Pub Date : 2018-12-19DOI: 10.3390/mol2net-04-06077
Inês D. S. Pires, M. Machuqueiro
{"title":"pH-dependent permeability of outer membrane protein G: an in silico study","authors":"Inês D. S. Pires, M. Machuqueiro","doi":"10.3390/mol2net-04-06077","DOIUrl":"https://doi.org/10.3390/mol2net-04-06077","url":null,"abstract":"","PeriodicalId":20475,"journal":{"name":"Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76344527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-12-19DOI: 10.3390/mol2net-04-06085
Rui J. S. Loureiro, Diogo Vila-Viçosa, M. Machuqueiro, E. Shakhnovich, P. Faísca
{"title":"The importance of unstructured termini in the aggregation cascade of beta-2-microglobulin: insights from molecular simulations of D76N mutant","authors":"Rui J. S. Loureiro, Diogo Vila-Viçosa, M. Machuqueiro, E. Shakhnovich, P. Faísca","doi":"10.3390/mol2net-04-06085","DOIUrl":"https://doi.org/10.3390/mol2net-04-06085","url":null,"abstract":"","PeriodicalId":20475,"journal":{"name":"Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87696467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-12-19DOI: 10.3390/mol2net-04-06078
Tatiana F. Vieira, Rita P. Magalhães, N. Cerqueira, S. Sousa
Graphical Abstract Abstract. G-protein-coupled receptors (GPCRs) constitute a large family of structurally similar proteins that respond to diverse physiological and environmental stimulants and that includes many therapeutic targets. In fact, 40% of all modern medicinal drugs are thought to target G-protein-coupled receptors (GPCRs), making this large family of proteins a particular appealing target for drug discovery efforts [1, 2]. Protein-ligand docking is a computational method that tries to predict and rank the structure resulting from the association between a ligand and a target protein [3]. Virtual screening (VS) can use docking to evaluate databases with millions of compounds to identify promising new molecules that could bind to a specific target of pharmacological interest, including GPCRs [4]. This strategy if often used to limit the amount of molecules that has to be tested experimentally and to reduce the cost in the identification of new lead molecules for drug development. This work reports a detailed comparison of the popular Autodock [5] and Vina [6] software programs in
{"title":"Evaluation of Different Scoring Functions for Docking and Virtual Screening against GPCR Drug Targets","authors":"Tatiana F. Vieira, Rita P. Magalhães, N. Cerqueira, S. Sousa","doi":"10.3390/mol2net-04-06078","DOIUrl":"https://doi.org/10.3390/mol2net-04-06078","url":null,"abstract":"Graphical Abstract Abstract. G-protein-coupled receptors (GPCRs) constitute a large family of structurally similar proteins that respond to diverse physiological and environmental stimulants and that includes many therapeutic targets. In fact, 40% of all modern medicinal drugs are thought to target G-protein-coupled receptors (GPCRs), making this large family of proteins a particular appealing target for drug discovery efforts [1, 2]. Protein-ligand docking is a computational method that tries to predict and rank the structure resulting from the association between a ligand and a target protein [3]. Virtual screening (VS) can use docking to evaluate databases with millions of compounds to identify promising new molecules that could bind to a specific target of pharmacological interest, including GPCRs [4]. This strategy if often used to limit the amount of molecules that has to be tested experimentally and to reduce the cost in the identification of new lead molecules for drug development. This work reports a detailed comparison of the popular Autodock [5] and Vina [6] software programs in","PeriodicalId":20475,"journal":{"name":"Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82043393","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-12-18DOI: 10.3390/MOL2NET-04-06075
C. Sousa, António J. M. Ribeiro, A. Fortes, N. Cerqueira, M. Alves
{"title":"Experimental and Computational Studies Addressed to 1,3-Dipolar Cycloadditions of D-Erythrose 1,3-Dioxane 1,5-Lactone with Regio- andStereo-selectivity","authors":"C. Sousa, António J. M. Ribeiro, A. Fortes, N. Cerqueira, M. Alves","doi":"10.3390/MOL2NET-04-06075","DOIUrl":"https://doi.org/10.3390/MOL2NET-04-06075","url":null,"abstract":"","PeriodicalId":20475,"journal":{"name":"Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90897261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-12-17DOI: 10.3390/MOL2NET-04-05923
Deyani Nocedo-Mena, E. Garza, Mauricio González-Ferrara, M. D. R. Camacho-Corona
Terpenoids play a crucial role in the performance of diverse ecological functions in response to biotic and abiotic factors. They are classified as secondary metabolism products. Among their functions are: be pollinating attractants, herbivore deterrents, insecticides / repellents, antibacterial compounds. Like many other natural products, they show biological activities, which have been exploited in the prevention and treatment of human diseases. As part of the phytochemical study performed on the Cissus incisa specie, the characterization using GC/MS of a triterpenes mixture of the chloroform / methanol 1:1 extract was carried out. In addition, the antibacterial activity was evaluated against nine strains of multi-resistant clinical isolates. As a result, C. incisa can be considered for further investigations as a source of compounds with antibacterial properties
{"title":"Antibacterial activities of triterpenes from leaves of Cissus incisa","authors":"Deyani Nocedo-Mena, E. Garza, Mauricio González-Ferrara, M. D. R. Camacho-Corona","doi":"10.3390/MOL2NET-04-05923","DOIUrl":"https://doi.org/10.3390/MOL2NET-04-05923","url":null,"abstract":"Terpenoids play a crucial role in the performance of diverse ecological functions in response to biotic and abiotic factors. They are classified as secondary metabolism products. Among their functions are: be pollinating attractants, herbivore deterrents, insecticides / repellents, antibacterial compounds. Like many other natural products, they show biological activities, which have been exploited in the prevention and treatment of human diseases. As part of the phytochemical study performed on the Cissus incisa specie, the characterization using GC/MS of a triterpenes mixture of the chloroform / methanol 1:1 extract was carried out. In addition, the antibacterial activity was evaluated against nine strains of multi-resistant clinical isolates. As a result, C. incisa can be considered for further investigations as a source of compounds with antibacterial properties","PeriodicalId":20475,"journal":{"name":"Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86291775","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-12-17DOI: 10.3390/MOL2NET-04-05924
Deyani Nocedo-Mena, Mauricio González-Ferrara, M. D. R. Camacho-Corona
Cissus incisa is an endemic plant from Mexico and the southern United States. In traditional Mexican medicine it is used to treat respiratory and skin infections, although it has not been scientifically validated until now. The current study was undertaken primarily to investigate the phytochemistry composition of this plant. From GC/MS technique was identified several compounds, among them, series of triterpenoids. These compounds are widely distributed in the plant kingdom. They have been investigated for their biological activities, such as anticancer and antimicrobial.
{"title":"Triterpenoids identified by GC-MS in chloroform/methanol extract from leaves of Cissus incisa","authors":"Deyani Nocedo-Mena, Mauricio González-Ferrara, M. D. R. Camacho-Corona","doi":"10.3390/MOL2NET-04-05924","DOIUrl":"https://doi.org/10.3390/MOL2NET-04-05924","url":null,"abstract":"Cissus incisa is an endemic plant from Mexico and the southern United States. In traditional Mexican medicine it is used to treat respiratory and skin infections, although it has not been scientifically validated until now. The current study was undertaken primarily to investigate the phytochemistry composition of this plant. From GC/MS technique was identified several compounds, among them, series of triterpenoids. These compounds are widely distributed in the plant kingdom. They have been investigated for their biological activities, such as anticancer and antimicrobial.","PeriodicalId":20475,"journal":{"name":"Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83954609","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-12-17DOI: 10.3390/mol2net-04-05926
Efrain Solares, E. Fernández, Jorge Navarro
Graphical Abstract Insert grafical abstract figure here Abstract. Portfolio optimization is one of the most addressed areas in operational research, mainly because of its practical relevance and interesting theoretical challenges. Recently, Solares et al . (2018) have proposed using probabilistic confidence intervals as criteria to select the most convenient portfolio. An approach following this idea allows the investor to consider not only the expected impact of the portfolios but also the risk of not obtaining that expected impact. Moreover, it identifies the behavior of the investor in presence of risk and gives her/him support depending on her/his own preferences. On the other hand, there are situations where the investor is not satisfied with the knowledge provided by probabilistic information (e.g., such information is precarious or the investor gives importance to other information, such as financial data). In this case, the investor may be interested in considering many criteria in order to select the most convenient portfolio.
{"title":"Portfolio optimization with incorporation of preferences and many criteria","authors":"Efrain Solares, E. Fernández, Jorge Navarro","doi":"10.3390/mol2net-04-05926","DOIUrl":"https://doi.org/10.3390/mol2net-04-05926","url":null,"abstract":"Graphical Abstract Insert grafical abstract figure here Abstract. Portfolio optimization is one of the most addressed areas in operational research, mainly because of its practical relevance and interesting theoretical challenges. Recently, Solares et al . (2018) have proposed using probabilistic confidence intervals as criteria to select the most convenient portfolio. An approach following this idea allows the investor to consider not only the expected impact of the portfolios but also the risk of not obtaining that expected impact. Moreover, it identifies the behavior of the investor in presence of risk and gives her/him support depending on her/his own preferences. On the other hand, there are situations where the investor is not satisfied with the knowledge provided by probabilistic information (e.g., such information is precarious or the investor gives importance to other information, such as financial data). In this case, the investor may be interested in considering many criteria in order to select the most convenient portfolio.","PeriodicalId":20475,"journal":{"name":"Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83964474","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-12-17DOI: 10.3390/MOL2NET-04-06009
Alejandro Valdés-Jiménez, Josep-L. Larriba-Pey, M. Reyes-Parada, Gabriel Núñez-Vivanco
Most of drugs interact with more than one molecular target. This fact typically would be seen like as an undesired feature of a pharmacological treatment, however, current trends in drug discovery has put hope and several efforts in the improved efficiency and efficacy that have been showed by some promiscuous drugs. Indeed, several approaches for predict the polypharmacological profile of drugs have been recently developed. In this line, the structure of proteins has gained special interest. The structure of proteins is several times more conserved than their sequence. Moreover, even in those cases where a close evolutionary relationship exists between two proteins, it is possible that their global structures are not conserving, and only share partial three-dimensional (3D) patterns, which define in most cases, their biological functions. Interestingly, several tools have been developed for the identification of similar 3D patterns, however, usually demand a known query or only consider the observed data (e.g. orthosteric binding sites in PDB, annotated motif, known ligands, etc.). Nevertheless, some approaches shows that 3D amino acids conservation is a enough prove for consider these residues as part of an active site or a binding site of a protein structure, even when no prior knowledge of functional residues are available. Thus, considering all unknown or unobserved 3D patterns (e.g. allosteric binding sites), for the discovery, search and characterization of putative common binding sites between a set of protein structures, cold be more informative than explore only known sites. Here, we present 3D-PP, a new free access web server to discover all conserved 3D amino acid patterns among a set of protein structures including those coming from both, X-ray crystallographic experiments and in silico comparative modelling. The preprocessing modules of 3D-PP were developed in Python and all data generated are processed and organized automatically in a scalable high-performance graph database. References (1–5) 1. Anighoro A, Bajorath J, Rastelli G. Polypharmacology: Challenges and Opportunities in Drug Discovery. J Med Chem [Internet]. 2014;dx.doi.org/10.1021/jm5006463. Available from: http://www.ncbi.nlm.nih.gov/pubmed/24946140 2. Konc J, Janežic D. Binding site comparison for function prediction and pharmaceutical discovery. Curr Opin Struct Biol [Internet]. 2014 Apr [cited 2014 Sep 3];25:34–9. Available from: http://www.ncbi.nlm.nih.gov/pubmed/24878342 3. Nadzirin N, Gardiner EJ, Willett P, Artymiuk PJ, Firdaus-Raih M. SPRITE and ASSAM: Web servers for side chain 3D-motif searching in protein structures. Nucleic Acids Res. 2012;40(W1). 4. Martinez-bazan N, Muntes-mulero V, Gomez-villamor S. DEX : High-Performance Exploration on Large Graphs for Information Retrieval. Artif Intell [Internet]. 2007;573–82. Available from: http://portal.acm.org/citation.cfm?doid=1321440.1321521 5. Nunez-Vivanco G, Valdes-Jimenez A, Besoain F, Reyes-Parada
{"title":"3D-PP: a tool for discovering conserved 3D protein patterns","authors":"Alejandro Valdés-Jiménez, Josep-L. Larriba-Pey, M. Reyes-Parada, Gabriel Núñez-Vivanco","doi":"10.3390/MOL2NET-04-06009","DOIUrl":"https://doi.org/10.3390/MOL2NET-04-06009","url":null,"abstract":"Most of drugs interact with more than one molecular target. This fact typically would be seen like as an undesired feature of a pharmacological treatment, however, current trends in drug discovery has put hope and several efforts in the improved efficiency and efficacy that have been showed by some promiscuous drugs. Indeed, several approaches for predict the polypharmacological profile of drugs have been recently developed. In this line, the structure of proteins has gained special interest. \u0000The structure of proteins is several times more conserved than their sequence. Moreover, even in those cases where a close evolutionary relationship exists between two proteins, it is possible that their global structures are not conserving, and only share partial three-dimensional (3D) patterns, which define in most cases, their biological functions. Interestingly, several tools have been developed for the identification of similar 3D patterns, however, usually demand a known query or only consider the observed data (e.g. orthosteric binding sites in PDB, annotated motif, known ligands, etc.). Nevertheless, some approaches shows that 3D amino acids conservation is a enough prove for consider these residues as part of an active site or a binding site of a protein structure, even when no prior knowledge of functional residues are available. Thus, considering all unknown or unobserved 3D patterns (e.g. allosteric binding sites), for the discovery, search and characterization of putative common binding sites between a set of protein structures, cold be more informative than explore only known sites. \u0000Here, we present 3D-PP, a new free access web server to discover all conserved 3D amino acid patterns among a set of protein structures including those coming from both, X-ray crystallographic experiments and in silico comparative modelling. The preprocessing modules of 3D-PP were developed in Python and all data generated are processed and organized automatically in a scalable high-performance graph database. \u0000References \u0007(1–5) \u0000\u00071. Anighoro A, Bajorath J, Rastelli G. Polypharmacology: Challenges and Opportunities in Drug Discovery. J Med Chem [Internet]. 2014;dx.doi.org/10.1021/jm5006463. Available from: http://www.ncbi.nlm.nih.gov/pubmed/24946140 \u00002. Konc J, Janežic D. Binding site comparison for function prediction and pharmaceutical discovery. Curr Opin Struct Biol [Internet]. 2014 Apr [cited 2014 Sep 3];25:34–9. Available from: http://www.ncbi.nlm.nih.gov/pubmed/24878342 \u00003. Nadzirin N, Gardiner EJ, Willett P, Artymiuk PJ, Firdaus-Raih M. SPRITE and ASSAM: Web servers for side chain 3D-motif searching in protein structures. Nucleic Acids Res. 2012;40(W1). \u00004. Martinez-bazan N, Muntes-mulero V, Gomez-villamor S. DEX : High-Performance Exploration on Large Graphs for Information Retrieval. Artif Intell [Internet]. 2007;573–82. Available from: http://portal.acm.org/citation.cfm?doid=1321440.1321521 \u00005. Nunez-Vivanco G, Valdes-Jimenez A, Besoain F, Reyes-Parada ","PeriodicalId":20475,"journal":{"name":"Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85347341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-12-17DOI: 10.3390/MOL2NET-04-05921
Viviana Quevedo, Bernabé Ortega-Tenezaca
{"title":"Incidence of the use of didactic material for students with hearing disability at the basic intercultural education center of deaf","authors":"Viviana Quevedo, Bernabé Ortega-Tenezaca","doi":"10.3390/MOL2NET-04-05921","DOIUrl":"https://doi.org/10.3390/MOL2NET-04-05921","url":null,"abstract":"","PeriodicalId":20475,"journal":{"name":"Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86839326","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-12-17DOI: 10.3390/MOL2NET-04-06006
R. Concu, M. Cordeiro
Molecular imprinted polymers (MIP
分子印迹聚合物(MIP
{"title":"From All Atom to Coarse Grain: Molecular Dynamic Simulation of Imprinting Process on a Silica Xerogel","authors":"R. Concu, M. Cordeiro","doi":"10.3390/MOL2NET-04-06006","DOIUrl":"https://doi.org/10.3390/MOL2NET-04-06006","url":null,"abstract":"Molecular imprinted polymers (MIP","PeriodicalId":20475,"journal":{"name":"Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74081595","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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