1
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Lopes TJS, Rios RA, Rios TN, Alencar BM, Ferreira MV, Morishita E. Computational analyses reveal fundamental properties of the AT structure related to thrombosis. BIOINFORMATICS ADVANCES 2022; 3:vbac098. [PMID: 36698764 PMCID: PMC9838315 DOI: 10.1093/bioadv/vbac098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/28/2022] [Accepted: 12/22/2022] [Indexed: 12/25/2022]
Abstract
Summary Blood coagulation is a vital process for humans and other species. Following an injury to a blood vessel, a cascade of molecular signals is transmitted, inhibiting and activating more than a dozen coagulation factors and resulting in the formation of a fibrin clot that ceases the bleeding. In this process, antithrombin (AT), encoded by the SERPINC1 gene is a key player regulating the clotting activity and ensuring that it stops at the right time. In this sense, mutations to this factor often result in thrombosis-the excessive coagulation that leads to the potentially fatal formation of blood clots that obstruct veins. Although this process is well known, it is still unclear why even single residue substitutions to AT lead to drastically different phenotypes. In this study, to understand the effect of mutations throughout the AT structure, we created a detailed network map of this protein, where each node is an amino acid, and two amino acids are connected if they are in close proximity in the three-dimensional structure. With this simple and intuitive representation and a machine-learning framework trained using genetic information from more than 130 patients, we found that different types of thrombosis have emerging patterns that are readily identifiable. Together, these results demonstrate how clinical features, genetic data and in silico analysis are converging to enhance the diagnosis and treatment of coagulation disorders. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
| | - Ricardo A Rios
- Institute of Computing, Federal University of Bahia, Salvador 40170-110, Brazil
| | - Tatiane N Rios
- Institute of Computing, Federal University of Bahia, Salvador 40170-110, Brazil
| | - Brenno M Alencar
- Institute of Computing, Federal University of Bahia, Salvador 40170-110, Brazil
| | - Marcos V Ferreira
- Institute of Computing, Federal University of Bahia, Salvador 40170-110, Brazil
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2
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Zhu H, Zhang Y, Li W, Huang N. A Comprehensive Survey of Prospective Structure-Based Virtual Screening for Early Drug Discovery in the Past Fifteen Years. Int J Mol Sci 2022; 23:15961. [PMID: 36555602 PMCID: PMC9781938 DOI: 10.3390/ijms232415961] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Structure-based virtual screening (SBVS), also known as molecular docking, has been increasingly applied to discover small-molecule ligands based on the protein structures in the early stage of drug discovery. In this review, we comprehensively surveyed the prospective applications of molecular docking judged by solid experimental validations in the literature over the past fifteen years. Herein, we systematically analyzed the novelty of the targets and the docking hits, practical protocols of docking screening, and the following experimental validations. Among the 419 case studies we reviewed, most virtual screenings were carried out on widely studied targets, and only 22% were on less-explored new targets. Regarding docking software, GLIDE is the most popular one used in molecular docking, while the DOCK 3 series showed a strong capacity for large-scale virtual screening. Besides, the majority of identified hits are promising in structural novelty and one-quarter of the hits showed better potency than 1 μM, indicating that the primary advantage of SBVS is to discover new chemotypes rather than highly potent compounds. Furthermore, in most studies, only in vitro bioassays were carried out to validate the docking hits, which might limit the further characterization and development of the identified active compounds. Finally, several successful stories of SBVS with extensive experimental validations have been highlighted, which provide unique insights into future SBVS drug discovery campaigns.
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Affiliation(s)
- Hui Zhu
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
- National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Yulin Zhang
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
- National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Wei Li
- RPXDs (Suzhou) Co., Ltd., Suzhou 215028, China
| | - Niu Huang
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
- National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
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3
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Moorthy NSHN, Brás NF, Ramos MJ, Fernandes PA. Structure based virtual screening of natural product molecules as glycosidase inhibitors. In Silico Pharmacol 2021; 9:56. [PMID: 34722112 DOI: 10.1007/s40203-021-00115-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/01/2021] [Indexed: 11/30/2022] Open
Abstract
Objective of the present investigation comprised of the application of in silico methods to discover novel natural product (NP) based potential inhibitors for carbohydrate mediated diseases. Structure based drug design studies (molecular docking and structure based pharmacophore analysis) were carried out on a series of natural product compounds to identify significant bioactive molecules to inhibit α-mannosidase (I and II) and β-galactosidase enzymes. Furthermore, protein ligand interaction fingerprint analysis, molecular dynamics simulations and molecular access system (MACCS) fingerprint analysis were performed to understand the binding behaviors of the studied molecules. The results derived from these analyses showed that the identified compounds exhibit significant binding interactions with the active site residues. The compounds, NP-51, NP-81 and NP-165 have shown significant docking score against the studied enzymes (α-mannosidases-I, α-mannosidases-II and β-galactosidases). The fingerprint studies showed that the presence of rings (aromatic or aliphatic) with sulfur atoms, nitrogen atoms, methyl groups, etc. have favorable effects on the α-mannosidase II inhibitory activity. However, the presence of halogen atoms substituted in the molecules have reduced inhibitory ability against α-mannosidase II. The compound, NP-165 has significant activity against both enzymes (α-mannosidases and β-galactosidases). These studies accomplished that the compounds identified through in silico methodologies can be used to develop semisynthetic derivatives of the glycosidase inhibitors and can be screened for the treatment of different carbohydrate mediated diseases. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-021-00115-9.
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Affiliation(s)
- N S Hari Narayana Moorthy
- Department of Pharmacy, Indira Gandhi National Tribal University, Amarkantak, MP 484887 India.,UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 6874169-007 Porto, Portugal
| | - Natércia F Brás
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 6874169-007 Porto, Portugal
| | - Maria J Ramos
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 6874169-007 Porto, Portugal
| | - Pedro A Fernandes
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 6874169-007 Porto, Portugal
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4
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Prediction and characterization of influenza virus polymerase inhibitors through blind docking and ligand based virtual screening. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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5
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Kellici TF, Pilka ES, Bodkin MJ. Small-molecule modulators of serine protease inhibitor proteins (serpins). Drug Discov Today 2020; 26:442-454. [PMID: 33259801 DOI: 10.1016/j.drudis.2020.11.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 10/11/2020] [Accepted: 11/10/2020] [Indexed: 02/06/2023]
Abstract
Serine protease inhibitors (serpins) are a large family of proteins that regulate and control crucial physiological processes, such as inflammation, coagulation, thrombosis and thrombolysis, and immune responses. The extraordinary impact that these proteins have on numerous crucial pathways makes them an attractive target for drug discovery. In this review, we discuss recent advances in research on small-molecule modulators of serpins, examine their mode of action, analyse the structural data from crystallised protein-ligand complexes, and highlight the potential obstacles and possible therapeutic perspectives. The application of in silico methods for rational drug discovery is also summarised. In addition, we stress the need for continued research in this field.
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6
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Molecular insight into silk fibroin based delivery vehicle for amphiphilic drugs: Synthesis, characterization and molecular dynamics studies. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2019.112156] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Ramos RS, Macêdo WJC, Costa JS, da Silva CHTDP, Rosa JMC, da Cruz JN, de Oliveira MS, de Aguiar Andrade EH, E Silva RBL, Souto RNP, Santos CBR. Potential inhibitors of the enzyme acetylcholinesterase and juvenile hormone with insecticidal activity: study of the binding mode via docking and molecular dynamics simulations. J Biomol Struct Dyn 2019; 38:4687-4709. [PMID: 31674282 DOI: 10.1080/07391102.2019.1688192] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Models validation in QSAR, pharmacophore, docking and others can ensure the accuracy and reliability of future predictions in design and selection of molecules with biological activity. In this study, pyriproxyfen was used as a pivot/template to search the database of the Maybridge Database for potential inhibitors of the enzymes acetylcholinesterase and juvenile hormone as well. The initial virtual screening based on the 3D shape resulted in 2000 molecules with Tanimoto index ranging from 0.58 to 0.88. A new reclassification was performed on the overlapping of positive and negative charges, which resulted in 100 molecules with Tanimoto's electrostatic score ranging from 0.627 to 0.87. Using parameters related to absorption, distribution, metabolism and excretion and the pivot molecule, the molecules selected in the previous stage were evaluated regarding these criteria, and 21 were then selected. The pharmacokinetic and toxicological properties were considered and for 12 molecules, the DEREK software not fired any alert of toxicity, which were thus considered satisfactory for prediction of biological activity using the Web server PASS. In the molecular docking with insect acetylcholinesterase, the Maybridge3_002654 molecule had binding affinity of -11.1 kcal/mol, whereas in human acetylcholinesterase, the Maybridge4_001571molecule show in silico affinity of -10.2 kcal/mol, and in the juvenile hormone, the molecule MCULE-8839595892 show in silico affinity value of -11.6 kcal/mol. Subsequent long-trajectory molecular dynamics studies indicated considerable stability of the novel molecules compared to the controls.AbbreviationsQSARquantitative structure-activity relationshipsPASSprediction of activity spectra for substancesCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ryan S Ramos
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá, Brazil.,Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Brazil.,Laboratory of Molecular Modeling and Simulation System, Federal Rural University of Amazônia, Capanema, Brazil
| | - Williams J C Macêdo
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Brazil.,Laboratory of Molecular Modeling and Simulation System, Federal Rural University of Amazônia, Capanema, Brazil
| | - Josivan S Costa
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Brazil.,Laboratory of Molecular Modeling and Simulation System, Federal Rural University of Amazônia, Capanema, Brazil
| | - Carlos H T de P da Silva
- Computational Laboratory of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences of Ribeirão Preto, São Paulo, Brazil
| | - Joaquín M C Rosa
- Department of Pharmaceutical Organic Chemistry, University of Granada, Granada, Spain
| | | | - Mozaniel S de Oliveira
- Program of Post-Graduation in Food Science and Technology, Federal University of Pará, Belém, Brazil
| | - Eloisa H de Aguiar Andrade
- Adolpho Ducke Laboratory, Emílio Goeldi Paraense Museum, Belém, Brazil.,Program of Post-Graduation in Biodiversity and Biotechnology (BIONORTE), Federal University of Pará, Belém, Brazil
| | - Raullyan B L E Silva
- Center of Biodiversity, Institute for Scientific and Technological Research of Amapá (IEPA), Brazil
| | | | - Cleydson B R Santos
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá, Brazil.,Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Brazil
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8
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Labeling IL-18 with alkaloids: toward the use of cytokines as carrier molecules in chemotherapy. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2483-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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9
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Size and Flexibility Define the Inhibition of the H3N2 Influenza Endonuclease Enzyme by Calix[n]arenes. Antibiotics (Basel) 2019; 8:antibiotics8020073. [PMID: 31163674 PMCID: PMC6627454 DOI: 10.3390/antibiotics8020073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/29/2019] [Accepted: 05/30/2019] [Indexed: 12/21/2022] Open
Abstract
Inhibition of H3N2 influenza PA endonuclease activity by a panel of anionic calix[n]arenes and β-cyclodextrin sulfate has been studied. The joint experimental and theoretical results reveal that the larger, more flexible and highly water-soluble sulfonato-calix[n]arenes have high inhibitory activity, with para-sulfonato-calix[8]arene, SC8, having an IC50 value of 6.4 μM. Molecular docking calculations show the SC8 can interact at both the polyanion binding site and also the catalytic site of H3N2 influenza PA endonuclease.
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10
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Banegas-Luna AJ, Cerón-Carrasco JP, Puertas-Martín S, Pérez-Sánchez H. BRUSELAS: HPC Generic and Customizable Software Architecture for 3D Ligand-Based Virtual Screening of Large Molecular Databases. J Chem Inf Model 2019; 59:2805-2817. [DOI: 10.1021/acs.jcim.9b00279] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Antonio J. Banegas-Luna
- Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Católica San Antonio de Murcia (UCAM), Campus de los Jerónimos s/n, 30107 Murcia, Spain
| | - José P. Cerón-Carrasco
- Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Católica San Antonio de Murcia (UCAM), Campus de los Jerónimos s/n, 30107 Murcia, Spain
| | - Savíns Puertas-Martín
- Supercomputing - Algorithms Research Group (SAL), Department of Informatics, University of Almería, Agrifood Campus of International Excellence, ceiA3, Almería, 04120, Spain
| | - Horacio Pérez-Sánchez
- Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Católica San Antonio de Murcia (UCAM), Campus de los Jerónimos s/n, 30107 Murcia, Spain
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11
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Wang XS, Guan SY, Liu A, Yue J, Hu LN, Zhang K, Yang LK, Lu L, Tian Z, Zhao MG, Liu SB. Anxiolytic effects of Formononetin in an inflammatory pain mouse model. Mol Brain 2019; 12:36. [PMID: 30961625 PMCID: PMC6454770 DOI: 10.1186/s13041-019-0453-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 03/25/2019] [Indexed: 12/24/2022] Open
Abstract
Chronic pain is commonly accompanied with anxiety disorder, which complicates treatment. In this study, we investigated the analgesic and anxiolytic effects of Formononetin (FMNT), an active component of traditional Chinese medicine red clover (Trifolium pratense L.) that is capable of protecting neurons from N-methyl-D-aspartate (NMDA)-evoked excitotoxic injury, on mice suffering from complete Freund’s adjuvant (CFA)-induced chronic inflammatory pain. The results show that FMNT administration significantly reduces anxiety-like behavior but does not affect the nociceptive threshold in CFA-injected mice. The treatment reverses the upregulation of NMDA, GluA1, and GABAA receptors, as well as PSD95 and CREB in the basolateral amygdala (BLA). The effects of FMNT on NMDA receptors and CREB binding protein (CBP) were further confirmed by the potential structure combination between these compounds, which was analyzed by in silico docking technology. FMNT also inhibits the activation of the NF-κB signaling pathway and microglia in the BLA of mice suffering from chronic inflammatory pain. Therefore, the anxiolytic effects of FMNT are partially due to the attenuation of inflammation and neuronal hyperexcitability through the inhibition of NMDA receptor and CBP in the BLA.
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Affiliation(s)
- Xin-Shang Wang
- Department of Pharmacology, School of Pharmacy, and Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Shao-Yu Guan
- Department of Pharmacology, School of Pharmacy, and Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - An Liu
- Department of Pharmacology, School of Pharmacy, and Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Jiao Yue
- Department of Pharmacology, School of Pharmacy, and Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Li-Ning Hu
- Department of Pharmacology, School of Pharmacy, and Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Kun Zhang
- Department of Pharmacology, School of Pharmacy, and Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Liu-Kun Yang
- Department of Pharmacology, School of Pharmacy, and Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Liang Lu
- Department of Pharmacology, School of Pharmacy, and Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Zhen Tian
- Department of Pharmacology, School of Pharmacy, and Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710032, China.,The 154th Central Hospital of PLA, Xinyang, 464000, China
| | - Ming-Gao Zhao
- Department of Pharmacology, School of Pharmacy, and Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Shui-Bing Liu
- Department of Pharmacology, School of Pharmacy, and Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710032, China.
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12
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Wu J, Xie D, Chen X, Tang YJ, Wang L, Xie J, Wei D. Inhibitory mechanism of a substrate-type angiotensin I-converting enzyme inhibitory peptide. Process Biochem 2019. [DOI: 10.1016/j.procbio.2018.12.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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13
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Sharma A, Kumar V, Pratap S, Kumar P. The inhibitory and binding studies of methyl-sulfone hydroxamate based inhibitors against LpxC from drug resistant Moraxella catarrhalis using biophysical, biochemical and in silico approaches. Int J Biol Macromol 2018; 118:1747-1762. [DOI: 10.1016/j.ijbiomac.2018.07.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/06/2018] [Accepted: 07/07/2018] [Indexed: 01/17/2023]
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14
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Mehta P, Srivastava S, Sharma M, Singh I, Malik R. Identification of chemically diverse GABA A agonists as potential anti-epileptic agents using structure-guided virtual screening, ADMET, quantum mechanics and clinical validation through off-target analysis. Int J Biol Macromol 2018; 119:1113-1128. [PMID: 30098361 DOI: 10.1016/j.ijbiomac.2018.08.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/06/2018] [Accepted: 08/07/2018] [Indexed: 11/19/2022]
Abstract
Development of resistance against existing anti-epileptic drugs has alarmed the scientific innovators to find novel potential chemical starting points for the treatment of epilepsy and GABAA inhibition is a promising drug target strategy against epilepsy. The crystal structure of a subtype-selective β3-homopentameric ligand-gated ion channel of GABAA receptor has been used for the first time for screening the Asinex library for discovery of GABAA agonists as potential anti-epileptic agents. Co-crystallized ligand established the involvement of part of the β7-β8 loop (Glu155 and Tyr157) and β9-β10 loop (Phe200 and Tyr205) residues as the crucial amino acids in effective binding, an essential feature, being hydrogen bond or ionic interaction with Glu155 residue. Top ranked hits were further subjected to binding energy estimation, ADMET analysis and ligand efficiency matric calculations as consecutive filters. About 19 compounds qualifying all parameters possessed interaction of one positively charged group with Glu155 with good CNS drug-like properties. Simulation studies were performed on the apo protein, its complex with co-crystallized ligand and the best hit qualifying all screening parameters. The best hit was also analyzed using Quantum mechanical studies, off-target analysis and hit modification. The off-target analysis emphasized that these agents did not have any other predicted side-effects.
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Affiliation(s)
- Pakhuri Mehta
- Department of Pharmacy, Central University of Rajasthan, NH-8, Bandar Sindri, Ajmer, Rajasthan 305817, India
| | - Shubham Srivastava
- Department of Pharmacy, Central University of Rajasthan, NH-8, Bandar Sindri, Ajmer, Rajasthan 305817, India
| | - Manish Sharma
- School of Pharmacy, Maharishi Markandeshwar University, Sadopur, Ambala, Haryana 134007, India
| | - Inderpal Singh
- Bioinformatics Infrastructure Facility, Department of Biotechnology, Shri Mata Vaishno Devi University (SMVDU), Kakryal, Katra, Jammu & Kashmir 182320, India
| | - Ruchi Malik
- Department of Pharmacy, Central University of Rajasthan, NH-8, Bandar Sindri, Ajmer, Rajasthan 305817, India.
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15
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Abstract
Beyond finding inhibitors that show high binding affinity to the respective target, there is the challenge of optimizing their properties with respect to metabolic and toxicological issues, as well as further off-target effects. To reduce the experimental effort of synthesizing and testing actual substances in corresponding assays, virtual screening has become an indispensable toolbox in preclinical development. The scope of application covers the prediction of molecular properties including solubility, metabolic liability and binding to antitargets, such as the hERG channel. Furthermore, prediction of binding sites and drugable targets are emerging aspects of virtual screening. Issues involved with the currently applied computational models including machine learning algorithms are outlined, such as limitations to the accuracy of prediction and overfitting.
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16
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Sarukhanyan E, Shityakov S, Dandekar T. In Silico Designed Axl Receptor Blocking Drug Candidates Against Zika Virus Infection. ACS OMEGA 2018; 3:5281-5290. [PMID: 30023915 PMCID: PMC6044927 DOI: 10.1021/acsomega.8b00223] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 04/13/2018] [Indexed: 05/24/2023]
Abstract
After a large outbreak in Brazil, novel drugs against Zika virus became extremely necessary. Evaluation of virus-based pharmacological strategies concerning essential host factors brought us to the idea that targeting the Axl receptor by blocking its dimerization function could be critical for virus entry. Starting from experimentally validated compounds, such as RU-301, RU-302, warfarin, and R428, we identified a novel compound 2' (R428 derivative) to be the most potent for this task amongst a number of alternative compounds and leads. The improved affinity of compound 2' was confirmed by molecular docking as well as molecular dynamics simulation techniques using implicit solvation models. The current study summarizes a new possibility for inhibition of the Axl function as a potential target for future antiviral therapies.
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Affiliation(s)
- Edita Sarukhanyan
- Department
of Bioinformatics, Biocenter, University
of Würzburg, Am
Hubland, 97074 Würzburg, Germany
| | - Sergey Shityakov
- Department
of Anesthesia and Critical Care, University
Hospital Würzburg, Oberdürrbacher Str. 6, 97080 Würzburg, Germany
| | - Thomas Dandekar
- Department
of Bioinformatics, Biocenter, University
of Würzburg, Am
Hubland, 97074 Würzburg, Germany
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17
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Cerón-Carrasco JP, Pérez-Sánchez H, Zúñiga J, Requena A. Antibodies as Carrier Molecules: Encapsulating Anti-Inflammatory Drugs inside Herceptine. J Phys Chem B 2018; 122:2064-2072. [DOI: 10.1021/acs.jpcb.7b10749] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- José Pedro Cerón-Carrasco
- Bioinformatics
and High Performance Computing Research Group (BIO-HPC), Universidad Católica San Antonio de Murcia (UCAM) Campus de los Jerónimos, 30107 Murcia, Spain
| | - Horacio Pérez-Sánchez
- Bioinformatics
and High Performance Computing Research Group (BIO-HPC), Universidad Católica San Antonio de Murcia (UCAM) Campus de los Jerónimos, 30107 Murcia, Spain
| | - José Zúñiga
- Departamento
de Química Física, Universidad de Murcia, 30100 Murcia, Spain
| | - Alberto Requena
- Departamento
de Química Física, Universidad de Murcia, 30100 Murcia, Spain
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18
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Khan MF, Nahar N, Rashid RB, Chowdhury A, Rashid MA. Computational investigations of physicochemical, pharmacokinetic, toxicological properties and molecular docking of betulinic acid, a constituent of Corypha taliera (Roxb.) with Phospholipase A2 (PLA2). BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2018; 18:48. [PMID: 29391000 PMCID: PMC5795847 DOI: 10.1186/s12906-018-2116-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 01/26/2018] [Indexed: 11/10/2022]
Abstract
BACKGROUND Betulinic acid (BA) is a natural triterpenoid compound and exhibits a wide range of biological and medicinal properties including anti-inflammatory activity. Therefore, this theoretical investigation is performed to evaluate (a) physicochemical properties such as acid dissociation constant (pKa), distribution coefficient (logD), partition coefficient (logP), aqueous solubility (logS), solvation free energy, dipole moment, polarizability, hyperpolarizability and different reactivity descriptors, (b) pharmacokinetic properties like human intestinal absorption (HIA), cellular permeability, skin permeability (PSkin), plasma protein binding (PPB), penetration of the blood brain barrier (BBB), (c) toxicological properties including mutagenicity, carcinogenicity, risk of inhibition of hERG gene and (d) molecular mechanism of anti-inflammatory action which will aid the development of analytical method and the synthesis of BA derivatives. METHODS The physicochemical properties were calculated using MarvinSketch 15.6.29 and Gaussian 09 software package. The pharmacokinetic and toxicological properties were calculated on online server PreADMET. Further, the molecular docking study was conducted on AutoDock vina in PyRx 0.8. RESULTS The aqueous solubility increased with increasing pH due to the ionization of BA leading to decrease in distribution coefficient. The solvation energies in water, dimethyl sulfoxide (DMSO), acetonitrile, n-octanol, chloroform and carbon tetrachloride were - 41.74 kJ/mol, - 53.80 kJ/mol, - 66.27 kJ/mol, - 69.64 kJ/mol, - 65.96 kJ/mol and - 60.13 kJ/mol, respectively. From the results of polarizability and softness, it was clear that BA is less stable and hence, kinetically more reactive in water. BA demonstrated good human intestinal absorption (HIA) and moderate cellular permeability. Further, BA also exhibited positive CNS activity due to high permeability through BBB. The toxicological study revealed that BA was a mutagenic compound but noncarcinogenic in mice model. Moreover, molecular docking study of BA with PLA2 revealed that BA interacts with GLY22 & GLY29 through hydrogen bond formation and LEU2, PHE5, HIS6, ALA17, ALA18, HIS47 and TYR51 through different types of hydrophobic interactions. The binding affinity of BA was - 41.00 kJ/mol which is comparable to the binding affinity of potent inhibitor 6-Phenyl-4(R)-(7-Phenyl-heptanoylamino)-hexanoic acid (BR4) (- 33.89 kJ/mol). CONCLUSIONS Our computed properties may assist the development of analytical method to assay BA or to develop BA derivatives with better pharmacokinetic and toxicological profile.
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Arantes PR, Pérez-Sánchez H, Verli H. Antithrombin conformational modulation by D-myo-inositol 3,4,5,6-tetrakisphosphate (TMI), a novel scaffold for the development of antithrombotic agents. J Biomol Struct Dyn 2017; 36:4045-4056. [DOI: 10.1080/07391102.2017.1407259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Pablo Ricardo Arantes
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, CP 15005, Porto Alegre 91500-970, RS, Brazil
| | - Horacio Pérez-Sánchez
- Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Católica de Murcia (UCAM), Murcia, Spain
| | - Hugo Verli
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, CP 15005, Porto Alegre 91500-970, RS, Brazil
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Discovery of potential Zika virus RNA polymerase inhibitors by docking-based virtual screening. Comput Biol Chem 2017; 71:144-151. [DOI: 10.1016/j.compbiolchem.2017.10.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 09/14/2017] [Accepted: 10/18/2017] [Indexed: 11/20/2022]
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Wahlmüller FC, Sokolikova B, Rieger D, Geiger M. New lipid interaction partners stimulate the inhibition of activated protein C by cell-penetrating protein C inhibitor. Thromb Haemost 2017; 111:41-52. [DOI: 10.1160/th13-06-0478] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 08/24/2013] [Indexed: 12/18/2022]
Abstract
SummaryProtein C inhibitor (PCI, SerpinA5) is a heparin-binding serpin which can penetrate through cellular membranes. Selected negatively charged phospholipids like unsaturated phosphatidylserine and oxidised phosphatidylethanolamine bind to PCI and stimulate its inhibitory activity towards different proteases. The interaction of phospholipids with PCI might also alter the lipid distribution pattern of blood cells and influence the remodelling of cellular membranes. Here we showed that PCI is an additional binding partner of phosphatidic acid (PA), cardiolipin (CL), and phosphoinositides (PIPs). Protein lipid overlay assays exhibited a unique binding pattern of PCI towards different lipid species. In addition PA, CL, and unsaturated, monophosphorylated PIPs stimulated the inhibitory property of PCI towards activated protein C in a heparin like manner. As shown for kallistatin (SerpinA4) and vaspin (SerpinA12), the incubation of cells with PCI led to the activation of protein kinase B (AKT), which could be achieved through direct interaction of PCI with PIPs. This model is supported by the fact that PCI stimulated the PIP-dependent 5-phosphatase SHIP2 in vitro, which would result in AKT activation. Hence the interaction of PCI with different lipids might not only stimulate the inhibition of potential target protease by PCI, but could also alter intracellular lipid signalling.
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Multi-functional activities of citrus flavonoid narirutin in Alzheimer’s disease therapeutics: An integrated screening approach and in vitro validation. Int J Biol Macromol 2017; 103:733-743. [DOI: 10.1016/j.ijbiomac.2017.05.110] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/15/2017] [Accepted: 05/17/2017] [Indexed: 01/13/2023]
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Zhang X, Perez-Sanchez H, Lightstone FC. A Comprehensive Docking and MM/GBSA Rescoring Study of Ligand Recognition upon Binding Antithrombin. Curr Top Med Chem 2017; 17:1631-1639. [PMID: 27852201 PMCID: PMC5403970 DOI: 10.2174/1568026616666161117112604] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 06/12/2016] [Accepted: 06/19/2016] [Indexed: 11/22/2022]
Abstract
Background: A high-throughput virtual screening pipeline has been extended from single energetically minimized structure Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) rescoring to ensemble-average MM/GBSA rescoring. The correlation coefficient (R2) of calculated and experimental binding free energies for a series of antithrombin ligands has been improved from 0.36 to 0.69 when switching from the single-structure MM/GBSA rescoring to ensemble-average one. The electrostatic interactions in both solute and solvent are identified to play an important role in determining the binding free energy after the decomposition of the calculated binding free energy. The increasing negative charge of the compounds provides a more favorable electrostatic energy change but creates a higher penalty for the solvation free energy. Such a penalty is compensated by the electrostatic energy change, which results in a better binding affinity. A highly hydrophobic ligand is determined by the docking program to be a non-specific binder. Results: Our results have demonstrated that it is very important to keep a few top poses for rescoring, if the binding is non-specific or the binding mode is not well determined by the docking calculation.
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Affiliation(s)
- Xiaohua Zhang
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory (LLNL), Livermore, CA, United States
| | - Horacio Perez-Sanchez
- Bioinformatics and High Performance Computing Research Group, Department of Computer Science, Universidad Católica San Antonio de Murcia (UCAM), Spain
| | - Felice C Lightstone
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory (LLNL), Livermore 94550, CA, United States
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Rauf A, Hadda TB, Uddin G, Cerón-Carrasco JP, Peña-García J, Pérez-Sánchez H, Khan H, Bawazeer S, Patel S, Mubarak MS, Abu-Izneid T, Mabkhot YN. Sedative-hypnotic-like effect and molecular docking of di-naphthodiospyrol from Diospyros lotus in an animal model. Biomed Pharmacother 2017; 88:109-113. [DOI: 10.1016/j.biopha.2017.01.043] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 01/05/2017] [Accepted: 01/06/2017] [Indexed: 11/25/2022] Open
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Maiti J, Biswas S, Chaudhuri A, Chakraborty S, Chakraborty S, Das R. Environment sensitive fluorescent analogue of biologically active oxazoles differentially recognizes human serum albumin and bovine serum albumin: Photophysical and molecular modeling studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 175:191-199. [PMID: 28039847 DOI: 10.1016/j.saa.2016.12.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/24/2016] [Accepted: 12/20/2016] [Indexed: 06/06/2023]
Abstract
An environment sensitive fluorophore, 4-(5-(4-(dimethylamino)phenyl)oxazol-2-yl)benzoic acid (DMOBA), that closely mimics biologically active 2,5-disubstituited oxazoles has been designed to probe two homologous serum proteins, human serum albumin (HSA) and bovine serum albumin (BSA) by means of photophysical and molecular modeling studies. This fluorescent analogue exhibits solvent polarity sensitive fluorescence due to an intramolecular charge transfer in the excited state. In comparison to water, the steady state emission spectra of DMOBA in BSA is characterized by a greater blue shift (~10nm) and smaller Stokes' shift (~5980cm-1) in BSA than HSA (Stokes'shift~6600cm-1), indicating less polar and more hydrophobic environment of the dye in the former than the latter. The dye-protein binding interactions are remarkably stronger for BSA than HSA which is evident from higher value of the association constant for the DMOBA-BSA complex (Ka~5.2×106M-1) than the DMOBA-HSA complex (Ka~1.0×106M-1). Fӧrster resonance energy transfer studies revealed remarkably less efficient energy transfer (8%) between the donor tryptophans in BSA and the acceptor DMOBA dye than that (30%) between the single tryptophan moiety in HSA and the dye, which is consistent with a much larger distance between the donor (tryptophan)-acceptor (dye) pair in BSA (34.5Å) than HSA (25.4Å). Site specific competitive binding assays have confirmed on the location of the dye in Sudlow's site II of BSA and in Sudlow's site I of HSA, respectively. Molecular modeling studies have shown that the fluorescent analogue is tightly packed in the binding site of BSA due to strong steric complementarity, where, binding of DMOBA to BSA is primarily dictated by the van der Waals and hydrogen bonding interactions. In contrast, in HSA the steric complementarity is less significant and binding is primarily guided by polar interactions and van der Waals interactions appear to be less significant in the formation of the HSA-DMOBA complex. Electrostatic interactions contribute significantly in the binding of DMOBA to HSA (-2.09kcal/mol) compared to BSA (-0.47kcal/mol). Electrostatic surface potential calculation reveals that the DMOBA binding site within HSA is highly charged compared to BSA.
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Affiliation(s)
- Jyotirmay Maiti
- Department of Chemistry, West Bengal State University, Barasat, Kol-126, India
| | - Suman Biswas
- Department of Chemistry, West Bengal State University, Barasat, Kol-126, India
| | - Ankur Chaudhuri
- Department of Microbiology, West Bengal State University, Barasat, Kol-126, India
| | - Sandipan Chakraborty
- Department of Microbiology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700 019, India
| | - Sibani Chakraborty
- Department of Microbiology, West Bengal State University, Barasat, Kol-126, India
| | - Ranjan Das
- Department of Chemistry, West Bengal State University, Barasat, Kol-126, India.
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In vitro modulatory effects of functionalized pyrimidines and piperidine derivatives on Aryl hydrocarbon receptor (AhR) and glucocorticoid receptor (GR) activities. Bioorg Chem 2017; 71:285-293. [PMID: 28267985 DOI: 10.1016/j.bioorg.2017.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 02/06/2017] [Accepted: 02/18/2017] [Indexed: 11/21/2022]
Abstract
The development of biologically active molecules based on molecular recognition is an attractive and challenging task in medicinal chemistry and the molecules that can activate/deactivate certain receptors are of great medical interest. In this contribution, selected pyrimidine/piperidine derivatives were synthesized and tested for the ability to activate/deactivate Aryl hydrocarbon receptor (AhR) and Glucocorticoid receptor (GR). Tested compounds are shown to activate the receptors but to much lesser extent than positive controls, dioxin and dexamethasone for Ahr and GR, respectively. However, some of them antagonized the positive controls action. Although further in vivo studies are needed to fully characterize the bioactivities of these compounds, the reported in vitro evidences demonstrate that they might be used as the modulators of AhR and GR activities.
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Chakraborty S, Basu S. Dual inhibition of BACE1 and Aβ aggregation by β-ecdysone: Application of a phytoecdysteroid scaffold in Alzheimer’s disease therapeutics. Int J Biol Macromol 2017; 95:281-287. [DOI: 10.1016/j.ijbiomac.2016.11.061] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 01/01/2023]
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Collado-González M, Montalbán MG, Peña-García J, Pérez-Sánchez H, Víllora G, Díaz Baños FG. Chitosan as stabilizing agent for negatively charged nanoparticles. Carbohydr Polym 2016; 161:63-70. [PMID: 28189247 DOI: 10.1016/j.carbpol.2016.12.043] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 12/03/2016] [Accepted: 12/18/2016] [Indexed: 01/15/2023]
Abstract
Chitosan is a biocompatible polysaccharide with positive Z potential which can stabilize negative charged nanoparticles. Silk fibroin nanoparticles and citrate gold nanoparticles, both with negative Z potential, but they form aggregates at physiological ionic strength. In this work, we study the behavior of chitosan in solution when the ionic strength of the medium is increased and how the concentration of chitosan and the proportion of the two components (chitosan and AuNP or SFN) significantly affect the stability and size of the nanocomposites formed. In addition to experimental measurements, molecular modeling were used to gain insight into how chitosan interacts with silk fibroin monomers, and to identify the main energetic interactions involved in the process. The optimum values for obtaining the smallest and most homogeneous stable nanocomposites were obtained and two different ways of organization through which chitosan may exert its stabilizing effect were suggested.
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Affiliation(s)
| | | | - Jorge Peña-García
- Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Católica San Antonio de Murcia (UCAM), Murcia, Spain
| | - Horacio Pérez-Sánchez
- Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Católica San Antonio de Murcia (UCAM), Murcia, Spain
| | - Gloria Víllora
- Department of Chemical Engineering, University of Murcia, Murcia, Spain
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Martínez-Ballesta MDC, Pérez-Sánchez H, Moreno DA, Carvajal M. Plant plasma membrane aquaporins in natural vesicles as potential stabilizers and carriers of glucosinolates. Colloids Surf B Biointerfaces 2016; 143:318-326. [DOI: 10.1016/j.colsurfb.2016.03.056] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/15/2016] [Accepted: 03/18/2016] [Indexed: 02/02/2023]
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Martínez-Martínez I, González-Porras JR, Cebeira MJ, de Arriba F, Espín S, Bohdan N, Corrales FJ, Corral J, Vicente V. Identification of a new potential mechanism responsible for severe bleeding in myeloma: immunoglobulins bind the heparin binding domain of antithrombin activating this endogenous anticoagulant. Haematologica 2016; 101:e423-e426. [PMID: 27479819 DOI: 10.3324/haematol.2016.144873] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Irene Martínez-Martínez
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Arrixaca, Pamplona, Spain Grupo de Investigación CB15/00055 del Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | | | | | - Felipe de Arriba
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Arrixaca, Pamplona, Spain
| | - Salvador Espín
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Arrixaca, Pamplona, Spain
| | - Nataliya Bohdan
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Arrixaca, Pamplona, Spain
| | | | - Javier Corral
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Arrixaca, Pamplona, Spain Grupo de Investigación CB15/00055 del Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Vicente Vicente
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Arrixaca, Pamplona, Spain Grupo de Investigación CB15/00055 del Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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Budryn G, Zaczyńska D, Pałecz B, Rachwał-Rosiak D, Belica S, den-Haan H, Peña-García J, Pérez-Sánchez H. Interactions of free and encapsulated hydroxycinnamic acids from green coffee with egg ovalbumin, whey and soy protein hydrolysates. Lebensm Wiss Technol 2016. [DOI: 10.1016/j.lwt.2015.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Brovarets' OO, Pérez-Sánchez H, Hovorun DM. Structural grounds for the 2-aminopurine mutagenicity: a novel insight into the old problem of the replication errors. RSC Adv 2016. [DOI: 10.1039/c6ra17787e] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Mutagenic pressure of the 2AP molecule on DNA during its replication is realized via the more intensive generation of the T* mutagenic tautomers through the reaction 2AP·T(WC) → 2AP·T*(w).
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Affiliation(s)
- Ol'ha O. Brovarets'
- Department of Molecular and Quantum Biophysics
- Institute of Molecular Biology and Genetics
- National Academy of Sciences of Ukraine
- 03680 Kyiv
- Ukraine
| | - Horacio Pérez-Sánchez
- Computer Science Department
- Bioinformatics and High Performance Computing (BIO-HPC) Research Group
- Universidad Católica San Antonio de Murcia (UCAM)
- Murcia
- Spain
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics
- Institute of Molecular Biology and Genetics
- National Academy of Sciences of Ukraine
- 03680 Kyiv
- Ukraine
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Effect of inclusion of hydroxycinnamic and chlorogenic acids from green coffee bean in β-cyclodextrin on their interactions with whey, egg white and soy protein isolates. Food Chem 2015; 168:276-87. [DOI: 10.1016/j.foodchem.2014.07.056] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 05/24/2014] [Accepted: 07/08/2014] [Indexed: 01/28/2023]
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Zhang X, Péréz-Sánchez H, Lightstone FC. Molecular Dynamics Simulations of Ligand Recognition upon Binding Antithrombin: A MM/GBSA Approach. BIOINFORMATICS AND BIOMEDICAL ENGINEERING 2015. [DOI: 10.1007/978-3-319-16480-9_56] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Cerón-Carrasco JP, Cerezo J, Requena A, Zuñiga J, Contreras-García J, Chavan S, Manrubia-Cobo M, Pérez-Sánchez H. Labelling Herceptin with a novel oxaliplatin derivative: a computational approach towards the selective drug delivery. J Mol Model 2014; 20:2401. [PMID: 25149438 DOI: 10.1007/s00894-014-2401-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 07/28/2014] [Indexed: 11/30/2022]
Abstract
The clinical use of platinum(II)-based drugs has serious side effects due to the non-specific reactions with both malignant and normal cells. To circumvent such major drawback, novel metallodrugs might be combined with suitable carrier molecules, as antibodies, to ensure selective attacks on tumours while sparing healthy tissues. In this contribution, we investigate the stability of a novel oxaliplatin derivate drug embedded in Herceptin (trastuzumab), an antibody which is able to recognise breast cancer cells, by using a wide panel of theoretical tools: docking, molecular dynamics and quantum calculations. Our calculations reveal the binding mechanism: the drug initially interacts non-covalently with the Pro40A and Asp167A residues, and the nitrogen of His171B subsequently replaces one of the water molecules coordinated to the platinum center, where the latter step reversibly fixes the drug into the antibody. These data might be used to further rationalise the synthesis of improved drugs beyond classical platinum(II) derivatives by improving the ligand-protein coupling mode.
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Affiliation(s)
- José P Cerón-Carrasco
- Departamento de Química Física, Facultad de Química, Universidad de Murcia, 30100 Campus de Espinardo, Murcia, Spain,
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Heart health risk assessment system: a nonintrusive proposal using ontologies and expert rules. BIOMED RESEARCH INTERNATIONAL 2014; 2014:959645. [PMID: 25045715 PMCID: PMC4082843 DOI: 10.1155/2014/959645] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 05/10/2014] [Accepted: 05/18/2014] [Indexed: 11/17/2022]
Abstract
According to the World Health Organization, the world's leading cause of death is heart disease, with nearly two million deaths per year. Although some factors are not possible to change, there are some keys that help to prevent heart diseases. One of the most important keys is to keep an active daily life, with moderate exercise. However, deciding what a moderate exercise is or when a slightly abnormal heart rate value is a risk depends on the person and the activity. In this paper we propose a context-aware system that is able to determine the activity the person is performing in an unobtrusive way. Then, we have defined ontology to represent the available knowledge about the person (biometric data, fitness status, medical information, etc.) and her current activity (level of intensity, heart rate recommended for that activity, etc.). With such knowledge, a set of expert rules based on this ontology are involved in a reasoning process to infer levels of alerts or suggestions for the users when the intensity of the activity is detected as dangerous for her health. We show how this approach can be accomplished by using only everyday devices such as a smartphone and a smartwatch.
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A performance/cost evaluation for a GPU-based drug discovery application on volunteer computing. BIOMED RESEARCH INTERNATIONAL 2014; 2014:474219. [PMID: 25025055 PMCID: PMC4082831 DOI: 10.1155/2014/474219] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 05/10/2014] [Accepted: 05/19/2014] [Indexed: 11/18/2022]
Abstract
Bioinformatics is an interdisciplinary research field that develops tools for the analysis of large biological databases, and, thus, the use of high performance computing (HPC) platforms is mandatory for the generation of useful biological knowledge. The latest generation of graphics processing units (GPUs) has democratized the use of HPC as they push desktop computers to cluster-level performance. Many applications within this field have been developed to leverage these powerful and low-cost architectures. However, these applications still need to scale to larger GPU-based systems to enable remarkable advances in the fields of healthcare, drug discovery, genome research, etc. The inclusion of GPUs in HPC systems exacerbates power and temperature issues, increasing the total cost of ownership (TCO). This paper explores the benefits of volunteer computing to scale bioinformatics applications as an alternative to own large GPU-based local infrastructures. We use as a benchmark a GPU-based drug discovery application called BINDSURF that their computational requirements go beyond a single desktop machine. Volunteer computing is presented as a cheap and valid HPC system for those bioinformatics applications that need to process huge amounts of data and where the response time is not a critical factor.
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Navarro-González I, Pérez-Sánchez H, Martín-Pozuelo G, García-Alonso J, Periago MJ. The inhibitory effects of bioactive compounds of tomato juice binding to hepatic HMGCR: in vivo study and molecular modelling. PLoS One 2014; 9:e83968. [PMID: 24392102 PMCID: PMC3879275 DOI: 10.1371/journal.pone.0083968] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 11/18/2013] [Indexed: 02/03/2023] Open
Abstract
The hypocholesterolemic effect of tomato juice has been investigated in an intervention study with rats, along with the possible inhibition effect of bioactive tomato compounds binding to the HMGCR enzyme. Two experimental groups (n = 8 Sprague-Dawley rats) were fed ad libitum for five weeks, with water or tomato juice provided to the control and intervention groups, respectively. Total, LDL and HDL cholesterol, and total triglycerides were analysed in plasma, and the lycopene content and the expression and activity of the enzyme HMGCR were determined in liver samples. A computational molecular modelling was carried out to determine the interactions between HMGCR and lycopene, chlorogenic acid and naringenin. Total, LDL and HDL cholesterol were significantly lower in the intervention group after the intake of tomato juice. In addition, a significant reduction in HMGCR activity was observed, although this was not accompanied by changes in gene expression. The molecular modelling showed that components of tomato can bind to the active site of the enzyme and compete with the ligand HMGCoA. Lycopene, from tomato juice, accumulates in the liver and can inhibit the activity of the rate-limiting enzyme of cholesterol biosynthesis, HMGCR.
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Affiliation(s)
- Inmaculada Navarro-González
- Dept. of Food Science and Nutrition, Faculty of Veterinary Science. University of Murcia, Campus de Espinardo. Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
- * E-mail: (IG); (HPS)
| | - Horacio Pérez-Sánchez
- Computer Science Department, Catholic University of Murcia (UCAM), Murcia, Spain
- * E-mail: (IG); (HPS)
| | - Gala Martín-Pozuelo
- Dept. of Food Science and Nutrition, Faculty of Veterinary Science. University of Murcia, Campus de Espinardo. Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Javier García-Alonso
- Dept. of Food Science and Nutrition, Faculty of Veterinary Science. University of Murcia, Campus de Espinardo. Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Maria Jesús Periago
- Dept. of Food Science and Nutrition, Faculty of Veterinary Science. University of Murcia, Campus de Espinardo. Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
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