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Sladek V, Tokiwa H, Shimano H, Shigeta Y. Protein Residue Networks from Energetic and Geometric Data: Are They Identical? J Chem Theory Comput 2018; 14:6623-6631. [PMID: 30500196 DOI: 10.1021/acs.jctc.8b00733] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein residue networks (PRN) from energetic and geometric data are probably not identical. PRNs constructed from ab initio pair interaction energies are analyzed for the first time and compared to PRN based on center of mass separation. We use modern, previously unused algorithms such as global and local efficiencies to quantitatively confirm that both types of PRNs do exhibit small-world character. The main novelty finding is that interaction energy-based PRNs preserve small-world character even when clustered. A node hierarchy independent of the cutoff energy used for the edge creation is characteristic for them. Efficiency centrality identifies hubs responsible for such behavior. The interaction energy-based PRNs seem to comply with the scale-free network model with respect to efficiency centrality distribution as opposed to distance based PRNs. Community detection is introduced into protein network research as an extension beyond cluster analysis to study tertiary and quaternary structures.
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Affiliation(s)
- Vladimir Sladek
- Institute of Chemistry - Centre for Glycomics , Dubravska cesta 9 , 84538 Bratislava , Slovakia.,Agency for Medical Research and Development (AMED) , Chiyoda-ku , Japan
| | - Hiroaki Tokiwa
- Agency for Medical Research and Development (AMED) , Chiyoda-ku , Japan.,Department of Chemistry , Rikkyo University , Nishi-Ikebukuro , Toshima, Tokyo 171-8501 , Japan
| | - Hitoshi Shimano
- Agency for Medical Research and Development (AMED) , Chiyoda-ku , Japan.,Department of Internal Medicine, Faculty of Medicine , University of Tsukuba , 1-1-1 Tennodai , Tsukuba, Ibaraki 305-8575 , Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences , University of Tsukuba , Tennodai 1-1-1 , Tsukuba, Ibaraki 305-8577 , Japan
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Costa JDS, Ramos RDS, Costa KDSL, Brasil DDSB, Silva CHTDPD, Ferreira EFB, Borges RDS, Campos JM, Macêdo WJDC, Santos CBRD. An In Silico Study of the Antioxidant Ability for Two Caffeine Analogs Using Molecular Docking and Quantum Chemical Methods. Molecules 2018; 23:molecules23112801. [PMID: 30380600 PMCID: PMC6278550 DOI: 10.3390/molecules23112801] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 10/01/2018] [Accepted: 10/11/2018] [Indexed: 12/13/2022] Open
Abstract
The antioxidant activity of molecules constitutes an important factor for the regulation of redox homeostasis and reduction of the oxidative stress. Cells affected by oxidative stress can undergo genetic alteration, causing structural changes and promoting the onset of chronic diseases, such as cancer. We have performed an in silico study to evaluate the antioxidant potential of two molecules of the zinc database: ZINC08706191 (Z91) and ZINC08992920 (Z20). Molecular docking, quantum chemical calculations (HF/6-31G**) and Pearson’s correlation have been performed. Molecular docking results of Z91 and Z20 showed both the lower binding affinity (BA) and inhibition constant (Ki) values for the receptor-ligand interactions in the three tested enzymes (cytochrome P450—CP450, myeloperoxidase—MP and NADPH oxidase—NO) than the control molecules (5-fluorouracil—FLU, melatonin—MEL and dextromethorphan—DEX, for each receptor respectively). Molecular descriptors were correlated with Ki and strong correlations were observed for the CP450, MP and NO receptors. These and other results attest the significant antioxidant ability of Z91 and Z20, that may be indicated for further analyses in relation to the control of oxidative stress and as possible antioxidant agents to be used in the pharmaceutical industry.
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Affiliation(s)
- Josivan da Silva Costa
- Postgraduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Pará, Rua Augusto Corrêa, 01, Belém, Pará 66075110, Brazil.
- Laboratory of Modeling and Computational Chemistry, Department of Biological Sciences, Federal University of Amapá, Rod. Juscelino Kubitschek, Km 02, s/n, Macapá, Amapá 68902-280, Brazil.
- Laboratory of Molecular Modeling and Simulation System, Federal Rural University of Amazônia, Rua João Pessoa, 121, Capanema, Pará 68700-030, Brazil.
| | - Ryan da Silva Ramos
- Laboratory of Modeling and Computational Chemistry, Department of Biological Sciences, Federal University of Amapá, Rod. Juscelino Kubitschek, Km 02, s/n, Macapá, Amapá 68902-280, Brazil.
- Laboratory of Molecular Modeling and Simulation System, Federal Rural University of Amazônia, Rua João Pessoa, 121, Capanema, Pará 68700-030, Brazil.
| | - Karina da Silva Lopes Costa
- Laboratory of Modeling and Computational Chemistry, Department of Biological Sciences, Federal University of Amapá, Rod. Juscelino Kubitschek, Km 02, s/n, Macapá, Amapá 68902-280, Brazil.
| | | | | | - Elenilze Figueiredo Batista Ferreira
- Laboratory of Modeling and Computational Chemistry, Department of Biological Sciences, Federal University of Amapá, Rod. Juscelino Kubitschek, Km 02, s/n, Macapá, Amapá 68902-280, Brazil.
| | - Rosivaldo Dos Santos Borges
- Postgraduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Pará, Rua Augusto Corrêa, 01, Belém, Pará 66075110, Brazil.
| | - Joaquín María Campos
- Department of Pharmaceutical and Organic Chemistry, University of Granada, Campus of Cartuja, 18071 Granada, Spain.
| | - Williams Jorge da Cruz Macêdo
- Postgraduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Pará, Rua Augusto Corrêa, 01, Belém, Pará 66075110, Brazil.
- Laboratory of Molecular Modeling and Simulation System, Federal Rural University of Amazônia, Rua João Pessoa, 121, Capanema, Pará 68700-030, Brazil.
| | - Cleydson Breno Rodrigues Dos Santos
- Laboratory of Modeling and Computational Chemistry, Department of Biological Sciences, Federal University of Amapá, Rod. Juscelino Kubitschek, Km 02, s/n, Macapá, Amapá 68902-280, Brazil.
- Laboratory of Molecular Modeling and Simulation System, Federal Rural University of Amazônia, Rua João Pessoa, 121, Capanema, Pará 68700-030, Brazil.
- Department of Pharmaceutical and Organic Chemistry, University of Granada, Campus of Cartuja, 18071 Granada, Spain.
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Yao XQ, Momin M, Hamelberg D. Elucidating Allosteric Communications in Proteins with Difference Contact Network Analysis. J Chem Inf Model 2018; 58:1325-1330. [DOI: 10.1021/acs.jcim.8b00250] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xin-Qiu Yao
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Mohamed Momin
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Donald Hamelberg
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United States
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Dorantes-Gilardi R, Bourgeat L, Pacini L, Vuillon L, Lesieur C. In proteins, the structural responses of a position to mutation rely on the Goldilocks principle: not too many links, not too few. Phys Chem Chem Phys 2018; 20:25399-25410. [DOI: 10.1039/c8cp04530e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A disease has distinct genetic and molecular hallmarks such as sequence variants that are likely to produce the alternative protein structures accountable for individual responses to drugs and disease development.
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Affiliation(s)
| | | | - Lorenza Pacini
- Institut Rhônalpin des systèmes complexes
- IXXI-ENS-Lyon
- Lyon
- France
- AMPERE
| | - Laurent Vuillon
- LAMA
- Univ. Savoie Mont Blanc
- CNRS, LAMA
- 73376 Le Bourget du Lac
- France
| | - Claire Lesieur
- Institut Rhônalpin des systèmes complexes
- IXXI-ENS-Lyon
- Lyon
- France
- AMPERE
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