, we employed the extensive molecular docking analysis using AutoDock Vina to comparatively evaluate the interactions of resveratrol derivatives (22 molecules from the ZINC database) as ligands with SIRT1 (PDB ID: 5BTR) as a receptor. The ChemDraw and Chem3D tools were used to prepare 3D structures of all ligands and energetically minimize them by the MM2 force field. RESULTS The molecular docking and visualizations showed that conformational change in resveratrol derivatives significantly influenced the parameter for docking results. Several types of interactions, including conventional hydrogen bonds, carbon-hydrogen bonds, Pi-donor hydrogen bonds, and Pi-Alkyl, were found via docking analysis of resveratrol derivatives and SIRT1 receptors. The possible activation effect of resveratrol 4'-(6-galloylglucoside) with ZINC ID: ZINC230079516 with higher binding energy score (-46.8608 kJ/mol) to the catalytic domain (CD) of SIRT1 was achieved at the maximum value for SIRT1, as compared to resveratrol and its other derivatives. CONCLUSION Finally, resveratrol 4'-(6-galloylglucoside), as a derivative for resveratrol, has stably interacted with the CD of SIRT1 and might be a potential effective activator for SIRT1.
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Affiliation(s)
- Mozhdeh Zamani
- Autophagy Research Center, Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Pooneh Mokarram
- Autophagy Research Center, Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehdi Jamshidi
- Institute für Chemie, Universität Oldenburg, Carl-von-Ossietzky-Straße 9-11,26129 Oldenburg, Germany
| | - Morvarid Siri
- Autophagy Research Center, Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hadi Ghasemi
- Autophagy Research Center, Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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Rathi R. Potential inhibitors of FemC to combat Staphylococcus aureus: virtual screening, molecular docking, dynamics simulation, and MM-PBSA analysis. J Biomol Struct Dyn 2023; 41:10495-10506. [PMID: 36524526 DOI: 10.1080/07391102.2022.2157328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022]
Abstract
FemC is a methicillin resistance factor involved in the alterations of peptidoglycan and glutamine synthesis in Staphylococcus aureus. To identify the potent antibacterial agents, antibacterial molecules were screened against the predicted and validated FemC model. Based on docking scores, presence of essential interactions with active site residues of FemC, pharmacokinetic, and ADMET properties, six candidates were shortlisted and subjected to molecular dynamics to evaluate the stability of FemC-ligand complexes. Further, per residue decomposition analysis and Molecular Mechanics/Poisson-Boltzmann Surface Area (MMPBSA) analysis confirmed that S15, M16, S17, R31, R43, Q47, K48 and R49 of FemC played a vital role in the formation of lower energy stable FemC-inhibitor(s) complexes. Therefore, in the present study, the reported six molecules (Z317461228, Z92241701, Z30923155, Z30202349, Z2609517102 and Z92470167) may pave the path to design the scaffold of novel potent antimicrobials against S. aureus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ravi Rathi
- Amity School of Applied Sciences, Amity University Haryana, Gurgaon, Haryana, India
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Sarmah P, Konwar P, Saikia J, Borah T, Verma JS, Banik D. Screening of potent inhibitor from Aquilaria malaccensis Lam. against arachidonic inflammatory enzymes: an insight from molecular docking, ADMET, molecular dynamics simulation and MM-PBSA approaches. J Biomol Struct Dyn 2023:1-15. [PMID: 37885259 DOI: 10.1080/07391102.2023.2271977] [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: 05/02/2023] [Accepted: 08/29/2023] [Indexed: 10/28/2023]
Abstract
The three primary enzymes COX (cyclooxygenase), LOX (lipoxygenase) and CYT-P450 (cytochrome P450), which are part of the arachidonic inflammatory pathway, play crucial role in the development of asthma, rheumatoid arthritis and cardiovascular diseases. Ethnomedicinally, plant-derived chemicals have a major role in the treatment of fatal illnesses. Aquilaria malaccensis Lam. widely known as agarwood is prized for its fragrance and therapeutic properties. The phytochemicals and extracts of this plant have significant healing properties in the treatment of serious illnesses. In the current work, an in-silico approach including molecular docking, ADMET (absorption, distribution, metabolism, excretion and toxicity), molecular dynamics (MD) simulation and molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) was performed to screen 33 bioactive compounds from this plant against COX-2 and 5-LOX in order to find the most effective inhibitor. 2-(2-Phenylethyl)chromone was found to inhibit both 5-LOX and COX-2, showing the highest binding affinities (-9.1 kcal/mol and -9.0 kcal/mol, respectively) than standard Ibuprofen and nordihydroguaiaretic acid (NDGA). 2-(2-Phenylethyl)chromone showed the highest drug-likeness score and low risk of toxicity compared to other phytochemicals. MD modeling and MM-PBSA calculations showed that 2-(2-Phenylethyl)chromone had a strong persistent binding interaction with 5-LOX than COX-2, and this interaction is comparable to the bounded standards Ibuprofen and NDGA. From this study, we may infer that the 2-(2-Phenylethyl)chromone can serve as a potent inhibitor and has scope to be employed in the treatment of inflammatory ailments.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Prasanna Sarmah
- Agrotechnology and Rural Development Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Parthapratim Konwar
- Agrotechnology and Rural Development Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Jadumoni Saikia
- Agrotechnology and Rural Development Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Twinkle Borah
- Agrotechnology and Rural Development Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Jitendra Singh Verma
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Engineering Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
| | - Dipanwita Banik
- Agrotechnology and Rural Development Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Rathi R, Kumari R, Pathak SR, Dalal V. Promising antibacterials for LLM of Staphylococcus aureus using virtual screening, molecular docking, dynamics, and MMPBSA. J Biomol Struct Dyn 2023; 41:7277-7289. [PMID: 36073371 DOI: 10.1080/07391102.2022.2119278] [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: 04/08/2022] [Accepted: 08/25/2022] [Indexed: 10/14/2022]
Abstract
In S. aureus, lipophilic membrane (LLM) protein is a methicillin resistance factor and is an essential role in peptidoglycan metabolism. The virtual screening of antibacterial molecules against the model of LLM was performed to identify the potent antibacterial molecules. Molecular docking results of pharmacokinetic filtered molecules illustrated that five molecules had higher binding affinities than tunicamycin (TUM) and were stabled via non-covalent interactions (hydrogen bond and hydrophobic interactions) at the active site of LLM. Further, molecular dynamics results revealed that binding of identified antibacterial molecules with LLM resulted in stable LLM-inhibitor(s) complexes. Molecular Mechanics/Position-Boltzmann Surface Area (MMPBSA) analysis showed that LLM-inhibitor(s) complexes had high binding affinities in the range of -213.49 ± 2.24 to -227.42 ± 3.05 kJ/mol. The amino acid residues decomposition analysis confirmed that identified antibacterial molecules bound at the active site (Asn148, Leu149, Asp151, Asp208, His269, His271, and His272) of LLM. Noticeably, the current study found five antibacterial molecules (BDE 27575101, BDE 33638168, BDE 33672484, LAS 51502073, and BDE 25098678) were highly potent than TUM and even than earlier reported molecules. Therefore, here reported antibacterial molecules may be used directly or developed to inhibit LLM of S. aureus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ravi Rathi
- Amity School of Applied Sciences, Amity University Haryana, Haryana, India
| | - Reena Kumari
- Department of Mathematics and Statistics, Swami Vivekanand Subharti University, Meerut, India
| | - Seema R Pathak
- Amity School of Applied Sciences, Amity University Haryana, Haryana, India
| | - Vikram Dalal
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO, USA
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Siddiqui S, Riaz S, Ahmad R, Wani MJ, Hashmi MA, Zofair SFF, Mateen S, Moin S. Synergistic effect of chlorogenic acid and vitamin D3 (cholecalciferol) on in-vitro glycation may assist in prevention of polycystic ovarian syndrome (PCOS) progression - A biophysical, biochemical and in-silico study. Int J Biol Macromol 2023; 245:125497. [PMID: 37369258 DOI: 10.1016/j.ijbiomac.2023.125497] [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: 03/26/2023] [Revised: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 06/29/2023]
Abstract
Advanced glycation end products (AGEs) are formed through non-enzymatic glycation, that have been linked to various diseases, including polycystic ovarian syndrome (PCOS) playing a critical role leading to secondary comorbidities such as diabetes-related problems, cardiovascular complications, infertility, etc. As a result, there has been a lot of research into AGE-inhibiting phytochemicals for the remediation and obstruct progression of glycation-related illnesses. The current study is based on in-vitro protein model, in which human serum albumin have been used to investigate the cumulative effect of chlorogenic acid (CGA) and cholecalciferol (vitamin D) on glycation and evaluate their inhibitory impact on AGEs production in the presence of methylglyoxal. Through the application of several biochemical and biophysical techniques, we were able to examine the synergistic impact of both the compounds on albumin structure and its biochemical properties during different stages of glycation. According to Nitro-blue tetrazolium assay results indicate that CGA and vitamin D inhibited fructosamine (early glycation product) production. Moreover, free thiol and lysine residues were significantly increased whereas protein carbonyl levels were significantly decreased. Additive effect of CGA and vitamin D were associated with reduced AGEs fluorescence and increased tryptophan and tyrosine fluorescence. Amadori-albumin after treatment showed some evidence of regaining its alpha-helicity as measured by far-UV CD spectrum. Furthermore, secondary structural alterations were confirmed by Fourier transform infrared spectroscopy (FTIR). ANS (1-anilinonaphthalene-8-sulfonic acid) fluorescence spectra also displayed less revelation of hydrophobic patches. Bilirubin binding capacity was also restored which showed functional recovery of HSA. The electrophoretic mobility was also restored which is portrayed by SDS-PAGE. Additionally, to predict the anti-aggregation potential of CGA and vitamin D, congo red assay and ThT fluorescence was performed which reveal low aggregate formation after treatment. These results corroborated with scanning electron microscopy and confocal microscopy. Docking and simulation results also reveal spontaneous binding of CGA and vitamin D on subdomain IIA of HSA favoring their binding thermodynamically. All the findings suggest that chlorogenic acid and cholecalciferol given in combination might help in prevention of PCOS progression and its related complications.
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Affiliation(s)
- Sana Siddiqui
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Sana Riaz
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Rizwan Ahmad
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Mohd Junaid Wani
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Md Amiruddin Hashmi
- Interdisciplinary Biotechnology Unit, Faculty of Life Science, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Syeda Fauzia Farheen Zofair
- Interdisciplinary Biotechnology Unit, Faculty of Life Science, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Somaiya Mateen
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Shagufta Moin
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India.
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Gavande PV, Goyal A. Molecular dynamics-based structural insights of the first putative endoglucanase, PsGH5A of glycoside hydrolase family 5 from Pseudopedobacter saltans. J Mol Model 2023; 29:186. [PMID: 37221261 DOI: 10.1007/s00894-023-05575-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/27/2023] [Indexed: 05/25/2023]
Abstract
CONTEXT The putative endoglucanase, PsGH5A, from Pseudopedobacter saltans of family GH5 contains a catalytic module, PsGH5 (β/α)8-TIM barrel), at N-terminal followed by a family 6 carbohydrate-binding module (CBM6, β-sandwich). Superposition of PsGH5A with PDB homologs revealed Glu220 and Glu318 as evolutionarily conserved and catalytic residues performing the hydrolysis through retaining-type mechanism, a canonical property of GH5 family. PsGH5A showed higher affinity for longer cellooligosaccharides, as long as cellodecaose with binding free energy (∆G) of - 13.72 kcal/mol upon the molecular docking, thereby indicating the endo-mode of hydrolysis. The radius of gyration, Rg (2.7 nm), and solvent accessible surface area, SASA (229.6 nm2), of PsGH5A-Cellotetraose complex were determined by MD simulation which was lower than that of PsGH5A (Rg, 2.8 nm, SASA, 267 nm2) demonstrating the compactness and affinity of PsGH5A with the cellulosic ligands. Cellulose compatibility of PsGH5A was further confirmed by MMPBSA and per-residue decomposition analysis, where notable ∆G of - 54.38 kcal/mol for PsGH5A-Cellotetraose complex was observed. Thus, PsGH5A could be potentially an efficient endoglucanase as it accommodated larger cellooligosaccharides at its active-site. PsGH5A is the first putative endoglucanase studied here from P. saltans which could be genome-mined for lignocellulosic biomass saccharification in the renewable energy sector. METHODS The 3-D structure of PsGH5A generated by AlphaFold2, RaptorX, SwissModel, Phyre2 and Robetta tool; YASARA was used for energy minimization of built models. UCLA SAVES-v6 was used for quality assessment of models. Molecular Docking was performed using SWISS-DOCK server and Chimera software. Molecular Dynamics simulations and MMPBSA analysis of PsGH5A and PsGH5A-Cellotetraose complex were performed on GROMACS 2019.6.
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Affiliation(s)
- Parmeshwar Vitthal Gavande
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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Ribeiro R, Botelho FD, Pinto AMV, La Torre AMA, Almeida JSFD, LaPlante SR, Franca TCC, Veiga-Junior VF, Dos Santos MC. Molecular modeling study of natural products as potential bioactive compounds against SARS-CoV-2. J Mol Model 2023; 29:183. [PMID: 37212923 DOI: 10.1007/s00894-023-05586-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/09/2023] [Indexed: 05/23/2023]
Abstract
CONTEXT The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the COVID-19 infection and responsible for millions of victims worldwide, remains a significant threat to public health. Even after the development of vaccines, research interest in the emergence of new variants is still prominent. Currently, the focus is on the search for effective and safe drugs, given the limitations and side effects observed for the synthetic drugs administered so far. In this sense, bioactive natural products that are widely used in the pharmaceutical industry due to their effectiveness and low toxicity have emerged as potential options in the search for safe drugs against COVID-19. Following this line, we screened 10 bioactive compounds derived from cholesterol for molecules capable of interacting with the receptor-binding domain (RBD) of the spike protein from SARS-CoV-2 (SC2Spike), responsible for the virus's invasion of human cells. Rounds of docking followed by molecular dynamics simulations and binding energy calculations enabled the selection of three compounds worth being experimentally evaluated against SARS-CoV-2. METHODS The 3D structures of the cholesterol derivatives were prepared and optimized using the Spartan 08 software with the semi-empirical method PM3. They were then exported to the Molegro Virtual Docking (MVD®) software, where they were docked onto the RBD of a 3D structure of the SC2Spike protein that was imported from the Protein Data Bank (PDB). The best poses obtained from MVD® were subjected to rounds of molecular dynamics simulations using the GROMACS software, with the OPLS/AA force field. Frames from the MD simulation trajectories were used to calculate the ligand's free binding energies using the molecular mechanics - Poisson-Boltzmann surface area (MM-PBSA) method. All results were analyzed using the xmgrace and Visual Molecular Dynamics (VMD) software.
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Affiliation(s)
- Rayssa Ribeiro
- Department of Chemical Engineering, 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
| | - Amanda M V Pinto
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ, Brazil
| | - Antonia M A La Torre
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ, Brazil
| | - 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
| | - Steven R LaPlante
- INRS, Centre Armand-Frappier Santé Biotechnologie 531, Boulevard Des Prairies, Laval, QC, Canada
| | - Tanos C C Franca
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ, Brazil
- INRS, Centre Armand-Frappier Santé Biotechnologie 531, Boulevard Des Prairies, Laval, QC, Canada
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Valdir F Veiga-Junior
- Department of Chemical Engineering, Military Institute of Engineering, 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.
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11
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Lu Y, Shen Q, Zhai C, Yan H, Shen S. Ant nest-like hierarchical porous imprinted resin-dispersive solid-phase extraction for selective extraction and determination of polychlorinated biphenyls in milk. Food Chem 2023; 406:135076. [PMID: 36455312 DOI: 10.1016/j.foodchem.2022.135076] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022]
Abstract
Polychlorinated biphenyls (PCBs) are persistent toxic, organic chemicals that tend to accumulate in the food chain. This study reports the rapid and selective extraction and determination of PCBs (PCB81, 153, 105, 126, and 157) in milk samples by a dispersive solid-phase extraction (DSPE) coupled with gas chromatography-tandem mass spectrometry (GC-MS/MS). An ionic liquid-molecularly imprinted porous resin (IL-MIPPR) as a DSPE adsorbent was synthesized from m-aminophenol, formaldehyde, and 2,2'-benzidinedisulfonic acid as the monomer, crosslinker, and virtual template, respectively. The IL-MIPPR had a fast mass transfer (1.0 min) and good selectivity (imprinting factors of 1.8-3.0). The IL-MIPPR - DSPE - GC-MS/MS method exhibited good linearity (R2 ≥ 0.9995), the limit of detections (LODs) < 0.6 pg/g, and the recoveries ranged from 82.8 % to 106 % with relative standard deviations ≤ 6.6 %. This method is thus better than previously reported methods in terms of the LOD, the adsorbent dosage, and the extraction time.
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Affiliation(s)
- Yanke Lu
- Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, China; Key Laboratory of Public Health Safety of Hebei Province, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, College of Pharmaceutical Sciences, Hebei University, Baoding 071002, China
| | - Qi Shen
- Institute of Chemistry, Chinese Academy of Science, Beijing 100190, China
| | - Chengcheng Zhai
- Key Laboratory of Public Health Safety of Hebei Province, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, College of Pharmaceutical Sciences, Hebei University, Baoding 071002, China
| | - Hongyuan Yan
- Key Laboratory of Public Health Safety of Hebei Province, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, College of Pharmaceutical Sciences, Hebei University, Baoding 071002, China.
| | - Shigang Shen
- Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, China.
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12
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Wang S, Luan J, Chen L, Liu H, Li W, Wang J. Computational characteristics of the structure-activity relationship of inhibitors targeting Pks13-TE domain. Comput Biol Chem 2023; 104:107864. [PMID: 37028177 DOI: 10.1016/j.compbiolchem.2023.107864] [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: 02/11/2023] [Revised: 03/22/2023] [Accepted: 04/01/2023] [Indexed: 04/09/2023]
Abstract
Multiple studies have established the Pks13-TE domain as a promising target for anti-tuberculosis drug development. However, recent findings have revealed that the lead compound currently in the pipeline for Pks13-TE has significant cardiotoxicity issues. Given the pressing need for new chemical structures for Pks13-TE inhibitors, this study aims to provide a detailed understanding of the Pks13-TE domain binding site through the application of computational chemical biology techniques. Our results highlight the size and shape of the Pks13-TE domain binding pocket, key residues including Asp1644, Asn1640, Phe1670, and Tyr1674 within the pocket, and inhibitor pharmacophore characteristics such as aromatic ring sites, positively charged sites, and hydrogen bond donors. To our knowledge, these simulation results are novel and contribute to the discovery of next-generation Pks13-TE inhibitors without similar prior studies.
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Affiliation(s)
- Shizun Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China; School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Jiasi Luan
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China; School of Medical Devices, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Lu Chen
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China; School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Haihan Liu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China; School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Weixia Li
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China; School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China; School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China.
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13
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Kumari R, Rathi R, Pathak SR, Dalal V. Computational investigation of potent inhibitors against YsxC: structure-based pharmacophore modeling, molecular docking, molecular dynamics, and binding free energy. J Biomol Struct Dyn 2023; 41:930-941. [PMID: 34913841 DOI: 10.1080/07391102.2021.2015446] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
In S. aureus, ribosome biogenesis GTP-binding (YsxC), a GTPase interacts with 50S subunit and 30S subunit of ribosome, and β' subunit of RNA polymerase and played an important role in protein synthesis. For the identification of potent lead molecules, we have conducted pharmacophore modeling by consideration of pharmacophore features of GTP among YsxC-GTP complex. Virtual screening and molecular docking results displayed that five pharmacokinetic and ADMET filtered molecules-ZINC000006424138, ZINC000095502032, ZINC000225415132, ZINC000095475800, and ZINC000012990761-had higher binding affinities than GTP with YsxC. All the identified molecules shared similar pharmacophore features of GTP and were stabilized via hydrogen bonds and hydrophobic interactions with YsxC. Molecular dynamics analysis revealed that YsxC-inhibitor(s) complexes were lesser dynamics and higher stable than YsxC-GTP complex. Molecular Mechanics/Poisson-Boltzmann Surface Area (MMPBSA) results confirmed that identified molecules bound at the active site (Arg33, Ser34, Asn35, Val36, Lys38, Ser39, Thr40, Thr54, Ser55, Pro58, Lys60, Thr61, Thr144, Lys145, Ser178, and Ile179) of YsxC and formed the lower energy (-190.32 ± 3.46 to -217.03 ± 2.55 kJ/mol) complexes than YsxC-GTP (-157.16 ± 2.89 kJ/mol) complex. The identified molecules in this study can be further tested and utilized to design novel antimicrobial agents for S. aureus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Reena Kumari
- Department of Mathematics and Statistics, Swami Vivekanand Subharti University, Meerut, India
| | - Ravi Rathi
- Amity School of Applied Sciences, Amity University Haryana, Haryana, India
| | - Seema R Pathak
- Amity School of Applied Sciences, Amity University Haryana, Haryana, India
| | - Vikram Dalal
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO, USA
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14
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Vantaggiato L, Shaba E, Cameli P, Bergantini L, d’Alessandro M, Carleo A, Montuori G, Bini L, Bargagli E, Landi C. BAL Proteomic Signature of Lung Adenocarcinoma in IPF Patients and Its Transposition in Serum Samples for Less Invasive Diagnostic Procedures. Int J Mol Sci 2023; 24:ijms24020925. [PMID: 36674438 PMCID: PMC9861565 DOI: 10.3390/ijms24020925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a form of chronic and irreversible fibrosing interstitial pneumonia of unknown etiology. Although antifibrotic treatments have shown a reduction of lung function decline and a slow disease progression, IPF is characterize by a very high mortality. Emerging evidence suggests that IPF increases the risk of lung carcinogenesis. Both diseases show similarities in terms of risk factors, such as history of smoking, concomitant emphysema, and viral infections, besides sharing similar pathogenic pathways. Lung cancer (LC) diagnosis is often difficult in IPF patients because of the diffuse lung injuries and abnormalities due to the underlying fibrosis. This is reflected in the lack of optimal therapeutic strategies for patients with both diseases. For this purpose, we performed a proteomic study on bronchoalveolar lavage fluid (BALF) samples from IPF, LC associated with IPF (LC-IPF) patients, and healthy controls (CTRL). Molecular pathways involved in inflammation, immune response, lipid metabolism, and cell adhesion were found for the dysregulated proteins in LC-IPF, such as TTHY, APOA1, S10A9, RET4, GDIR1, and PROF1. The correlation test revealed a relationship between inflammation- and lipid metabolism-related proteins. PROF1 and S10A9, related to inflammation, were up-regulated in LC-IPF BAL and serum, while APOA1 and APOE linked to lipid metabolism, were highly abundant in IPF BAL and low abundant in IPF serum. Given the properties of cytokine/adipokine of the nicotinamide phosphoribosyltransferase, we also evaluated its serum abundance, highlighting its down-regulation in LC-IPF. Our retrospective analyses of BAL samples extrapolated some potential biomarkers of LC-IPF useful to improve the management of these contemporary pathologies. Their differential abundance in serum samples permits the measurement of these potential biomarkers with a less invasive procedure.
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Affiliation(s)
- Lorenza Vantaggiato
- Functional Proteomic Section, Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Enxhi Shaba
- Functional Proteomic Section, Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Paolo Cameli
- UOC Respiratory Diseases and Lung Transplantation, Department Internal and Specialist Medicine, University of Siena, 53100 Siena, Italy
| | - Laura Bergantini
- UOC Respiratory Diseases and Lung Transplantation, Department Internal and Specialist Medicine, University of Siena, 53100 Siena, Italy
| | - Miriana d’Alessandro
- UOC Respiratory Diseases and Lung Transplantation, Department Internal and Specialist Medicine, University of Siena, 53100 Siena, Italy
| | - Alfonso Carleo
- Department of Pneumology, Medical School Hannover (MHH), 30539 Hannover, Germany
| | - Giusy Montuori
- UOC Respiratory Diseases and Lung Transplantation, Department Internal and Specialist Medicine, University of Siena, 53100 Siena, Italy
| | - Luca Bini
- Functional Proteomic Section, Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Elena Bargagli
- UOC Respiratory Diseases and Lung Transplantation, Department Internal and Specialist Medicine, University of Siena, 53100 Siena, Italy
| | - Claudia Landi
- Functional Proteomic Section, Department of Life Sciences, University of Siena, 53100 Siena, Italy
- Correspondence:
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15
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Choudhary S, Kesavan AK, Juneja V, Thakur S. Molecular modeling, simulation and docking of Rv1250 protein from Mycobacterium tuberculosis. FRONTIERS IN BIOINFORMATICS 2023; 3:1125479. [PMID: 37122997 PMCID: PMC10130521 DOI: 10.3389/fbinf.2023.1125479] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/31/2023] [Indexed: 05/02/2023] Open
Abstract
Computational prediction and protein structure modeling have come to the aid of various biological problems in determining the structure of proteins. These technologies have revolutionized the biological world of research, allowing scientists and researchers to gain insights into their biological questions and design experimental research much more efficiently. Pathogenic Mycobacterium spp. is known to stay alive within the macrophages of its host. Mycobacterium tuberculosis is an acid-fast bacterium that is the most common cause of tuberculosis and is considered to be the main cause of resistance of tuberculosis as a leading health issue. The genome of Mycobacterium tuberculosis contains more than 4,000 genes, of which the majority are of unknown function. An attempt has been made to computationally model and dock one of its proteins, Rv1250 (MTV006.22), which is considered as an apparent drug-transporter, integral membrane protein, and member of major facilitator superfamily (MFS). The most widely used techniques, i.e., homology modeling, molecular docking, and molecular dynamics (MD) simulation in the field of structural bioinformatics, have been used in the present work to study the behavior of Rv1250 protein from M. tuberculosis. The structure of unknown TB protein, i.e., Rv1250 was retrived using homology modeling with the help of I-TASSER server. Further, one of the sites responsible for infection was identified and docking was done by using the specific Isoniazid ligand which is an inhibitor of this protein. Finally, the stability of protein model and analysis of stable and static interaction between protein and ligand molecular dynamic simulation was performed at 100 ns The designing of novel Rv1250 enzyme inhibitors is likely achievable with the use of proposed predicted model, which could be helpful in preventing the pathogenesis caused by M. tuberculosis. Finally, the MD simulation was done to evaluate the stability of the ligand for the specific protein.
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Affiliation(s)
- Sumita Choudhary
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Anup Kumar Kesavan
- Department of Biotechnology and Microbiology, Kannur University, Dr. E. K. Janaki Ammal Campus, PalayadKannur, Kerala, India
- *Correspondence: Anup Kumar Kesavan, ; Sheetal Thakur,
| | - Vijay Juneja
- Eastern Regional Research Center, United States Department of Agriculture, Agricultural Research Service, Wyndmoor, PA, United States
| | - Sheetal Thakur
- University Centre for Research & Development, Department of Biotechnology, Chandigarh University, Gharuan-Mohali, Punjab, India
- *Correspondence: Anup Kumar Kesavan, ; Sheetal Thakur,
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16
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Bisht N, Dalal V, Tewari L. Molecular modeling and dynamics simulation of alcohol dehydrogenase enzyme from high efficacy cellulosic ethanol-producing yeast mutant strain Pichia kudriavzevii BGY1-γm. J Biomol Struct Dyn 2022; 40:12022-12036. [PMID: 34424128 DOI: 10.1080/07391102.2021.1967196] [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] [Indexed: 12/24/2022]
Abstract
One of the major constraints limiting the use of abundantly available lignocellulosic biomass as potential feedstock for alcohol industry is the lack of C6/C5 co-sugar fermenting yeast. The present study explores a mutant yeast Pichia kudriavzevii BGY1-γm as a potential strain for bioconversion of glucose/xylose sugars of green biomass into ethanol under batch fermentation. The mutant strain having higher alcohol dehydrogenase activity (11.31%) showed significantly higher ethanol concentration during co-fermentation of glucose/xylose sugars (14.2%) as compared to the native strain. Based on 99% sequence similarity of ADH encoding gene from the mutant with the gene sequences from other yeast strains, the ADH enzyme was identified as ADH-1 type. The study reveals first three-dimensional model of ADH-1 utilizing glucose/xylose sugars from P. kudriavzevii BGY1-γm (PkADH mutant). The refined and validated model of PkADH mutant was used for molecular docking against the substrate (acetaldehyde) and product (ethanol). Molecular docking results showed that substrate and product exhibited a binding affinity of -4.55 and -4.5 kcal/mol with PkADH mutant. Acetaldehyde and ethanol interacted at the active site of PkADH mutant via hydrogen bonds (Ser42, His69 and Asp163) and hydrophobic interactions (Cys40, Ser42, His69, Cys95, Trp123 and Asp163) to form the stable protein-ligand complex. Molecular dynamics analysis revealed that PkADH-mutant acetaldehyde and PkADH-mutant ethanol complexes were more stable than PkADH mutant. MMPBSA binding energy confirmed that binding of substrate and product results in the formation of a lower energy stable protein-ligand complex.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Neha Bisht
- Department of Microbiology, College of Basic Sciences & Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttrakhand, India
| | - Vikram Dalal
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Lakshmi Tewari
- Department of Microbiology, College of Basic Sciences & Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttrakhand, India
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17
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Kumari R, Dalal V. Identification of potential inhibitors for LLM of Staphylococcus aureus: structure-based pharmacophore modeling, molecular dynamics, and binding free energy studies. J Biomol Struct Dyn 2022; 40:9833-9847. [PMID: 34096457 DOI: 10.1080/07391102.2021.1936179] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Staphylococcus aureus causes various life-threatening diseases in humans and developed resistance to several antibiotics. Lipophilic membrane (LLM) protein regulates bacterial lysis rate and methicillin resistance level in S. aureus. To identify potential lead molecules, we performed a structure-based pharmacophore modeling by consideration of pharmacophore properties from LLM-tunicamycin complex. Further, virtual screening of ZINC database against the LLM was conducted and compounds were assessed for Lipinski and ADMET properties. Based on pharmacokinetic, and molecular docking, five potential inhibitors (ZINC000072380005, ZINC000257219974, ZINC000176045471, ZINC000035296288, and ZINC000008789934) were identified. Molecular dynamics simulation (MDS) of these five molecules was performed to evaluate the dynamics and stability of protein after binding of the ligands. Several MDS analysis like RMSD, RMSF, Rg, SASA, and PCA confirm that identified compounds exhibit higher binding affinity as compared to tunicamycin for LLM. The binding free energy analysis reveals that five compounds exhibit higher binding energy in the range of -218.76 to -159.52 kJ/mol, which is higher as compared to tunicamycin (-116.13 kJ/mol). Individual residue decomposition analysis concludes that Asn148, Asp151, Asp208, His271, and His272 of LLM play a significant role in the formation of lower energy LLM-inhibitor(s) complexes. These predicted molecules displayed pharmacological and structural properties and may be further used to develop novel antimicrobial compounds against S. aureus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Reena Kumari
- Department of Mathematics and Statistics, Swami Vivekanand Subharti University, Meerut, India
| | - Vikram Dalal
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO, USA
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Dalal V, Kumari R. Screening and Identification of Natural Product‐Like Compounds as Potential Antibacterial Agents Targeting FemC of
Staphylococcus aureus
: An in‐Silico Approach. ChemistrySelect 2022. [DOI: 10.1002/slct.202201728] [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)
- Vikram Dalal
- Department of Anesthesiology Washington University in St. Louis Missouri 63110 USA
| | - Reena Kumari
- Department of Mathematics and Statistics Swami Vivekanand Subharti University Meerut 250005 India
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19
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Neuroprotective effects of phenolic glycosides from Populus tomentiglandulosa roots in HT22 mouse hippocampal neuronal cells. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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20
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Singh V, Dhankhar P, Dalal V, Tomar S, Kumar P. In-silico functional and structural annotation of hypothetical protein from Klebsiella pneumonia: A potential drug target. J Mol Graph Model 2022; 116:108262. [PMID: 35839717 DOI: 10.1016/j.jmgm.2022.108262] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 06/20/2022] [Accepted: 06/23/2022] [Indexed: 12/15/2022]
Abstract
Klebsiella pneumonia is known to cause several nosocomial infections in immunocompromised patients. It has developed resistance against a broad range of presently available antibiotics, resulting in high mortality rates in patients and declared an urgent threat. Therefore, exploration of possible novel drug targets against this opportunistic bacteria needs to be undertaken. In the present study, we performed an extensive in-silico analysis for functional and structural annotation and characterized HP CP995_08280 from K. pneumonia as a drug target and aimed to identify potent drug candidates. The functional and structural studies using several bioinformatics tools and databases predicted that HP CP995_08280 is a cytosolic protein that belongs to the β-lactamase family and shares structural similarity with FmtA protein from Staphylococcus aureus (PDB ID: 5ZH8). The structure of HP CP995_08280 was successfully modeled followed by structure-based virtual screening, docking, molecular dynamics, and Molecular mechanic/Poisson-Boltzmann surface area (MMPBSA) were performed to identify the potential compounds. We have found five potent antibacterial molecules, namely BDD 24083171, BDD 24085737, BDE 25098678, BDE 33638819, and BDE 33672484, which exhibited high binding affinity (>-7.5 kcal/mol) and were stabilized by hydrogen bonding and hydrophobic interactions with active site residues (Ser42, Lys45, Tyr126, and Asp128) of protein. Molecular dynamics and MMPBSA revealed that HP CP995_08280 - ligand(s) complexes were less dynamic and more stable than native HP CP995_08280. Hence, the present study may serve as a potential lead for developing inhibitors against drug-resistant Klebsiella pneumonia.
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Affiliation(s)
- Vishakha Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, 247667, India
| | - Poonam Dhankhar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, 247667, India
| | - Vikram Dalal
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, 247667, India
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, 247667, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, 247667, India.
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21
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Wang S, Wang MY, Shi YF, Han F, Ye HL, Cai YQ, Wu D, Tian LL, Zhang X, Tang YY. Identification of 2,2',4,5,5'-Pentachlorobiphenyl (PCB101) metabolites and their transmission characteristics in silver crucian carp (Carassius auratus gibelio). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 307:119583. [PMID: 35680065 DOI: 10.1016/j.envpol.2022.119583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/24/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Polychlorinated biphenyls (PCBs) have been attracting global concern due to their persistence and toxicity. However, the study on the metabolites of PCBs in freshwater fish is limited. In this study, the metabolites of 2,2',4,5,5'-Pentachlorobiphenyl (PCB101) in silver crucian carp (Carassius auratus gibelio) were identified for the first time. After intraperitoneal injection of PCB101 (2 mg/kg), the results showed that it could be metabolized to at least three types of metabolites, including hydroxylated (OH-), methoxylated (MeO-) and methyl sulfonated (MeSO2-) PCB101. The OH- metabolites identified in most tissues were 3-OH-PCB101and 4-OH-PCB101, such as liver, gallbladder, blood and muscle. MeSO2- metabolites identified in gallbladder, blood and brain were 3-MeSO2-PCB101 and 4-MeSO2-PCB101. Meanwhile, the MeO- metabolite identified in liver, gallbladder, blood and spleen of silver crucian carp was 4-MeO-PCB101. The investigation of the types and structures of PCB101 and its metabolites, as well as the tissue distribution and accumulation characteristics in silver crucian carp are beneficial to understand the transformation and metabolic mechanisms of PCBs in aquatic organisms. It is of great significance to identify potential pollution hazards of precursor compounds and their metabolites on aquatic products and ensure the quality and safety of aquatic products.
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Affiliation(s)
- Shuai Wang
- Fishery Products Quality Inspection and Test Centre (Shanghai), East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs of China, No. 300 Jungong Road, Yangpu District, Shanghai, 200090, China; College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; Linquan County Agricultural Product Quality and Safety Inspection Station, Linquan, Anhui province, China
| | - Meng-Yuan Wang
- Fishery Products Quality Inspection and Test Centre (Shanghai), East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs of China, No. 300 Jungong Road, Yangpu District, Shanghai, 200090, China; College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Yong-Fu Shi
- Fishery Products Quality Inspection and Test Centre (Shanghai), East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs of China, No. 300 Jungong Road, Yangpu District, Shanghai, 200090, China.
| | - Feng Han
- Fishery Products Quality Inspection and Test Centre (Shanghai), East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs of China, No. 300 Jungong Road, Yangpu District, Shanghai, 200090, China; College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Hong-Li Ye
- Fishery Products Quality Inspection and Test Centre (Shanghai), East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs of China, No. 300 Jungong Road, Yangpu District, Shanghai, 200090, China
| | - You-Qiong Cai
- Fishery Products Quality Inspection and Test Centre (Shanghai), East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs of China, No. 300 Jungong Road, Yangpu District, Shanghai, 200090, China
| | - Di Wu
- Fishery Products Quality Inspection and Test Centre (Shanghai), East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs of China, No. 300 Jungong Road, Yangpu District, Shanghai, 200090, China; College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Liang-Liang Tian
- Fishery Products Quality Inspection and Test Centre (Shanghai), East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs of China, No. 300 Jungong Road, Yangpu District, Shanghai, 200090, China
| | - Xuan Zhang
- Fishery Products Quality Inspection and Test Centre (Shanghai), East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs of China, No. 300 Jungong Road, Yangpu District, Shanghai, 200090, China
| | - Yun-Yu Tang
- Fishery Products Quality Inspection and Test Centre (Shanghai), East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs of China, No. 300 Jungong Road, Yangpu District, Shanghai, 200090, China
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22
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Adnan M, Koli S, Mohammad T, Siddiqui AJ, Patel M, Alshammari N, Bardakci F, Elasbali AM, Hassan MI. Searching for Novel Anaplastic Lymphoma Kinase Inhibitors: Structure-Guided Screening of Natural Compounds for a Tyrosine Kinase Therapeutic Target in Cancers. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:461-470. [PMID: 35925819 DOI: 10.1089/omi.2022.0067] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase molecular target with broad importance for drug discovery, especially in the field of cancer therapeutics. ALK belongs to the insulin receptor superfamily that is involved in various malignancies, including non-small cell lung cancer, anaplastic large cell lymphoma, and neuroblastoma. ALK has been shown to play a role in cancer progression and metastasis, making it one of the prime targets to develop novel anticancer therapeutics. In this context, natural compounds can be an important resource to unravel novel ALK inhibitors. In this study, we report a structure-based virtual screening of natural compounds from the ZINC database, with an eye to potential inhibitors of ALK. Molecular docking was performed on a natural compound library, and top hits holding good binding affinity, docking score, and specificity toward ALK were selected. The hits were further evaluated based on the PAINS (pan-assay interference compounds) filter, ADMET (absorption, distribution, metabolism, excretion, toxicity) properties, PASS (prediction of activity spectra for substances) analysis, and two-dimensional interaction of protein-ligand complexes. Importantly, two natural compounds (ZINC03845566 and ZINC03999625) were identified as potential candidates for ALK, having appreciable affinity and specificity toward the ALK binding pocket and depicting drug-like properties as predicted from ADMET analysis and their physicochemical parameters. An all-atom molecular dynamics simulation for 100 ns on ALK promised stable ALK-ligand complexes. Hence, we conclude that ZINC03845566 and ZINC03999625 can act as potential ALK inhibitors against cancers where ALK plays a role, for example, in lung cancer, among others. All in all, these findings inform future discovery and translational research for ALK inhibitors as anticancer drugs.
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Affiliation(s)
- Mohd Adnan
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
- Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha'il, Ha'il, Saudi Arabia
| | - Saadgee Koli
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Arif Jamal Siddiqui
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Mitesh Patel
- Department of Biotechnology, Parul Institute of Applied Sciences and Centre of Research for Development, Parul University, Vadodara, India
| | - Nawaf Alshammari
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Fevzi Bardakci
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | | | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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23
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Kumari R, Kumar V, Dhankhar P, Dalal V. Promising antivirals for PLpro of SARS-CoV-2 using virtual screening, molecular docking, dynamics, and MMPBSA. J Biomol Struct Dyn 2022:1-17. [PMID: 35510600 DOI: 10.1080/07391102.2022.2071340] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The recent pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (COVID-19) is a viral respiratory disease that has been spread all over the globe. Therefore, it is an urgent requirement to identify and develop drugs for this contagious infection. The papain-like protease (PLpro) of SARS-CoV-2 performs critical functions in virus replication and immune evasion, making it an enticing therapeutic target. SARS-CoV-2 and SARS-CoV PLpro proteases have significant similarities, and an inhibitor discovered for SARS-CoV PLpro is an exciting first step toward therapeutic development. Here, a set of antiviral molecules were screened at the catalytic and S-binding allosteric sites of papain-like protease (PLpro). Molecular docking results suggested that five molecules (44560613, 136277567, S5652, SC75741, and S3833) had good binding affinities at both sites of PLpro. Molecular dynamics analysis like root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), and hydrogen bond results showed that identified molecules with PLpro tend to form stable PLpro-inhibitor(s) complexes. Molecular Mechanics/Position-Boltzmann Surface Area (MMPBSA) analysis confirmed that antiviral molecules bound PLpro complex had lower energy (-184.72 ± 7.81 to -215.67 ± 6.73 kJ/mol) complexes. Noticeably, computational approaches revealed promising antivirals candidates for PLpro, which may be further tested by biochemical and cell-based assays to assess their potential for SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Reena Kumari
- Department of Mathematics and Statistics, Swami Vivekanand Subharti University, Meerut, India
| | - Viney Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, India
| | - Poonam Dhankhar
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA
| | - Vikram Dalal
- Department of Anesthesiology, Washington University in St. Louis, St. Louis MO, USA
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24
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Kumari R, Rathi R, Pathak SR, Dalal V. Structural-based virtual screening and identification of novel potent antimicrobial compounds against YsxC of Staphylococcus aureus. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132476] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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25
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Yang F, Cui Y, Yu H, Guo Y, Cheng Y, Yao W, Xie Y. Identifying potential thyroid hormone disrupting effects among diphenyl ether structure pesticides and their metabolites in silico. CHEMOSPHERE 2022; 288:132575. [PMID: 34656618 DOI: 10.1016/j.chemosphere.2021.132575] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/23/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
The environmental and dietary pesticide exposures can cause thyroid hormones (THs) disorders, which are associated with the high incidence of thyroid diseases worldwide. The structures of diphenyl ether pesticides and their metabolites are very similar to the structure of THs. Based on this, in silico molecular simulation approaches were used to predict, screen, evaluate and identify the binding interactions of 98 diphenyl ether structure pesticides and their metabolites (DEPMs) with 10 THs related proteins in the study. The research results indicated that these DEPMs such as fluoroglycofen (FOG), rafoxanide, diclofop, ethoxyfen and difenopenten were considered to have the greater potentials to interfere with the related proteins of THs biosynthesis, blood transport, receptor binding and metabolism. And FOG can interact with thyroid hormone receptor beta (TRβ) to form non-bond interactions. Furthermore, the results of molecular dynamics simulations showed that there were strong and stable interactions between FOG and TRβ. These results suggested that the herbicide FOG was likely to disturb THs nuclear receptor. And benzene rings and hydrophobic groups might be the characteristic chemical functional groups for DEPMs to disrupt TRβ. The relevant results of this study can be used to provide references for environmental toxicology evaluation, food safety risk assessment, and formulation and revision of pesticides and their metabolites residue limits in agricultural products and food.
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Affiliation(s)
- Fangwei Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, No.1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; Engineering Research Center of Dairy Quality and Safety Control Technology, Ministry of Education, Inner Mongolia University, No.235 Daxue West Road, Hohhot, 010021, Inner Mongolia Autonomous Region, China; School of Food Science and Technology, Jiangnan University, No.1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; Joint International Research Laboratory of Food Safety, Jiangnan University, No.1800 Lihu Avenue, Wux, 214122, Jiangsu Province, China
| | - Yiwen Cui
- State Key Laboratory of Food Science and Technology, Jiangnan University, No.1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; School of Food Science and Technology, Jiangnan University, No.1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; Joint International Research Laboratory of Food Safety, Jiangnan University, No.1800 Lihu Avenue, Wux, 214122, Jiangsu Province, China
| | - Hang Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, No.1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; School of Food Science and Technology, Jiangnan University, No.1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; Joint International Research Laboratory of Food Safety, Jiangnan University, No.1800 Lihu Avenue, Wux, 214122, Jiangsu Province, China
| | - Yahui Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, No.1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; Engineering Research Center of Dairy Quality and Safety Control Technology, Ministry of Education, Inner Mongolia University, No.235 Daxue West Road, Hohhot, 010021, Inner Mongolia Autonomous Region, China; School of Food Science and Technology, Jiangnan University, No.1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; Joint International Research Laboratory of Food Safety, Jiangnan University, No.1800 Lihu Avenue, Wux, 214122, Jiangsu Province, China
| | - Yuliang Cheng
- State Key Laboratory of Food Science and Technology, Jiangnan University, No.1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; School of Food Science and Technology, Jiangnan University, No.1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; Joint International Research Laboratory of Food Safety, Jiangnan University, No.1800 Lihu Avenue, Wux, 214122, Jiangsu Province, China
| | - Weirong Yao
- State Key Laboratory of Food Science and Technology, Jiangnan University, No.1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; School of Food Science and Technology, Jiangnan University, No.1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; Joint International Research Laboratory of Food Safety, Jiangnan University, No.1800 Lihu Avenue, Wux, 214122, Jiangsu Province, China
| | - Yunfei Xie
- State Key Laboratory of Food Science and Technology, Jiangnan University, No.1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; Engineering Research Center of Dairy Quality and Safety Control Technology, Ministry of Education, Inner Mongolia University, No.235 Daxue West Road, Hohhot, 010021, Inner Mongolia Autonomous Region, China; School of Food Science and Technology, Jiangnan University, No.1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; Joint International Research Laboratory of Food Safety, Jiangnan University, No.1800 Lihu Avenue, Wux, 214122, Jiangsu Province, China.
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26
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Gupta DN, Dalal V, Savita BK, Dhankhar P, Ghosh DK, Kumar P, Sharma AK. In-silico screening and identification of potential inhibitors against 2Cys peroxiredoxin of Candidatus Liberibacter asiaticus. J Biomol Struct Dyn 2021; 40:8725-8739. [PMID: 33939584 DOI: 10.1080/07391102.2021.1916597] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Huanglongbing (HLB) is a worldwide citrus plant disease-related to non-culturable and fastidious α-proteobacteria Candidatus Liberibacter asiaticus (CLas). In CLas, Peroxiredoxin (Prx) plays a major role in the reduction of the level of reactive species such as reactive oxygen species (ROS), free radicals and peroxides, etc. Here, we have used structure-based drug designing approach was used to screen and identify the potent molecules against 2Cys Prx. The virtual screening of fragments library was performed against the three-dimensional validated model of Prx. To evaluate the binding affinity, the top four molecules (N-Boc-2-amino isobutyric acid (B2AI), BOC-L-Valine (BLV), 1-(boc-amino) cyclobutane carboxylic acid (1BAC), and N-Benzoyl-DL-alanine (BDLA)) were docked at the active site of Prx. The molecular docking results revealed that all the identified molecules had a higher binding affinity than Tert butyl hydroperoxide (TBHP), a substrate of Prx. Molecular dynamics analysis such as RMSD, Rg, SASA, hydrogen bonds, and PCA results indicated that Prx-inhibitor(s) complexes had lesser fluctuations and were more stable and compact than Prx-TBHP complex. MMPBSA results confirmed that the identified compounds could bind at the active site of Prx to form a lower energy Prx-inhibitor(s) complex than Prx-TBHP complex. The identified potent molecules may pave the path for the development of antimicrobial agents against CLA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Deena Nath Gupta
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Vikram Dalal
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Brajesh Kumar Savita
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Poonam Dhankhar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Dilip Kumar Ghosh
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, Nagpur, India
| | - Pravindra Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Ashwani Kumar Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
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27
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Vergoten G, Bailly C. Binding of hydroxychloroquine and chloroquine dimers to palmitoyl-protein thioesterase 1 (PPT1) and its glycosylated forms: a computational approach. J Biomol Struct Dyn 2021; 40:8197-8205. [PMID: 33876698 DOI: 10.1080/07391102.2021.1908167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The lysosomal enzyme palmitoyl-protein thioesterase 1 (PPT1) removes thioester-linked fatty acid groups from membrane-bound proteins to facilitate their proteolysis. A lack of PPT1 (due to gene mutations) causes the progressive death of cortical neurons and is responsible for infantile neural ceroid lipofuscinosis (INCL), a severe neurodegenerative disorder in children. Conversely, PPT1 is often over-expressed in cancer, and considered as a valid target to control tumor growth. Potent and selective inhibitors of PPT1 have been designed, in particular 4-amino-7-chloro-quinoline derivatives such as hydroxychloroquine (HCQ) and the dimeric analogues Lys05 and DC661. We have modeled the interaction of these three compounds with the enzyme, taking advantage of the PPT1 crystallographic structure. The molecules can fit into the palmitate site of the protein, with the dimeric compounds forming more stable complexes than the monomer. But the molecular modeling suggests that the most favorable binding sites are located outside the active site. Two sites centered on residues Met112 and Gln144 were identified, offering suitable cavities for drug binding. According to the calculated empirical energies of interaction (ΔE), the dimer DC661 forms the most stable complex at site Met112 of palmitate-bound PPT1. N-glycosylated forms of PPT1 were elaborated. Paucimannosidic glycans (M2FA and M3F) and a bulkier tetra-antennary complex glycan were introduced at asparagine residues N197, N212 and N232. These N-glycans do not impede drug binding, thus suggesting that all glycoforms of PPT1 can be targeted with these compounds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gérard Vergoten
- Inserm, INFINITE - U1286, Institut de Chimie Pharmaceutique Albert Lespagnol (ICPAL), Faculté de Pharmacie, University of Lille, Lille, France
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