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Matin MM, Chakraborty P, Alam MS, Islam MM, Hanee U. Novel mannopyranoside esters as sterol 14α-demethylase inhibitors: Synthesis, PASS predication, molecular docking, and pharmacokinetic studies. Carbohydr Res 2020; 496:108130. [PMID: 32863019 PMCID: PMC7427576 DOI: 10.1016/j.carres.2020.108130] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/02/2020] [Accepted: 08/09/2020] [Indexed: 12/18/2022]
Abstract
Direct unimolar one-step valeroylation of methyl α-d-mannopyranoside (MDM) furnished mainly 6-O-valeroate. However, similar reaction catalyzed by DMAP resulted 3,6-di-O-valeroate (21%) and 6-O-valeroate (47%) indicating reactivity sequence as 6-OH>3-OH>2-OH,4-OH. To get potential antimicrobial agents, 6-O-valeroate was converted into four 2,3,4-di-O-acyl esters, and 3,6-di-O-valeroate was converted into 2,4-di-O-acetate. Direct tetra-O-valeroylation of MDM gave a mixture of 2,3,4,6-tetra-O-valeroate and 2,3,6-tri-O-valeroate indicating that the C2-OH is more reactive than the equatorial C4-OH. The activity spectra analysis along with in vitro antimicrobial evaluation clearly indicated that these novel MDM esters had better antifungal activities over antibacterial agents. In this connection, molecular docking indicated that these MDM esters acted as competitive inhibitors of sterol 14α-demethylase (CYP51), an essential enzyme for clinical target to cure several infectious diseases. Furthermore, pharmacokinetic studies revealed that these MDM esters may be worth considering as potent candidates for oral and topical administration. Structure activity relationship (SAR) affirmed that saturated valeric chain (C5) in combination with caprylic (C8) chains was more promising CYP51 inhibitor over conventional antifungal antibiotics.
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Affiliation(s)
- Mohammed M Matin
- Bioorganic and Medicinal Chemistry Laboratory, Department of Chemistry, Faculty of Science, University of Chittagong, Chattogram, 4331, Bangladesh.
| | - Priyanka Chakraborty
- Bioorganic and Medicinal Chemistry Laboratory, Department of Chemistry, Faculty of Science, University of Chittagong, Chattogram, 4331, Bangladesh
| | - Muhammad S Alam
- Molecular Modeling & Drug Design Laboratory, Bangladesh Council of Scientific & Industrial Research (BCSIR) Laboratories, Chattogram, 4220, Bangladesh
| | - Mohammad M Islam
- Department of Biochemistry and Molecular Biology, Faculty of Biological Science, University of Chittagong, Chattogram, 4331, Bangladesh
| | - Umme Hanee
- Bioorganic and Medicinal Chemistry Laboratory, Department of Chemistry, Faculty of Science, University of Chittagong, Chattogram, 4331, Bangladesh
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Sharma M, Mittal A, Singh A, Jainarayanan AK, Sharma S, Paliwal S. Pharmacophore-driven identification of N-methyl-D-receptor antagonists as potent neuroprotective agents validated using in vivo studies. Biol Methods Protoc 2020; 5:bpaa013. [PMID: 32913897 PMCID: PMC7474860 DOI: 10.1093/biomethods/bpaa013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 06/25/2020] [Accepted: 07/02/2020] [Indexed: 01/18/2023] Open
Abstract
Alzheimer's disease (AD), apparently the most widespread reason behind dementia, is delineated by a continuous cognitive weakening in the aged. During its progression, N-methyl-D-aspartate receptor (NMDAR) antagonists are known to play a pivotal part in the mechanisms of learning and memory. Since there is an unmet medical need for the treatment of AD, we aim to identify possible chemical compounds targeted toward N-methyl-D-aspartate receptors. Three-dimensional models are developed to unveil some of the essential characteristics of the N-methyl-D-aspartate receptors by using a collection of already discovered N-methyl-D-aspartate receptor inhibitors. This is followed by virtual screening, which results in novel chemical compounds having the potential to inhibit N-methyl-D-aspartate receptors. Molecular docking studies and analysis promulgated two lead compounds with a high LibDock score. The compounds are shortlisted based on high estimated activity, fit values, LibDock score, no violation of Lipinski's, and availability for procuring. Finally, the shortlisted compounds are tested by employing in vivo studies, which we further propose as potential NMDA inhibitors for treating AD.
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Affiliation(s)
- Mukta Sharma
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, Rajasthan, India
| | - Anupama Mittal
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, Rajasthan, India
| | - Aarti Singh
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, Rajasthan, India
| | | | - Swapnil Sharma
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, Rajasthan, India
| | - Sarvesh Paliwal
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, Rajasthan, India
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Site-directed mutations of anti-amantadine scFv antibody by molecular dynamics simulation: prediction and validation. J Mol Model 2020; 26:49. [PMID: 32020367 DOI: 10.1007/s00894-020-4286-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 01/10/2020] [Indexed: 10/25/2022]
Abstract
A recombinant single-chain variable fragment (scFv) antibody was produced from a hybridoma cell strain secreting the monoclonal antibody for amantadine (AMD), and then its recognition mechanisms for AMD were studied using the molecular docking and molecular dynamics. Complex dockings revealed that three regions are involved in antibody recognition; framework 2 of the VL chain (LFR2) GLU40 and TYR42, complementarity-determining region of the VL chain (LCDR3) TYR116, and framework 2 of the VH chain (HFR2) HIS40 and TRP52 were the key amino acid residues. The results of molecular dynamics show that the most important amino acid residues in the interaction between AMD and scFv are HIS40 and TYR116. On the basis of the results of virtual mutation, the scFv antibody was evolved by directional mutagenesis of amino acid residue GLY107 to PHE. Indirect competitive ELISA (icELISA) results indicated that the scFv mutant had highly increased affinity for AMD with up to 3.9-fold improved sensitivity. Thus, the scFv antibody can be applied for mechanistic studies of intermolecular interactions, and our work offered affinity maturated antibodies by site mutations, which were beneficial for valuable anti-AMD antibody design and preparation in future.
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In vitro evaluation of arylsubstituted imidazoles derivatives as antiprotozoal agents and docking studies on sterol 14α-demethylase (CYP51) from Trypanosoma cruzi, Leishmania infantum, and Trypanosoma brucei. Parasitol Res 2019; 118:1533-1548. [PMID: 30903349 DOI: 10.1007/s00436-019-06206-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 01/04/2019] [Indexed: 12/28/2022]
Abstract
There is an urgent need to discover and develop new drugs to combat parasitic diseases as Chagas disease (Trypanosoma cruzi), sleeping sickness (Trypanosoma brucei), and leishmaniasis (Leishmania ssp.). These diseases are considered among the 13 most unattended diseases worldwide according to the WHO. In the present work, the synthesis of 14 arylsubstituted imidazoles and its molecular docking onto sterol 14α-demethylase (CYP51) was executed. In addition, the compounds, antiprotozoal activity against T. brucei, T. cruzi, Trypanosoma brucei rhodesiense, and Leishmania infantum was evaluated. In vitro antiparasitic results of the arylsubstituted imidazoles against T. brucei, T. cruzi, T.b. rhodesiense, and L. infantum indicated that all samples from arylsubstituted imidazole compounds presented interesting antiparasitic activity to various extent. The ligands 5a, 5c, 5e, 5f, 5g, 5i, and 5j exhibited strong activity against T. brucei, T. cruzi, T.b. rhodesiense, and L. infantum with IC50 values ranging from 0.86 to 10.23 μM. Most samples were cytotoxic against MRC-5 cell lines (1.12 < CC50 < 51.09 μM) and only ligand 5c showed a good selectivity against all tested parasites. According to the results of the molecular docking, the aromatic substituents in positions 1, 4, and 5 have mainly stabilizing hydrophobic interactions with the enzyme matrix, while the oxygen from NO2, SO3H, and OH groups interacts with the Fe2+ ion of the Heme group.
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Özdemir A, Sever B, Altıntop MD. New Benzodioxole-based Pyrazoline Derivatives: Synthesis and Anticandidal, In silico ADME, Molecular Docking Studies. LETT DRUG DES DISCOV 2018. [DOI: 10.2174/1570180815666180326152726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background:
Azoles are commonly used in the treatment and prevention of fungal
infections. They suppress fungal growth by acting on the heme group of lanosterol 14α-demethylase
enzyme (CYP51), thus blocking the biosynthesis of ergosterol.
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Objectives: Due to the importance of pyrazolines in the field of antifungal drug design, we aimed to
design and synthesize new pyrazoline-based anticandidal agents.
Methods:
New pyrazoline derivatives were synthesized via the reaction of 1-(chloroacetyl)-3-(2-
thienyl)-5-(1,3-benzodioxol-5-yl)-2-pyrazoline with aryl thiols. These compounds were evaluated
for their in vitro antifungal effects on Candida species. Docking studies were performed to predict
the affinity of the most effective anticandidal agents to substrate binding site of CYP51. Furthermore,
MTT assay was performed to determine the cytotoxic effects of the compounds on NIH/3T3
mouse embryonic fibroblast cell line. A computational study for the prediction of ADME properties
of all compounds was also carried out.
Results:
Compounds 5, 8, 10 and 12 were found as the most potent anticandidal agents against
Candida albicans and Candida glabrata in this series with the same MIC values of ketoconazole
and they also exhibited low toxicity against NIH/3T3 cells. Docking results indicated that all these
compounds showed good binding affinity into the active site of CYP51. In particular, chloro
substituted compounds 8 and 12 bind to CYP51 through direct coordination with the heme group.
According to in silico studies, compound 8 only violated one parameter of Lipinski’s rule of five,
making it a potential orally bioavailable agent.
Conclusion:
Compound 8 was defined as a promising candidate for further in vitro and in vivo
studies.
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Affiliation(s)
- Ahmet Özdemir
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey
| | - Belgin Sever
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey
| | - Mehlika Dilek Altıntop
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey
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Nicola AM, Albuquerque P, Paes HC, Fernandes L, Costa FF, Kioshima ES, Abadio AKR, Bocca AL, Felipe MS. Antifungal drugs: New insights in research & development. Pharmacol Ther 2018; 195:21-38. [PMID: 30347212 DOI: 10.1016/j.pharmthera.2018.10.008] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The need for better antifungal therapy is commonly accepted in view of the high mortality rates associated with systemic infections, the low number of available antifungal classes, their associated toxicity and the increasing number of infections caused by strains with natural or acquired resistance. The urgency to expand the range of therapeutic options for the treatment of fungal infections has led researchers in recent decades to seek alternative antifungal targets when compared to the conventional ones currently used. Although new potential targets are reported, translating the discoveries from bench to bedside is a long process and most of these drugs fail to reach the patients. In this review, we discuss the development of antifungal drugs focusing on the approach of drug repurposing and the search for novel drugs for classical targets, the most recently described gene targets for drug development, the possibilities of immunotherapy using antibodies, cytokines, therapeutic vaccines and antimicrobial peptides.
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Affiliation(s)
| | - Patrícia Albuquerque
- Faculty of Ceilândia, University of Brasília, Brazil; Graduate Programme in Microbial Biology, University of Brasília, Brazil
| | - Hugo Costa Paes
- Division of Clinical Medicine, University of Brasília Medical School, Brazil
| | - Larissa Fernandes
- Faculty of Ceilândia, University of Brasília, Brazil; Graduate Programme in Microbial Biology, University of Brasília, Brazil
| | - Fabricio F Costa
- Graduate Programme in Genomic Science and Biotechnology, Catholic University of Brasília, Brazil; MATTER, Chicago, IL, USA; Cancer Biology and Epigenomics Program, Ann & Robert Lurie Children's Hospital of Chicago Research Center, Northwestern University's Feinberg School of Medicine, Chicago, Illinois, USA
| | - Erika Seki Kioshima
- Department of Clinical Analysis and Biomedicine, State University of Maringá, Paraná, Brazil
| | - Ana Karina Rodrigues Abadio
- School for Applied Social and Agricultural Sciences, State University of Mato Grosso, Nova Mutum Campus, Mato Grosso, Brazil
| | | | - Maria Sueli Felipe
- Graduate Programme in Genomic Science and Biotechnology, Catholic University of Brasília, Brazil; Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brazil.
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Pandey B, Sharma P. Structural insights into impact of Y134F mutation and discovery of novel fungicidal compounds against CYP51 in Puccinia triticina. J Cell Biochem 2017; 119:2588-2603. [PMID: 28980720 DOI: 10.1002/jcb.26422] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Accepted: 09/22/2017] [Indexed: 12/22/2022]
Abstract
Sterol 14α-Demethylase Cytochrome P450 (CYP51) protein involved in ergosterol biosynthesis pathways turn out to be a crucial target for the fungicidal compound. However, the recognition mechanism and dynamic behavior of CYP51 in wheat leaf rust pathogen, Puccinia triticina, is still obscure. Previously, a mutation at position 134 (Y134F) was reported in five European isolates of P. triticina, conversely, structural basis of this mutation remains unclear. To address this problem, three-dimensional structure of CYP51 protein from P. triticina was successfully built using homology modeling approach. To assess the protein structure stability, wild and mutant-type CYP51 proteins bound with azole fungicide was subjected to 50 ns molecular dynamics (MD) simulations run. Observably, the comparative protein-ligand interaction analysis and binding free energy results revealed that impact of the mutation on the thermodynamics and conformational stability of the CYP51 protein was negligible. In addition, we carried out structure-based virtual screening and identified potent novel fungicidal compounds from four different databases and libraries. Consequently, through MD simulation and thermodynamic integration, four novel compounds such as CoCoCo54211 (CoCoCo database), ZINC04089470 (ZINC database), Allyl pyrocatechol 3,4 diacetate (Natural compound library), and 9-octadecenoic acid (Traditional Chinese Medicine database) has been predicted as potent fungicidal compound against CYP51 with XPGlide docking score of -11.41, -13.64, -7.40, and -6.55 kcal/mol, respectively. These compounds were found to form hydrogen bonds with heme group of CYP51, subsequently disturbing the stability and survival of fungus and can be used to control leaf rust in wheat.
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Affiliation(s)
- Bharati Pandey
- Plant Biotechnology Unit, ICAR-Indian Institute of Wheat Barley Research, Karnal, Haryana, India
| | - Pradeep Sharma
- Plant Biotechnology Unit, ICAR-Indian Institute of Wheat Barley Research, Karnal, Haryana, India
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8
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Cost effective characterization process and molecular dynamic simulation of detergent compatible alkaline protease from Bacillus pumilus strain MP27. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.04.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Kumar R, Biswas K, Singh PK, Singh PK, Elumalai S, Shukla P, Pabbi S. Lipid production and molecular dynamics simulation for regulation of accD gene in cyanobacteria under different N and P regimes. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:94. [PMID: 28428819 PMCID: PMC5393026 DOI: 10.1186/s13068-017-0776-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 04/05/2017] [Indexed: 05/11/2023]
Abstract
BACKGROUND Microalgae grown under different nutrient deficient conditions present a good source of natural lipids with applications for several types of biofuels. The expression of acetyl-CoA carboxylase gene can further provide an insight to the mechanisms leading to enhanced lipid production under such stresses. In this study, two nutrients viz. nitrogen and phosphorus were modulated to see its effect on lipid productivity in selected cyanobacteria and its correlation with Accase followed by molecular dynamics simulation. RESULTS Selected cyanobacteria viz. Oscillatoria sp. (SP8), Anabaena sp. (SP12), Anabaena sp. (SP13), Microcoleus sp. (SP18), and Nostoc sp. (SP20) varied in their ability to accumulate lipids which ranged from a lowest of 0.13% in Anabaena sp. (SP13) to the maximum of 7.24% in Microcoleus sp. (SP18). Microcoleus sp. (SP18) also recorded highest lipid accumulation at both N (6 mM NaNO3) and P (0.20 mM K2HPO4) limiting conditions. The overall expression of accD was found to be upregulated in both Oscillatoria sp. (SP8) and Microcoleus sp. (SP18) for all nitrogen concentrations but was differentially regulated with both positive and negative induction under phosphorus stress conditions. Maximum induction was observed in Microcoleus sp. (SP18) at 0.20 mM K2HPO4. The obtained 3D structure of SP8 protein (21.8 kDa) showed six alpha helices, while SP18 protein (16.7 kDa) exhibited four alpha helices and four beta sheets. The phi (ϕ)/psi(ψ) angles of the amino acid residues observed in Ramachandran plot analysis showed that both SP8 and SP18 proteins were highly stable with more than 90% amino acids in allowed regions. The molecular dynamics simulation results also indicated the stability of ligand-bound protein complexes. CONCLUSION It has been demonstrated that cyanobacterial isolates are affected differently by nutrient limitation leading to variation in their lipid productivity. The same has been revealed by the behavior of accD gene expression which was regulated more by nutrients concentrations rather than the organism. However, the ligand-bound protein complexes were stable throughout MD simulations.
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Affiliation(s)
- Roshan Kumar
- Centre for Conservation and Utilisation of Blue Green Algae, Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
- Department of Plant Biology and Biotechnology, Presidency College, Chennai, 600005 India
| | - Koushik Biswas
- Department of Biotechnology, Shri JJT University, Jhunjhunu, Rajasthan 333001 India
| | - Puneet Kumar Singh
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001 India
| | - Pankaj Kumar Singh
- ICAR-National Research Centre on Plant Biotechnology (NRCPB), New Delhi, 110012 India
| | - Sanniyasi Elumalai
- Department of Plant Biology and Biotechnology, Presidency College, Chennai, 600005 India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001 India
| | - Sunil Pabbi
- Centre for Conservation and Utilisation of Blue Green Algae, Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
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Yuan Y, Han R, Cao Q, Yu J, Mao J, Zhang T, Wang S, Niu Y, Liu D. Pharmacophore-Based Virtual Screening of Novel Inhibitors and Docking Analysis for CYP51A from Penicillium italicum. Mar Drugs 2017; 15:E107. [PMID: 28379163 PMCID: PMC5408253 DOI: 10.3390/md15040107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/24/2017] [Accepted: 03/30/2017] [Indexed: 01/07/2023] Open
Abstract
Sterol 14α-demethylases from Cytochrome P450 family (CYP51s) are essential enzymes in sterol biosynthesis and well-known as the target of antifungal drugs. The 3D structure of CYP51A from Penicillium italicum (PiCYP51A) was constructed through homology modeling based on the crystal structure of human CYP51A (PDB: 3LD6). Molecular dynamics (MD) simulation was operated to relax the initial model and followed by quality assessment using PROCHECK program. On the basis of the docking information on the currently available CYP51s with the patent demethylase inhibitors (DMIs), pharmacophore-based virtual screening combined with docking analysis was performed to pick out twelve new compounds from ZINC database. Six hits revealed in the ligand database suggested potential ability to inhibit PiCYP51A. Compared to patent fungicide triazolone, the top three lead compounds had similar or higher affinity with the target enzyme, and accordingly, exhibited comparable or lower EC50 values to P. italicum isolates. The results could provide references for de novo antifungal drug design.
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Affiliation(s)
- Yongze Yuan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Science, Central China Normal University, Wuhan 430079, China.
| | - Rui Han
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Science, Central China Normal University, Wuhan 430079, China.
| | - Qianwen Cao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Science, Central China Normal University, Wuhan 430079, China.
| | - Jinhui Yu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Science, Central China Normal University, Wuhan 430079, China.
| | - Jiali Mao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Science, Central China Normal University, Wuhan 430079, China.
| | - Tingfu Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Science, Central China Normal University, Wuhan 430079, China.
| | - Shengqiang Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Science, Central China Normal University, Wuhan 430079, China.
| | - Yuhui Niu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Science, Central China Normal University, Wuhan 430079, China.
| | - Deli Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Science, Central China Normal University, Wuhan 430079, China.
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Li L, Liu J, Nie S, Ding L, Wang L, Liu J, Liu W, Zhang T. Direct inhibition of Keap1–Nrf2 interaction by egg-derived peptides DKK and DDW revealed by molecular docking and fluorescence polarization. RSC Adv 2017. [DOI: 10.1039/c7ra04352j] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
DKK and DDW, egg-derived direct inhibitors of the Keap1–Nrf2 interaction, screening by fluorescence polarization assays and cell experiments.
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Affiliation(s)
- Liangyu Li
- Jilin Key Laboratory of Nutrition and Functional Food
- Jilin University
- Changchun 130062
- People's Republic of China
| | - Jingbo Liu
- Jilin Key Laboratory of Nutrition and Functional Food
- Jilin University
- Changchun 130062
- People's Republic of China
| | - Shaoping Nie
- State Key Laboratory Food Science & Technology
- Nanchang University
- Nanchang 330047
- People's Republic of China
| | - Long Ding
- Jilin Key Laboratory of Nutrition and Functional Food
- Jilin University
- Changchun 130062
- People's Republic of China
| | - Liying Wang
- Jilin Key Laboratory of Nutrition and Functional Food
- Jilin University
- Changchun 130062
- People's Republic of China
| | - Jiyun Liu
- Jilin Key Laboratory of Nutrition and Functional Food
- Jilin University
- Changchun 130062
- People's Republic of China
| | - Wenchao Liu
- Jilin Key Laboratory of Nutrition and Functional Food
- Jilin University
- Changchun 130062
- People's Republic of China
| | - Ting Zhang
- Jilin Key Laboratory of Nutrition and Functional Food
- Jilin University
- Changchun 130062
- People's Republic of China
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Tiwari R, Kumar K, Singh S, Nain L, Shukla P. Molecular Detection and Environment-Specific Diversity of Glycosyl Hydrolase Family 1 β-Glucosidase in Different Habitats. Front Microbiol 2016; 7:1597. [PMID: 27790196 PMCID: PMC5062022 DOI: 10.3389/fmicb.2016.01597] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 09/26/2016] [Indexed: 12/23/2022] Open
Abstract
β-glucosidase is a crucial element of the microbial cellulose multienzyme complex since it is responsible for the regulation of the entire cellulose hydrolysis process. Therefore, the aim of the present work was to explore the diversity and distribution of glycosyl hydrolase family 1 β-glucosidase genes in three different environmental niches including, Himalayan soil, cow dung and compost by metagenomic approach. Preliminary evaluation through metabolic profiling using BIOLOG based utilization patterns of carbon, nitrogen, phosphorus and sulfur revealed the environment and substrate specific nature of the indigenous microbial population. Furthermore, clonal library selection, screening and sequence analysis revealed that most of the GH1 β-glucosidase proteins had low identities with the available database. Analysis of the distribution of GH1 β-glucosidase gene fragments and β-glucosidase producing microbial community revealed the environment specific nature. The OTUs obtained from Himalayan soil and compost metagenomic libraries were grouped into 19 different genera comprising 6 groups. The cow dung sample displayed the least diversity of GH1 β-glucosidase sequences, with only 14 genera, distributed among three groups- Bacteroidetes, Firmicutes, and Actinobacteria. The metagenomic study coupled with metabolic profiling of GH1 β-glucosidase illustrated the existence of intricate relationship between the geochemical environmental factors and inherent microbial community.
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Affiliation(s)
- Rameshwar Tiwari
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand UniversityRohtak, India; Division of Microbiology, ICAR-Indian Agricultural Research InstituteNew Delhi, India
| | - Kanika Kumar
- ICAR-National Research Centre on Plant Biotechnology, LBS Centre, Indian Agricultural Research Institute New Delhi, India
| | - Surender Singh
- Division of Microbiology, ICAR-Indian Agricultural Research Institute New Delhi, India
| | - Lata Nain
- Division of Microbiology, ICAR-Indian Agricultural Research Institute New Delhi, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University Rohtak, India
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Rabelo VW, Santos TF, Terra L, Santana MV, Castro HC, Rodrigues CR, Abreu PA. Targeting CYP51 for drug design by the contributions of molecular modeling. Fundam Clin Pharmacol 2016; 31:37-53. [PMID: 27487199 DOI: 10.1111/fcp.12230] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 07/15/2016] [Accepted: 08/01/2016] [Indexed: 11/28/2022]
Abstract
CYP51 is an enzyme of sterol biosynthesis pathway present in animals, plants, protozoa and fungi. This enzyme is described as an important drug target that is still of interest. Therefore, in this work, we reviewed the structure and function of CYP51 and explored the molecular modeling approaches for the development of new antifungal and antiprotozoans that target this enzyme. Crystallographic structures of CYP51 of some organisms have already been described in the literature, which enable the construction of homology models of other organisms' enzymes and molecular docking studies of new ligands. The binding mode and interactions of some new series of azoles with antifungal or antiprotozoan activities has been studied and showed important residues of the active site. Molecular modeling is an important tool to be explored for the discovery and optimization of CYP51 inhibitors with better activities, pharmacokinetics, and toxicological profiles.
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Affiliation(s)
- Vitor W Rabelo
- Laboratório de Modelagem Molecular e Pesquisa em Ciências Farmacêuticas (LAMCIFAR), Universidade Federal do Rio de Janeiro, Campus Macaé Professor Aloísio Teixeira, Avenida São José do Barreto 767, CEP 27965-045, Macaé, RJ, Brazil
| | - Taísa F Santos
- Laboratório de Modelagem Molecular e Pesquisa em Ciências Farmacêuticas (LAMCIFAR), Universidade Federal do Rio de Janeiro, Campus Macaé Professor Aloísio Teixeira, Avenida São José do Barreto 767, CEP 27965-045, Macaé, RJ, Brazil
| | - Luciana Terra
- Laboratório de Antibióticos, Bioquímica, Ensino e Modelagem Molecular (LabiEMol), Instituto de Biologia, Universidade Federal Fluminense, Campus Valonguinho Outeiro de São João Baptista s/n, Centro, CEP 24210130, Niterói, RJ, Brazil
| | - Marcos V Santana
- Laboratório de Antibióticos, Bioquímica, Ensino e Modelagem Molecular (LabiEMol), Instituto de Biologia, Universidade Federal Fluminense, Campus Valonguinho Outeiro de São João Baptista s/n, Centro, CEP 24210130, Niterói, RJ, Brazil
| | - Helena C Castro
- Laboratório de Antibióticos, Bioquímica, Ensino e Modelagem Molecular (LabiEMol), Instituto de Biologia, Universidade Federal Fluminense, Campus Valonguinho Outeiro de São João Baptista s/n, Centro, CEP 24210130, Niterói, RJ, Brazil
| | - Carlos R Rodrigues
- Laboratório de Modelagem Molecular e QSAR (ModMolQSAR), Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, CEP 21941-599, Rio de Janeiro, RJ, Brazil
| | - Paula A Abreu
- Laboratório de Modelagem Molecular e Pesquisa em Ciências Farmacêuticas (LAMCIFAR), Universidade Federal do Rio de Janeiro, Campus Macaé Professor Aloísio Teixeira, Avenida São José do Barreto 767, CEP 27965-045, Macaé, RJ, Brazil
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