1
|
Yuan Y, Yiasmin MN, Tristanto NA, Chen Y, Liu Y, Guan S, Wang Z, Hua X. Computational simulations on the taste mechanism of steviol glycosides based on their interactions with receptor proteins. Int J Biol Macromol 2024; 255:128110. [PMID: 37981277 DOI: 10.1016/j.ijbiomac.2023.128110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/13/2023] [Accepted: 11/13/2023] [Indexed: 11/21/2023]
Abstract
Steviol glycoside (SG) is a potential natural sugar substitute. The taste of various SG structures differ significantly, while their mechanism has not been thoroughly investigated. To investigate the taste mechanism, molecular docking simulations of SGs with sweet taste receptor TAS1R2 and bitter taste receptor TAS2R4 were conducted. The result suggested that four flexible coils (regions) in TAS1R2 constructed a geometry open pocket in space responsible for the binding of sweeteners. Amino acids that form hydrogen bonds with sweeteners are located in different receptor regions. In bitterness simulation, fewer hydrogen bonds were formed with the increased size of SG molecules. Particularly, there was no interaction between RM and TAS2R4 due to its size, which explains the non-bitterness of RM. Molecular dynamics simulations further indicated that the number of hydrogen bonds between SGs and TAS1R2 was maintained during a simulation time of 50 ns, while sucrose was gradually released from the binding site, leading to the break of interaction. Conclusively, the high sweetness intensity of SG can be attributed to its durative concurrent interaction with the receptor's binding site, and such behavior was determined by the structure feature of SG.
Collapse
Affiliation(s)
- Yuying Yuan
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Mst Nushrat Yiasmin
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | | | - Yujie Chen
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Jiangsu Sevtia Biotechnology Co., Ltd., Wuxi 214181, China
| | - Yaxian Liu
- Department of Biotechnology and Enzyme Science, University of Hohenheim, Institute of Food Science and Biotechnology, Garbenstr. 25, 70599 Stuttgart, Germany
| | - Shuyi Guan
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zijie Wang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiao Hua
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| |
Collapse
|
2
|
Smith JD, Brawley J, Bordenave KC, Olsen RK, Intasiri A, Cremo CR, Bell TW. Isoform selectivities of novel 4-hydroxycoumarin imines as inhibitors of myosin II. Eur J Med Chem 2023; 247:115008. [PMID: 36543032 PMCID: PMC9889102 DOI: 10.1016/j.ejmech.2022.115008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
Muscle myosin inhibition could be used to treat many medical conditions involving hypercontractile states, including muscle spasticity, chronic musculoskeletal pain, and hypertrophic cardiomyopathy. A series of 13 advanced analogs of 3-(N-butylethanimidoyl)ethyl)-4-hydroxy-2H-chromen-2-one (BHC) were synthesized to explore extended imine nitrogen side chains and compare aldimines vs. ketimines. None of the new analogs inhibit nonmuscle myosin in a cytokinesis assay. ATPase structure-activity relationships reveal that selectivity for cardiac vs. skeletal myosin can be tuned with subtle structural changes. None of the compounds inhibited smooth muscle myosin II. Docking the compounds to homology models of cardiac and skeletal myosin II gave rationales for the effects of side arm length on inhibition selectivity and for cardiac vs. skeletal myosin. Properties including solubility, stability and toxicity, suggest that certain BHC analogs may be useful as candidates for preclinical studies or as lead compounds for advanced candidates for drugs with cardiac or skeletal muscle myosin selectivity.
Collapse
Affiliation(s)
- Joshua D Smith
- Department of Pharmacology, University of Nevada, School of Medicine, Reno, NV, 89557-0318, USA
| | - Jhonnathan Brawley
- Department of Chemistry, University of Nevada, Reno, NV, 89557-0216, USA
| | - Kate C Bordenave
- Department of Pharmacology, University of Nevada, School of Medicine, Reno, NV, 89557-0318, USA
| | - Ryan K Olsen
- Department of Chemistry, University of Nevada, Reno, NV, 89557-0216, USA
| | - Amarawan Intasiri
- Department of Chemistry, University of Nevada, Reno, NV, 89557-0216, USA
| | - Christine R Cremo
- Department of Pharmacology, University of Nevada, School of Medicine, Reno, NV, 89557-0318, USA.
| | - Thomas W Bell
- Department of Chemistry, University of Nevada, Reno, NV, 89557-0216, USA.
| |
Collapse
|
3
|
Carpentier M, Chomilier J. Analyses of Mutation Displacements from Homology Models. Methods Mol Biol 2023; 2627:195-210. [PMID: 36959449 DOI: 10.1007/978-1-0716-2974-1_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
Evaluation of the structural perturbations introduced by a single amino acid mutation is the main issue for protein structural biology. We propose here to present some recent advances in methods, allowing the splitting of distortion between the actual substitution effect and the contribution of the local flexibility of the position where the mutation occurs. Its main drawback is the need of many structures with a single mutation in each of them. To bypass this difficulty, we propose to use molecular modeling tools, with several software enabling us to build a model from a template, given the sequence. As a proof of concept, we rely on a gold standard, the human lysozyme. Both wild-type and three mutant structures are available in the PDB. Two of these mutations result in amyloid fibril formation, and the last one is neutral. As a conclusion, irrespective of the algorithm used for modeling, side chain conformations at the site of mutation are reliable, although long-range effects are out of reach of these tools.
Collapse
Affiliation(s)
- Mathilde Carpentier
- Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, Paris, France.
| | - Jacques Chomilier
- Sorbonne Université, BiBiP, IMPMC, UMR 7590, CNRS, MNHN, Paris, France
| |
Collapse
|
4
|
Sun B, Liu Y, Fan H, An Y, Liu W, Wang Q, Han J. The discovery of novel antifungal phenylpyridines derivatives based on CYP53 binding model. Eur J Med Chem 2022; 242:114676. [PMID: 35994951 DOI: 10.1016/j.ejmech.2022.114676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/08/2022] [Accepted: 08/08/2022] [Indexed: 11/15/2022]
Abstract
Benzoates as toxic intermediate are naturally produced by fungal intracellular metabolism, and CYP53 can specific transform the substrates. In the study, we constructed the CYP53 homology model and analyzed the corresponding active region. At the same time, the molecular docking and the structure-based pharmacophore model (SBP) were performed to explore the bind mode of representative CYP53 inhibitors. On the basis, a series of phenylpyridines derivatives were designed as novel CYP53 inhibitors, and their molecular structures were synthesized and evaluated. Compared with the positive control groups, their antifungal activity showed the obvious upward trend. In particular, target compounds (13a, 15b) possessed the excellent biological activity against pathogenic fungi and drug-resistant fungi in vivo and in vitro. The preliminary action mechanism has confirmed that target compounds could inhibit CYP53 activity, and block the metabolism of toxic intermediates (Benzoates). This further induced the accumulation of reactive oxygen species (ROS) through the pattern of mitochondrial depolarization, which eventually caused fungal lysis and death. In summary, the study provided the reasonable computational models, and effectively guided the generation of novel CYP53 antifungal inhibitors.
Collapse
Affiliation(s)
- Bin Sun
- Institute of BioPharmaceutical Research, Liaocheng University, 1 Hunan Road, Liaocheng, 252000, PR China.
| | - Yating Liu
- Institute of BioPharmaceutical Research, Liaocheng University, 1 Hunan Road, Liaocheng, 252000, PR China
| | - Haiyan Fan
- Institute of BioPharmaceutical Research, Liaocheng University, 1 Hunan Road, Liaocheng, 252000, PR China
| | - Yunfei An
- Institute of BioPharmaceutical Research, Liaocheng University, 1 Hunan Road, Liaocheng, 252000, PR China
| | - Wenxia Liu
- Institute of BioPharmaceutical Research, Liaocheng University, 1 Hunan Road, Liaocheng, 252000, PR China
| | - Qingpeng Wang
- Institute of BioPharmaceutical Research, Liaocheng University, 1 Hunan Road, Liaocheng, 252000, PR China
| | - Jun Han
- Institute of BioPharmaceutical Research, Liaocheng University, 1 Hunan Road, Liaocheng, 252000, PR China
| |
Collapse
|
5
|
Li X, Zhang Q, Xu Z, Jiang G, Gan L, Tian Y, Shi B. High-expression and characterization of a novel serine protease from Ornithinibacillus caprae L9 T with eco-friendly applications. Environ Sci Pollut Res Int 2022; 29:35996-36012. [PMID: 35060042 DOI: 10.1007/s11356-021-17495-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/08/2021] [Indexed: 06/14/2023]
Abstract
In the current work, a novel thermophilic serine protease gene (P3862) from Ornithinibacillus caprae L9T was functionally expressed in Bacillus subtilis SCK6. The monomeric enzyme of about 29 kDa was purified to homogeneity with 43.91% of recovery and 2.81-folds of purification. Characterization of the purified protease revealed the optimum activity at pH 7 and 65 °C. The protease exhibited excellent activity and stability in the presence of Na+, Mg2+, Ca2+, ethanediol, n-hexane, Tween-20, Tween-80 and Triton X-100. P3862 displayed favorable caseinolytic activity, moderate keratinolytic activity but no collagenolytic activity. Besides, the homology model of P3862 possessed a globular configuration and characteristic of α/β hydrolase fold, and displayed stable interactions with casein, glycoprotein and keratin rather than collagen. Moreover, the crude enzyme could completely dehair goatskin within 6 h, resulting in decrease in BOD5, COD and TSS loads by 72.86, 74.07, and 73.79%, respectively, as compared with Na2S treatment. Biocatalytic applications revealed that it could effectively remove egg-stains from fabrics at 37 °C for 30 min with low supplementation (300 U/mL), and was able to degrade the feathers of duck and chicken. Overall, these outstanding properties make P3862 valuable in the development of environmentally friendly biotechnologies .
Collapse
Affiliation(s)
- Xiaoguang Li
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, People's Republic of China
| | - Qian Zhang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education and College of Life Sciences, Sichuan University, Chengdu, 610065, People's Republic of China
| | - Zhe Xu
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, People's Republic of China
| | - Guangyang Jiang
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, People's Republic of China
| | - Longzhan Gan
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, People's Republic of China
| | - Yongqiang Tian
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, People's Republic of China.
| | - Bi Shi
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, People's Republic of China.
| |
Collapse
|
6
|
Kelder J, Pang Y, Dong J, Schaftenaar G, Thomas P. Molecular modeling, mutational analysis and steroid specificity of the ligand binding pocket of mPRα (PAQR7): Shared ligand binding with AdipoR1 and its structural basis. J Steroid Biochem Mol Biol 2022; 219:106082. [PMID: 35189329 DOI: 10.1016/j.jsbmb.2022.106082] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 12/14/2022]
Abstract
The 7-transmembrane architecture of adiponectin receptors (AdipoRs), determined from their X-ray crystal structures, was used for homology modeling of another progesterone and adipoQ receptor (PAQR) family member, membrane progesterone receptor alpha (mPRα). The mPRα model identified excess positively charged residues on the cytosolic side, suggesting it has the same membrane orientation as AdipoRs with an intracellular N-terminus. The homology model showed identical amino acid residues to those forming the zinc binding pocket in AdipoRs, which strongly implies that zinc is also present in mPRα. The homology model showed a critical H-bond interaction between the glutamine (Q) residue at 206 in the binding pocket and the 20-carbonyl of progesterone. Mutational analysis showed no progesterone binding to the arginine (R) 206 mutant and modeling predicted this was due to the strong positive charge of arginine stabilizing the presence of an oleic acid (C18:1) molecule in the binding pocket, as observed in the X-rays of AdipoRs. High Zn2+ concentrations are predicted to form a salt with the carboxylate group of the oleic acid, thereby eliminating its binding to the free fatty acid (FFA) binding pocket, and allowing progesterone to bind. This is supported by experiments showing 100 µM Zn2+ addition restored [3H]-progesterone binding of the Q206R mutant to levels in WT mPRα and increased [3H]-progesterone binding to mPRγ and AdipoR1 which have arginine residues in this region. The model predicts hydrophobic interactions of progesterone with amino acid residues surrounding the binding pocket, including valine 146 in TM3, which when mutated into a polar serine resulted in a complete loss of [3H]-progesterone binding. The mPRα model showed there is no hydrogen bond donor in the vicinity of the 3-keto group of progesterone and ligand structure-activity studies with 3-deoxy steroids revealed that, unlike the nuclear progesterone receptor, the 3-carbonyl oxygen is not essential for binding to mPRα. Interestingly, the small synthetic AdipoR agonist, AdipoRon, displayed binding affinity for mPRα and mimicked progesterone signaling, whereas D-e-MAPP, a ceramidase inhibitor, blocked progesterone signaling. Thus, critical residues around the binding pocket and steroid structures that bind mPRα, as well as similarities with AdipoRs, can be predicted from the homology model.
Collapse
Affiliation(s)
- Jan Kelder
- Theoretical & Computational Chemistry, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Yefei Pang
- University of Texas at Austin Marine Science Institute, 750 Channel View Drive, Port Aransas, TX 78373, USA
| | - Jing Dong
- University of Texas at Austin Marine Science Institute, 750 Channel View Drive, Port Aransas, TX 78373, USA
| | - Gijs Schaftenaar
- Theoretical & Computational Chemistry, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Peter Thomas
- University of Texas at Austin Marine Science Institute, 750 Channel View Drive, Port Aransas, TX 78373, USA.
| |
Collapse
|
7
|
Dragojević J, Marakovic N, Popović M, Smital T. Zebrafish (Danio rerio) Oatp2b1 as a functional ortholog of the human OATP2B1 transporter. Fish Physiol Biochem 2021; 47:1837-1849. [PMID: 34546486 DOI: 10.1007/s10695-021-01015-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
OATP2B1 belongs to a highly conserved organic anion transporting polypeptide (OATP) family of transporters, involved in the cellular uptake of both endogenous and exogenous compounds. The reported substrates of human OATP2B1 include steroid conjugates, bile salts, and thyroid hormones, as well as pharmaceuticals. Human OATP2B1 has orthologous genes in other vertebrate species, including zebrafish (Danio rerio), a widely used model organism in biomedical and environmental research. Our previous studies showed that zebrafish Oatp2b1 was phylogenetically closest to mammalian OATP2B1/Oatp2b1 and that it shares a similar tissue expression pattern. In this study, we aimed at discovering whether zebrafish Oatp2b1 could be a functional ortholog of human and rodent OATP2B1. To test this hypothesis, our primary goal was to obtain the first in vitro and in silico insights related to the structure and potential substrate preferences of zebrafish Oatp2b1. We generated cells transiently and stably transfected with zebrafish Oatp2b1 cloned from zebrafish liver, constructed an Oatp2b1 homology model, developed transport activity assays with model fluorescent substrate Lucifer yellow, and finally utilized this assay to analyze the interaction of zebrafish Oatp2b1 with both physiological and xenobiotic substances. Apart from structure similarities, our data revealed the strongest interaction of zebrafish Oatp2b1 with bile acids, steroid sulfates, thyroid hormones, and bilirubin, as well as xenobiotics bromosulfophthalein and sulfasalazine, which indicates its functional orthology with human OATP2B1.
Collapse
Affiliation(s)
- Jelena Dragojević
- Laboratory for Molecular Ecotoxicology, Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia
| | - Nikola Marakovic
- Institute for Medical Research and Occupational Health, Ksaverska cesta 2, 10000, Zagreb, Croatia
| | - Marta Popović
- Laboratory for Molecular Ecotoxicology, Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia
| | - Tvrtko Smital
- Laboratory for Molecular Ecotoxicology, Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia.
| |
Collapse
|
8
|
Kaji MD, Noonan JD, Geary TG, Beech RN. Structural mechanism underlying the differential effects of ivermectin and moxidectin on the C. elegans glutamate-gated chloride channel GLC-2. Biomed Pharmacother 2022; 145:112380. [PMID: 34749053 DOI: 10.1016/j.biopha.2021.112380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/19/2021] [Accepted: 10/25/2021] [Indexed: 11/02/2022] Open
Abstract
BACKGROUND AND PURPOSE Nematode glutamate-gated chloride channels (GluCls) are targets of ivermectin (IVM) and moxidectin (MOX), structurally dissimilar macrocyclic lactone (ML) anthelmintics. IVM and MOX possess different pharmacokinetics and efficacy profiles but are thought to have the same binding site, through which they allosterically activate GluCls, apart from the GLC-2 receptor, which is antagonized by IVM. Our goal was to determine GLC-2 sensitivity to MOX, investigate residues involved in antagonism of GLC-2, and to identify differences in receptor-level pharmacology between IVM and MOX. EXPERIMENTAL APPROACH Two-electrode voltage clamp electrophysiology was used to study the pharmacology of Caenorhabditis elegans GLC-2 receptors heterologously expressed in Xenopus laevis oocytes. In silico homology modeling identified Cel-GLC-2 residues Met291 and Gln292 at the IVM binding site that differ from other GluCls; we mutated these residues to those found in ML-sensitive GluCls, and those of filarial nematode GLC-2. KEY RESULTS We discovered that MOX inhibits wild-type C. elegans GLC-2 receptors roughly 10-fold more potently than IVM, and with greater maximal inhibition of glutamate activation (MOX = 86.9 ± 2.5%; IVM = 57.8 ± 5.9%). IVM was converted into an agonist in the Met291Gln mutant, but MOX remained an antagonist. Glutamate responses were abrogated in a Met291Leu Gln292Thr double mutant (mimicking filarial nematode GLC-2), but MOX and IVM were converted into positive allosteric modulators of glutamate at this construct. CONCLUSIONS AND IMPLICATIONS Our data provides new insights into differences in receptor-level pharmacology between IVM and MOX and identify residues responsible for ML antagonism of GLC-2.
Collapse
|
9
|
Mirabile S, Vittorio S, Paola Germanò M, Adornato I, Ielo L, Rapisarda A, Gitto R, Pintus F, Fais A, De Luca L. Evaluation of 4-(4-Fluorobenzyl)piperazin-1-yl]-Based Compounds as Competitive Tyrosinase Inhibitors Endowed with Antimelanogenic Effects. ChemMedChem 2021; 16:3083-3093. [PMID: 34223697 PMCID: PMC8518915 DOI: 10.1002/cmdc.202100396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/02/2021] [Indexed: 11/11/2022]
Abstract
There is a considerable attention for the development of inhibitors of tyrosinase (TYR) as therapeutic strategy for the treatment of hyperpigmentation disorders in humans. Continuing in our efforts to identify TYR inhibitors, we describe the design, synthesis and pharmacophore exploration of new small molecules structurally characterized by the presence of the 4-fluorobenzylpiperazine moiety as key pharmacophoric feature for the inhibition of TYR from Agaricus bisporus (AbTYR). Our investigations resulted in the discovery of the competitive inhibitor [4-(4-fluorobenzyl)piperazin-1-yl]-(3-chloro-2-nitro-phenyl)methanone 26 (IC50 =0.18 μM) that proved to be ∼100-fold more active than reference compound kojic acid (IC50 =17.76 μM). Notably, compound 26 exerted antimelanogenic effect on B16F10 cells in absence of cytotoxicity. Docking analysis suggested its binding mode into AbTYR and into modelled human TYR.
Collapse
Affiliation(s)
- Salvatore Mirabile
- Department of ChemicalBiological, Pharmaceutical and Environmental SciencesUniversity of MessinaViale Palatucci 1398168MessinaItaly
| | - Serena Vittorio
- Department of ChemicalBiological, Pharmaceutical and Environmental SciencesUniversity of MessinaViale Palatucci 1398168MessinaItaly
| | - Maria Paola Germanò
- Department of ChemicalBiological, Pharmaceutical and Environmental SciencesUniversity of MessinaViale Palatucci 1398168MessinaItaly
| | - Ilenia Adornato
- Department of ChemicalBiological, Pharmaceutical and Environmental SciencesUniversity of MessinaViale Palatucci 1398168MessinaItaly
| | - Laura Ielo
- Department of ChemistryUniversity of TurinVia P. Giuria 710125TurinItaly
| | - Antonio Rapisarda
- Department of ChemicalBiological, Pharmaceutical and Environmental SciencesUniversity of MessinaViale Palatucci 1398168MessinaItaly
| | - Rosaria Gitto
- Department of ChemicalBiological, Pharmaceutical and Environmental SciencesUniversity of MessinaViale Palatucci 1398168MessinaItaly
| | - Francesca Pintus
- Department of Life and Environment SciencesUniversity of Cagliari09042MonserratoCagliariItaly
| | - Antonella Fais
- Department of Life and Environment SciencesUniversity of Cagliari09042MonserratoCagliariItaly
| | - Laura De Luca
- Department of ChemicalBiological, Pharmaceutical and Environmental SciencesUniversity of MessinaViale Palatucci 1398168MessinaItaly
| |
Collapse
|
10
|
Simov V, Altman MD, Bianchi E, DelRizzo S, DiNunzio EN, Feng G, Goldenblatt P, Ingenito R, Johnson SA, Mansueto MS, Mayhood T, Mortison JD, Serebrov V, Sondey C, Sriraman V, Tucker TJ, Walji A, Wan H, Yue Y, Stoeck A, DiMauro EF. Discovery and characterization of novel peptide inhibitors of the NRF2/MAFG/DNA ternary complex for the treatment of cancer. Eur J Med Chem 2021; 224:113686. [PMID: 34303079 DOI: 10.1016/j.ejmech.2021.113686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/03/2021] [Accepted: 07/03/2021] [Indexed: 11/16/2022]
Abstract
Pathway activating mutations of the transcription factor NRF2 and its negative regulator KEAP1 are strongly correlative with poor clinical outcome with pemetrexed/carbo(cis)platin/pembrolizumab (PCP) chemo-immunotherapy in lung cancer. Despite the strong genetic support and therapeutic potential for a NRF2 transcriptional inhibitor, currently there are no known direct inhibitors of the NRF2 protein or its complexes with MAF and/or DNA. Herein we describe the design of a novel and high-confidence homology model to guide a medicinal chemistry effort that resulted in the discovery of a series of peptides that demonstrate high affinity, selective binding to the Antioxidant Response Element (ARE) DNA and thereby displace NRF2-MAFG from its promoter, which is an inhibitory mechanism that to our knowledge has not been previously described. In addition to their activity in electrophoretic mobility shift (EMSA) and TR-FRET-based assays, we show significant dose-dependent ternary complex disruption of NRF2-MAFG binding to DNA by SPR, as well as cellular target engagement by thermal destabilization of HiBiT-tagged NRF2 in the NCI-H1944 NSCLC cell line upon digitonin permeabilization, and SAR studies leading to improved cellular stability. We report the characterization and unique profile of lead peptide 18, which we believe to be a useful in vitro tool to probe NRF2 biology in cancer cell lines and models, while also serving as an excellent starting point for additional in vivo optimization toward inhibition of NRF2-driven transcription to address a significant unmet medical need in non-small cell lung cancer (NSCLC).
Collapse
Affiliation(s)
- Vladimir Simov
- Merck & Co., Inc., Chemistry, 33 Avenue Louis Pasteur, Boston, MA 02127, USA.
| | - Michael D Altman
- Merck & Co., Inc., Chemistry, 33 Avenue Louis Pasteur, Boston, MA 02127, USA
| | - Elisabetta Bianchi
- Peptides and Small Molecules R&D, IRBM, Via Pontina, 30,600, 00071 Pomezia RM, Italy
| | - Sonia DelRizzo
- Peptides and Small Molecules R&D, IRBM, Via Pontina, 30,600, 00071 Pomezia RM, Italy
| | - Edward N DiNunzio
- Merck & Co., Inc., Chemistry, 2000 Galloping Hill Road, K-15, Kenilworth, NJ 07033, USA
| | - Guo Feng
- Merck & Co., Inc., Quantitative Biosciences, 33 Avenue Louis Pasteur, Boston, MA 02127, USA
| | - Peter Goldenblatt
- Merck & Co., Inc., Quantitative Biosciences, 33 Avenue Louis Pasteur, Boston, MA 02127, USA
| | - Raffaele Ingenito
- Peptides and Small Molecules R&D, IRBM, Via Pontina, 30,600, 00071 Pomezia RM, Italy
| | - Scott A Johnson
- Merck & Co., Inc., Chemistry, 33 Avenue Louis Pasteur, Boston, MA 02127, USA
| | - My Sam Mansueto
- Merck & Co., Inc., Quantitative Biosciences, 33 Avenue Louis Pasteur, Boston, MA 02127, USA
| | - Todd Mayhood
- Merck & Co., Inc., Chemistry, 2000 Galloping Hill Road, K-15, Kenilworth, NJ 07033, USA
| | - Jonathan D Mortison
- Merck & Co., Inc., Chemistry, 33 Avenue Louis Pasteur, Boston, MA 02127, USA
| | - Victor Serebrov
- Merck & Co., Inc., Quantitative Biosciences, 33 Avenue Louis Pasteur, Boston, MA 02127, USA
| | - Christopher Sondey
- Merck & Co., Inc., Quantitative Biosciences, 33 Avenue Louis Pasteur, Boston, MA 02127, USA
| | - Venkat Sriraman
- Merck & Co., Inc., Quantitative Biosciences, 33 Avenue Louis Pasteur, Boston, MA 02127, USA
| | - Thomas J Tucker
- Merck & Co., Inc., Chemistry, 770 Sumneytown Pike, West Point, PA 19486, USA
| | - Abbas Walji
- Merck & Co., Inc., Chemistry, 770 Sumneytown Pike, West Point, PA 19486, USA
| | - Hui Wan
- Merck & Co., Inc., PPDM, 126 East Lincoln Avenue, Rahway, NJ 07065, USA
| | - Yingzi Yue
- Merck & Co., Inc., Biology, 33 Avenue Louis Pasteur, Boston, MA 02127, USA
| | - Alexander Stoeck
- Merck & Co., Inc., Biology, 33 Avenue Louis Pasteur, Boston, MA 02127, USA
| | - Erin F DiMauro
- Merck & Co., Inc., Chemistry, 33 Avenue Louis Pasteur, Boston, MA 02127, USA
| |
Collapse
|
11
|
Kawabata H, Miyake R, Asada K, Dekishima Y, Miyaike M, Kato R. Asymmetric synthesis of intermediate for (1R,2S)-ethyl 1-amino-2-vinylcyclopropanecarboxylate by desymmetrization using engineered esterase from Bacillus subtilis. J Biosci Bioeng 2021; 131:599-604. [PMID: 33744099 DOI: 10.1016/j.jbiosc.2021.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/08/2021] [Accepted: 02/14/2021] [Indexed: 01/04/2023]
Abstract
(1R,2S)-Ethyl 1-amino-2-vinylcyclopropanecarboxylate (VCPA), is a key intermediate for anti-hepatitis C virus drugs. In this study, we developed an efficient manufacturing method of intermediate for (1R,2S)-VCPA by enzymatic desymmetrization of a malonate diester derivative. In synthesis scheme of VCPA (1S,2S)-1-(ethoxycarbonyl)-2-vinylcyclopropanecarboxylic acid (VCPME) is the monoester intermediate, which is converted from 2-vinylcyclopropane-1,1-dicarboxylate diethyl ester (VCPDE). As a result of esterase screening for producing (1S,2S)-VCPME from VCPDE by enzymatic desymmetrization, p-nitrobenzyl esterase from Bacillus subtilis NBRC3027 (PNBE3027) showed high enantioselectivity (more than 90% e.e.). Based on the homology model of PNBE3027, a library of mutants with the substitution of L70, L270, L273, and L313 in substrate-binding pocket was created for improvement in enantioselectivity. (1S,2S)-VCPME produced by the best variant harboring L70D, L270Q, L273R, and L313M showed 98.9% e.e. of enanthiopurity. Furthermore, preparative scale production of (1S,2S)-VCPME using the quadruple mutant was achieved. Our investigations present a new efficient process for (1R,2S)-VCPA using esterase and diverse to be applied for the industrial scale production.
Collapse
Affiliation(s)
- Hiroshi Kawabata
- Mitsubishi Chemical Corporation, Yokohama R&D Center, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-8502, Japan; API Corporation, 13-4 Uchikanda 1-chome, Chiyoda-ku, Tokyo 101-0047, Japan
| | - Ryoma Miyake
- Mitsubishi Chemical Corporation, Yokohama R&D Center, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-8502, Japan.
| | - Kuniko Asada
- Mitsubishi Chemical Corporation, Yokohama R&D Center, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-8502, Japan
| | - Yasumasa Dekishima
- Mitsubishi Chemical Corporation, Yokohama R&D Center, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-8502, Japan
| | - Mitsuko Miyaike
- Mitsubishi Chemical Corporation, Yokohama R&D Center, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-8502, Japan
| | - Ryohei Kato
- Mitsubishi Chemical Corporation, Yokohama R&D Center, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-8502, Japan
| |
Collapse
|
12
|
Khan A, Khan H, Faheem M, Zeb A, Badshah M, Chung YR. Isolation and Characterization of an Acidic, Salt-Tolerant Endoglucanase Cel5A from a Bacterial Strain Martelella endophytica YC6887 Genome. Mol Biotechnol 2021; 63:305-315. [PMID: 33523417 DOI: 10.1007/s12033-020-00295-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2020] [Indexed: 11/29/2022]
Abstract
A Martelella endophytica (M. endophytica) strain YC6887 was previously isolated from the roots of a halophyte, Rosa rugosa, which was sequenced and characterized. The genomic and proteomic analysis showed a carbohydrate-degrading enzyme, endoglucanase Cel5A which was further characterized. The protein analysis revealed that this endoglucanase belongs to glycosidic hydrolase family 5 (GH5) with catalytic domain. This gene encodes 349-residue polypeptide and shows closest similarity with cellulases of other Martelella species. The protein was purified to homogeneity and shown that it was a 39 kDa protein. The purified recombinant Cel5A endoglucanase exhibited maximum activity at 50 °C and pH 4.5. The enzyme was salt tolerant and retained more than 50% residual activity up to 15% NaCl. The homology model structure of Cel5A displayed that it is stable and compact protein structure consisting of eleven α-helical structures and eight β-sheets. According to the predicted ligand binding site after superimposition with Pseudomonas stutzeri endoglucanase Cel5A (PDB ID: 4LX4), it consisted of five amino acid Asn157, Tyr116, Glu158, Glu270 and Trp303 that may be the expected active site of Cel5A from YC6887. This presented that our strain M. endophytica YC6887 that produces cellulase partially degrade the insoluble polysaccharides into reducing sugars.
Collapse
Affiliation(s)
- Ajmal Khan
- Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Centre, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea. .,Department of Biotechnology, Bacha Khan University, Charsada, KPK, Pakistan.
| | - Haji Khan
- Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Centre, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea.,Centre for Biotechnology and Microbiology, University of Swat, Swat, KPK, 19200, Pakistan
| | - Muhammad Faheem
- Department of Biological Sciences, National University of Medical Sciences, The Mall, Rawalpindi, 46000, Pakistan
| | - Amir Zeb
- Division of Life Science, Division of Applied Life Sciences (BK21 Plus), Research Institute of Natural Sciences, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Malik Badshah
- Sustainable Bioenergy and Biorefinery Laboratory, Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Young Ryun Chung
- Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Centre, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
| |
Collapse
|
13
|
Qi Z, Xu Y, Wang X, Jiang J, Meng F, Zhang Q, Huang B. Structural analysis of toll-like receptor 18 from soiny mullet (Liza haematocheila): Giving insights on the ligand binding mechanism of fish specific TLRs. Fish Shellfish Immunol 2020; 107:490-496. [PMID: 33098989 DOI: 10.1016/j.fsi.2020.10.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 06/11/2023]
Abstract
Toll-like receptors (TLRs) are important pattern recognition receptors (PRRs) of innate immune system, playing crucial roles in immune defense against pathogens. TLR18, a member of TLR1 family, is fish-specific TLR and involves in the immune response against bacterial infection. Currently, the structural biology of fish TLR18 is poorly elaborated. In this study, the structure and ligand binding of TLR18 (smTLR18) of soiny mullet (Liza haematocheila), an economically valuable aquaculture mugilid species, were analyzed. The extracellular domain (ECD) of smTLR18 formed an open-loop horseshoe-shaped structure with the concave surfaces made up of 19 parallel β-strands (LRR1-LRR19), lacking Z-loop that seen in human TLR9. The intracellular Toll/interleukin (IL)-1 (TIR) domain contained a central 4-parallel β-sheet (βA-βD) surrounded by 5 α-helices (αA-αE). Molecular docking analysis revealed that both ECD domain and TIR domain of smTLR18 could form homodimers. For the ECD homodimer, the main residues involved in dimer formation were located from LRR10 to LRR14. For the TIR homodimer, the residues involved in dimer formation were located in BB loop, αB helix, αC helix and DD loop. Ligand binding analyses revealed that peptidoglycans (PGNs) and lipopolysaccharides (LPS), two main bacterial pathogen-associated molecular patterns (PAMPs), were the potential ligands of smTLR18. The van der Waals and Coulombic interactions contributed to the interactions between smTLR18 and PGNs, while only van der Waals dominated the interactions between smTLR18 and LPS. The residues involved in ligands binding were located from LRR9 to LRR13. Our results provided the structural bases for elucidate the ligand binding of fish TLR18.
Collapse
Affiliation(s)
- Zhitao Qi
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, Yancheng Institute of Technology, Yancheng, Jiangsu Province, 224051, China.
| | - Yang Xu
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, Yancheng Institute of Technology, Yancheng, Jiangsu Province, 224051, China
| | - Xin Wang
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, Yancheng Institute of Technology, Yancheng, Jiangsu Province, 224051, China
| | - Junyao Jiang
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, 999077, China
| | - Fancui Meng
- Tianjin Institute of Pharmaceutical Research, Tianjin, 300193, China
| | - Qihuan Zhang
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, Yancheng Institute of Technology, Yancheng, Jiangsu Province, 224051, China
| | - Bei Huang
- Fisheries College, Jimei University, Xiamen, Fujian Province, 361021, China.
| |
Collapse
|
14
|
Comoletti D, Trobiani L, Chatonnet A, Bourne Y, Marchot P. Comparative mapping of selected structural determinants on the extracellular domains of cholinesterase-like cell-adhesion molecules. Neuropharmacology 2020; 184:108381. [PMID: 33166544 DOI: 10.1016/j.neuropharm.2020.108381] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/10/2020] [Accepted: 10/29/2020] [Indexed: 11/18/2022]
Abstract
Cell adhesion generally involves formation of homophilic or heterophilic protein complexes between two cells to form transcellular junctions. Neural cell-adhesion members of the α/β-hydrolase fold superfamily of proteins use their extracellular or soluble cholinesterase-like domain to bind cognate partners across cell membranes, as illustrated by the neuroligins. These cell-adhesion molecules currently comprise the synaptic organizers neuroligins found in all animal phyla, along with three proteins found only in invertebrates: the guidance molecule neurotactin, the glia-specific gliotactin, and the basement membrane protein glutactin. Although these proteins share a cholinesterase-like fold, they lack one or more residues composing the catalytic triad responsible for the enzymatic activity of the cholinesterases. Conversely, they are found in various subcellular localisations and display specific disulfide bonding and N-glycosylation patterns, along with individual surface determinants possibly associated with recognition and binding of protein partners. Formation of non-covalent dimers typical of the cholinesterases is documented for mammalian neuroligins, yet whether invertebrate neuroligins and their neurotactin, gliotactin and glutactin relatives also form dimers in physiological conditions is unknown. Here we provide a brief overview of the localization, function, evolution, and conserved versus individual structural determinants of these cholinesterase-like cell-adhesion proteins. This article is part of the special issue entitled 'Acetylcholinesterase Inhibitors: From Bench to Bedside to Battlefield'.
Collapse
Affiliation(s)
- Davide Comoletti
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6012, New Zealand; Child Health Institute of New Jersey, New Brunswick, NJ 08901, USA; Department of Neuroscience and Cell Biology Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA.
| | - Laura Trobiani
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6012, New Zealand
| | - Arnaud Chatonnet
- Lab 'Dynamique Musculaire et Métabolisme', Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE) / Université Montpellier, Montpellier, France
| | - Yves Bourne
- Lab 'Architecture et Fonction des Macromolécules Biologiques (AFMB)', Centre National de la Recherche Scientifique (CNRS)/Aix-Marseille Univ, Faculté des Sciences - Campus Luminy, Marseille, France
| | - Pascale Marchot
- Lab 'Architecture et Fonction des Macromolécules Biologiques (AFMB)', Centre National de la Recherche Scientifique (CNRS)/Aix-Marseille Univ, Faculté des Sciences - Campus Luminy, Marseille, France.
| |
Collapse
|
15
|
Bazin MA, Cojean S, Pagniez F, Bernadat G, Cavé C, Ourliac-Garnier I, Nourrisson MR, Morgado C, Picot C, Leclercq O, Baratte B, Robert T, Späth GF, Rachidi N, Bach S, Loiseau PM, Le Pape P, Marchand P. In vitro identification of imidazo[1,2-a]pyrazine-based antileishmanial agents and evaluation of L. major casein kinase 1 inhibition. Eur J Med Chem 2020; 210:112956. [PMID: 33148491 DOI: 10.1016/j.ejmech.2020.112956] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/19/2020] [Accepted: 10/19/2020] [Indexed: 12/15/2022]
Abstract
Leishmaniasis constitutes a severe public health problem, with an estimated prevalence of 12 million cases. This potentially fatal disease has a worldwide distribution and in 2012, the fatal Visceral Leishmaniasis (VL) was declared as new emerging disease in Europe, mainly due to global warming, with expected important public health impact. The available treatments are toxic, costly or lead to parasite resistance, thus there is an urgent need for new drugs with new mechanism of action. Previously, we reported the discovery of CTN1122, a potent imidazo[1,2-a]pyrazine-based antileishmanial hit compound targeting L-CK1.2 at low micromolar ranges. Here, we described structurally related, safe and selective compounds endowed with antiparasitic properties, better than miltefosine, the reference therapy by oral route. L-CK1.2 homology model gave the first structural explanations of the role of 4-pyridyl (CTN1122) and 2-aminopyrimidin-4-yl (compound 21) moieties, at the position 3 of the central core, in the low micromolar to nanomolar L-CK1.2 inhibition, whereas N-methylpyrazole derivative 11 remained inactive against the parasite kinase.
Collapse
Affiliation(s)
- Marc-Antoine Bazin
- Université de Nantes, Cibles et Médicaments des Infections et du Cancer, IICiMed, EA 1155, F-44000, Nantes, France
| | - Sandrine Cojean
- BioCIS Biomolécules: Conception, Isolement, Synthèse, Chimiothérapie Antiparasitaire, UMR CNRS 8076, Univ. Paris-Sud, Université Paris-Saclay, Faculté de Pharmacie, F-92296, Châtenay-Malabry, France
| | - Fabrice Pagniez
- Université de Nantes, Cibles et Médicaments des Infections et du Cancer, IICiMed, EA 1155, F-44000, Nantes, France
| | - Guillaume Bernadat
- BioCIS Biomolécules: Conception, Isolement, Synthèse, Chimiothérapie Antiparasitaire, UMR CNRS 8076, Univ. Paris-Sud, Université Paris-Saclay, Faculté de Pharmacie, F-92296, Châtenay-Malabry, France
| | - Christian Cavé
- BioCIS Biomolécules: Conception, Isolement, Synthèse, Chimiothérapie Antiparasitaire, UMR CNRS 8076, Univ. Paris-Sud, Université Paris-Saclay, Faculté de Pharmacie, F-92296, Châtenay-Malabry, France
| | - Isabelle Ourliac-Garnier
- Université de Nantes, Cibles et Médicaments des Infections et du Cancer, IICiMed, EA 1155, F-44000, Nantes, France
| | - Marie-Renée Nourrisson
- Université de Nantes, Cibles et Médicaments des Infections et du Cancer, IICiMed, EA 1155, F-44000, Nantes, France
| | - Cathy Morgado
- Université de Nantes, Cibles et Médicaments des Infections et du Cancer, IICiMed, EA 1155, F-44000, Nantes, France
| | - Carine Picot
- Université de Nantes, Cibles et Médicaments des Infections et du Cancer, IICiMed, EA 1155, F-44000, Nantes, France
| | - Olivier Leclercq
- Institut Pasteur and Institut National de Santé et Recherche Médicale INSERM U1201, Unité de Parasitologie Moléculaire et Signalisation, F-75015, Paris, France
| | - Blandine Baratte
- Sorbonne Université, CNRS, UMR8227, Integrative Biology of Marine Models Laboratory (LBI2M), Station Biologique de Roscoff, F-29680, Roscoff, France; Sorbonne Université, CNRS, FR2424, Kinase Inhibitor Specialized Screening Facility - KISSf, Station Biologique, F-29680, Roscoff, France
| | - Thomas Robert
- Sorbonne Université, CNRS, UMR8227, Integrative Biology of Marine Models Laboratory (LBI2M), Station Biologique de Roscoff, F-29680, Roscoff, France; Sorbonne Université, CNRS, FR2424, Kinase Inhibitor Specialized Screening Facility - KISSf, Station Biologique, F-29680, Roscoff, France
| | - Gérald F Späth
- Institut Pasteur and Institut National de Santé et Recherche Médicale INSERM U1201, Unité de Parasitologie Moléculaire et Signalisation, F-75015, Paris, France
| | - Najma Rachidi
- Institut Pasteur and Institut National de Santé et Recherche Médicale INSERM U1201, Unité de Parasitologie Moléculaire et Signalisation, F-75015, Paris, France
| | - Stéphane Bach
- Sorbonne Université, CNRS, UMR8227, Integrative Biology of Marine Models Laboratory (LBI2M), Station Biologique de Roscoff, F-29680, Roscoff, France; Sorbonne Université, CNRS, FR2424, Kinase Inhibitor Specialized Screening Facility - KISSf, Station Biologique, F-29680, Roscoff, France
| | - Philippe M Loiseau
- BioCIS Biomolécules: Conception, Isolement, Synthèse, Chimiothérapie Antiparasitaire, UMR CNRS 8076, Univ. Paris-Sud, Université Paris-Saclay, Faculté de Pharmacie, F-92296, Châtenay-Malabry, France
| | - Patrice Le Pape
- Université de Nantes, Cibles et Médicaments des Infections et du Cancer, IICiMed, EA 1155, F-44000, Nantes, France
| | - Pascal Marchand
- Université de Nantes, Cibles et Médicaments des Infections et du Cancer, IICiMed, EA 1155, F-44000, Nantes, France.
| |
Collapse
|
16
|
Banerjee S, Garrigues RJ, Chanakira MN, Negron-Olivo JJ, Odeh YH, Spuches AM, Martin Roop R, Pitzer JE, Martin DW, Dasgupta S. Investigating the roles of the conserved Cu 2+-binding residues on Brucella FtrA in producing conformational stability and functionality. J Inorg Biochem 2020; 210:111162. [PMID: 32623149 PMCID: PMC7484176 DOI: 10.1016/j.jinorgbio.2020.111162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 06/07/2020] [Accepted: 06/11/2020] [Indexed: 11/17/2022]
Abstract
Brucella is a zoonotic pathogen requiring iron for its survival and acquires this metal through the expression of several high-affinity uptake systems. Of these, the newly discovered ferrous iron transporter, FtrABCD, is proposed to take part in ferrous iron uptake. Sequence homology shows that, FtrA, the proposed periplasmic ferrous-binding component, is a P19-type protein (a periplasmic protein from C. jejuni which shows Cu2+ dependent iron affinity). Previous structural and biochemical studies on other P19 systems have established a Cu2+ dependent Mn2+ affinity as well as formation of homodimers for these systems. The Cu2+ coordinating amino acids from these proteins are conserved in Brucella FtrA, hinting towards similar properties. However, there has been no experimental evidence, till date, establishing metal affinities and the possibility of dimer formation by Brucella FtrA. Using wild-type FtrA and Cu2+-binding mutants (H65A, E67A, H118A, and H151A) we investigated the metal affinities, folding stabilities, dimer forming abilities, and the molecular basis of the Cu2+ dependence for this P19-type protein employing homology modeling, analytical gel filtration, calorimetric, and spectroscopic methods. The data reported here confirm a Cu2+-dependent, low-μM Mn2+ (Fe2+ mimic) affinity for the wild-type FtrA. In addition, our data clearly show the loss of Mn2+ affinity, and the formation of less stable protein conformations as a result of mutating these conserved Cu2+-binding residues, indicating the important roles these residues play in producing a native and functional fold of Brucella FtrA.
Collapse
Affiliation(s)
- Sambuddha Banerjee
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA.
| | - Ryan J Garrigues
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA
| | - Mina N Chanakira
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
| | | | - Yasmene H Odeh
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
| | - Anne M Spuches
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
| | - R Martin Roop
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA
| | - Joshua Edison Pitzer
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA
| | - Daniel W Martin
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA
| | - Saumya Dasgupta
- Department of Chemistry, Amity Institute of Applied Sciences, Amity University Kolkata, WB, 700135, India
| |
Collapse
|
17
|
Liu X, Wilson MW, Liu K, Lee P, Yeomans L, Hagen SE, Lin CM, Wen B, Sun D, White AD, Showalter HD, Antonetti DA. Synthesis and structure-activity relationships of thieno[2,3-d]pyrimidines as atypical protein kinase C inhibitors to control retinal vascular permeability and cytokine-induced edema. Bioorg Med Chem 2020; 28:115480. [PMID: 32327351 DOI: 10.1016/j.bmc.2020.115480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 03/25/2020] [Accepted: 03/27/2020] [Indexed: 11/28/2022]
Abstract
Studies demonstrate that small molecule targeting of atypical protein kinase C (aPKC) may provide an effective means to control vascular permeability, prevent edema, and reduce inflammation providing novel and important alternatives to anti-VEGF therapies for certain blinding eye diseases. Based on a literature tricyclic thieno[2,3-d]pyrimidine lead (1), an ATP-competitive inhibitor of the aPKC iota (ι) and aPKC zeta (ζ) isoforms, we have synthesized a small series of compounds in 1-2 steps from a readily available chloro intermediate. A single pyridine congener was also made using 2D NMR to assign regiochemistry. Within the parent pyrimidine series, a range of potencies was observed against aPKCζ whereas the pyridine congener was inactive. Selected compounds were also tested for their effect toward VEGF-induced permeability in BREC cells. The most potent of these (7l) was further assayed against the aPKCι isoform and showed a favorable selectivity profile against a panel of 31 kinases, including kinases from the AGC superfamily, with a focus on PKC isoforms and kinases previously shown to affect permeability. Further testing of 7l in a luciferase assay in HEK293 cells showed an ability to prevent TNF-α induced NFκB activation while not having any effect on cell survival. Intravitreal administration of 7l to the eye yielded a complete reduction in permeability in a test to determine whether the compound could block VEGF- and TNFα-induced permeability across the retinal vasculature in a rat model. The compound in mice displayed good microsomal stability and in plasma moderate exposure (AUC and Cmax), low clearance, a long half-life and high oral bioavailability. With IV dosing, higher levels were observed in the brain and eye relative to plasma, with highest levels in the eye by either IV or PO dosing. With a slow oral absorption profile, 7l accumulates in the eye to maintain a high concentration after dosing with higher levels than in plasma. Compound 7l may represent a class of aPKC inhibitors for further investigation.
Collapse
Affiliation(s)
- Xuwen Liu
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105, USA
| | - Michael W Wilson
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Vahlteich Medicinal Chemistry Core, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kun Liu
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Vahlteich Medicinal Chemistry Core, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pil Lee
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Vahlteich Medicinal Chemistry Core, University of Michigan, Ann Arbor, MI 48109, USA
| | - Larisa Yeomans
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Susan E Hagen
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Vahlteich Medicinal Chemistry Core, University of Michigan, Ann Arbor, MI 48109, USA
| | - Cheng-Mao Lin
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105, USA
| | - Bo Wen
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Duxin Sun
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andrew D White
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Vahlteich Medicinal Chemistry Core, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hollis D Showalter
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - David A Antonetti
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105, USA; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA.
| |
Collapse
|
18
|
Abelak KK, Bishop-Bailey D, Nobeli I. Molecular dynamics simulations of the interaction of wild type and mutant human CYP2J2 with polyunsaturated fatty acids. BMC Res Notes 2019; 12:760. [PMID: 31753010 PMCID: PMC6873649 DOI: 10.1186/s13104-019-4797-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 11/11/2019] [Indexed: 01/20/2023] Open
Abstract
OBJECTIVES The data presented here is part of a study that was aimed at characterizing the molecular mechanisms of polyunsaturated fatty acid metabolism by CYP2J2, the main cytochrome P450 enzyme active in the human cardiovasculature. This part comprises the molecular dynamics simulations of the binding of three eicosanoid substrates to wild type and mutant forms of the enzyme. These simulations were carried out with the aim of dissecting the importance of individual residues in the active site and the roles they might play in dictating the binding and catalytic specificity exhibited by CYP2J2. DATA DESCRIPTION The data comprise: (a) a new homology model of CYP2J2, (b) a number of predicted low-energy complexes of CYP2J2 with arachidonic acid, docosahexaenoic acid and eicosapentaenoic acid, produced with molecular docking and (c) a series of molecular dynamics simulations of the wild type and four mutants interacting with arachidonic acid as well as simulations of the wild type interacting with the two other eicosanoid ligands. The simulations may be helpful in identifying the determinants of substrate specificity of this enzyme and in unraveling the role of individual mutations on its function. They may also help guide the generation of mutants with altered substrate preferences.
Collapse
Affiliation(s)
- K. K. Abelak
- Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, London, NW1 0TU UK
| | - D. Bishop-Bailey
- Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, London, NW1 0TU UK
| | - I. Nobeli
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, Malet Street, London, WC1E 7HX UK
| |
Collapse
|
19
|
Katrolia P, Liu X, Zhao Y, Kopparapu NK, Zheng X. Gene cloning, expression and homology modeling of first fibrinolytic enzyme from mushroom (Cordyceps militaris). Int J Biol Macromol 2020; 146:897-906. [PMID: 31726136 DOI: 10.1016/j.ijbiomac.2019.09.212] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 09/09/2019] [Accepted: 09/21/2019] [Indexed: 01/12/2023]
Abstract
Fibrinolytic enzymes are important thrombolytic agents for blood-clotting disorders like cardiovascular diseases. Availability of novel recombinant fibrinolytic enzymes can overcome the shortcomings of current thrombolytic drugs. With the objective of facilitating their cost-effective production for therapeutic applications and for gaining deeper insight into their structure-function, we have cloned and expressed the first fibrinolytic protease gene from Cordyceps militaris. Cordyceps militaris fibrinolytic enzyme (CmFE) has one open reading frame of 759 bp encoding "pre-pro-protein" of 252 amino acids. Recombinant CmFE was expressed as 28 kDa extracellular enzyme in Pichia pastoris which was capable of degrading fibrin clot. A structure homology model of CmFE was developed using urokinase-type plasminogen activator. The active site contains catalytic triad His41, Asp83, Ser177 and consensus sequence of GDSGG. The substrate binding residues are Asp (171), Gly (194) and Ser (192). Its trypsin-like specificity is determined by the critical Asp171 in S1 subsite. The "oxyanion hole" is formed by backbone amide hydrogen atoms of Gly-175 and Ser-177. CmFE contains six conserved cysteines forming three disulfide linkages. This is the first study describing cloning, expression and prediction of structure-function relationship of a mushroom fibrinolytic protease. Hence it has great relevance in application of fibrinolytic enzymes as thrombolytic agents.
Collapse
|
20
|
Anzai T, Matsumura Y. Topological analysis of TMEM180, a newly identified membrane protein that is highly expressed in colorectal cancer cells. Biochem Biophys Res Commun 2019; 520:566-572. [PMID: 31615651 DOI: 10.1016/j.bbrc.2019.10.070] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 10/07/2019] [Indexed: 01/08/2023]
Abstract
New target molecules for diagnosis of and drug development for colorectal cancer (CRC) are always in great demand. Previously, we identified a new colorectal cancer-specific protein, TMEM180, and successfully developed an anti-TMEM180 monoclonal antibody (mAb) for the diagnosis and treatment of CRC. Although TMEM180 is classified as a member of the cation symporter family and multi-pass membrane protein, little is known about its function. In this study, we examined topology of this membrane protein and analyzed its function. Using a homology model of human TMEM180, we experimentally determined that the protein has 12 transmembrane domains, and that its N-terminal and C-termini are exposed extracellularly. Moreover, we found that the putative cation-binding site of TMEM180 is conserved among orthologs, and that its position is similar to that of melibiose transporter MelB. These results suggest that TMEM180 acts as a cation symporter. Our topological analysis based on the homology model provides insight into functional and structural roles of TMEM180 that may help to elucidate the pathology of CRC.
Collapse
Affiliation(s)
- Takahiro Anzai
- Division of Developmental Therapeutics, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, 6-5-1, Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan; Department of Integrated Bioscience, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Yasuhiro Matsumura
- Division of Developmental Therapeutics, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, 6-5-1, Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan; Department of Integrated Bioscience, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan.
| |
Collapse
|
21
|
Holt MC, Ho CS, Morano MI, Barrett SD, Stein AJ. Improved homology modeling of the human & rat EP 4 prostanoid receptors. BMC Mol Cell Biol 2019; 20:37. [PMID: 31455205 PMCID: PMC6712885 DOI: 10.1186/s12860-019-0212-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 07/11/2019] [Indexed: 12/02/2022] Open
Abstract
Background The EP4 prostanoid receptor is one of four GPCRs that mediate the diverse actions of prostaglandin E2 (PGE2). Novel selective EP4 receptor agonists would assist to further elucidate receptor sub-type function and promote development of therapeutics for bone healing, heart failure, and other receptor associated conditions. The rat EP4 (rEP4) receptor has been used as a surrogate for the human EP4 (hEP4) receptor in multiple SAR studies. To better understand the validity of this traditional approach, homology models were generated by threading for both receptors using the RaptorX server. These models were fit to an implicit membrane using the PPM server and OPM database with refinement of intra and extracellular loops by Prime (Schrödinger). To understand the interaction between the receptors and known agonists, induced-fit docking experiments were performed using Glide and Prime (Schrödinger), with both endogenous agonists and receptor sub-type selective, small-molecule agonists. The docking scores and observed interactions were compared with radioligand displacement experiments and receptor (rat & human) activation assays monitoring cAMP. Results Rank-ordering of in silico compound docking scores aligned well with in vitro activity assay EC50 and radioligand binding Ki. We observed variations between rat and human EP4 binding pockets that have implications in future small-molecule receptor-modulator design and SAR, specifically a S103G mutation within the rEP4 receptor. Additionally, these models helped identify key interactions between the EP4 receptor and ligands including PGE2 and several known sub-type selective agonists while serving as a marked improvement over the previously reported models. Conclusions This work has generated a set of novel homology models of the rEP4 and hEP4 receptors. The homology models provide an improvement upon the previously reported model, largely due to improved solvation. The hEP4 docking scores correlates best with the cAMP activation data, where both data sets rank order Rivenprost>CAY10684 > PGE1 ≈ PGE2 > 11-deoxy-PGE1 ≈ 11-dexoy-PGE2 > 8-aza-11-deoxy-PGE1. This rank-ordering matches closely with the rEP4 receptor as well. Species-specific differences were noted for the weak agonists Sulprostone and Misoprostol, which appear to dock more readily within human receptor versus rat receptor. Electronic supplementary material The online version of this article (10.1186/s12860-019-0212-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Melissa C Holt
- Cayman Chemical Co, 1180 E. Ellsworth Rd, Ann Arbor, MI, 48108, USA
| | - Chi S Ho
- Cayman Chemical Co, 1180 E. Ellsworth Rd, Ann Arbor, MI, 48108, USA
| | - M Inés Morano
- Cayman Chemical Co, 1180 E. Ellsworth Rd, Ann Arbor, MI, 48108, USA
| | | | - Adam J Stein
- Cayman Chemical Co, 1180 E. Ellsworth Rd, Ann Arbor, MI, 48108, USA.
| |
Collapse
|
22
|
Bandyopadhyay AK, Islam RNU, Mitra D, Banerjee S, Yasmeen S, Goswami A. Insights from the salt bridge analysis of malate dehydrogenase from H. salinarum and E.coli. Bioinformation 2019; 15:95-103. [PMID: 31435155 PMCID: PMC6677910 DOI: 10.6026/97320630015095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/11/2019] [Accepted: 02/11/2019] [Indexed: 11/23/2022] Open
Abstract
Halophilic proteins have greater abundance of acidic over basic residues in sequence. In structure, the surface is decorated by negative
charges, with lower content of Lysine. Using sequence BLOCKs and 3D model of malate dehydrogenase from halophilic archaea
(Halobacterium salinarum; hsMDH) and X-ray structure from mesophilic bacteria (E. coli; ecMDH), we show that not only acidic and basic
residues have higher mean relative abundance (MRA) and thus, impart higher polarity to the sequences, but also show their presence in
the surface of the structure of hsMDH relative to its mesophilic counterpart. These observations may indicate that both the acidic and the
basic residues have a concerted role in the stability of hsMDH. Analysis on salt bridges from hsMDH and ecMDH show that in the former,
salt bridges are highly intricate, newly engineered and global in nature. Although, these salt bridges are abundant in hsMDH, in the active
site the design remains unperturbed. In high salt where hydrophobic force is weak, these salt bridges seem to play a major role in the
haloadaptation of the tertiary structure of hsMDH. This is the first report of such an observation.
Collapse
Affiliation(s)
| | | | - Debanjan Mitra
- Department of Biotechnology,The University of Burdwan,Burdwan, West Bengal,India
| | - Sahini Banerjee
- Department of Biological Sciences,ISI,Kolkata,West Bengal,India
| | - Saba Yasmeen
- Department of Botany and Microbiology,Acharya Nagarjun University,Nagarjun Nagar,Andra Pradesh,India
| | - Arunava Goswami
- Department of Biological Sciences,ISI,Kolkata,West Bengal,India
| |
Collapse
|
23
|
El-Gamal MI, Ullah S, Zaraei SO, Jalil S, Zaib S, Zaher DM, Omar HA, Anbar HS, Pelletier J, Sévigny J, Iqbal J. Synthesis, biological evaluation, and docking studies of new raloxifene sulfonate or sulfamate derivatives as inhibitors of nucleotide pyrophosphatase/phosphodiesterase. Eur J Med Chem 2019; 181:111560. [PMID: 31382118 DOI: 10.1016/j.ejmech.2019.07.063] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/11/2019] [Accepted: 07/22/2019] [Indexed: 12/21/2022]
Abstract
A new series of raloxifene sulfonate/sulfamate derivatives were designed and synthesized. The target compounds were tested for inhibitory effect against nucleotide pyrophosphatase/phosphodiesterase-1 and -3 (NPP1 and NPP3) enzymes. Furthermore, all the ten target compounds were subjected to cytotoxic studies on various cancer cell lines, and the most potent derivatives were explored for their potency against these cancer cell lines as well as F180 fibroblasts to investigate the selectivity indexes. Compound 1f exerted the highest potency against HT-29 colon cancer cell line (IC50 = 1.4 μM) with 8.43-fold selectivity towards HT-29 than F180 fibroblasts. Compound 1f exerted sub-micromolar IC50 values against NPP1 and NPP3 (IC50 = 0.29 μM and 0.71 μM, respectively). The most potent inhibitors were docked in developed homology model of NPP1 and crystal structure of NPP3. All the docked analogues manifested remarkable interactions within the active pocket of NPP1 and NPP3.
Collapse
Affiliation(s)
- Mohammed I El-Gamal
- College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates; Faculty of Pharmacy, University of Mansoura, Mansoura, 35516, Egypt.
| | - Saif Ullah
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan
| | - Seyed-Omar Zaraei
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Saquib Jalil
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan
| | - Sumera Zaib
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan
| | - Dana M Zaher
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Hany A Omar
- College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates; Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt
| | - Hanan S Anbar
- Faculty of Pharmacy, University of Mansoura, Mansoura, 35516, Egypt
| | - Julie Pelletier
- Centre de Recherche du CHU de Québec - Université Laval, Québec, QC, G1V 4G2, Canada
| | - Jean Sévigny
- Centre de Recherche du CHU de Québec - Université Laval, Québec, QC, G1V 4G2, Canada; Département de microbiologie-infectiologie et d'immunologie, Faculté de Médecine, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Jamshed Iqbal
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan.
| |
Collapse
|
24
|
Banerjee S, Roy A, Madhusudhan MS, Bairagya HR, Roy A. Structural insights of a cellobiose dehydrogenase enzyme from the basidiomycetes fungus Termitomyces clypeatus. Comput Biol Chem 2019; 82:65-73. [PMID: 31272063 DOI: 10.1016/j.compbiolchem.2019.05.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 02/18/2019] [Accepted: 05/28/2019] [Indexed: 02/03/2023]
Abstract
Filamentous fungi secrete various oxidative enzymes to degrade the glycosidic bonds of polysaccharides. Cellobiose dehydrogenase (CDH) (E.C.1.1.99.18) is one of the important lignocellulose degrading enzymes produced by various filamentous fungi. It contains two stereo specific ligand binding domains, cytochrome and dehydrogenase - one for heme and the other for flavin adenine dinucleotide (FAD) respectively. The enzyme is of commercial importance for its use in amperometric biosensor, biofuel production, lactose determination in food, bioremediation etc. Termitomyces clypeatus, an edible fungus belonging to the basidiomycetes group, is a good producer of CDH. In this paper we have analyzed the structural properties of this enzyme from T. clypeatus and identified a distinct carbohydrate binding module (CBM) which is not present in most fungi belonging to the basidiomycetes group. In addition, the dehydrogenase domain of T. clypeatus CDH exhibited the absence of cellulose binding residues which is in contrast to the dehydrogenase domains of CDH of other basidiomycetes. Sequence analysis of cytochrome domain showed that the important residues of this domain were conserved like in other fungal CDHs. Phylogenetic tree, constructed using basidiomycetes and ascomycetes CDH sequences, has shown that very surprisingly the CDH from T. clypeatus, which is classified as a basidiomycetes fungus, is clustered with the ascomycetes group. A homology model of this protein has been constructed using the CDH enzyme of ascomycetes fungus Myricoccum thermophilum as a template since it has been found to be the best match sequence with T. clypeatus CDH. We also have modelled the protein with its substrate, cellobiose, which has helped us to identify the substrate interacting residues (L354, P606, T629, R631, Y649, N732, H733 and N781) localized within its dehydrogenase domain. Our computational investigation revealed for the first time the presence of all three domains - cytochrome, dehydrogenase and CBM - in the CDH of T. clypeatus, a basidiomycetes fungus. In addition to discovering the unique structural attributes of this enzyme from T. clypeatus, our study also discusses the possible phylogenetic status of this fungus.
Collapse
|
25
|
Sherin DR, Geethu CK, Prabhakaran J, Mann JJ, Dileep Kumar JS, Manojkumar TK. Molecular docking, dynamics simulations and 3D-QSAR modeling of arylpiperazine derivatives of 3,5-dioxo-(2H,4H)-1,2,4-triazine as 5-HT 1AR agonists. Comput Biol Chem 2018; 78:108-115. [PMID: 30502727 DOI: 10.1016/j.compbiolchem.2018.11.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/09/2018] [Accepted: 11/18/2018] [Indexed: 12/31/2022]
Abstract
Serotonin receptor, 5-HT1AR, agonists and partial agonists have established drug candidates for psychiatric and neurologic disorders. Recently, we reported the synthesis and evaluation of arylpiperazine derivatives of 3,5-dioxo-(2H,4H)-1,2,4-triazine as 5-HT1AR ligands. Herein, we generated a homology model of the receptor and docked the ligands against it, predicted the stability of the receptor model and complexes by molecular dynamics and generated a 3D-QSAR model for the arylpiperazine derivatives of 3,5-dioxo-(2H,4H)-1,2,4-triazine. The model suggests the hydrophobic part that arises from the aromatic region and the electron withdrawing parts play a vital role in the agonist activity of the lead molecules.
Collapse
Affiliation(s)
- D R Sherin
- Centre for Data Engineering and Computational Modeling, Indian Institute of Information Technology and Management-Kerala, India
| | - C K Geethu
- Centre for Data Engineering and Computational Modeling, Indian Institute of Information Technology and Management-Kerala, India
| | - Jaya Prabhakaran
- Molecular Imaging and Neuropathology Division, New York State Psychiatric Institute & Department of Psychiatry, Columbia University College of Physicians and Surgeons, New York, USA
| | - J John Mann
- Molecular Imaging and Neuropathology Division, New York State Psychiatric Institute & Department of Psychiatry, Columbia University College of Physicians and Surgeons, New York, USA
| | - J S Dileep Kumar
- Molecular Imaging and Neuropathology Division, New York State Psychiatric Institute & Department of Psychiatry, Columbia University College of Physicians and Surgeons, New York, USA.
| | - T K Manojkumar
- Centre for Data Engineering and Computational Modeling, Indian Institute of Information Technology and Management-Kerala, India.
| |
Collapse
|
26
|
Irfanullah, Zeb A, Shinwari N, Shah K, Gilani SZT, Khan S, Lee KW, Raza SI, Hussain S, Liaqat K, Ahmad W. Molecular and in silico analyses validates pathogenicity of homozygous mutations in the NPR2 gene underlying variable phenotypes of Acromesomelic dysplasia, type Maroteaux. Int J Biochem Cell Biol 2018; 102:76-86. [PMID: 30016695 DOI: 10.1016/j.biocel.2018.07.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/12/2018] [Accepted: 07/13/2018] [Indexed: 01/13/2023]
Abstract
Homozygous and/or heterozygous loss of function mutations in the natriuretic peptide receptor B (NPR2) have been reported in causing acromesomelic dysplasia, type Maroteaux with variable clinical features and idiopathic short stature with nonspecific skeletal deformities. On the other hand, gain of function mutations in the same gene result in overgrowth disorder suggesting that NPR2 and its ligand, natriuretic peptide precursor C (CNP), are the key players of endochondral bone growth. However, the precise mechanism behind phenotypic variability of the NPR2 mutations is not fully understood so far. In the present study, three consanguineous families of Pakistani origin (A, B, C) with variable phenotypes of acromesomelic dysplasia, type Maroteaux were evaluated at clinical and molecular levels. Linkage analysis followed by Sanger sequencing of the NPR2 gene revealed three homozygous mutations including p.(Leu314 Arg), p.(Arg371*), and p.(Arg1032*) in family A, B and C, respectively. In silico structural and functional analyses substantiated that a novel missense mutation [p.(Leu314 Arg)] in family A allosterically affects binding of NPR2 homodimer to its ligand (CNP) which ultimately results in defective guanylate cyclase activity. A nonsense mutation [p.(Arg371*)] in family B entirely removed the transmembrane domain, protein kinase domain and guanylate cyclase domains of the NPR2 resulting in abolishing its guanylate cyclase activity. Another novel mutation [p.(Arg1032*)], found in family C, deteriorated the guanylate cyclase domain of the protein and probably plundered its guanylate cyclase activity. These results suggest that guanylate cyclase activity is the most critical function of the NPR2 and phenotypic severity of the NPR2 mutations is proportional to the reduction in its guanylate cyclase activity.
Collapse
Affiliation(s)
- Irfanullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, Pakistan; Department of Chemistry, Shaheed Benazir Bhutto University, Sheringal, Upper Dir, Pakistan
| | - Amir Zeb
- Division of Life Sciences, Division of Applied Life Sciences (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Republic of Korea
| | - Naila Shinwari
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, Pakistan
| | - Khadim Shah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, Pakistan
| | - Syed Zohaib Tayyab Gilani
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, Pakistan
| | - Saadullah Khan
- Department of Biotechnology & Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, KPK, Pakistan
| | - Keun Woo Lee
- Division of Life Sciences, Division of Applied Life Sciences (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Republic of Korea
| | - Syed Irfan Raza
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, Pakistan
| | - Shabir Hussain
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, Pakistan
| | - Khurram Liaqat
- Department of Biotechnology, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, Pakistan
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, Pakistan.
| |
Collapse
|
27
|
Kirsch SA, Kugemann A, Carpaneto A, Böckmann RA, Dietrich P. Phosphatidylinositol-3,5-bisphosphate lipid-binding-induced activation of the human two-pore channel 2. Cell Mol Life Sci 2018; 75:3803-3815. [PMID: 29705952 DOI: 10.1007/s00018-018-2829-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/29/2018] [Accepted: 04/23/2018] [Indexed: 11/24/2022]
Abstract
Mammalian two-pore channels (TPCs) are activated by the low-abundance membrane lipid phosphatidyl-(3,5)-bisphosphate (PI(3,5)P2) present in the endo-lysosomal system. Malfunction of human TPC1 or TPC2 (hTPC) results in severe organellar storage diseases and membrane trafficking defects. Here, we compared the lipid-binding characteristics of hTPC2 and of the PI(3,5)P2-insensitive TPC1 from the model plant Arabidopsis thaliana. Combination of simulations with functional analysis of channel mutants revealed the presence of an hTPC2-specific lipid-binding pocket mutually formed by two channel regions exposed to the cytosolic side of the membrane. We showed that PI(3,5)P2 is simultaneously stabilized by positively charged amino acids (K203, K204, and K207) in the linker between transmembrane helices S4 and S5 and by S322 in the cytosolic extension of S6. We suggest that PI(3,5)P2 cross links two parts of the channel, enabling their coordinated movement during channel gating.
Collapse
Affiliation(s)
- Sonja A Kirsch
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Andreas Kugemann
- Molecular Plant Physiology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Armando Carpaneto
- Institute of Biophysics, National Research Council, Genoa, Italy.,Department of Earth, Environment and Life Sciences-DISTAV, University of Genoa, Genoa, Italy
| | - Rainer A Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany.
| | - Petra Dietrich
- Molecular Plant Physiology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany.
| |
Collapse
|
28
|
Abstract
General anesthetics are thought to allosterically bind and potentiate the inhibitory currents of the GABAA receptor through drug-specific binding sites. The physiologically relevant isoform of the GABAA receptor is a transmembrane ligand-gated ion channel consisting of five subunits (γ-α-β-α-β linkage) symmetrically arranged around a central chloride-conducting pore. Although the exact molecular structure of this heteropentameric GABAA receptor remains unknown, molecular modeling has allowed significant advancements in understanding anesthetic binding and action. Using the open-channel conformations of the homologous glycine and glutamate-gated chloride receptors as templates, a homology model of the GABAA receptor was constructed using the Discovery Studio computational chemistry software suite. Consensus structural alignment of the homology templates allowed for the construction of a three-dimensional heteropentameric GABAA receptor model with (γ2-β3-α1-β3-α1) subunit linkage. An anesthetic binding site was identified within the transmembrane α/β intersubunit space by the convergence of three residues shown to be essential for anesthetic activity in previous studies with mutant mice (β3-N265, β3-M286, α1-L232). Propofol derivatives docked into this binding site showed log-linear correlation with experimentally derived GABAA receptor potentiation (EC50) values, suggesting this binding site may be important for receptor activation. The receptor-based pharmacophore was analyzed with surface maps displaying the predominant anesthetic-protein interactions, revealing an amphiphilic binding cavity incorporating the three residues involved in anesthetic modulation. Quantum mechanics calculations of the bonding patterns found in complementary high-resolution receptor systems further elucidated the complex nature of anesthetic-protein interactions.
Collapse
Affiliation(s)
- Victoria S Fahrenbach
- Stanford University School of Medicine, Stanford, CA, United States; Palo Alto VA Health Care System, Palo Alto, CA, United States
| | - Edward J Bertaccini
- Stanford University School of Medicine, Stanford, CA, United States; Palo Alto VA Health Care System, Palo Alto, CA, United States.
| |
Collapse
|
29
|
Giovanola M, Vollero A, Cinquetti R, Bossi E, Forrest LR, Di Cairano ES, Castagna M. Threonine 67 is a key component in the coupling of the NSS amino acid transporter KAAT1. Biochim Biophys Acta Biomembr 2018; 1860:1179-1186. [PMID: 29409909 DOI: 10.1016/j.bbamem.2018.01.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 01/26/2018] [Accepted: 01/28/2018] [Indexed: 01/30/2023]
Affiliation(s)
- M Giovanola
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Via Trentacoste 2, 20134, Milano, Italy
| | - A Vollero
- Department of Biotechnology and Life Sciences, University of Insubria, Via J.H. Dunant 3, 21100, Varese, Italy
| | - R Cinquetti
- Department of Biotechnology and Life Sciences, University of Insubria, Via J.H. Dunant 3, 21100, Varese, Italy
| | - E Bossi
- Department of Biotechnology and Life Sciences, University of Insubria, Via J.H. Dunant 3, 21100, Varese, Italy
| | - L R Forrest
- Computational Structural Biology Section, NIH NINDS, 35 Convent Drive, Bethesda, MD 20892-3761, USA
| | - E S Di Cairano
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Via Trentacoste 2, 20134, Milano, Italy
| | - M Castagna
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Via Trentacoste 2, 20134, Milano, Italy.
| |
Collapse
|
30
|
Loo JSE, Emtage AL, Ng KW, Yong ASJ, Doughty SW. Assessing GPCR homology models constructed from templates of various transmembrane sequence identities: Binding mode prediction and docking enrichment. J Mol Graph Model 2017; 80:38-47. [PMID: 29306746 DOI: 10.1016/j.jmgm.2017.12.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/27/2017] [Accepted: 12/26/2017] [Indexed: 11/15/2022]
Abstract
GPCR crystal structures have become more readily accessible in recent years. However, homology models of GPCRs continue to play an important role as many GPCR structures remain unsolved. The new crystal structures now available provide not only additional templates for homology modelling but also the opportunity to assess the performance of homology models against their respective crystal structures and gain insight into the performance of such models. In this study we have constructed homology models from templates of various transmembrane sequence identities for eight GPCR targets to better understand the relationship between transmembrane sequence identity and model quality. Model quality was assessed relative to the crystal structure in terms of structural accuracy as well as performance in two typical structure-based drug design applications: ligand binding pose prediction and docking enrichment in virtual screening. Crystal structures significantly outperformed homology models in both assessments. Accurate ligand binding pose prediction was possible but difficult to achieve using homology models, even with the use of induced fit docking. In virtual screening using homology models still conferred significant enrichment compared to random selection, with a clear benefit also observed in using models optimized through induced fit docking. Our results indicate that while homology models that are reasonably accurate structurally can be constructed, without significant refinement homology models will be outperformed by crystal structures in ligand binding pose prediction and docking enrichment regardless of the template used, primarily due to the extremely high level of structural accuracy needed for such applications.
Collapse
Affiliation(s)
- Jason S E Loo
- School of Pharmacy, Taylor's University, No.1 Jalan Taylor's, 47500 Subang Jaya, Selangor, Malaysia.
| | - Abigail L Emtage
- School of Pharmacy, The University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor, Malaysia
| | - Kar Weng Ng
- School of Pharmacy, Taylor's University, No.1 Jalan Taylor's, 47500 Subang Jaya, Selangor, Malaysia
| | - Alene S J Yong
- School of Pharmacy, Taylor's University, No.1 Jalan Taylor's, 47500 Subang Jaya, Selangor, Malaysia
| | - Stephen W Doughty
- Penang Medical College, No. 4 Jalan Sepoy Lines, 10450 George Town, Penang, Malaysia
| |
Collapse
|
31
|
Wang T, Liu H, Duan Y. Assessment of the transmembrane domain structures in GPCR Dock 2013 models. J Struct Biol 2017; 201:210-220. [PMID: 29174398 DOI: 10.1016/j.jsb.2017.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 11/15/2017] [Accepted: 11/20/2017] [Indexed: 01/08/2023]
Abstract
The community-wide blind prediction of G-protein coupled receptor (GPCR) structures and ligand docking has been conducted three times and the quality of the models was primarily assessed by the accuracy of ligand binding modes. The seven transmembrane (TM) helices of the receptors were taken as a whole; thus the model quality within the 7TM domains has not been evaluated. Here we evaluate the 7TM domain structures in the models submitted for the last round of prediction - GPCR Dock 2013. Applying the 7 × 7 RMSD matrix analysis described in our prior work, we show that the models vary widely in prediction accuracy of the 7TM structures, exhibiting diverse structural differences from the targets. For the prediction of the 5-hydroxytryptamine receptors, the top 7TM models are rather close to the targets, which however are not ranked top by ligand-docking. On the other hand, notable deviations of the TMs are found in in the previously identified top docking models that closely resemble other receptors. We further reveal reasons of success and failure in ligand docking for the models. This current assessment not only complements the previous assessment, but also provides important insights into the current status of GPCR modeling and ligand docking.
Collapse
Affiliation(s)
- Ting Wang
- Genome Center, 451 East Health Science Drive, University of California, Davis, CA 95616, United States; Sichuan University of Science and Engineering, 180 Xueyuan Street, Huixing Road, Zigong 643000, Sichuan Province, China.
| | - Haiguang Liu
- Complex Systems Division, Beijing Computational Science Research Center, 10 W. Dongbeiwang Rd, Haidian District, Beijing 100193, China
| | - Yong Duan
- Genome Center, 451 East Health Science Drive, University of California, Davis, CA 95616, United States
| |
Collapse
|
32
|
Holien JK, Seibt B, Roberts V, Salvaris E, Parker MW, Cowan PJ, Dwyer KM. AMP and adenosine are both ligands for adenosine 2B receptor signaling. Bioorg Med Chem Lett 2018; 28:202-6. [PMID: 29191553 DOI: 10.1016/j.bmcl.2017.11.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 11/01/2017] [Accepted: 11/08/2017] [Indexed: 02/07/2023]
Abstract
Adenosine is considered the canonical ligand for the adenosine 2B receptor (A2BR). A2BR is upregulated following kidney ischemia augmenting post ischemic blood flow and limiting tubular injury. In this context the beneficial effect of A2BR signaling has been attributed to an increase in the pericellular concentration of adenosine. However, following renal ischemia both kidney adenosine monophosphate (AMP) and adenosine levels are substantially increased. Using computational modeling and calcium mobilization assays, we investigated whether AMP could also be a ligand for A2BR. The computational modeling suggested that AMP interacts with more favorable energy to A2BR compared with adenosine. Furthermore, AMPαS, a non-hydrolyzable form of AMP, increased calcium uptake by Chinese hamster ovary (CHO) cells expressing the human A2BR, indicating preferential signaling via the Gq pathway. Therefore, a putative AMP-A2BR interaction is supported by the computational modeling data and the biological results suggest this interaction involves preferential Gq activation. These data provide further insights into the role of purinergic signaling in the pathophysiology of renal IRI.
Collapse
|
33
|
Gondim ACS, Romero-Canelón I, Sousa EHS, Blindauer CA, Butler JS, Romero MJ, Sanchez-Cano C, Sousa BL, Chaves RP, Nagano CS, Cavada BS, Sadler PJ. The potent anti-cancer activity of Dioclea lasiocarpa lectin. J Inorg Biochem 2017; 175:179-189. [PMID: 28756174 DOI: 10.1016/j.jinorgbio.2017.07.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 07/03/2017] [Accepted: 07/10/2017] [Indexed: 02/07/2023]
Abstract
The lectin DLasiL was isolated from seeds of the Dioclea lasiocarpa collected from the northeast coast of Brazil and characterized for the first time by mass spectrometry, DNA sequencing, inductively coupled plasma-mass spectrometry, electron paramagnetic resonance, and fluorescence spectroscopy. The structure of DLasiL lectin obtained by homology modelling suggested strong conservation of the dinuclear Ca/Mn and sugar-binding sites, and dependence of the solvent accessibility of tryptophan-88 on the oligomerisation state of the protein. DLasiL showed highly potent (low nanomolar) antiproliferative activity against several human carcinoma cell lines including A2780 (ovarian), A549 (lung), MCF-7 (breast) and PC3 (prostate), and was as, or more, potent than the lectins ConBr (Canavalia brasiliensis), ConM (Canavalia maritima) and DSclerL (Dioclea sclerocarpa) against A2780 and PC3 cells. Interestingly, DLasiL lectin caused a G2/M arrest in A2780 cells after 24h exposure, activating caspase 9 and delaying the on-set of apoptosis. Confocal microscopy showed that fluorescently-labelled DLasiL localized around the nuclei of A2780 cells at lectin doses of 0.5-2× IC50 and gave rise to enlarged nuclei and spreading of the cells at high doses. These data reveal the interesting antiproliferative activity of DLasiL lectin, and suggest that further investigations to explore the potential of DLasiL as a new anticancer agent are warranted.
Collapse
Affiliation(s)
- Ana C S Gondim
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, 60455-760 Fortaleza, Ceará, Brazil; Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK; Department of Organic and Inorganic Chemistry, Federal University of Ceará, 60455-900 Fortaleza, Ceará, Brazil
| | | | - Eduardo H S Sousa
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK; Department of Organic and Inorganic Chemistry, Federal University of Ceará, 60455-900 Fortaleza, Ceará, Brazil
| | | | - Jennifer S Butler
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - María J Romero
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | | | - Bruno L Sousa
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, 60455-760 Fortaleza, Ceará, Brazil
| | - Renata P Chaves
- Department of Fishing and Engineering, Federal University of Ceará, 60455-900 Fortaleza, Ceará, Brazil
| | - Celso S Nagano
- Department of Fishing and Engineering, Federal University of Ceará, 60455-900 Fortaleza, Ceará, Brazil
| | - Benildo S Cavada
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, 60455-760 Fortaleza, Ceará, Brazil.
| | - Peter J Sadler
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK.
| |
Collapse
|
34
|
Abstract
The Reggio group has constructed computer models of the inactive and G-protein-activated states of the cannabinoid CB1 and CB2 receptors, as well as, several orphan receptors that recognize a subset of cannabinoid compounds, including GPR55 and GPR18. These models have been used to design ligands, mutations, and covalent labeling studies. The resultant second-generation models have been used to design ligands with improved affinity, efficacy, and subtype selectivity. Herein, we provide a guide for the development of GPCR models using the most recent orphan receptor studied in our lab, GPR3. GPR3 is an orphan receptor that belongs to the Class A family of G-protein-coupled receptors. It shares high sequence similarity with GPR6, GPR12, the lysophospholipid receptors, and the cannabinoid receptors. GPR3 is predominantly expressed in mammalian brain and oocytes and it is known as a Gαs-coupled receptor activated constitutively in cells. GPR3 represents a possible target for the treatment of different pathological conditions such as Alzheimer's disease, oocyte maturation, or neuropathic pain. However, the lack of potent and selective GPR3 ligands is delaying the exploitation of this promising therapeutic target. In this context, we aim to develop a homology model that helps us to elucidate the structural determinants governing ligand-receptor interactions at GPR3. In this chapter, we detail the methods and rationale behind the construction of the GPR3 active-and inactive-state models. These homology models will enable the rational design of novel ligands, which may serve as research tools for further understanding of the biological role of GPR3.
Collapse
Affiliation(s)
- Paula Morales
- University of North Carolina at Greensboro, Greensboro, NC, United States.
| | - Dow P Hurst
- University of North Carolina at Greensboro, Greensboro, NC, United States
| | - Patricia H Reggio
- University of North Carolina at Greensboro, Greensboro, NC, United States
| |
Collapse
|
35
|
Fakhouri L, Cook CD, Al-Huniti MH, Console-Bram LM, Hurst DP, Spano MBS, Nasrallah DJ, Caron MG, Barak LS, Reggio PH, Abood ME, Croatt MP. Design, synthesis and biological evaluation of GPR55 agonists. Bioorg Med Chem 2017; 25:4355-67. [PMID: 28673732 DOI: 10.1016/j.bmc.2017.06.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 06/05/2017] [Accepted: 06/12/2017] [Indexed: 12/23/2022]
Abstract
GPR55, a G protein-coupled receptor, is an attractive target to alleviate inflammatory and neuropathic pain and treat osteoporosis and cancer. Identifying a potent and selective ligand will aid to further establish the specific physiological roles and pharmacology of the receptor. Towards this goal, a targeted library of 22 compounds was synthesized in a modular fashion to obtain structure-activity relationship information. The general route consisted of coupling a variety of p-aminophenyl sulfonamides to isothiocyanates to form acylthioureas. For the synthesis of a known naphthyl ethyl alcohol motif, route modification led to a shorter and more efficient process. The 22 analogues were analyzed for their ability to serve as agonists at GPR55 and valuable information for both ends of the molecule was ascertained.
Collapse
|
36
|
Hansen NL, Nissen JN, Hamberger B. Two residues determine the product profile of the class II diterpene synthases TPS14 and TPS21 of Tripterygium wilfordii. Phytochemistry 2017; 138:52-56. [PMID: 28279524 DOI: 10.1016/j.phytochem.2017.02.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/16/2017] [Accepted: 02/22/2017] [Indexed: 05/22/2023]
Abstract
The medicinal plant Tripterygium wilfordii (Celastraceae) contains a pair of class II diterpene synthases (diTPS) of specialized labdane-type metabolism that, despite remarkably close homology, form strikingly different products. TwTPS21 catalyzes bicyclization of the linear C20 precursor geranylgeranyl diphosphate to ent-copal-8-ol diphosphate, while TwTPS14 forms kolavenyl diphosphate. To determine the amino acid signature controlling the functional divergence of the homologues, we modeled their structures based on an existing crystal structure of the Arabidopsis ent-copalyl diphosphate synthase, archetypal of diTPSs in general metabolism of gibberellin phytohormones. Of the residues differing between TwTPS21 and TwTPS14 two located to the predicted active site, and we hypothesized that these are responsible for the functional differentiation of the enzymes. Using site-directed mutagenesis, we generated a panel of six variants, where one, or both positions were exchanged between the enzymes. In coupled heterologous assays with a corresponding class I diTPS, TwTPS2, complete product interchange was observed in variants with both reciprocal mutations, while substitutions of either residue gave mixed product profiles. Two mutants, TwTPS14:Y265H and TwTPS21:A325V, also produced ent-copalyl diphosphate, highlighting the evolutionary potential of enzymes of this family to drive rapid diversification of plant diterpene biosynthesis through neo-functionalization. Our study contributes to the understanding of structure-function relation in plant class II diTPSs and complements previous mutational studies of Arabidopsis ent-copalyl diphosphate synthase with additional examples from the specialized metabolism of T. wilfordii.
Collapse
Affiliation(s)
- Nikolaj L Hansen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Denmark; Center for Synthetic Biology "bioSYNergy" and Copenhagen Plant Sciences Centre, Denmark
| | - Jakob N Nissen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Denmark; Center for Synthetic Biology "bioSYNergy" and Copenhagen Plant Sciences Centre, Denmark
| | - Björn Hamberger
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Denmark; Center for Synthetic Biology "bioSYNergy" and Copenhagen Plant Sciences Centre, Denmark.
| |
Collapse
|
37
|
Abstract
To find an effective drug for Zika virus, it is important to understand how numerous proteins which are critical for the virus' structure and function interact with their counterparts. One approach to inhibiting the flavivirus is to deter its ability to bind onto glycoproteins; however, the crystal structures of envelope proteins of the ever-evolving viral strains that decipher glycosidic or drug-molecular interactions are not always available. To fill this gap, we are reporting a holistic, simulation-based approach to predict compounds that will inhibit ligand binding onto a structurally unresolved protein, in this case the Zika virus envelope protein (ZVEP), by developing a three-dimensional general structure and analyzing sites at which ligands and small drug-like molecules interact. By examining how glycan molecules and small-molecule probes interact with a freshly resolved ZVEP homology model, we report the susceptibility of ZVEP to inhibition via two small molecules, ZINC33683341 and ZINC49605556-by preferentially binding onto the primary receptor responsible for the virus' virulence. Antiviral activity was confirmed when ZINC33683341 was tested in cell culture. We anticipate the results to be a starting point for drug discovery targeting Zika virus and other emerging pathogens.
Collapse
Affiliation(s)
- Sandun Fernando
- Biological Engineering, Texas A&M University, 303C Scoates Hall, 2117 TAMU, College Station, TX, 77843, USA.
| | - Teshan Fernando
- Biological Engineering, Texas A&M University, 303C Scoates Hall, 2117 TAMU, College Station, TX, 77843, USA
| | - Michal Stefanik
- Department of Virology, Veterinary Research Institute, Hudcova 70, 62100, Brno, Czech Republic
| | - Ludek Eyer
- Department of Virology, Veterinary Research Institute, Hudcova 70, 62100, Brno, Czech Republic.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, 37005, Ceske Budejovice, Czech Republic
| | - Daniel Ruzek
- Department of Virology, Veterinary Research Institute, Hudcova 70, 62100, Brno, Czech Republic.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, 37005, Ceske Budejovice, Czech Republic
| |
Collapse
|
38
|
Banerjee S, Sen Gupta PS, Bandyopadhyay AK. Insight into SNPs and epitopes of E protein of newly emerged genotype-I isolates of JEV from Midnapur, West Bengal, India. BMC Immunol 2017; 18:13. [PMID: 28264652 PMCID: PMC5339996 DOI: 10.1186/s12865-017-0197-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 02/16/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Japanese encephalitis virus (JEV) is a mosquito-borne flavivirus that causes Japanese Encephalitis (JE) and Acute Encephalitis Syndrome (AES) in humans. Genotype-I (as co-circulating cases with Genotype-III) was isolated in 2010 (JEV28, JEV21) and then in 2011 (JEV45) from Midnapur district, West Bengal (WB) for the first time from clinical patients who were previously been vaccinated with live attenuated SA14-14-2 strain. We apply bioinformatics and immunoinformatics on sequence and structure of E protein for analysis of crucial substitutions that might cause the genotypic transition, affecting protein-function and altering specificity of epitopes. RESULTS Although frequency of substitutions in E glycoprotein of JEV28, JEV21 and JEV45 isolates vary, its homologous patterns remain exactly similar as earlier Japan isolate (Ishikawa). Sequence and 3D model-structure based analyses of E protein show that only four of all substitutions are critical for genotype-I specific effect of which N103K is common among all isolates indicating its role in the transition of genotype-III to genotype-I. Predicted B-cell and T-cell epitopes are seen to harbor these critical substitutions that affect overall conformational stability of the protein. These epitopes were subjected to conservation analyses using a large set of the protein from Asian continent. CONCLUSIONS The study identifies crucial substitutions that contribute to the emergence of genotype-I. Predicted epitopes harboring these substitutions may alter specificity which might be the reason of reported failure of vaccine. Conservation analysis of these epitopes would be useful for design of genotype-I specific vaccine.
Collapse
Affiliation(s)
- Shyamashree Banerjee
- Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, 713104, India
| | - Parth Sarthi Sen Gupta
- Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, 713104, India
| | | |
Collapse
|
39
|
Hinz KM, Neef D, Rutz C, Furkert J, Köhrle J, Schülein R, Krause G. Molecular features of the L-type amino acid transporter 2 determine different import and export profiles for thyroid hormones and amino acids. Mol Cell Endocrinol 2017; 443:163-174. [PMID: 28108384 DOI: 10.1016/j.mce.2017.01.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 01/11/2017] [Accepted: 01/17/2017] [Indexed: 10/20/2022]
Abstract
The L-type amino acid transporter 2 (LAT2) imports amino acids (AA) and also certain thyroid hormones (TH), e.g. 3,3'-T2 and T3, but not rT3 and T4. We utilized LAT2 mutations (Y130A, N133S, F242W) that increase 3,3'-T2 import and focus here on import and export capacity for AA, T4, T3, BCH and derivatives thereof to delineate molecular features. Transport studies and analysis of competitive inhibition of import by radiolabelled TH and AA were performed in Xenopus laevis oocytes. Only Y130A, a pocket widening mutation, enabled import for T4 and increased it for T3. Mutant F242W showed increased 3,3'-T2 import but no import rates for other TH derivatives. No export was detected for any TH by LAT2-wild type (WT). Mutations Y130A and N133S enabled only the export of 3,3'-T2, while N133S also increased AA export. Thus, distinct molecular LAT2-features determine bidirectional AA transport but only an unidirectional 3,3'-T2 and T3 import.
Collapse
Affiliation(s)
- Katrin M Hinz
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Dominik Neef
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Claudia Rutz
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Jens Furkert
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Josef Köhrle
- Institut für Experimentelle Endokrinologie, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Ralf Schülein
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Gerd Krause
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Berlin, Germany.
| |
Collapse
|
40
|
Shukla E, Agrawal SB, Gaikwad SM. Conformational and functional transitions and in silico analysis of a serine protease from Conidiobolus brefeldianus (MTCC 5185). Int J Biol Macromol 2017; 98:387-397. [PMID: 28153464 DOI: 10.1016/j.ijbiomac.2017.01.124] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 01/06/2017] [Accepted: 01/27/2017] [Indexed: 11/25/2022]
Abstract
This work describes functional and structural transitions of a novel protease isolated from Conidiobolus brefeldianus MTCC 5185 (Cprot), in detail using biophysical and bioinformatics tools. The commercial importance of Cprot in silk and leather industries made it an interesting candidate for structural investigations. Cprot possesses 8.2% α-helix, 31.1% β-sheet and 23.8% turns. The enzyme was found to be active over a wide pH range and up to 55°C. The protease was also stable in organic solvents up to 50% (v/v) concentration of alcohols and DMSO for >24h and in 2M guanidine hydrochloride for >12h. Cprot was also resistant to trypsin, chymotrypsin, proteinase K and fluorinated alcohols (5-10%). The melting temperatures observed for the native Cprot and for the enzyme treated under various stress conditions correlated well with the corresponding structural and functional transitions obtained. The structural information was supported by the homology model of its closest homologue from C. coronatus; revealing its similarity to PA clan of proteases (Proteases of mixed nucleophile, superfamily A), with His-64, Asp-113 and Ser-208 as putative catalytic triad. Three tryptophan residues in Cprot are surrounded by positively charged residues, as evident from solute quenching studies and homology model.
Collapse
Affiliation(s)
- Ekta Shukla
- Academy of Scientific and Innovative Research (AcSIR), Division of Biochemical Sciences, CSIR-National Chemical laboratory, Pune 411008, India
| | - Sanskruthi B Agrawal
- Academy of Scientific and Innovative Research (AcSIR), Division of Biochemical Sciences, CSIR-National Chemical laboratory, Pune 411008, India
| | - Sushama M Gaikwad
- Academy of Scientific and Innovative Research (AcSIR), Division of Biochemical Sciences, CSIR-National Chemical laboratory, Pune 411008, India.
| |
Collapse
|
41
|
Ekins S, Godbole AA, Kéri G, Orfi L, Pato J, Bhat RS, Verma R, Bradley EK, Nagaraja V. Machine learning and docking models for Mycobacterium tuberculosis topoisomerase I. Tuberculosis (Edinb) 2017; 103:52-60. [PMID: 28237034 DOI: 10.1016/j.tube.2017.01.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 01/14/2017] [Accepted: 01/18/2017] [Indexed: 11/30/2022]
Abstract
There is a shortage of compounds that are directed towards new targets apart from those targeted by the FDA approved drugs used against Mycobacterium tuberculosis. Topoisomerase I (Mttopo I) is an essential mycobacterial enzyme and a promising target in this regard. However, it suffers from a shortage of known inhibitors. We have previously used computational approaches such as homology modeling and docking to propose 38 FDA approved drugs for testing and identified several active molecules. To follow on from this, we now describe the in vitro testing of a library of 639 compounds. These data were used to create machine learning models for Mttopo I which were further validated. The combined Mttopo I Bayesian model had a 5 fold cross validation receiver operator characteristic of 0.74 and sensitivity, specificity and concordance values above 0.76 and was used to select commercially available compounds for testing in vitro. The recently described crystal structure of Mttopo I was also compared with the previously described homology model and then used to dock the Mttopo I actives norclomipramine and imipramine. In summary, we describe our efforts to identify small molecule inhibitors of Mttopo I using a combination of machine learning modeling and docking studies in conjunction with screening of the selected molecules for enzyme inhibition. We demonstrate the experimental inhibition of Mttopo I by small molecule inhibitors and show that the enzyme can be readily targeted for lead molecule development.
Collapse
Affiliation(s)
- Sean Ekins
- Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, CA 94403, USA; Collaborations in Chemistry, 5616 Hilltop Needmore Road, Fuquay-Varina, NC 27526, USA.
| | - Adwait Anand Godbole
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - György Kéri
- Vichem Chemie Research Ltd., Herman Ottó u. 15, H-1022, Budapest, Hungary; Semmelweis Univ, Dept Med Chem, MTA SE Pathobiochem Res Grp, H-1092, Budapest, Hungary
| | - Lászlo Orfi
- Vichem Chemie Research Ltd., Herman Ottó u. 15, H-1022, Budapest, Hungary; Semmelweis Univ, Dept Med Chem, MTA SE Pathobiochem Res Grp, H-1092, Budapest, Hungary
| | - János Pato
- Vichem Chemie Research Ltd., Herman Ottó u. 15, H-1022, Budapest, Hungary
| | - Rajeshwari Subray Bhat
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Rinkee Verma
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | | | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, 560064, India.
| |
Collapse
|
42
|
Abstract
Linkage and genome-wide association studies have identified a genetic risk locus for late-onset Parkinson's disease in chromosome 12, originally identified as PARK6. The causative gene was identified to code for a large multifunctional protein, LRRK2 (leucine-rich repeat kinase 2). The combined genetic and biochemical evidence supports a hypothesis in which the LRRK2 kinase function is causally involved in the pathogenesis of sporadic and familial forms of PD, and therefore that LRRK2 kinase inhibitors could be useful for treatment. Although LRRK2 has so far not been crystallised, the use of homology modelling and crystallographic surrogates has allowed the optimisation of chemical structures such that compounds of high selectivity with good brain penetration and appropriate pharmacokinetic properties are now available for understanding the biology of LRRK2 in vitro and in vivo. This chapter reviews LRRK2 biology, the structural biology of LRRK2 and gives an overview of inhibitors of LRRK2.
Collapse
Affiliation(s)
- K V Christensen
- Neuroscience Drug Discovery, H. Lundbeck A/S, Valby, Denmark
| | - G P Smith
- Neuroscience Drug Discovery, H. Lundbeck A/S, Valby, Denmark
| | | |
Collapse
|
43
|
Lingineni K, Belekar V, Tangadpalliwar SR, Garg P. The role of multidrug resistance protein (MRP-1) as an active efflux transporter on blood-brain barrier (BBB) permeability. Mol Divers 2017; 21:355-65. [PMID: 28050687 DOI: 10.1007/s11030-016-9715-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 12/16/2016] [Indexed: 01/30/2023]
Abstract
Drugs acting on central nervous system (CNS) may take longer duration to reach the market as these compounds have a higher attrition rate in clinical trials due to the complexity of the brain, side effects, and poor blood-brain barrier (BBB) permeability compared to non-CNS-acting compounds. The roles of active efflux transporters with BBB are still unclear. The aim of the present work was to develop a predictive model for BBB permeability that includes the MRP-1 transporter, which is considered as an active efflux transporter. A support vector machine model was developed for the classification of MRP-1 substrates and non-substrates, which was validated with an external data set and Y-randomization method. An artificial neural network model has been developed to evaluate the role of MRP-1 on BBB permeation. A total of nine descriptors were selected, which included molecular weight, topological polar surface area, ClogP, number of hydrogen bond donors, number of hydrogen bond acceptors, number of rotatable bonds, P-gp, BCRP, and MRP-1 substrate probabilities for model development. We identified 5 molecules that fulfilled all criteria required for passive permeation of BBB, but they all have a low logBB value, which suggested that the molecules were effluxed by the MRP-1 transporter.
Collapse
|
44
|
Dow BA, Sehanobish E, Davidson VL. In Silico Approaches to Identify Mutagenesis Targets to Probe and Alter Protein-Cofactor and Protein-Protein Functional Relationships. Methods Mol Biol 2017; 1498:181-90. [PMID: 27709576 DOI: 10.1007/978-1-4939-6472-7_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
When performing site-directed mutagenesis experiments to study protein structure-function relationships, ideally one would know the structure of the protein under study. It is also very useful to have structures of multiple related proteins in order to determine whether or not particular amino acid residues are conserved in the structures either in the active site of an enzyme at the surface of a protein or at a putative protein-protein interface. While many protein structures are available in the Protein Data Base (PDB), a structure of the protein of interest may not be available. In the study of reversible and often transient protein-protein interactions it is rare to have a structure of the complex of the two interacting proteins. In this chapter, methods are described for comparing protein structures, generating putative structures of proteins with homology models based on the protein primary sequence, and generating docking models to predict interaction sites between proteins and cofactor-protein interactions. The rationale used to predict mutagenesis targets from these structures and models is also described.
Collapse
|
45
|
Levoin N, Labeeuw O, Billot X, Calmels T, Danvy D, Krief S, Berrebi-Bertrand I, Lecomte JM, Schwartz JC, Capet M. Discovery of nanomolar ligands with novel scaffolds for the histamine H4 receptor by virtual screening. Eur J Med Chem 2016; 125:565-572. [PMID: 27718472 DOI: 10.1016/j.ejmech.2016.09.074] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/21/2016] [Accepted: 09/22/2016] [Indexed: 12/29/2022]
Abstract
The involvement of histamine H4 receptor (H4R) in immune cells chemotaxis and mediator release makes it an attractive target for the treatment of inflammation disorders. A decade of medicinal chemistry efforts has led to several promising ligands, although the chemical structures described so far possesses a singular limited diversity. We report here the discovery of novel structures, belonging to completely different scaffolds. The virtual screening was planed as a two-steps process. First, using a "scout screening" methodology, we have experimentally probed the H4R ligand binding site using a small size chemical library with very diverse structures, and identified a hit that further assist us in refining a raw 3D homology model. Second, the refined 3D model was used to conduct a widened virtual screening. This two-steps strategy proved to be very successful, both in terms of structural diversity and hit rate (23%). Moreover, the hits have high affinity for the H4R, with most potent ligands in the nanomolar range.
Collapse
Affiliation(s)
- Nicolas Levoin
- Bioprojet-Biotech, 4rue du Chesnay Beauregard, 35762 Saint-Gregoire Cedex, France.
| | - Olivier Labeeuw
- Bioprojet-Biotech, 4rue du Chesnay Beauregard, 35762 Saint-Gregoire Cedex, France
| | - Xavier Billot
- Bioprojet-Biotech, 4rue du Chesnay Beauregard, 35762 Saint-Gregoire Cedex, France
| | - Thierry Calmels
- Bioprojet-Biotech, 4rue du Chesnay Beauregard, 35762 Saint-Gregoire Cedex, France
| | - Denis Danvy
- Bioprojet-Biotech, 4rue du Chesnay Beauregard, 35762 Saint-Gregoire Cedex, France
| | - Stéphane Krief
- Bioprojet-Biotech, 4rue du Chesnay Beauregard, 35762 Saint-Gregoire Cedex, France
| | | | - Jeanne-Marie Lecomte
- Bioprojet-Biotech, 4rue du Chesnay Beauregard, 35762 Saint-Gregoire Cedex, France
| | | | - Marc Capet
- Bioprojet-Biotech, 4rue du Chesnay Beauregard, 35762 Saint-Gregoire Cedex, France
| |
Collapse
|
46
|
Abstract
Zika virus (ZIKV) is an arbovirus that has infected hundreds of thousands of people and is a rapidly expanding epidemic across Central and South America. ZIKV infection has caused serious, albeit rare, complications including Guillain-Barré syndrome and congenital microcephaly. There are currently no vaccines or antiviral agents to treat or prevent ZIKV infection, but there are several ZIKV non-structural proteins that may serve as promising antiviral drug targets. In this work, we have carried out an in-silico search for potential anti-Zika viral agents from natural sources. We have generated ZIKV protease, methyltransferase, and RNA-dependent RNA polymerase using homology modeling techniques and we have carried out molecular docking analyses of our in-house virtual library of phytochemicals with these protein targets as well as with ZIKV helicase. Overall, 2263 plant-derived secondary metabolites have been docked. Of these, 43 compounds that have drug-like properties have exhibited remarkable docking profiles to one or more of the ZIKV protein targets, and several of these are found in relatively common herbal medicines, suggesting promise for natural and inexpensive antiviral therapy for this emerging tropical disease.
Collapse
Affiliation(s)
- Kendall G Byler
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL, 35899, USA
| | - Ifedayo Victor Ogungbe
- Department of Chemistry & Biochemistry, Jackson State University, Jackson, MS, 39217, USA
| | - William N Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL, 35899, USA.
| |
Collapse
|
47
|
Singla R, Jaitak V. Synthesis of rebaudioside A from stevioside and their interaction model with hTAS2R4 bitter taste receptor. Phytochemistry 2016; 125:106-111. [PMID: 26976334 DOI: 10.1016/j.phytochem.2016.03.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 01/15/2016] [Accepted: 03/07/2016] [Indexed: 06/05/2023]
Abstract
Steviol glycosides (SG's) from Stevia rebaudiana (Bertoni) have been used as a natural low-calorie sweeteners. Its aftertaste bitterness restricts its use for human consumption and limits its application in food and pharmaceutical products. In present study, we have performed computational analysis in order to investigate the interaction of two major constituents of SG's against homology model of the hTAS2R4 receptor. Molecular simulation study was performed using stevioside and rebaudioside A revealed that, sugar moiety at the C-3'' position in rebaudioside A causes restriction of its entry into the receptor site thereby unable to trigger the bitter reception signaling cascade. Encouraged by the current finding, we have also developed a greener route using β-1,3-glucanase from Irpex lacteus for the synthesis of de-bittered rebaudioside A from stevioside. The rebaudioside A obtained was of high quality with percent conversion of 62.5%. The results here reported could be used for the synthesis of rebaudioside A which have large application in food and pharmaceutical industry.
Collapse
Affiliation(s)
- Ramit Singla
- Centre for Pharmaceutical Sciences and Natural Products, School of Basic and Applied Sciences, Central University of Punjab, Bathinda(Pb) 151 001, India
| | - Vikas Jaitak
- Centre for Pharmaceutical Sciences and Natural Products, School of Basic and Applied Sciences, Central University of Punjab, Bathinda(Pb) 151 001, India.
| |
Collapse
|
48
|
Verma A, Chandra S, Suthar MK, Doharey PK, Siddiqi MI, Saxena JK. NADP⁺ binding effects tryptophan accessibility, folding and stability of recombinant B. malayi G6PD. Int J Biol Macromol 2016; 85:645-54. [PMID: 26763177 DOI: 10.1016/j.ijbiomac.2015.12.087] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 12/28/2015] [Accepted: 12/30/2015] [Indexed: 11/21/2022]
Abstract
Brugia malayi Glucose 6-phosphate dehydrogenase apoenzyme (BmG6PD) was expressed and purified by affinity chromatography to study the differences in kinetic properties of enzyme and the effect of the cofactor NADP(+) binding on enzyme stability. The presence of cofactor NADP(+) influenced the tertiary structure of enzyme due to significant differences in the tryptophan microenvironment. However, NADP(+) binding have no effect on secondary structure of the enzyme. Quenching with acrylamide indicated that two or more tryptophan residues became accessible upon cofactor binding. Unfolding and cross linking study of BmG6PD showed that NADP(+) stabilized the protein in presence of high concentration of urea/GdmCl. A homology model of BmG6PD constructed using human G6PD (PDB id: 2BH9) as a template indicated 34% α-helix, 19% β-sheet and 47% random coil conformations in the predicted model of the enzyme. In the predicted model binding of NADP(+) to BmG6PD was less tight with the structural sites (-10.96 kJ/mol binding score) as compared with the coenzyme site (-15.47 kJ/mol binding score).
Collapse
|
49
|
Jaitak V. Interaction model of steviol glycosides from Stevia rebaudiana (Bertoni) with sweet taste receptors: A computational approach. Phytochemistry 2015; 116:12-20. [PMID: 26021732 DOI: 10.1016/j.phytochem.2015.05.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 05/08/2015] [Accepted: 05/14/2015] [Indexed: 06/04/2023]
Abstract
Docking studies were performed on natural sweeteners from Stevia rebaudiana by constructing homology models of T1R2 and T1R3 subunits of human sweet taste receptors. Ramachandran plot, PROCHECK results and ERRAT overall quality factor were used to validate the quality of models. Furthermore, docking results of steviol glycosides (SG's) were correlated significantly with data available in the literature which enabled to predict the exact sweetness rank order of SG's. The binding pattern indicated that Asn 44, Ans 52, Ala 345, Pro 343, Ile 352, Gly 346, Gly 47, Ala 354, Ser 336, Thr 326 and Ser 329 are the main interacting amino acid residues in case of T1R2 and Arg 56, Glu 105, Asp 215, Asp 216, Glu 148, Asp 258, Lys 255, Ser 104, Glu 217, Leu 51, Arg 52 for T1R3, respectively. Amino acids interact with SG's mainly by forming hydrogen bonds with the hydroxyl group of glucose moieties. Significant variation in docked poses of all the SG's were found. In this study, we have proposed the mechanism of the sweetness of the SG's in the form of multiple point stimulation model by considering the diverse binding patterns of various SG's, as well as their structural features. It will give further insight in understanding the differences in the quality of taste and will be used to improve the taste of SG's using semi-synthetic approaches.
Collapse
Affiliation(s)
- Vikas Jaitak
- Centre for Chemical and Pharmaceutical Sciences, Central University of Punjab, Bathinda (Pb) 151001, India.
| |
Collapse
|
50
|
Raeppel SL, Therrien E, Raeppel F. Design and synthesis of constrained analogs of LCRF-0004 as potent RON tyrosine kinase inhibitors. Bioorg Med Chem Lett 2015; 25:3706-10. [PMID: 26112445 DOI: 10.1016/j.bmcl.2015.06.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 06/08/2015] [Indexed: 01/09/2023]
Abstract
New fused bicyclic lactam head groups as rigidified analogs of thieno[3,2-b]pyridine-based kinase inhibitor LCRF-0004 were designed and synthesized. Depending on the functionalities and the size of these bicyclic head groups, potent inhibitors of RON tyrosine kinase with various level of selectivity against c-Met tyrosine kinase were obtained.
Collapse
|